Mahtab, S. et al. Causes of death identified in neonates enrolled through Child Health and Mortality Prevention Surveillance (CHAMPS), December 2016 –December 2021. PLOS Glob. Public Health 3, e0001612 (2023).
Perin, J. et al. Global, regional, and national causes of under-5 mortality in 2000-19: an updated systematic analysis with implications for the Sustainable Development Goals. Lancet Child Adolesc. Health 6, 106–115 (2022).
Huynh, B.-T. et al. Severe bacterial neonatal infections in Madagascar, Senegal, and Cambodia: A multicentric community-based cohort study. PLOS Med 18, e1003681 (2021).
Sands, K. et al. Early-Onset Neonatal Sepsis in Low- and Middle-Income Countries: Current Challenges and Future Opportunities. Infect. Drug Resist. 15, 933–946 (2022).
Wen, S. C. H. et al. Gram-negative neonatal sepsis in low- And lower-middle-income countries and WHO empirical antibiotic recommendations: A systematic review and meta-analysis. PLoS Med 18, e1003787 (2021).
Zaidi, A. K. M. et al. Hospital-acquired neonatal infections in developing countries. Lancet Lond. Engl. 365, 1175–1188 (2005).
Milton, R. et al. Neonatal sepsis and mortality in low-income and middle-income countries from a facility-based birth cohort: an international multisite prospective observational study. Lancet Glob. Health 10, e661–e672 (2022).
Breurec, S. et al. High third-generation cephalosporin resistant Enterobacteriaceae prevalence rate among neonatal infections in Dakar, Senegal. BMC Infect. Dis. 16, 587 (2016).
Huynh, B. et al. Bacterial Infections in Neonates, Madagascar, 2012-2014. Emerg. Infect. Dis. 24, 710–717 (2018).
Vardakas, K. Z., Tansarli, G. S., Rafailidis, P. I. & Falagas, M. E. Carbapenems versus alternative antibiotics for the treatment of bacteraemia due to Enterobacteriaceae producing extended-spectrum β-lactamases: a systematic review and meta-analysis. J. Antimicrob. Chemother. 67, 2793–2803 (2012).
GBD 2021 Antimicrobial Resistance Collaborators Global burden of bacterial antimicrobial resistance 1990-2021: a systematic analysis with forecasts to 2050. Lancet Lond. Engl. 404, 1199–1226 (2024).
Gans, H. A. & Darmstadt, G. L. Bacterial Sepsis in the Neonate. in Fetal and Neonatal Brain Injury (eds. Stevenson, D. K., Druzin, M. L., Sunshine, P., Hintz, S. R. & Benitz, W. E.) 456–480 (Cambridge University Press, Cambridge, 2017). https://doi.org/10.1017/9781316275498.031.
Singh, M., Alsaleem, M. & Gray, C. P. Neonatal Sepsis. in StatPearls (StatPearls Publishing, Treasure Island (FL), 2025).
de Lauzanne, A. et al. Prevalence and factors associated with faecal carriage of extended-spectrum β-lactamase-producing Enterobacterales among peripartum women in the community in Cambodia. J. Antimicrob. Chemother. 77, 2658–2666 (2022).
Milenkov, M. et al. Prevalence, Risk Factors, and Genetic Characterization of Extended-Spectrum Beta-Lactamase Escherichia coli Isolated From Healthy Pregnant Women in Madagascar. Front. Microbiol. 12, (2021).
Chomkatekaew, C. et al. Detection of maternal transmission of resistant Gram-negative bacteria in a Cambodian hospital setting. Front. Microbiol. 14, 1158056 (2023).
Patangia, D. V., Ryan, C. A., Dempsey, E., Stanton, C. & Ross, R. P. Vertical transfer of antibiotics and antibiotic resistant strains across the mother/baby axis. Trends Microbiol 30, 47–56 (2022).
Danino, D. et al. Mother-to-child transmission of extended-spectrum-beta-lactamase-producing Enterobacteriaceae. J. Hosp. Infect. 100, 40–46 (2018).
Rettedal, S. et al. Extended-spectrum β-lactamase-producing Enterobacteriaceae among pregnant women in Norway: prevalence and maternal–neonatal transmission. J. Perinatol. 35, 907–912 (2015).
Arredondo-Alonso, S., Willems, R. J., van Schaik, W. & Schürch, A. C. On the (im)possibility of reconstructing plasmids from whole-genome short-read sequencing data. Microb. Genomics 3, e000128 (2017).
Koren, S. & Phillippy, A. M. One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly. Curr. Opin. Microbiol. 23, 110–120 (2015).
Harimanana, A. et al. Neonatal acquisition of extended-spectrum beta-lactamase-producing Enterobacteriaceae in the community of a low-income country (NeoLIC): protocol for a household cohort study in Moramanga, Madagascar. BMJ Open 12, e061463 (2022).
