Early-life gut microbiome modulation reduces the abundance of antibiotic-resistant bacteria

Casaburi, Giorgio; Duar, Rebbeca M.; Vance, Daniel P.; Mitchell, Ryan; Contreras, Lindsey; Frese, Steven A.; Smilowitz, Jennifer T.; Underwood, Mark A.

doi:10.1186/s13756-019-0583-6

Cited by 101Gut microbiota and healthAntibiotic Resistance in BacteriaInfant Nutrition and Health

Early-life gut microbiome modulation reduces the abundance of antibiotic-resistant bacteria

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Casaburi, Giorgio, Duar, Rebbeca M., Vance, Daniel P., Mitchell, Ryan, Contreras, Lindsey, Frese, Steven A., Smilowitz, Jennifer T., Underwood, Mark A.·2019·Antimicrobial Resistance & Infection Control

DOI 10.1186/s13756-019-0583-6PMC PMC6693174

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Abstract

Antibiotic-resistant (AR) bacteria are a global threat. AR bacteria can be acquired in early life and have long-term sequelae. Limiting the spread of antibiotic resistance without triggering the development of additional resistance mechanisms is of immense clinical value. Here, we show how the infant gut microbiome can be modified, resulting in a significant reduction of AR genes (ARGs) and the potentially pathogenic bacteria that harbor them. The gut microbiome was characterized using shotgun metagenomics of fecal samples from two groups of healthy, term breastfed infants. One group was fed B. infantis EVC001 in addition to receiving lactation support (n = 29, EVC001-fed), while the other received lactation support alone (n = 31, controls). Coliforms were isolated from fecal samples and genome sequenced, as well as tested for minimal inhibitory concentrations against clinically relevant antibiotics. Infants fed B. infantis EVC001 exhibited a change to the gut microbiome, resulting in a 90% lower level of ARGs compared to controls. ARGs that differed significantly between groups were predicted to confer resistance to beta lactams, fluoroquinolones, or multiple drug classes, the majority of which belonged to Escherichia, Clostridium, and Staphylococcus. Minimal inhibitory concentration assays confirmed the resistance phenotypes among isolates with these genes. Notably, we found extended-spectrum beta lactamases among healthy, vaginally delivered breastfed infants who had never been exposed to antibiotics. Colonization of the gut of breastfed infants by a single strain of B. longum subsp. infantis had a profound impact on the fecal metagenome, including a reduction in ARGs. This highlights the importance of developing novel approaches to limit the spread of these genes among clinically relevant bacteria. Future studies are needed to determine whether colonization with B. infantis EVC001 decreases the incidence of AR infections in breastfed infants. This clinical trial was registered at ClinicalTrials.gov , NCT02457338.

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Bifidobacterium supplementation has been associated with lower ARG abundance in the infant gut microbiome, likely due to the competitive exclusion of ARG-rich pathobionts.
“Bifidobacterium, and Bifidobacterium supplementation has been associated with lower ARG abundance in the infant gut microbiome, likely due to the competitive exclusion of ARG-rich pathobionts56–59.”
From Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants. (2025) · cites this paper as [56]
The Results report that breastfed infants fed B. infantis EVC001 had 90% fewer ARGs than controls, and significantly lower levels of ARG-associated Enterobacteriaceae. The Discussion also reports reductions in Proteobacteria and Firmicutes. These findings support the association with fewer ARG-rich bacteria, but the paper does not establish competitive exclusion as the mechanism. (LLM, conf=0.82)
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Why Don't All Infants Have Bifidobacteria in Their Stool?
