Stoll, B. J. et al. Early-onset neonatal sepsis 2015 to 2017, the rise of Escherichia coli, and the need for novel prevention strategies. JAMA Pediatr. 174, e200593 (2020).
Biondi, E. et al. Epidemiology of bacteremia in febrile infants in the United States. Pediatrics 132, 990–996 (2013).
Secher, T., Brehin, C. & Oswald, E. Early settlers: which E. coli strains do you not want at birth? Am. J. Physiol. 311, G123–G129 (2016).
Al-Balawi, M. & Morsy, F. M. Prenatal versus postnatal initial colonization of healthy neonates’ colon ecosystem by the enterobacterium Escherichia coli. Microbiol. Spectr. 9, e0037921 (2021).
Backhed, F. et al. Dynamics and stabilization of the human gut microbiome during the first year of life. Cell Host Microbe 17, 852 (2015).
Elahi, S. et al. Immunosuppressive CD71+ erythroid cells compromise neonatal host defence against infection. Nature 504, 158–162 (2013).
Kollmann, T. R., Kampmann, B., Mazmanian, S. K., Marchant, A. & Levy, O. Protecting the newborn and young infant from infectious diseases: lessons from immune ontogeny. Immunity 46, 350–363 (2017).
Olin, A. et al. Stereotypic immune system development in newborn children. Cell 174, 1277–1292.e14 (2018).
Araujo David, B. et al. Kupffer cell reverse migration into the liver sinusoids mitigates neonatal sepsis and meningitis. Sci. Immunol. 9, eadq9704 (2024).
Sonnenborn, U. Escherichia coli strain Nissle 1917-from bench to bedside and back: history of a special Escherichia coli strain with probiotic properties. FEMS Microbiol. Lett. 363, fnw212 (2016).
Kaper, J. B., Nataro, J. P. & Mobley, H. L. Pathogenic Escherichia coli. Nat. Rev. Microbiol. 2, 123–140 (2004).
Tenaillon, O., Skurnik, D., Picard, B. & Denamur, E. The population genetics of commensal Escherichia coli. Nat. Rev. Microbiol. 8, 207–217 (2010).
Sawhney, S. S. et al. Gut microbiome evolution from infancy to 8 years of age. Nat. Med. 31, 2004–2015 (2025).
Hunstad, D. A. & Justice, S. S. Intracellular lifestyles and immune evasion strategies of uropathogenic Escherichia coli. Annu. Rev. Microbiol. 64, 203–221 (2010).
Biggel, M. et al. Horizontally acquired papGII-containing pathogenicity islands underlie the emergence of invasive uropathogenic Escherichia coli lineages. Nat. Commun. 11, 5968 (2020).
Mu, A. et al. Integrative omics identifies conserved and pathogen-specific responses of sepsis-causing bacteria. Nat. Commun. 14, 1530 (2023).
Bonten, M. et al. Epidemiology of Escherichia coli bacteremia: a systematic literature review. Clin. Infect. Dis. 72, 1211–1219 (2021).
Feldman, S. F. et al. A nationwide population-based study of Escherichia coli bloodstream infections: incidence, antimicrobial resistance and mortality. Clin. Microbiol. Infect. 28, 879.e1–879.e7 (2022).
Wertheim, H. F. et al. Risk and outcome of nosocomial Staphylococcus aureus bacteraemia in nasal carriers versus non-carriers. Lancet 364, 703–705 (2004).
Cohen, I. R. & Norins, L. C. Natural human antibodies to gram-negative bacteria: immunoglobulins G, A, and M. Science 152, 1257–1259 (1966).
Haas, A. et al. Systemic antibody responses to gut commensal bacteria during chronic HIV-1 infection. Gut 60, 1506–1519 (2011).
Koch, M. A. et al. Maternal IgG and IgA antibodies dampen mucosal T helper cell responses in early life. Cell 165, 827–841 (2016).
Zeng, M. Y. et al. Gut microbiota-induced immunoglobulin G controls systemic infection by symbiotic bacteria and pathogens. Immunity 44, 647–658 (2016).
Zheng, W. et al. Microbiota-targeted maternal antibodies protect neonates from enteric infection. Nature 577, 543–548 (2020).