World Health Organization. WHO Recommendations for Management of Serious Bacterial Infections in Infants Aged 0-59 Days. (World Health Organization, Geneva, 2024). Accessible from: Accessible from: https://iris.who.int/bitstream/handle/10665/379727/9789240102903-eng.pdf?sequence=1%20Maternal%20colonization%20with%20extended-spectrum%20%CE%B2-lactamase-producing%20Enterobacteriaceae%20in%20term%20vs%20preterm%20pregnancies.
Magiorakos, A.-P. et al. Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance. Clin. Microbiol. Infect. 18, 268–281 (2012).
Russell, N. et al. Early-versus late-onset sepsis in neonates – time to shift the paradigm?. Clin. Microbiol. Infect. 30, 38–43 (2024).
Frank Wolf, M. et al. Vertical Transmission of Extended-Spectrum, Beta-Lactamase-Producing Enterobacteriaceae during Preterm Delivery: A Prospective Study. Microorganisms 9, 506 (2021).
Sgayer, I. et al. Maternal colonization with extended-spectrum β-lactamase-producing Enterobacteriaceae in term versus preterm pregnancies. Int. J. Gynaecol. Obstet. Organ Int. Fed. Gynaecol. Obstet. 161, 447–454 (2023).
Matok, L. A. et al. Mother-to-Neonate Transmission of Antibiotic-Resistant Bacteria: A Cross-Sectional Study. Microorganisms 9, 1245 (2021).
Denkel, L. A. et al. The mother as most important risk factor for colonization of very low birth weight (VLBW) infants with extended-spectrum -lactamase-producing Enterobacteriaceae (ESBL-E). J. Antimicrob. Chemother. 69, 2230–2237 (2014).
Bezabih, Y. M. et al. Comparison of the global prevalence and trend of human intestinal carriage of ESBL-producing Escherichia coli between healthcare and community settings: a systematic review and meta-analysis. JAC-Antimicrob. Resist 4, dlac048 (2022).
Carvalho, M. J. et al. Antibiotic resistance genes in the gut microbiota of mothers and linked neonates with or without sepsis from low- and middle-income countries. Nat. Microbiol. 7, 1337–1347 (2022).
Okomo, U. A. et al. Maternal colonization and early-onset neonatal bacterial sepsis in the Gambia, West Africa: a genomic analysis of vertical transmission. Clin. Microbiol. Infect. 29, 386.e1–386.e9 (2023).
Leo, S., Curtis, N. & Zimmermann, P. The neonatal intestinal resistome and factors that influence it-a systematic review. Clin. Microbiol. Infect. Publ. Eur. Soc. Clin. Microbiol. Infect. Dis. 28, 1539–1546 (2022).
Pärnänen, K. et al. Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements. Nat. Commun. 9, 3891 (2018).
Bargheet, A. et al. Development of early life gut resistome and mobilome across gestational ages and microbiota-modifying treatments. eBioMedicine 92, 104613 (2023).
Carattoli, A. Plasmids and the spread of resistance. Int. J. Med. Microbiol. 303, 298–304 (2013).
Smillie, C. S. et al. Ecology drives a global network of gene exchange connecting the human microbiome. Nature 480, 241–244 (2011).
He, W., Russel, J., Klincke, F., Nesme, J. & Sørensen, S. J. Insights into the ecology of the infant gut plasmidome. Nat. Commun. 15, 6924 (2024).
Akintayo, I. et al. Tracking clonal and plasmid transmission in colistin- and carbapenem-resistant Klebsiella pneumoniae. mSystems 10, e01128-24 (2025).
Milenkov, M. et al. Implementation of the WHO Tricycle protocol for surveillance of extended-spectrum β-lactamase producing Escherichia coli in humans, chickens, and the environment in Madagascar: a prospective genomic epidemiology study. Lancet Microbe 5, 100850 (2024).
Turner, P. et al. High Prevalence of Antimicrobial-resistant Gram-negative Colonization in Hospitalized Cambodian Infants. Pediatr. Infect. Dis. J. 35, 856–861 (2016).
Herindrainy, P. et al. Acquisition of extended spectrum beta-lactamase-producing enterobacteriaceae in neonates: A community based cohort in Madagascar. PLOS ONE 13, e0193325 (2018).
Albers, L. L. The duration of labor in healthy women. J. Perinatol. J. Calif. Perinat. Assoc. 19, 114–119 (1999).
Boulanger, H. et al. Immunologic aspects of preeclampsia. AJOG Glob. Rep. 4, 100321 (2024).
Kennedy, K. M. et al. Parity modulates impact of BMI and gestational weight gain on gut microbiota in human pregnancy. Gut Microbes 15, 2259316 (2023).
Berry, A. S. F. et al. Remodeling of the maternal gut microbiome during pregnancy is shaped by parity. Microbiome 9, 146 (2021).
