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Stinson LF, Ma J, Lai CT, Rea A, Perrella SL, Geddes DT. Milk microbiome transplantation: recolonizing donor milk with mother's own milk microbiota. Appl Microbiol Biotechnol 2024; 108:74. [PMID: 38194146 PMCID: PMC10776751 DOI: 10.1007/s00253-023-12965-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/29/2023] [Accepted: 12/10/2023] [Indexed: 01/10/2024]
Abstract
Donor human milk (DHM) provides myriad nutritional and immunological benefits for preterm and low birthweight infants. However, pasteurization leaves DHM devoid of potentially beneficial milk microbiota. In the present study, we performed milk microbiome transplantation from freshly collected mother's own milk (MOM) into pasteurized DHM. Small volumes of MOM (5%, 10%, or 30% v/v) were inoculated into pasteurized DHM and incubated at 37 °C for up to 8 h. Further, we compared microbiome recolonization in UV-C-treated and Holder-pasteurized DHM, as UV-C treatment has been shown to conserve important biochemical components of DHM that are lost during Holder pasteurization. Bacterial culture and viability-coupled metataxonomic sequencing were employed to assess the effectiveness of milk microbiome transplantation. Growth of transplanted MOM bacteria occurred rapidly in recolonized DHM samples; however, a greater level of growth was observed in Holder-pasteurized DHM compared to UV-C-treated DHM, potentially due to the conserved antimicrobial properties in UV-C-treated DHM. Viability-coupled metataxonomic analysis demonstrated similarity between recolonized DHM samples and fresh MOM samples, suggesting that the milk microbiome can be successfully transplanted into pasteurized DHM. These results highlight the potential of MOM microbiota transplantation to restore the microbial composition of UV-C-treated and Holder-pasteurized DHM and enhance the nutritional and immunological benefits of DHM for preterm and vulnerable infants. KEY POINTS: • Mother's own milk microbiome can be successfully transplanted into donor human milk. • Recolonization is equally successful in UV-C-treated and Holder-pasteurized milk. • Recolonization time should be restricted due to rapid bacterial growth.
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Affiliation(s)
- Lisa F Stinson
- School of Molecular Sciences, The University of Western Australia, Perth, Australia.
| | - Jie Ma
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
| | - Ching Tat Lai
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
| | - Alethea Rea
- Mathematics and Statistics, Murdoch University, Perth, Australia
| | - Sharon L Perrella
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
| | - Donna T Geddes
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
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2
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Samarra A, Cabrera-Rubio R, Martínez-Costa C, Collado MC. Unravelling the evolutionary dynamics of antibiotic resistance genes in the infant gut microbiota during the first four months of life. Ann Clin Microbiol Antimicrob 2024; 23:72. [PMID: 39138497 PMCID: PMC11323388 DOI: 10.1186/s12941-024-00725-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 07/12/2024] [Indexed: 08/15/2024] Open
Abstract
BACKGROUND Alongside microbiota development, the evolution of the resistome is crucial in understanding the early-life acquisition and persistence of Antibiotic Resistance Genes (ARGs). Therefore, the aim of this study is to provide a comprehensive view of the evolution and dynamics of the neonatal resistome from 7 days to 4 months of age using a high-throughput qPCR platform. METHODS In the initial phase, a massive screening of 384 ARGs using a high-throughput qPCR in pooled healthy mother-infant pairs feces from the MAMI cohort was carried out to identify the most abundant and prevalent ARGs in infants and in mothers. This pre-analysis allowed for later targeted profiling in a large number of infants in a longitudinal manner during the first 4 months of life. 16S rRNA V3-V4 amplicon sequencing was performed to asses microbial composition longitudinally. Potential factors influencing the microbiota and ARGs in this period were also considered, such as mode of birth and breastfeeding type. RESULTS Following the massive screening, the top 45 abundant ARGs and mobile genetic elements were identified and studied in 72 infants during their first months of life (7 days, 1, 2, and 4 months). These genes were associated with resistance to aminoglycosides, beta-lactams and tetracyclines, among others, as well as integrons, and other mobile genetic elements. Changes in both ARG composition and quantity were observed during the first 4 months of life: most ARGs abundance increased over time, but mobile genetic elements decreased significantly. Further exploration of modulating factors highlighted the effect on ARG composition of specific microbial genus, and the impact of mode of birth at 7 days and 4 months. The influence of infant formula feeding was observed at 4-month-old infants, who exhibited a distinctive resistome composition. CONCLUSIONS This study illustrates the ARG evolution and dynamics in the infant gut by use of a targeted, high-throughput, quantitative PCR-based method. An increase in antibiotic resistance over the first months of life were observed with a fundamental role of delivery mode in shaping resistance profiles. Further, we highlighted the influence of feeding methods on the resistome development. These findings offer pivotal insights into dynamics of and factors influencing early-life resistome, with potential avenues for intervention strategies.
