Hornik CP, Fort P, Clark RH, et al. Early and late onset sepsis in very-low-birth-weight infants from a large group of neonatal intensive care units. Early Hum Dev. 2012;88(Suppl 2):S69-74. https://doi.org/10.1016/S0378-3782(12)70019-1.

Article  PubMed  PubMed Central  Google Scholar 

Gan MY, Lee WL, Yap BJ, et al. Contemporary trends in global mortality of sepsis among young infants less than 90 days: a systematic review and meta-analysis. Front Pediatr. 2022;10: 890767. https://doi.org/10.3389/fped.2022.890767.

Article  PubMed  PubMed Central  Google Scholar 

Klinger G, Levy I, Sirota L, et al. Epidemiology and risk factors for early onset sepsis among very-low-birthweight infants. Am J Obstet Gynecol. 2009;201(1):38 e1-46. https://doi.org/10.1016/j.ajog.2009.03.006.

Article  PubMed  Google Scholar 

Stoll BJ, Hansen N, Fanaroff AA, et al. Late-onset sepsis in very low birth weight neonates: the experience of the NICHD Neonatal Research Network. Pediatrics. 2002;110(2 Pt 1):285–91. https://doi.org/10.1542/peds.110.2.285.

Article  PubMed  Google Scholar 

Goh GL, Lim CSE, Sultana R, De La Puerta R, Rajadurai VS, Yeo KT. Risk factors for mortality from late-onset sepsis among preterm very-low-birthweight infants: a single-center cohort study from Singapore. Front Pediatr. 2021;9: 801955. https://doi.org/10.3389/fped.2021.801955.

Article  PubMed  Google Scholar 

Boghossian NS, Page GP, Bell EF, et al. Late-onset sepsis in very low birth weight infants from singleton and multiple-gestation births. J Pediatr. 2013;162(6):1120–4, 1124 e1. https://doi.org/10.1016/j.jpeds.2012.11.089.

Article  PubMed  PubMed Central  Google Scholar 

Carl MA, Ndao IM, Springman AC, et al. Sepsis from the gut: the enteric habitat of bacteria that cause late-onset neonatal bloodstream infections. Clin Infect Dis. 2014;58(9):1211–8. https://doi.org/10.1093/cid/ciu084.

Article  PubMed  PubMed Central  Google Scholar 

Smith A, Saiman L, Zhou J, Della-Latta P, Jia H, Graham PL 3rd. Concordance of gastrointestinal tract colonization and subsequent bloodstream infections with gram-negative bacilli in very low birth weight infants in the neonatal intensive care unit. Pediatr Infect Dis J. 2010;29(9):831–5. https://doi.org/10.1097/INF.0b013e3181e7884f.

Article  PubMed  PubMed Central  Google Scholar 

Graspeuntner S, Waschina S, Kunzel S, et al. Gut dysbiosis with bacilli dominance and accumulation of fermentation products precedes late-onset sepsis in preterm infants. Clin Infect Dis. 2019;69(2):268–77. https://doi.org/10.1093/cid/ciy882.

Article  CAS  PubMed  Google Scholar 

Mai V, Torrazza RM, Ukhanova M, et al. Distortions in development of intestinal microbiota associated with late onset sepsis in preterm infants. PLoS ONE. 2013;8(1): e52876. https://doi.org/10.1371/journal.pone.0052876.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Stewart CJ, Embleton ND, Marrs ECL, et al. Longitudinal development of the gut microbiome and metabolome in preterm neonates with late onset sepsis and healthy controls. Microbiome. 2017;5(1):75. https://doi.org/10.1186/s40168-017-0295-1.

Article  PubMed  PubMed Central  Google Scholar 

Mukhopadhyay S, Lee JJ, Hartman E, et al. Preterm infants at low risk for early-onset sepsis differ in early fecal microbiome assembly. Gut Microbes. 2022;14(1):2154091. https://doi.org/10.1080/19490976.2022.2154091.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Graham PL 3rd, Della-Latta P, Wu F, Zhou J, Saiman L. The gastrointestinal tract serves as the reservoir for Gram-negative pathogens in very low birth weight infants. Pediatr Infect Dis J. 2007;26(12):1153–6. https://doi.org/10.1097/INF.0b013e31814619d4.

Article  PubMed  Google Scholar 

El Manouni El Hassani S, Niemarkt HJ, Berkhout DJC, et al. Profound pathogen-specific alterations in intestinal microbiota composition precede late-onset sepsis in preterm infants: a longitudinal, multicenter, case-control study. Clin Infect Dis. 2021;73(1):e224–32. https://doi.org/10.1093/cid/ciaa1635.

Article  CAS  PubMed  Google Scholar 

Madan JC, Salari RC, Saxena D, et al. Gut microbial colonisation in premature neonates predicts neonatal sepsis. Arch Dis Child Fetal Neonatal Ed. 2012;97(6):F456–62. https://doi.org/10.1136/fetalneonatal-2011-301373.