Jia, X. et al. Comparison of Fecal Microbiota Communities between Primiparous and Multiparous Cows during Non-Pregnancy and Pregnancy. Anim. Open Access J. MDPI 13, 869 (2023).
Mealy, G. et al. Impact of previous pregnancy and BMI on cellular and serum immune activity from early to late pregnancy. Sci. Rep. 14, 16055 (2024).
Hijazi, S. M., Fawzi, M. A., Ali, F. M. & Galil, K. H. A. E. Multidrug-resistant ESBL-producing Enterobacteriaceae and associated risk factors in community infants in Lebanon. J. Infect. Dev. Ctries. 10, 947–955 (2016).
Bäckhed, F. et al. Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life. Cell Host Microbe 17, 690–703 (2015).
Dominguez-Bello, M. G. et al. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc. Natl Acad. Sci. 107, 11971–11975 (2010).
Chereau, F. et al. Colonization of Extended-Spectrum-β-Lactamase- and NDM-1-Producing Enterobacteriaceae among Pregnant Women in the Community in a Low-Income Country: a Potential Reservoir for Transmission of Multiresistant Enterobacteriaceae to Neonates. Antimicrob. Agents Chemother. 59, 3652–3655 (2015).
Hashimoto, M., Hasegawa, H. & Maeda, S. High temperatures promote cell-to-cell plasmid transformation in Escherichia coli. Biochem. Biophys. Res. Commun. 515, 196–200 (2019).
Ratkowsky, D. A., Olley, J., McMeekin, T. A. & Ball, A. Relationship between temperature and growth rate of bacterial cultures. J. Bacteriol. 149, 1–5 (1982).
Shah, P. S. et al. Seasonal variations in healthcare-associated infection in neonates in Canada. Arch. Dis. Child. – Fetal Neonatal Ed. 98, F65–F69 (2013).
Karanika, S., Karantanos, T., Arvanitis, M., Grigoras, C. & Mylonakis, E. Fecal Colonization With Extended-spectrum Beta-lactamase–Producing Enterobacteriaceae and Risk Factors Among Healthy Individuals: A Systematic Review and Metaanalysis. Clin. Infect. Dis. 63, 310–318 (2016).
Scherff, N., Rothgänger, J., Weniger, T., Mellmann, A. & Harmsen, D. Real-time plasmid transmission detection pipeline. Microbiol. Spectr. 12, e02100–e02124 (2024).
Patnode, C. D. et al. Breastfeeding and Health Outcomes for Infants and Children: A Systematic Review. Pediatrics (2025) https://doi.org/10.1542/peds.2025-071516.
Nadimpalli, M. L. et al. Can breastfeeding protect against antimicrobial resistance?. BMC Med 18, 392 (2020).
Silago, V. et al. Bacteremia in critical care units at Bugando Medical Centre, Mwanza, Tanzania: the role of colonization and contaminated cots and mothers’ hands in cross-transmission of multidrug resistant Gram-negative bacteria. Antimicrob. Resist. Infect. CONTROL 9, (2020).
Orwa, S. A. et al. Global prevalence of antibiotic consumption during pregnancy: A systematic review and meta-analysis. J. Infect. 89, 106189 (2024).
Jazmati, N., Jazmati, T. & Hamprecht, A. Importance of pre-enrichment for detection of third-generation cephalosporin-resistant Enterobacteriaceae (3GCREB) from rectal swabs. Eur. J. Clin. Microbiol. Infect. Dis. 36, 1847–1851 (2017).
Jain, C., Rodriguez-R, L. M., Phillippy, A. M., Konstantinidis, K. T. & Aluru, S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat. Commun. 9, 5114 (2018).
Feldgarden, M. et al. AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Sci. Rep. 11, 12728 (2021).
Carattoli, A. et al. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob. Agents Chemother. 58, 3895–3903 (2014).
Criscuolo, A. A fast alignment-free bioinformatics procedure to infer accurate distance-based phylogenetic trees from genome assemblies. Res. Ideas Outcomes 5, e36178 (2019).
Criscuolo, A. On the transformation of MinHash-based uncorrected distances into proper evolutionary distances for phylogenetic inference. F1000Research 9, 1309 (2020).
Minh, B. Q. et al. IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. Mol. Biol. Evol. 37, 1530–1534 (2020).
Treangen, T. J., Ondov, B. D., Koren, S. & Phillippy, A. M. The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biol. 15, 524 (2014).
Wick, R. R., Judd, L. M., Gorrie, C. L. & Holt, K. E. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLOS Comput. Biol. 13, e1005595 (2017).
Vasimuddin, Md., Misra, S., Li, H. & Aluru, S. Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. in 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS) 314–324 (2019). https://doi.org/10.1109/IPDPS.2019.00041.
Abram, K. et al. Mash-based analyses of Escherichia coli genomes reveal 14 distinct phylogroups. Commun. Biol. 4, 1–12 (2021).