Effects of Probiotic Supplementation on the Gut Microbiota and Antibiotic Resistome Development in Preterm Infants

Eirin Esaiassen, Erik Hjerde, Jorunn Pauline Cavanagh, Tanja Pedersen, Jannicke H Andresen, Siren I Rettedal, Ragnhild Støen, Britt Nakstad, Nils P Willassen, Claus Klingenberg, Eirin Esaiassen, Erik Hjerde, Jorunn Pauline Cavanagh, Tanja Pedersen, Jannicke H Andresen, Siren I Rettedal, Ragnhild Støen, Britt Nakstad, Nils P Willassen, Claus Klingenberg

Abstract

Objectives: In 2014 probiotic supplementation (Lactobacillus acidophilus and Bifidobacterium longum subspecies infantis; InfloranⓇ) was introduced as standard of care to prevent necrotizing enterocolitis (NEC) in extremely preterm infants in Norway. We aimed to evaluate the influence of probiotics and antibiotic therapy on the developing gut microbiota and antibiotic resistome in extremely preterm infants, and to compare with very preterm infants and term infants not given probiotics. Study design: A prospective, observational multicenter study in six tertiary-care neonatal units. We enrolled 76 infants; 31 probiotic-supplemented extremely preterm infants <28 weeks gestation, 35 very preterm infants 28-31 weeks gestation not given probiotics and 10 healthy full-term control infants. Taxonomic composition and collection of antibiotic resistance genes (resistome) in fecal samples, collected at 7 and 28 days and 4 months age, were analyzed using shotgun-metagenome sequencing. Results: Median (IQR) birth weight was 835 (680-945) g and 1,290 (1,150-1,445) g in preterm infants exposed and not exposed to probiotics, respectively. Two extremely preterm infants receiving probiotic developed NEC requiring surgery. At 7 days of age we found higher median relative abundance of Bifidobacterium in probiotic supplemented infants (64.7%) compared to non-supplemented preterm infants (0.0%) and term control infants (43.9%). Lactobacillus was only detected in small amounts in all groups, but the relative abundance increased up to 4 months. Extremely preterm infants receiving probiotics had also much higher antibiotic exposure, still overall microbial diversity and resistome was not different than in more mature infants at 4 weeks and 4 months. Conclusion: Probiotic supplementation may induce colonization resistance and alleviate harmful effects of antibiotics on the gut microbiota and antibiotic resistome. Clinical Trial Registration: Clinicaltrials.gov: NCT02197468. https://ichgcp.net/clinical-trials-registry/NCT02197468.

Keywords: bifidobacteria; colonization resistance; gut microbiota; lactobacilli; preterm infant; shotgun metagenome sequencing; taxonomy.

Figures

Figure 1
Figure 1
CONSORT study flow diagram. PEP, probiotic extremely preterm; NPVP, non-probiotic very preterm; FTC, full term control; NICU, Neonatal Intensive care Unit.
Figure 2
Figure 2
(A–C) Median relative abundance of dominant taxa at genus level. Box plot diagram where the inside bar represent median, the outer horizontal line of the box represents the 25th and the 75th percentile. (A) Median relative abundance at 7 days. (B) Median relative abundance at 28 days. (C) Median relative abundance at 4 months.
Figure 3
Figure 3
(A–D) Alpha diversity calculated by Shannon diversity index and beta diversity between PEP, NPVP, and FTC infants calculated by non-metrical multidimensional scaling (NMDS). Box plot diagram where the inside bar represent median, the outer horizontal line of the box represents the 25th and the 75th percentile. Error bars represent the standard error. Differences between groups at a given time point and at different time points were tested with linear mixed model. (A) Shannon diversity index of three groups of infants at three sampling points. (B) Beta diversity (NMDS) at 7 days. (C) Beta diversity (NMDS) at 28 days. (D) Beta diversity (NMDS) at 4 months.