Article  PubMed  Google Scholar 

Selma-Royo M, Calatayud Arroyo M, Garcia-Mantrana I, et al. Perinatal environment shapes microbiota colonization and infant growth: impact on host response and intestinal function. Microbiome. 2020;8(1):167. https://doi.org/10.1186/s40168-020-00940-8.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Avershina E, Storro O, Oien T, et al. Bifidobacterial succession and correlation networks in a large unselected cohort of mothers and their children. Appl Environ Microbiol. 2013;79(2):497–507. https://doi.org/10.1128/AEM.02359-12.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gasparrini AJ, Wang B, Sun X, et al. Persistent metagenomic signatures of early-life hospitalization and antibiotic treatment in the infant gut microbiota and resistome. Nat Microbiol. 2019;4(12):2285–97. https://doi.org/10.1038/s41564-019-0550-2.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gibson MK, Wang B, Ahmadi S, et al. Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome. Nat Microbiol. 2016;1:16024. https://doi.org/10.1038/nmicrobiol.2016.24.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Mallick H, Rahnavard A, McIver LJ, et al. Multivariable association discovery in population-scale meta-omics studies. PLoS Comput Biol. 2021;17(11): e1009442. https://doi.org/10.1371/journal.pcbi.1009442.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Olm MR, Crits-Christoph A, Bouma-Gregson K, Firek BA, Morowitz MJ, Banfield JF. inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains. Nat Biotechnol. 2021;39(6):727–36. https://doi.org/10.1038/s41587-020-00797-0.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lou YC, Olm MR, Diamond S, et al. Infant gut strain persistence is associated with maternal origin, phylogeny, and traits including surface adhesion and iron acquisition. Cell Rep Med. 2021;2(9): 100393. https://doi.org/10.1016/j.xcrm.2021.100393.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jimenez E, Delgado S, Maldonado A, et al. Staphylococcus epidermidis: a differential trait of the fecal microbiota of breast-fed infants. BMC Microbiol. 2008;8:143. https://doi.org/10.1186/1471-2180-8-143.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Tazi A, Plainvert C, Anselem O, et al. Risk factors for infant colonization by hypervirulent CC17 Group B Streptococcus: toward the understanding of late-onset disease. Clin Infect Dis. 2019;69(10):1740–8. https://doi.org/10.1093/cid/ciz033.

Article  CAS  PubMed  Google Scholar 

Jeffreys AJ, Royle NJ, Patel I, et al. Principles and recent advances in human DNA fingerprinting. EXS. 1991;58:1–19. https://doi.org/10.1007/978-3-0348-7312-3_1.

Article  CAS  PubMed  Google Scholar 

Fouhy F, Guinane CM, Hussey S, et al. High-throughput sequencing reveals the incomplete, short-term recovery of infant gut microbiota following parenteral antibiotic treatment with ampicillin and gentamicin. Antimicrob Agents Chemother. 2012;56(11):5811–20. https://doi.org/10.1128/AAC.00789-12.

Article  CAS  PubMed  PubMed Central  Google Scholar 

McDonnell L, Gilkes A, Ashworth M, et al. Association between antibiotics and gut microbiome dysbiosis in children: systematic review and meta-analysis. Gut Microbes Jan-Dec. 2021;13(1):1–18. https://doi.org/10.1080/19490976.2020.1870402.

Article  CAS  Google Scholar 

Costeloe K, Bowler U, Brocklehurst P, et al. A randomised controlled trial of the probiotic Bifidobacterium breve BBG-001 in preterm babies to prevent sepsis, necrotising enterocolitis and death: the Probiotics in Preterm infantS (PiPS) trial. Health Technol Assess. 2016;20(66):1–194. https://doi.org/10.3310/hta20660.

Article  PubMed  PubMed Central  Google Scholar 

Sowden M, van Weissenbruch MM, Bulabula ANH, van Wyk L, Twisk J, van Niekerk E. Effect of a multi-strain probiotic on the incidence and severity of necrotizing enterocolitis and feeding intolerances in preterm neonates. Nutrients. 2022. https://doi.org/10.3390/nu14163305.

Article  PubMed  PubMed Central  Google Scholar 

Jacobs SE, Tobin JM, Opie GF, et al. Probiotic effects on late-onset sepsis in very preterm infants: a randomized controlled trial. Pediatrics. 2013;132(6):1055–62. https://doi.org/10.1542/peds.2013-1339.

Article  PubMed  Google Scholar 

Rao SC, Athalye-Jape GK, Deshpande GC, Simmer KN, Patole SK. Probiotic supplementation and late-onset sepsis in preterm infants: a meta-analysis. Pediatrics. 2016;137(3): e20153684. https://doi.org/10.1542/peds.2015-3684.

Article  PubMed  Google Scholar 

Wong CB, Iwabuchi N, Xiao JZ. Exploring the science behind Bifidobacterium breve M-16V in infant health. Nutrients. 2019. https://doi.org/10.3390/nu11081724.

Article