Tannock, G. W., Lee, P. S., Wong, K. H., & Lawley, B. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00834 · Cited by 46 · see citing works
Strategies for managing today's infections
Carmeli, Y. (2008) · Clinical Microbiology and Infection · doi:10.1111/j.1469-0691.2008.01957.x · Cited by 45 · see citing works
Antibiotic resistance potential of the healthy preterm infant gut microbiome
Rose, G., Shaw, A., Sim, K., Wooldridge, D. J., Li, M.-S., Gharbia, S. E., Misra, R., & Kroll, J. S. (2017) · PeerJ · doi:10.7717/peerj.2928 · Cited by 44 · see citing works
Tetracycline resistance genes acquired at birth
Alicea-Serrano, A. M., Contreras, M., Magris, M., Hidalgo, G., & Domínguez-Bello, M. G. (2013) · Archives of Microbiology · doi:10.1007/s00203-012-0864-4 · Cited by 41 · see citing works
Colonization of breastfed infants by Bifidobacterium longum subsp. infantis EVC001 reduces virulence gene abundance
Casaburi, G., & Frese, S. A. (2018) · Human Microbiome Journal · doi:10.1016/j.humic.2018.05.001 · Cited by 38 · see citing works
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GenCoF: a graphical user interface to rapidly remove human genome contaminants from metagenomic datasets
Czajkowski, M. D., Vance, D., Frese, S. A., & Casaburi, G. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty963 · Cited by 37 · see citing works
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The Clostridium perfringens TetA(P) efflux protein contains a functional variant of the Motif A region found in major facilitator superfamily transport proteins
Bannam, T. L., Johanesen, P., Salvado, C. L., Pidot, S. J., Farrow, K. A., & Rood, J. I. (2003) · Microbiology · doi:10.1099/mic.0.26614-0 · Cited by 34 · see citing works
Different Functions of MdtB and MdtC Subunits in the Heterotrimeric Efflux Transporter MdtB2C Complex ofEscherichia coli
Kim, H., & Nikaido, H. (2012) · Biochemistry · doi:10.1021/bi300379y · Cited by 33 · see citing works
Translational metagenomics and the human resistome: confronting the menace of the new millennium
Willmann, M., & Peter, S. (2016) · Journal of Molecular Medicine · doi:10.1007/s00109-016-1478-0 · Cited by 25 · see citing works
Commentary: Remembrance of microbes past
Tannock, G. W. (2004) · International Journal of Epidemiology · doi:10.1093/ije/dyh380 · Cited by 22 · see citing works
Metagenomic Comparison of Antibiotic Resistance Genes Associated with Liquid and Dewatered Biosolids
McCall, C. A., Bent, E., Jørgensen, T. S., Dunfield, K. E., & Habash, M. (2016) · Journal of Environmental Quality · doi:10.2134/jeq2015.05.0255 · Cited by 15 · see citing works
Significance of Lactose in Dairy Products
McSweeney, P. L. H., & Fox, P. A. (2009) · Springer eBooks · doi:10.1007/978-0-387-84865-5_3 · Cited by 11 · see citing works

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Bifidobacteria-mediated immune system imprinting early in life
Henrick, B. M., Rodriguez, L., Lakshmikanth, T., Pou, C., Henckel, E., Arzoomand, A., Olin, A., Wang, J., Mikeš, J., Tan, Z., et al. (2021) · Cell · doi:10.1016/j.cell.2021.05.030 · Cited by 808 · see citing works
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Impact of antibiotics on the human microbiome and consequences for host health
Patangia, D. V., Ryan, C. A., Dempsey, E. M., Ross, R. P., & Stanton, C. (2022) · MicrobiologyOpen · doi:10.1002/mbo3.1260 · Cited by 806 · see citing works
Clinical implications of preterm infant gut microbiome development
Healy, D., Ryan, C. A., Ross, R. P., Stanton, C., & Dempsey, E. M. (2021) · Nature Microbiology · doi:10.1038/s41564-021-01025-4 · Cited by 132 · see citing works
Early‐Life Gut Microbiome—The Importance of Maternal and Infant Factors in Its Establishment
Kapourchali, F. R., & Cresci, G. (2020) · Nutrition in Clinical Practice · doi:10.1002/ncp.10490 · Cited by 133 · see citing works