Hofstra, H. & Dankert, J. Antigenic cross-reactivity of major outer membrane proteins in enterobacteriaceae species. J. Gen. Microbiol. 111, 293–302 (1979).
Baker, C. J. & Kasper, D. L. Correlation of maternal antibody deficiency with susceptibility to neonatal group B streptococcal infection. N. Engl. J. Med. 294, 753–756 (1976).
Chace, D. H., De Jesus, V. R. & Spitzer, A. R. Clinical chemistry and dried blood spots: increasing laboratory utilization by improved understanding of quantitative challenges. Bioanalysis 6, 2791–2794 (2014).
Nhu, N. T. K. High-risk Escherichia coli clones that cause neonatal meningitis and association with recrudescent infection. eLife 12, RP91853 (2024).
Cole, B. K., Ilikj, M., McCloskey, C. B. & Chavez-Bueno, S. Antibiotic resistance and molecular characterization of bacteremia Escherichia coli isolates from newborns in the United States. PLoS ONE 14, e0219352 (2019).
Malaure, C. et al. Early-onset infection caused by Escherichia coli sequence type 1193 in late preterm and full-term neonates. Emerg. Infect. Dis. 30, 20–28 (2024).
Mulvey, M. A., Schilling, J. D. & Hultgren, S. J. Establishment of a persistent Escherichia coli reservoir during the acute phase of a bladder infection. Infect. Immun. 69, 4572–4579 (2001).
Day, M. W., Jackson, L. A., Akins, D. R., Dyer, D. W. & Chavez-Bueno, S. Whole-genome sequences of the archetypal K1 Escherichia coli neonatal isolate RS218 and contemporary neonatal bacteremia clinical isolates SCB11, SCB12, and SCB15. Genome Announc. 3, e01598-14 (2015).
Williams, M. et al. Whole-genome sequencing-based phylogeny, antibiotic resistance, and invasive phenotype of Escherichia coli strains colonizing the cervix of women in preterm labor. BMC Microbiol. 21, 330 (2021).
Chavez-Bueno, S., Day, M. W., Toby, I. T., Akins, D. R. & Dyer, D. W. Genome sequence of SCB34, a sequence type 131 multidrug-resistant Escherichia coli isolate causing neonatal early-onset sepsis. Genome Announc. https://doi.org/10.1128/genomeA.00514-14 (2014).
Gu, H. et al. Rational design and evaluation of an artificial Escherichia coli K1 protein vaccine candidate based on the structure of OmpA. Front. Cell Infect. Microbiol. 8, 172 (2018).
Mayorga, M., Wheatley, J. L., Maldonado, B. N. & Chavez-Bueno, S. Bovine lactoferrin maintains antibacterial effect against neonatal Escherichia coli septicaemia isolates despite the presence of iron acquisition genes. J. Med. Microbiol. https://doi.org/10.1099/jmm.0.002116 (2026).
Sarkar, S., Ulett, G. C., Totsika, M., Phan, M. D. & Schembri, M. A. Role of capsule and O antigen in the virulence of uropathogenic Escherichia coli. PLoS ONE 9, e94786 (2014).
Phan, M. D. et al. The serum resistome of a globally disseminated multidrug resistant uropathogenic Escherichia coli clone. PLoS Genet. 9, e1003834 (2013).
Pautsch, A. & Schulz, G. E. Structure of the outer membrane protein A transmembrane domain. Nat. Struct. Biol. 5, 1013–1017 (1998).
Netea, M. G. et al. Defining trained immunity and its role in health and disease. Nat. Rev. Immunol. 20, 375–388 (2020).
Rusconi, B. et al. Intergenerational protective anti-gut commensal immunoglobulin G originates in early life. Proc. Natl Acad. Sci. USA 121, e2309994121 (2024).
Cohen, I. R. & Norins, L. C. Antibiodies of the IgG, IgM, and IgA classes in newborn and adult sera reactive with gram-negative bacteria. J. Clin. Invest. 47, 1053–1062 (1968).
Crook, N. et al. Adaptive strategies of the candidate probiotic E. coli Nissle in the mammalian gut. Cell Host Microbe 25, 499–512.e8 (2019).
Caballero-Flores, G. et al. Maternal immunization confers protection to the offspring against an attaching and effacing pathogen through delivery of IgG in breast milk. Cell Host Microbe 25, 313–323.e4 (2019).