References

    1. Groer MW, Luciano AA, Dishaw LJ, Ashmeade TL, Miller E, Gilbert JA. Development of the preterm infant gut microbiome: a research priority. Microbiome (2014) 2:38. 10.1186/2049-2618-2-38
    1. Olin A, Henckel E, Chen Y, Lakshmikanth T, Pou C, Mikes J, et al. Stereotypic immune system development in newborn children. Cell (2018) 5:1277–92.e14. 10.1016/j.cell.2018.06.045
    1. Pammi M, Cope J, Tarr PI, Warner BB, Morrow AL, Mai V, et al. Intestinal dysbiosis in preterm infants preceding necrotizing enterocolitis: a systematic review and meta-analysis. Microbiome (2017) 1:31 10.1186/s40168-017-0248-8
    1. AlFaleh K, Anabrees J. Probiotics for prevention of necrotizing enterocolitis in preterm infants. Cochrane Database Syst Rev. (2014) 10:CD005496 10.1002/14651858.CD005496.pub4
    1. Aceti A, Gori D, Barone G, Callegari ML, Di Mauro A, Fantini MP, et al. . Probiotics for prevention of necrotizing enterocolitis in preterm infants: systematic review and meta-analysis. Ital J Pediatr. (2015) 41:89. 10.1186/s13052-015-0199-2
    1. Sawh SC, Deshpande S, Jansen S, Reynaert CJ, Jones PM. Prevention of necrotizing enterocolitis with probiotics: a systematic review and meta-analysis. PeerJ. (2016) 4:e2429. 10.7717/peerj.2429
    1. Lau CS, Chamberlain RS. Probiotic administration can prevent necrotizing enterocolitis in preterm infants: a meta-analysis. J Pediatr Surg. (2015) 8:1405–12. 10.1016/j.jpedsurg.2015.05.008
    1. Olsen R, Greisen G, Schroder M, Brok J. Prophylactic probiotics for preterm infants: a systematic review and meta-analysis of observational studies. Neonatology (2016) 2:105–12. 10.1159/000441274
    1. Costeloe K, Bowler U, Brocklehurst P, Hardy P, Heal P, Juszczak E, 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) 66:1–194. 10.3310/hta20660.
    1. Denkel LA, Schwab F, Garten L, Geffers C, Gastmeier P, Piening B. Protective effect of dual-strain probiotics in preterm infants: a multi-center time series analysis. PLoS ONE (2016) 6:e0158136 10.1371/journal.pone.0158136
    1. Tarnow-Mordi W, Soll RF. Probiotic supplementation in preterm infants: it is time to change practice. J Pediatr. (2014) 5:959–60. 10.1016/j.jpeds.2013.12.050
    1. Viswanathan S, Lau C, Akbari H, Hoyen C, Walsh MC. Survey and evidence based review of probiotics used in very low birth weight preterm infants within the United States. J Perinatol. (2016) 12:1106–11. 10.1038/jp.2016.144.
    1. Esaiassen E, Cavanagh P, Hjerde E, Simonsen GS, Stoen R, Klingenberg C. Bifidobacterium longum subspecies infantis bacteremia in 3 extremely preterm infants receiving probiotics. Emerg Infect Dis. (2016) 9:1664–6. 10.3201/eid2209.160033
    1. Zbinden A, Zbinden R, Berger C, Arlettaz R. Case series of Bifidobacterium longum bacteremia in three preterm infants on probiotic therapy. Neonatology (2015) 1:56–9. 10.1159/000367985
    1. Kolacek S, Hojsak I, Berni Canani R, Guarino A, Indrio F, et al. Commercial probiotic products: a call for improved quality control. a position paper by the ESPGHAN working group for probiotics and prebiotics. J Pediatr Gastroenterol Nutr. (2017) 1:117–24. 10.1097/mpg.0000000000001603
    1. Vallabhaneni S, Walker TA, Lockhart SR, Ng D, Chiller T, Melchreit R, et al. Notes from the field: fatal gastrointestinal mucormycosis in a premature infant associated with a contaminated dietary supplement–Connecticut, 2014. MMWR Morb Mortal Wkly Rep. (2015) 6:155–6.
    1. Frost BL, Modi BP, Jaksic T, Caplan MS. New medical and surgical insights into neonatal necrotizing enterocolitis: a review. JAMA Pediatr. (2017) 1:83–8. 10.1001/jamapediatrics.2016.2708
    1. Hsieh EM, Hornik CP, Clark RH, Laughon MM, Benjamin DK, Jr, Smith PB. Medication use in the neonatal intensive care unit. Am J Perinatol. (2014) 9:811–21. 10.1055/s-0033-1361933.
    1. Esaiassen E, Fjalstad JW, Juvet LK, van den Anker JN, Klingenberg C. Antibiotic exposure in neonates and early adverse outcomes: a systematic review and meta-analysis. J Antimicrob Chemother. (2017) 72:1858–70. 10.1093/jac/dkx088