Antibiotic Resistance in Plant Pathogenic Bacteria: Recent Data and Environmental Impact of Unchecked Use and the Potential of Biocontrol Agents as an Eco-Friendly Alternative
Islam, T., Haque, M. A., Barai, H. R., Istiaq, A., & Kim, J.-J. (2024) · Plants · doi:10.3390/plants13081135 · Cited by 82 · see citing works
Metagenomic insights of the infant microbiome community structure and function across multiple sites in the United States
Casaburi, G., Duar, R. M., Brown, H. K., Mitchell, R. D., Kazi, S., Chew, S., Cagney, O., Flannery, R. L., Sylvester, K. G., Frese, S. A., et al. (2021) · Scientific Reports · doi:10.1038/s41598-020-80583-9 · Cited by 75 · see citing works
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Antimicrobial resistance in enteric bacteria: current state and next-generation solutions
Wallace, M. J., Fishbein, S. R. S., & Dantas, G. A. (2020) · Gut Microbes · doi:10.1080/19490976.2020.1799654 · Cited by 78 · see citing works
Comparative Genome Analysis of Bifidobacterium longum subsp. infantis Strains Reveals Variation in Human Milk Oligosaccharide Utilization Genes among Commercial Probiotics
Duar, R. M., Casaburi, G., Mitchell, R. D., Scofield, L. N. C., Ramírez, C. A. O., Barile, D., Henrick, B. M., & Frese, S. A. (2020) · Nutrients · doi:10.3390/nu12113247 · Cited by 70 · see citing works
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Colonization Resistance in the Infant Gut: The Role of B. infantis in Reducing pH and Preventing Pathogen Growth
Duar, R. M., Kyle, D., & Casaburi, G. (2020) · High-Throughput · doi:10.3390/ht9020007 · Cited by 70 · see citing works
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The infant gut resistome is associated with E. coli and early-life exposures
Lebeaux, R. M., Coker, M. O., Dade, E. F., Palys, T. J., Morrison, H. G., Ross, B. D., Baker, E., Karagas, M. R., Madan, J. C., & Hoen, A. G. (2021) · BMC Microbiology · doi:10.1186/s12866-021-02129-x · Cited by 68 · see citing works
Early life gut microbiome and its impact on childhood health and chronic conditions
Núñez, H., Nieto, P. A., Mars, R. A. T., Ghavami, M., Hoy, C. S., & Sukhum, K. V. (2025) · Gut Microbes · doi:10.1080/19490976.2025.2463567 · Cited by 74 · see citing works
Early probiotic supplementation with B. infantis in breastfed infants leads to persistent colonization at 1 year
O’Brien, C. E., Meier, A., Cernioglo, K., Mitchell, R. D., Casaburi, G., Frese, S. A., Henrick, B. M., Underwood, M. A., & Smilowitz, J. T. (2021) · Pediatric Research · doi:10.1038/s41390-020-01350-0 · Cited by 66 · see citing works
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Impact of Probiotic B. infantis EVC001 Feeding in Premature Infants on the Gut Microbiome, Nosocomially Acquired Antibiotic Resistance, and Enteric Inflammation
Nguyen, M., Holdbrooks, H., Mishra, P. K., Abrantes, M. A., Eskew, S., Garma, M., Oca, C.-G., McGuckin, C., Hein, C. T., Mitchell, R. D., et al. (2021) · Frontiers in Pediatrics · doi:10.3389/fped.2021.618009 · Cited by 61 · see citing works
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Maternal-infant antibiotic resistance genes transference: what do we know?
Samarra, A., Esteban-Torres, M., Cabrera‐Rubio, R., Bernabeu, M., Arboleya, S., Gueimonde, M., & Collado, M. C. (2023) · Gut Microbes · doi:10.1080/19490976.2023.2194797 · Cited by 58 · see citing works
Integrating the Ecosystem Services Framework to Define Dysbiosis of the Breastfed Infant Gut: The Role of B. infantis and Human Milk Oligosaccharides
Duar, R. M., Henrick, B. M., Casaburi, G., & Frese, S. A. (2020) · Frontiers in Nutrition · doi:10.3389/fnut.2020.00033 · Cited by 50 · see citing works
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Bifidobacterium catabolism of human milk oligosaccharides overrides endogenous competitive exclusion driving colonization and protection