Sanidad, K. Z. et al. Maternal gut microbiome-induced IgG regulates neonatal gut microbiome and immunity. Sci. Immunol. 7, eabh3816 (2022).
Smith, P., DiLillo, D. J., Bournazos, S., Li, F. & Ravetch, J. V. Mouse model recapitulating human Fcγ receptor structural and functional diversity. Proc. Natl Acad. Sci. USA 109, 6181–6186 (2012).
Erickson, J. J. et al. Pregnancy enables antibody protection against intracellular infection. Nature 606, 769–775 (2022).
Lawrence, S. M., Corriden, R. & Nizet, V. Age-appropriate functions and dysfunctions of the neonatal neutrophil. Front. Pediatr. 5, 23 (2017).
McGreal, E. P., Hearne, K. & Spiller, O. B. Off to a slow start: under-development of the complement system in term newborns is more substantial following premature birth. Immunobiology 217, 176–186 (2012).
Balogh, P., Tew, J. G. & Szakal, A. K. Simultaneous blockade of Fcγ receptors and indirect labeling of mouse lymphocytes by the selective detection of allotype-restricted epitopes on the kappa chain of rat monoclonal antibodies. Cytometry 47, 107–110 (2002).
Berry, G. T. Galactosemia: when is it a newborn screening emergency? Mol. Genet. Metab. 106, 7–11 (2012).
Xu, Y. et al. Antibiotic exposure prevents acquisition of beneficial metabolic functions in the preterm infant gut microbiome. Microbiome 10, 103 (2022).
Hwang, J. et al. Predictive factors for perinatal bacterial transmission from colonized mothers to delivered very-low-birth-weight infants: a retrospective cohort study. Sci. Rep. 14, 16835 (2024).
Malek, A., Sager, R., Kuhn, P., Nicolaides, K. H. & Schneider, H. Evolution of maternofetal transport of immunoglobulins during human pregnancy. Am. J. Reprod. Immunol. 36, 248–255 (1996).
Zhang, S. L. et al. Maternal and neonatal IgG against Klebsiella pneumoniae are associated with lower risk of neonatal sepsis: a case-control study of hospitalized neonates in Botswana. PLOS Glob. Public Health 4, e0003350 (2024).
Madhi, S. A. et al. Influenza vaccination of pregnant women and protection of their infants. N. Engl. J. Med. 371, 918–931 (2014).
Pasetti, M. F. et al. Maternal determinants of infant immunity: Implications for effective immunization and maternal-child health. Vaccine 38, 4491–4494 (2020).
Atyeo, C. G. et al. Maternal immune response and placental antibody transfer after COVID-19 vaccination across trimester and platforms. Nat. Commun. 13, 3571 (2022).
Kollmann, T. R., Marchant, A. & Way, S. S. Vaccination strategies to enhance immunity in neonates. Science 368, 612–615 (2020).
Qiu, L. et al. Vaccines against extraintestinal pathogenic Escherichia coli (ExPEC): progress and challenges. Gut Microbes 16, 2359691 (2024).
Wessels, M. R. et al. Studies of group B streptococcal infection in mice deficient in complement component C3 or C4 demonstrate an essential role for complement in both innate and acquired immunity. Proc. Natl Acad. Sci. USA 92, 11490–11494 (1995).
Fonseca, M. I. et al. Cell-specific deletion of C1qa identifies microglia as the dominant source of C1q in mouse brain. J. Neuroinflammation 14, 48 (2017).
Kitamura, D., Roes, J., Kuhn, R. & Rajewsky, K. A B cell-deficient mouse by targeted disruption of the membrane exon of the immunoglobulin mu chain gene. Nature 350, 423–426 (1991).
Nitschke, L., Carsetti, R., Ocker, B., Kohler, G. & Lamers, M. C. CD22 is a negative regulator of B-cell receptor signalling. Curr. Biol. 7, 133–143 (1997).
Totsika, M. et al. Insights into a multidrug resistant Escherichia coli pathogen of the globally disseminated ST131 lineage: genome analysis and virulence mechanisms. PLoS ONE 6, e26578 (2011).
Nhu, N. T. K. et al. Discovery of new genes involved in Curli production by a uropathogenic escherichia coli strain from the highly virulent O45:K1:H7 lineage. mBio https://doi.org/10.1128/mBio.01462-18 (2018).