    1. Cotten CM, Taylor S, Stoll B, Goldberg RN, Hansen NI, Sanchez PJ, et al. Prolonged duration of initial empirical antibiotic treatment is associated with increased rates of necrotizing enterocolitis and death for extremely low birth weight infants. Pediatrics (2009) 1:58–66. 10.1542/peds.2007-3423
    1. Gibson MK, Wang B, Ahmadi S, Burnham CA, Tarr PI, Warner BB, et al. . Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome. Nat Microbiol. (2016) 1:16024. 10.1038/nmicrobiol.2016.24
    1. Fjalstad JW, Esaiassen E, Juvet LK, van den Anker JN, Klingenberg C. Antibiotic therapy in neonates and impact on gut microbiota and antibiotic resistance development: a systematic review. J Antimicrob Chemother. (2017) 73:569–80. 10.1093/jac/dkx426
    1. Kelly BJ, Gross R, Bittinger K, Sherrill-Mix S, Lewis JD, Collman RG, et al. Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOV. Bioinformatics (2015) 15:2461–8. 10.1093/bioinformatics/btv183
    1. Klingenberg C. Preterm Infant Gut (PINGU) - a Norwegian Multi Centre Study (PINGU). Available online at:
    1. Hill CJ, Brown JR, Lynch DB, Jeffery IB, Ryan CA, Ross RP, et al. Effect of room temperature transport vials on DNA quality and phylogenetic composition of faecal microbiota of elderly adults and infants. Microbiome (2016) 1:19 10.1186/s40168-016-0164-3
    1. Neu J, Walker WA. Necrotizing enterocolitis. N Engl J Med. (2011) 3:255–64. 10.1056/NEJMra1005408
    1. Truong DT, Franzosa EA, Tickle TL, Scholz M, Weingart G, Pasolli E, et al. MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Nat Methods (2015) 10:902–3. 10.1038/nmeth.3589
    1. McArthur AG, Waglechner N, Nizam F, Yan A, Azad MA, Baylay AJ, et al. The comprehensive antibiotic resistance database. Antimicrob Agents Chemother. (2013) 7:3348–57. 10.1128/aac.00419-13
    1. Kaminski J, Gibson MK, Franzosa EA, Segata N, Dantas G, Huttenhower C. High-specificity targeted functional profiling in microbial communities with shortBRED. PLoS Comput Biol. (2015) 12:e1004557 10.1371/journal.pcbi.1004557
    1. Klingenberg C. Manual of Neonatal Medicine. 5th Edn. Tromsø: Paediatric Deptartment, University Hospital of Northern Norway; (2017).
    1. Abdulkadir B, Nelson A, Skeath T, Marrs EC, Perry JD, Cummings SP, et al. Routine use of probiotics in preterm infants: longitudinal impact on the microbiome and metabolome. Neonatology (2016) 4:239–47. 10.1159/000442936
    1. de Man P, Verhoeven BA, Verbrugh HA, Vos MC, van den Anker JN. An antibiotic policy to prevent emergence of resistant bacilli. Lancet (2000) 9208:973–8. 10.1016/S0140-6736(00)90015-1
    1. Parks DH, Tyson GW, Hugenholtz P, Beiko RG. STAMP: statistical analysis of taxonomic and functional profiles. Bioinformatics (2014) 21:3123–4. 10.1093/bioinformatics/btu494
    1. Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Series B (1995) 57:289–300.
    1. Huson DH, Auch AF, Qi J, Schuster SC. MEGAN analysis of metagenomic data. Genome Res. (2007) 3:377–86. 10.1101/gr.5969107
    1. Weng M, Walker WA. The role of gut microbiota in programming the immune phenotype. J Dev Orig Health Dis. (2013) 3:203–14. 10.1017/s2040174412000712
    1. Hill CJ, Lynch DB, Murphy K, Ulaszewska M, Jeffery IB, O'Shea CA, et al. Evolution of gut microbiota composition from birth to 24 weeks in the INFANTMET Cohort. Microbiome (2017) 1:4 10.1186/s40168-016-0213-y
    1. Arboleya S, Binetti A, Salazar N, Fernandez N, Solis G, Hernandez-Barranco A, et al. Establishment and development of intestinal microbiota in preterm neonates. FEMS Microbiol Ecol. (2012) 3:763–72. 10.1111/j.1574-6941.2011.01261.x
    1. Stewart CJ, Embleton ND, Marrs EC, Smith DP, Nelson A, Abdulkadir B, et al. Temporal bacterial and metabolic development of the preterm gut reveals specific signatures in health and disease. Microbiome (2016) 1:67 10.1186/s40168-016-0216-8
    1. Jacobs SE, Tobin JM, Opie GF, Donath S, Tabrizi SN, Pirotta M, et al. Probiotic effects on late-onset sepsis in very preterm infants: a randomized controlled trial. Pediatrics (2013) 6:1055–62. 10.1542/peds.2013-1339
    1. Bertelli C, Pillonel T, Torregrossa A, Prod'hom G, Fischer CJ, Greub G, et al. Bifidobacterium longum bacteremia in preterm infants receiving probiotics. Clin Infect Dis. (2015) 6:924–7. 10.1093/cid/ciu946