Heiss, B. E., Ehrlich, A. M., Maldonado-Gómez, M. X., Taft, D. H., Larke, J. A., Goodson, M. L., Slupsky, C. M., Tancredi, D. J., Raybould, H. E., & Mills, D. A. (2021) · Gut Microbes · doi:10.1080/19490976.2021.1986666 · Cited by 50 · see citing works
Bifidobacterium and Lactobacillus Probiotics and Gut Dysbiosis in Preterm Infants
Rossum, T. V., Haiß, A., Knoll, R. L., Marißen, J., Podlesny, D., Pagel, J., Bleskina, M., Vens, M., Fortmann, M. I., Siller, B., et al. (2024) · Archives of Pediatrics and Adolescent Medicine · doi:10.1001/jamapediatrics.2024.2626 · Cited by 47 · see citing works
Bifidobacterium longum subsp. infantis EVC001 Administration Is Associated with a Significant Reduction in the Incidence of Necrotizing Enterocolitis in Very Low Birth Weight Infants
Tobias, J. D., Olyaei, A. F., Laraway, B. J., Jordan, B. K., Dickinson, S., Golzarri‐Arroyo, L., Fialkowski, E., Owora, A. H., & Scottoline, B. P. (2022) · The Journal of Pediatrics · doi:10.1016/j.jpeds.2021.12.070 · Cited by 43 · see citing works
Inulin Fermentation by Lactobacilli and Bifidobacteria from Dairy Calves
Zhu, Y., Liu, J., Lopez, J. M., & Mills, D. A. (2020) · Applied and Environmental Microbiology · doi:10.1128/aem.01738-20 · Cited by 40 · see citing works
Increased Incidence of Methicillin-Resistant Staphylococcus aureus in Knee and Hip Prosthetic Joint Infection
Hays, M. R., Kildow, B. J., Hartman, C. W., Lyden, E. R., Springer, B. D., Fehring, T. K., & Garvin, K. L. (2023) · The Journal of Arthroplasty · doi:10.1016/j.arth.2023.02.025 · Cited by 39 · see citing works
Translating neonatal microbiome science into commercial innovation: metabolism of human milk oligosaccharides as a basis for probiotic efficacy in breast-fed infants
Mills, D. A., German, J. B., Lebrilla, C. B., & Underwood, M. A. (2023) · Gut Microbes · doi:10.1080/19490976.2023.2192458 · Cited by 38 · see citing works
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Human Milk Oligosaccharide Utilization in Intestinal Bifidobacteria Is Governed by Global Transcriptional Regulator NagR
Arzamasov, A. A., Nakajima, A., Sakanaka, M., Ojima, M. N., Katayama, T., Rodionov, D. A., & Osterman, A. L. (2022) · mSystems · doi:10.1128/msystems.00343-22 · Cited by 41 · see citing works
Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants.
Kiu, R., Darby, E. M., Alcon-Giner, C., Acuna-Gonzalez, A., Camargo, A., Lamberte, L. E., Phillips, S., Sim, K., Shaw, A. G., Clarke, P., et al. (2025) · Nature communications · doi:10.1038/s41467-025-62584-2 · Cited by 36 · see citing works
“Bi ﬁ do-bacterium , and Bi ﬁ dobacterium supplementation has been associated with lower ARG abundance in the infant gut microbiome, likely due to the competitive exclusion of ARG-rich pathobionts 56 – 59 .”
Gut microbiome function and composition in infants from rural Kenya and association with human milk oligosaccharides
Derrien, M., Mikulic, N., Uyoga, M. A., Chenoll, E., Climent, E., Howard-Varona, A., Nyilima, S., Stoffel, N. U., Karanja, S., Kottler, R., et al. (2023) · Gut Microbes · doi:10.1080/19490976.2023.2178793 · Cited by 36 · see citing works
Antimicrobial Resistance Genes (ARGs), the Gut Microbiome, and Infant Nutrition
Theophilus, R. J., & Taft, D. H. (2023) · Nutrients · doi:10.3390/nu15143177 · Cited by 35 · see citing works
Litter Commensal Bacteria Can Limit the Horizontal Gene Transfer of Antimicrobial Resistance to Salmonella in Chickens
Oladeinde, A., Abdo, Z., Zwirzitz, B., Woyda, R., Lakin, S. M., Press, M. O., Cox, N. A., Thomas, J. C., Looft, T. P., Rothrock, M. J., et al. (2022) · Applied and Environmental Microbiology · doi:10.1128/aem.02517-21 · Cited by 35 · see citing works
Can breastfeeding protect against antimicrobial resistance?