Mobley, H. L. et al. Pyelonephritogenic Escherichia coli and killing of cultured human renal proximal tubular epithelial cells: role of hemolysin in some strains. Infect. Immun. 58, 1281–1289 (1990).
Nhu, N. T. K. et al. A convergent evolutionary pathway attenuating cellulose production drives enhanced virulence of some bacteria. Nat. Commun. 15, 1441 (2024).
Choi, J., Schmukler, M. & Groisman, E. A. Degradation of gene silencer is essential for expression of foreign genes and bacterial colonization of the mammalian gut. Proc. Natl Acad. Sci. USA 119, e2210239119 (2022).
Budnick, J. A., Bina, X. R. & Bina, J. E. Complete genome sequence of Klebsiella pneumoniae strain ATCC 43816. Microbiol. Resour. Announc. https://doi.org/10.1128/MRA.01441-20 (2021).
Gort, A. S. & Miller, V. L. Identification and characterization of Yersinia enterocolitica genes induced during systemic infection. Infect Immun 68, 6633–6642 (2000).
Montano, J. et al. Salmonella enterica Serovar Typhimurium 14028s genomic regions required for colonization of lettuce leaves. Front. Microbiol. 11, 6 (2020).
Becavin, C. et al. Comparison of widely used Listeria monocytogenes strains EGD, 10403S, and EGD-e highlights genomic variations underlying differences in pathogenicity. mBio 5, e00969–00914 (2014).
Ren, Y. et al. Complete genome sequence of Enterobacter cloacae subsp. cloacae type strain ATCC 13047. J. Bacteriol. 192, 2463–2464 (2010).
Shao, T. Y. et al. Commensal Candida albicans positively calibrates systemic Th17 immunological responses. Cell Host Microbe 25, 404–417.e6 (2019).
Prasanphanich, N. S. et al. Preconceptual priming overrides susceptibility to Escherichia coli systemic infection during pregnancy. mBio https://doi.org/10.1128/mBio.00002-21 (2021).
Jiang, T. T. et al. Commensal fungi recapitulate the protective benefits of intestinal bacteria. Cell Host Microbe 22, 809–816.e4 (2017).
Wimmers, F. et al. Multi-omics analysis of mucosal and systemic immunity to SARS-CoV-2 after birth. Cell 186, 4632–4651.e23 (2023).
Langbo, C., Bach, J., Kleyn, M. & Downes, F. P. From newborn screening to population health research: implementation of the Michigan BioTrust for health. Public Health Rep. 128, 377–384 (2013).
Mei, J. V., Alexander, J. R., Adam, B. W. & Hannon, W. H. Use of filter paper for the collection and analysis of human whole blood specimens. J. Nutr. 131, 1631S–1636S (2001).
Mercader, S., Featherstone, D. & Bellini, W. J. Comparison of available methods to elute serum from dried blood spot samples for measles serology. J. Virol. Methods 137, 140–149 (2006).
Gruner, N., Stambouli, O. & Ross, R. S. Dried blood spots–preparing and processing for use in immunoassays and in molecular techniques. J. Vis. Exp. 97, e52619 (2015).
Lee, T. S. et al. BglBrick vectors and datasheets: a synthetic biology platform for gene expression. J. Biol. Eng. 5, 12 (2011).
Hegde, S. et al. Inhibition of RHOA activity preserves the survival and hemostasis function of long-term cold-stored platelets. Blood 144, 1732–1746 (2024).
Millius, A. & Weiner, O. D. Manipulation of neutrophil-like HL-60 cells for the study of directed cell migration. Methods Mol. Biol. 591, 147–158 (2010).
De Coster, W., D’Hert, S., Schultz, D. T., Cruts, M. & Van Broeckhoven, C. NanoPack: visualizing and processing long-read sequencing data. Bioinformatics 34, 2666–2669 (2018).
Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455–477 (2012).
Vaser, R., Sovic, I., Nagarajan, N. & Sikic, M. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res. 27, 737–746 (2017).
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).
Gurevich, A., Saveliev, V., Vyahhi, N. & Tesler, G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29, 1072–1075 (2013).
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).
Deatherage, D. E. & Barrick, J. E. Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq. Methods Mol. Biol. 1151, 165–188 (2014).
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).