    1. Wang Y, Hoenig JD, Malin KJ, Qamar S, Petrof EO, Sun J, et al. 16S rRNA gene-based analysis of fecal microbiota from preterm infants with and without necrotizing enterocolitis. ISME J. (2009) 8:944–54. 10.1038/ismej.2009.37
    1. Butel MJ, Suau A, Campeotto F, Magne F, Aires J, Ferraris L, et al. Conditions of bifidobacterial colonization in preterm infants: a prospective analysis. J Pediatr Gastroenterol Nutr. (2007) 5:577–82. 10.1097/MPG.0b013e3180406b20
    1. Swidsinski A, Loening-Baucke V, Lochs H, Hale LP. Spatial organization of bacterial flora in normal and inflamed intestine: a fluorescence in situ hybridization study in mice. World J Gastroenterol. (2005) 8:1131–40. 10.3748/wjg.v11.i8.1131
    1. Villmones HC, Haug ES, Ulvestad E, Grude N, Stenstad T, Halland A, et al. Species level description of the human ileal bacterial microbiota. Sci Rep. (2018) 1:4736 10.1038/s41598-018-23198-5
    1. Dutta S, Ray P, Narang A. Comparison of stool colonization in premature infants by three dose regimes of a probiotic combination: a randomized controlled trial. Am J Perinatol. (2015) 8:733–40. 10.1055/s-0034-1395473
    1. Costeloe K, Hardy P, Juszczak E, Wilks M, Millar MR. Bifidobacterium breve BBG-001 in very preterm infants: a randomised controlled phase 3 trial. Lancet (2016) 10019:649–60. 10.1016/s0140-6736(15)01027-2
    1. Gritz EC, Bhandari V. The human neonatal gut microbiome: a brief review. Front Pediatr. (2015) 3:17 10.3389/fped.2015.00017
    1. Deshpande GC, Rao SC, Keil AD, Patole SK. Evidence-based guidelines for use of probiotics in preterm neonates. BMC Med. (2011) 9:92. 10.1186/1741-7015-9-92
    1. Siggers RH, Siggers J, Thymann T, Boye M, Sangild PT. Nutritional modulation of the gut microbiota and immune system in preterm neonates susceptible to necrotizing enterocolitis. J Nutr Biochem. (2011) 6:511–21. 10.1016/j.jnutbio.2010.08.002
    1. Cilieborg MS, Boye M, Sangild PT. Bacterial colonization and gut development in preterm neonates. Early Hum Dev. (2012) 88:S41–9. 10.1016/j.earlhumdev.2011.12.027
    1. Watkins C, Murphy K, Dempsey EM, O'Shea CA, Murphy BP, O'Toole PW, et al. Dose-interval study of a dual probiotic in preterm infants. Arch Dis Child Fetal Neonatal Ed. (2018) 20:313468 10.1136/archdischild-2017-313468
    1. Hall MA, Cole CB, Smith SL, Fuller, Rolles CJ. Factors influencing the presence of faecal lactobacilli in early infancy. Arch Dis Childhood (1990) 2:185–88.
    1. Fouhy F, Guinane CM, Hussey S, Wall R, Ryan CA, Dempsey EM, 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) 11:5811–20. 10.1128/aac.00789-12
    1. Rose G, Shaw AG, Sim K, Wooldridge DJ, Li MS, Gharbia S, et al. . Antibiotic resistance potential of the healthy preterm infant gut microbiome. PeerJ. (2017) 5:e2928. 10.7717/peerj.2928
    1. Grazul H, Kanda LL, Gondek D. Impact of probiotic supplements on microbiome diversity following antibiotic treatment of mice. Gut Microbes (2016) 2:101–14. 10.1080/19490976.2016.1138197
    1. Fouhy F, Ogilvie LA, Jones B, Ross RP, Ryan AC, Dempsey EM, et al. . Identification of aminoglycoside and beta-lactam resistance genes from within an infant gut functional metagenomic library. PLoS ONE (2014) 9:e108016. 10.1371/journal.pone.0108016
    1. von Wintersdorff CJ, Wolffs PF, Savelkoul PH, Nijsen RR, Lau S, Gerhold K, et al. The gut resistome is highly dynamic during the first months of life. Future Microbiol. (2016) 4:501–10. 10.2217/fmb.15.154
    1. Moore AM, Patel S, Forsberg KJ, Wang B, Bentley G, Razia Y, et al. Pediatric fecal microbiota harbor diverse and novel antibiotic resistance genes. PLoS ONE (2013) 11:e78822 10.1371/journal.pone.0078822
    1. Pamer EG. Resurrecting the intestinal microbiota to combat antibiotic-resistant pathogens. Science (2016) 6285:535–8. 10.1126/science.aad9382
    1. Ravi A, Estensmo ELF, Abee-Lund TML, Foley SL, Allgaier B, Martin CR, et al. . Association of the gut microbiota mobilome with hospital location and birth weight in preterm infants. Pediatr Res. (2017) 82:829–838. 10.1038/pr.2017.146

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