Nadimpalli, M. L., Bourke, C. D., Robertson, R. C., Delarocque‐Astagneau, E., Manges, A. R., & Pickering, A. J. (2020) · BMC Medicine · doi:10.1186/s12916-020-01862-w · Cited by 35 · see citing works
Impact of antibiotics on off-target infant gut microbiota and resistance genes in cohort studies
Lebeaux, R. M., Madan, J. C., Nguyen, Q. P., Coker, M. O., Dade, E. F., Moroishi, Y., Palys, T. J., Ross, B. D., Pettigrew, M. M., Morrison, H. G., et al. (2022) · Pediatric Research · doi:10.1038/s41390-022-02104-w · Cited by 33 · see citing works
Breastfeeding and early Bifidobacterium-driven microbial colonization shape the infant gut resistome
Samarra, A., Alcañiz, A. J., Martínez-Costa, C., Marina, A., Comas, I., Segata, N., Quijada, N. M., & Collado, M. C. (2025) · Nature Communications · doi:10.1038/s41467-025-61154-w · Cited by 32 · see citing works
Helping Mom Help Baby: Nutrition-Based Support for the Mother-Infant Dyad During Lactation
Ford, E. L., Underwood, M. A., & German, J. B. (2020) · Frontiers in Nutrition · doi:10.3389/fnut.2020.00054 · Cited by 40 · see citing works
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Metabolic model of necrotizing enterocolitis in the premature newborn gut resulting from enteric dysbiosis
Casaburi, G., Wei, J., Kazi, S., Liu, J., Wang, K., Tao, G., Lin, P., Dunn, J., Henrick, B. M., Frese, S. A., et al. (2022) · Frontiers in Pediatrics · doi:10.3389/fped.2022.893059 · Cited by 27 · see citing works
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Sonocatalytic process of penicillin removal using - Fe2O3 / effect of different parameters / degradation mechanism/ kinetic study/optimisation with response surface model
Abdipour, H., & Hemati, H. (2023) · International Journal of Environmental & Analytical Chemistry · doi:10.1080/03067319.2023.2207465 · Cited by 27 · see citing works
The role of <i>Bifidobacterium</i> genus in modulating the neonate microbiota: implications for antibiotic resistance acquisition in early life
Samarra, A., Cabrera-Rubio, R., Martínez-Costa, C., & Collado, M. C. (2024) · Gut Microbes · doi:10.1080/19490976.2024.2357176 · Cited by 25 · see citing works
Building Robust Assemblages of Bacteria in the Human Gut in Early Life
Tannock, G. W. (2021) · Applied and Environmental Microbiology · doi:10.1128/aem.01449-21 · Cited by 23 · see citing works
Impact of Hospital Wastewater on the Occurrence and Diversity of Beta-Lactamase Genes During Wastewater Treatment with an Emphasis on Carbapenemase Genes: A Metagenomic Approach
Hubeny, J., Ciesielski, S., Harnisz, M., Korzeniewska, E., Dulski, T., Jałowiecki, Ł., & Płaza, G. A. (2021) · Frontiers in Environmental Science · doi:10.3389/fenvs.2021.738158 · Cited by 21 · see citing works
Infant age inversely correlates with gut carriage of resistance genes, reflecting modifications in microbial carbohydrate metabolism during early life
Xu, X., Feng, Q., Zhang, T., Gao, Y., Cheng, Q., Zhang, W., Wu, Q., Xu, K., Li, Y., Nguyen, N., et al. (2024) · iMeta · doi:10.1002/imt2.169 · Cited by 20 · see citing works
The Resistome of ESKAPEE Pathogens in Untreated and Treated Wastewater: A Polish Case Study
Hubeny, J., Korzeniewska, E., Ciesielski, S., Płaza, G. A., & Harnisz, M. (2022) · Biomolecules · doi:10.3390/biom12081160 · Cited by 19 · see citing works
B. infantis EVC001 Is Well-Tolerated and Improves Human Milk Oligosaccharide Utilization in Preterm Infants in the Neonatal Intensive Care Unit
Bajorek, S. A., Duar, R. M., Corrigan, M., Matrone, C., Winn, K. A., Norman, S. E., Mitchell, R. D., Cagney, O., Aksenov, A. A., Melnik, A. V., et al. (2022) · Frontiers in Pediatrics · doi:10.3389/fped.2021.795970 · Cited by 19 · see citing works
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Milk glycan metabolism by intestinal bifidobacteria: insights from comparative genomics
Arzamasov, A. A., & Osterman, A. L. (2022) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.1080/10409238.2023.2182272 · Cited by 18 · see citing works
