Major genetic meta-analysis reveals how antibiotic resistance in babies varies according to mode of birth, prematurity, and where they live

A meta-analysis of genetic studies analysing the microbiota (bacteria in the gut) of 1,275 infants from 10 countries finds that caesarean delivery and antibiotic use are driving the increase of antibiotic resistance genes load among infants, according to new research being presented at this year’s ESCMID Global Congress (formerly ECCMID) in Barcelona, Spain (27-30 April).

The study, by researchers from UiT The Artic University of Norway, highlights the urgent need for more research on targeted interventions to reduce antibiotic resistance in infants. They speculate that probiotics, for example, could reduce the abundance of antibiotic resistance genes and merit further investigation.

Antimicrobial resistance (AMR) is a global health emergency. Drug-resistant infections kill more than 1.27 million people a year worldwide. If no action is taken, antimicrobial resistance could overtake cancer as the leading cause of death worldwide by 2050, and is projected to kill 10 million people globally.

Immature immune system

Infants are highly susceptible to infections due to their immature immune system. At the same time, their gut microbiota is full of diverse bacteria, many of which harbour resistance against a broad range of antibiotics, even in the absence of antibiotic exposure. The gut resistome—the collection of antibiotic resistant genes (ARGs) harboured in the genomes of infant gut microbes—develops when microbes flood the gut immediately after birth, and is an important piece of the AMR puzzle.

The gut mobilome—the collection of diverse mobile genetic elements (MGEs) within the gut, plays a key role in the spread of ARGs. Bacteria swap genetic material, like ARGs, through horizontal gene transfer. With so many bacteria in close proximity, the gut provides ideal conditions for this exchange of ARGs.

While many intestinal bacteria harbouring ARGs do not pose a health threat, some ARGs are acquired by microbes with pathogenic potential. When these genes are transmitted to a pathogen, this has dire consequences for both the individual patient and society.

Understanding the factors influencing the development of the infant gut resistome and mobilome is therefore crucial for developing strategies to mitigate AMR prevalence.

Fragmented insights

Several previous clinical studies have provided important but fragmented insights into the gut resistome, but their small sample sizes and inherent biases (e.g., selection bias and confounding) limit the generalisability of the findings.

To overcome these limitations, researchers conducted a meta-analysis of infant cohorts based on metagenomics data from 14 studies spanning 10 countries and three continents.

They investigated the extent to which antibiotic use, birth mode, prematurity, feeding practices, and geography influenced the abundance and diversity of ARGs and MGEs in 3,981 gut metagenome faecal samples from 1,275 infants. To track the infants’ microbiomes, infants’ stools were sampled longitudinally up to 14 months of age.

Shotgun metagenomes

Researchers used published shotgun metagenomes (untargeted genetic sequencing of all bacteria living in the gut) to examine the associations between the diversity and load of ARGs and MGEs and antibiotic use, birth mode, prematurity, feeding practices, and geography, as well as to identify which bacterial species are major hosts of ARGs within infants’ gut.

Overall, the analyses found that use of antibiotics, Caesarean delivery, and prematurity was significantly associated with reduced beneficial gut microbe diversity compared to full-term, vaginally-born infants not exposed to antibiotics.

On the other hand, vaginal birth was linked to lower abundance but more diverse ARGs compared to C-section delivery.

Delivery mode

“Vaginally born infants are exposed to more vaginal and gut bacteria compared to C-section born babies, who are primarily exposed to skin bacteria,” explains lead author Ahmed Bargheet from UiT The Artic University of Norway. “Since bacteria correlate with the collection of antibiotic resistant genes in the gut, higher antibiotic resistant gene diversity in vaginally born infants is expected.

However, the presence of higher levels of certain commensal bacteria—which supply their host with essential nutrients and help defend the host against opportunistic pathogens—in vaginally born infants may suppress pathogenic bacteria (which are likely to carry a higher abundance of antibiotic resistant genes), thereby reducing the overall abundance.”

As expected, the analyses found that antibiotic use was linked to higher ARG and MGE abundance. However, antibiotic use had no significant impact on the ARGs’ diversity.

Breastfed infants

Surprisingly, exclusively breastfed infants showed no significant effects on ARG diversity or abundance.

Importantly, the researchers detected 199 clinically relevant ARGs (that confer resistance to clinically relevant antibiotics), whose diversity increased with age during the first two years of life. “The diversity of the ARGs increased over time, mirroring the diversity of the bacteria. However, the abundance of ARGs decreased over time, possibly due to a reduction in the abundance of pathogenic bacteria such as Escherichia coli,” says Bargheet.

Interestingly, two African cohorts (from Zimbabwe and South Africa) had a statistically significant and higher ARG and MGE abundance compared to the European cohorts. “It’s possible that Zimbabwe and South Africa used more antibiotics in their infant cohorts than the Europeans,” says Bargheet. “In Zimbabwe, the regulation and control of antibiotics is not as strict as in some regions of Europe, leading to a situation where antibiotics can often be purchased over the counter without a prescription, potentially exacerbating antimicrobial resistance.”

Usual suspect

The authors further confirmed E. coli as the main host of ARGs in the guts of infants, and concerningly, nearly half of the ARGs co-localised with plasmids, allowing efficient transfer between bacteria. Furthermore, E. coli strain diversity was found to be reduced during breastfeeding, but increased with age. Interestingly, antibiotic use had no significant impact on the E. coli strain diversity.

“Our meta-analysis of the available evidence clearly shows that C-section delivery, antibiotic use, and prematurity play an underappreciated role in antibiotic resistance in infants by altering early life resistome and mobilome, leading to an increased gut carriage of antibiotic resistance genes and mobile genetic elements”, says Bargheet.

“This has important implications for the antibiotic resistance crisis. By gaining insight into these factors, we aim to develop targeted interventions like probiotics, that could significantly reduce the number of deaths caused by antimicrobial resistance. This research not only addresses a pressing global health challenge but also sets the stage for breakthroughs in medical treatment and infection control. As we move forward, our focus remains on turning these findings into actionable strategies that can save lives and curb the spread of resistant infections.”

Despite the important findings, the authors note several limitations, including that the impact of hospitalisation and other clinical variables could not be examined in this analysis due to a lack of data.