Milk oligosaccharide-driven persistence of Bifidobacterium pseudocatenulatum modulates local and systemic microbial metabolites upon synbiotic treatment in conventionally colonized mice
Larke, J. A., Heiss, B. E., Ehrlich, A. M., Taft, D. H., Raybould, H. E., Mills, D. A., & Slupsky, C. M. (2023) · Microbiome · doi:10.1186/s40168-023-01624-9 · Cited by 19 · see citing works
Human Milk—The Biofluid That Nourishes Infants from the First Day of Life
Lugonja, N. M., Marinković, V., Pucarević, M., Miletić, S., Stojić, N., Crnković, D. M., & Vrvić, M. M. (2024) · Foods · doi:10.3390/foods13091298 · Cited by 19 · see citing works
Metagenomic analysis of the gut microbiota in piglets either challenged or not with enterotoxigenic Escherichia coli reveals beneficial effects of probiotics on microbiome composition, resistome, digestive function and oxidative stress responses
Apiwatsiri, P., Pupa, P., Sirichokchatchawan, W., Sawaswong, V., Nimsamer, P., Payungporn, S., Hampson, D. J., & Prapasarakul, N. (2022) · PLoS ONE · doi:10.1371/journal.pone.0269959 · Cited by 18 · see citing works
The association between early life antibiotic exposure and the gut resistome of young children: a systematic review
Lebeaux, R. M., Karalis, D., Lee, J., Whitehouse, H. C., Madan, J. C., Karagas, M. R., & Hoen, A. G. (2022) · Gut Microbes · doi:10.1080/19490976.2022.2120743 · Cited by 17 · see citing works
Impact of Early Feeding: Metagenomics Analysis of the Infant Gut Microbiome
Guglielmo, M. D. D., Franke, K., Robbins, A. K., & Crowgey, E. L. (2022) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2022.816601 · Cited by 17 · see citing works
The neonatal intestinal resistome and factors that influence it—a systematic review
Léo, S., Curtis, N. C., & Zimmermann, P. (2022) · Clinical Microbiology and Infection · doi:10.1016/j.cmi.2022.07.014 · Cited by 16 · see citing works
Genomic atlas of Bifidobacterium infantis and B. longum informs infant probiotic design
Shao, Y., Wang, S., Gichuki, B. M., Stares, M. D., Rozday, T. J., Kumar, N., Browne, H. P., Dawson, N. J. R., Njunge, J. M., Tigoi, C., et al. (2026) · Cell · doi:10.1016/j.cell.2026.01.007 · Cited by 17 · see citing works
Influence of age, socioeconomic status, and location on the infant gut resistome across populations
Patangia, D. V., Grimaud, G. M., Wang, S., Ross, R. P., & Stanton, C. (2024) · Gut Microbes · doi:10.1080/19490976.2023.2297837 · Cited by 15 · see citing works
Early life exposure of infants to benzylpenicillin and gentamicin is associated with a persistent amplification of the gut resistome
Patangia, D. V., Grimaud, G. M., O'Shea, C., Ryan, C. A., Dempsey, E. M., Stanton, C., & Ross, R. P. (2024) · Microbiome · doi:10.1186/s40168-023-01732-6 · Cited by 15 · see citing works
Inferring early-life host and microbiome functions by mass spectrometry-based metaproteomics and metabolomics
Pettersen, V. K., Antunes, L. C. M., Dufour, A., & Arrieta, M. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2021.12.012 · Cited by 14 · see citing works
Temporal dynamics and microbial interactions shaping the gut resistome in early infancy
Chatzigiannidou, I., Johansen, P. L., Dehli, R. I., Moll, J. M., Eriksen, C., Myers, P. N., Roager, H. M., Yang, L., Stokholm, J., Sørensen, S. J., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-63401-6 · Cited by 14 · see citing works
Delayed colonization of Bifidobacterium spp. and low prevalence of B. infantis among infants of Asian ancestry born in Singapore: insights from the GUSTO cohort study
Xu, J. Y., Duar, R. M., Quah, B., Gong, M., Tin, F., Chan, P., Sim, C. K., Tan, K. H., Chong, Y. S., Gluckman, P. D., et al. (2024) · Frontiers in Pediatrics · doi:10.3389/fped.2024.1421051 · Cited by 13 · see citing works
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Metagenomics analysis of the neonatal intestinal resistome
Léo, S., Çetiner, Ö. F., Pittet, L. F., Messina, N. L., Jakob, W., Falquet, L., Curtis, N. C., & Zimmermann, P. (2023) · Frontiers in Pediatrics · doi:10.3389/fped.2023.1169651 · Cited by 11 · see citing works
Use of probiotics to reduce infections and death and prevent colonization with extended-spectrum beta-lactamase (ESBL)-producing bacteria among newborn infants in Tanzania (ProRIDE Trial): study protocol for a randomized controlled clinical trial
Kuwelker, K., Langeland, N., Löhr, I. H., Gidion, J., Manyahi, J., Moyo, S. J., Blomberg, B., & Klingenberg, C. (2021) · Trials · doi:10.1186/s13063-021-05251-3 · Cited by 11 · see citing works
Modulation of gut microbiota: An emerging consequence in neonatal sepsis
Iqbal, F., Lewis, L., Siva, N., Vandana, K. E., Purkayastha, J., & Shenoy, P. A. (2023) · Clinical Epidemiology and Global Health · doi:10.1016/j.cegh.2023.101245 · Cited by 10 · see citing works
Unveiling the Gut Microbiota and Resistome of Wild Cotton Mice, Peromyscus gossypinus , from Heavy Metal- and Radionuclide-Contaminated Sites in the Southeastern United States
Thomas, J. C., Kieran, T. J., Finger, J. W., Bayona‐Vásquez, N. J., Oladeinde, A., Beasley, J. C., Seaman, J. C., McArthur, J. V., Rhodes, O. E., & Glenn, T. C. (2021) · Microbiology Spectrum · doi:10.1128/spectrum.00097-21 · Cited by 10 · see citing works
A novel bacteriocin produced by Bifidobacterium longum subsp. infantis has dual antimicrobial and immunomodulatory activityPreprint
Javvadi, S. G., Kujawska, M., Papp, D., Gontarczyk, A. M., Jordan, A., Lawson, M. A., O’Neill, I. J., Alcon-Giner, C., Kiu, R., Clarke, P., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.01.27.477972 · Cited by 10 · see citing works
Antibiotic standards stored as a mixture in water: methanol are unstable at various temperatures irrespective of pH and glass container silanization
Emami, S., Lerno, L., & Taha, A. Y. (2021) · Food Additives & Contaminants Part A · doi:10.1080/19440049.2021.1982150 · Cited by 9 · see citing works
Selection of antibiotic-resistant bacterial populations in the dairy cow gut following intramuscular ceftiofur treatment for metritis
Vasco, K. A., Bowcutt, B., Carbonell, S. L., Souza, L., Robison, C. I., Abuelo, Á., Erskine, R. J., Norby, B., Zhang, L., Ruegg, P. L., et al. (2024) · Journal of Dairy Science · doi:10.3168/jds.2023-24572 · Cited by 8 · see citing works
Reintroducing B. infantis to the cesarean-born neonate: an ecologically sound alternative to “vaginal seeding”
Duar, R. M., Kyle, D., & Tribe, R. M. (2020) · FEMS Microbiology Letters · doi:10.1093/femsle/fnaa032 · Cited by 8 · see citing works
Self-citation
Impact of a multi-strain probiotic administration on peri-rectal colonization with drug-resistant Gram-negative bacteria in preterm neonates
Sowden, M., van Niekerk, E., Bulabula, A. N. H., Dramowski, A., Whitelaw, A. C., Twisk, J. W. R., & van Weissenbruch, M. M. (2022) · Frontiers in Pediatrics · doi:10.3389/fped.2022.1002762 · Cited by 7 · see citing works
Human Gut Microbiome: A Potential Prospective to Counter Antibiotic-Resistant Pathogens
Yadav, M. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-819265-8.00005-x · Cited by 6 · see citing works
Detection of Carbapenem-resistant Enterobacteriaceae by Real-Time PCR and Assessment of Hospitalization Related Risk Factors Associated with their Fecal Carriage: A Case-control Study
Ravikant, R., Kumari, P., Kumar, M., Roy, P., & Jeya, M. (2022) · Journal of Pure and Applied Microbiology · doi:10.22207/jpam.16.2.37 · Cited by 8 · see citing works
Baseline azithromycin resistance in the gut microbiota of preterm born infants
Gallacher, D. J., Zhang, L., Aboklaish, A. F., Mitchell, E., Wach, R., Marchesi, J. R., & Kotecha, S. (2023) · Pediatric Research · doi:10.1038/s41390-023-02743-7 · Cited by 6 · see citing works
Understanding the influence of the microbiome on childhood infections
Heston, S. M., Hurst, J. H., & Kelly, M. S. (2024) · Expert Review of Anti-infective Therapy · doi:10.1080/14787210.2024.2340664 · Cited by 5 · see citing works
Probiotic supplementation in neonates and long‐term gut colonisation: A systematic review of randomised controlled trials
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Additional file 4 of Use of probiotics to reduce infections and death and prevent colonization with extended-spectrum beta-lactamase (ESBL)-producing bacteria among newborn infants in Tanzania (ProRIDE Trial): study protocol for a randomized controlled clinical trial
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Additional file 2 of Use of probiotics to reduce infections and death and prevent colonization with extended-spectrum beta-lactamase (ESBL)-producing bacteria among newborn infants in Tanzania (ProRIDE Trial): study protocol for a randomized controlled clinical trial
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Additional file 3 of Use of probiotics to reduce infections and death and prevent colonization with extended-spectrum beta-lactamase (ESBL)-producing bacteria among newborn infants in Tanzania (ProRIDE Trial): study protocol for a randomized controlled clinical trial
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Additional file 5 of Use of probiotics to reduce infections and death and prevent colonization with extended-spectrum beta-lactamase (ESBL)-producing bacteria among newborn infants in Tanzania (ProRIDE Trial): study protocol for a randomized controlled clinical trial
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Metagenomic analysis reveals reduction in antibiotic resistance genes in breastfed infants fed Bifidobacterium longum subsp. infantis EVC001
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Authors: Casaburi, G., Duar, R. M., Vance, D. P., Mitchell, R., Contreras, L., Frese, S. A., Smilowitz, J. T., & Underwood, M. A.
Affiliations: Infinant Health Inc. (United States) (US)
University of Nebraska–Lincoln (US)
University of California, Davis (US)
University of California Davis Medical Center (US)
Corresponding author: Smilowitz, Jennifer T.
Underwood, Mark A.
ORCID: Casaburi, Giorgio
Duar, Rebbeca M.
Mitchell, Ryan
Contreras, Lindsey
Frese, Steven A.
Smilowitz, Jennifer T.
Underwood, Mark A.
Venue: Antimicrobial Resistance & Infection Control
Publisher: Springer Science and Business Media LLC
Published: 2019-08-14
Volume: 8
Issue: 1
Pages: 131-131
ISSN: 2047-2994 (ISSN-L)
DOI: 10.1186/s13756-019-0583-6
PMC: PMC6693174
OpenAlex: W2967608930
Cited by: 101
References: 86
Citations by year: 2026: 12 · 2025: 6 · 2024: 14 · 2023: 16 · 2022: 20 · 2021: 21 · 2020: 12
FWCI: 4.39
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
creativecommons.org/licenses/by/4.0/ (tdm)
creativecommons.org/licenses/by/4.0/ (vor)
Locations: Antimicrobial Resistance and Infection Control (publishedVersion, cc-by)
Europe PMC (PubMed Central) (publishedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
eScholarship (California Digital Library) (submittedVersion, cc-by)
Funders: Evolve Biosystems (n/a)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Medicine › Antibiotic Resistance in Bacteria
Health Sciences › Nursing › Nutrition and Dietetics › Infant Nutrition and Health
Keywords: antibiotic resistance genes, infant gut microbiota, probiotic supplementation, breastfeeding, coliform bacteria, extended-spectrum beta-lactamase, minimum inhibitory concentration, Escherichia, Clostridium, Staphylococcus, vaginal delivery, antibiotic resistance spread
MeSH terms: Gastrointestinal Microbiome, Bifidobacterium longum subspecies infantis, Whole Genome Sequencing, Anti-Bacterial Agents, Bacteria, beta-Lactamases, Breast Feeding, Drug Resistance, Microbial, Feces, Humans, Infant, Newborn, Microbial Sensitivity Tests, Case-Control Studies, Probiotics, Metagenomics, High-Throughput Nucleotide Sequencing

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Early-life gut microbiome modulation reduces the abundance of antibiotic-resistant bacteria

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