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Affiliation(s)
- Anna Samarra
- Departament of Biotechnology, Institute of Agrochemistry and Food Technology- National Spanish Research Council (IATA-CSIC), Paterna, Valencia, Spain
| | - Raúl Cabrera-Rubio
- Departament of Biotechnology, Institute of Agrochemistry and Food Technology- National Spanish Research Council (IATA-CSIC), Paterna, Valencia, Spain
| | - Cecilia Martínez-Costa
- Department of Pediatrics, School of Medicine, University of Valencia, Valencia, Spain
- Pediatric Gastroenterology and Nutrition Section, Hospital Clínico Universitario Valencia, INCLIVA, Valencia, Spain
| | - Maria Carmen Collado
- Departament of Biotechnology, Institute of Agrochemistry and Food Technology- National Spanish Research Council (IATA-CSIC), Paterna, Valencia, Spain.
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Dubois L, Valles-Colomer M, Ponsero A, Helve O, Andersson S, Kolho KL, Asnicar F, Korpela K, Salonen A, Segata N, de Vos WM. Paternal and induced gut microbiota seeding complement mother-to-infant transmission. Cell Host Microbe 2024; 32:1011-1024.e4. [PMID: 38870892 DOI: 10.1016/j.chom.2024.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 04/03/2024] [Accepted: 05/07/2024] [Indexed: 06/15/2024]
Abstract
Microbial colonization of the neonatal gut involves maternal seeding, which is partially disrupted in cesarean-born infants and after intrapartum antibiotic prophylaxis. However, other physically close individuals could complement such seeding. To assess the role of both parents and of induced seeding, we analyzed two longitudinal metagenomic datasets (health and early life microbiota [HELMi]: N = 74 infants, 398 samples, and SECFLOR: N = 7 infants, 35 samples) with cesarean-born infants who received maternal fecal microbiota transplantation (FMT). We found that the father constitutes a stable source of strains for the infant independently of the delivery mode, with the cumulative contribution becoming comparable to that of the mother after 1 year. Maternal FMT increased mother-infant strain sharing in cesarean-born infants, raising the average bacterial empirical growth rate while reducing pathogen colonization. Overall, our results indicate that maternal seeding is partly complemented by that of the father and support the potential of induced seeding to restore potential deviations in this process.
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Affiliation(s)
- Léonard Dubois
- Department CIBIO, University of Trento, 38123 Trento, Italy
| | - Mireia Valles-Colomer
- Department CIBIO, University of Trento, 38123 Trento, Italy; MELIS Department, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Alise Ponsero
- Human Microbiota Research Program, Faculty of Medicine, University of Helsinki, 0014 Helsinki, Finland
| | - Otto Helve
- Children's Hospital, Pediatric Research Center, University of Helsinki, and Helsinki University Hospital, 00014 Helsinki, Finland; Department of Health Security, Finnish Institute for Health and Welfare, 0014 Helsinki, Finland
| | - Sture Andersson
- Children's Hospital, Pediatric Research Center, University of Helsinki, and Helsinki University Hospital, 00014 Helsinki, Finland
| | - Kaija-Leena Kolho
- Human Microbiota Research Program, Faculty of Medicine, University of Helsinki, 0014 Helsinki, Finland
| | | | - Katri Korpela
- Human Microbiota Research Program, Faculty of Medicine, University of Helsinki, 0014 Helsinki, Finland
| | - Anne Salonen
- Human Microbiota Research Program, Faculty of Medicine, University of Helsinki, 0014 Helsinki, Finland
| | - Nicola Segata
- Department CIBIO, University of Trento, 38123 Trento, Italy; Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, 20141 Milan, Italy.
| | - Willem M de Vos
- Human Microbiota Research Program, Faculty of Medicine, University of Helsinki, 0014 Helsinki, Finland; Laboratory of Microbiology, University of Wageningen, 6703 WE Wageningen, the Netherlands.
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Al Kady C, Moussally K, Chreif W, Farra A, Caluwaerts S, Wertheim H, Soukarieh D, Gordillo Gomez F, Dibiasi J, Lenglet A. Overuse of antibiotics for urinary tract infections in pregnant refugees, Lebanon. Bull World Health Organ 2024; 102:389-399. [PMID: 38812803 PMCID: PMC11132156 DOI: 10.2471/blt.23.291235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/21/2022] [Accepted: 02/22/2024] [Indexed: 05/31/2024] Open
Abstract
Objective To determine whether adding urine culture to urinary tract infection diagnosis in pregnant women from refugee camps in Lebanon reduced unnecessary antibiotic use. Methods We conducted a prospective, cross-sectional study between April and June 2022 involving pregnant women attending a Médecins Sans Frontières sexual reproductive health clinic in south Beirut. Women with two positive urine dipstick tests (i.e. a suspected urinary tract infection) provided urine samples for culture. Bacterial identification and antimicrobial sensitivity testing were conducted following European Committee on Antimicrobial Susceptibility Testing guidelines. We compared the characteristics of women with positive and negative urine culture findings and we calculated the proportion of antibiotics overprescribed or inappropriately used. We also estimated the cost of adding urine culture to the diagnostic algorithm. Findings The study included 449 pregnant women with suspected urinary tract infections: 18.0% (81/449) had positive urine culture findings. If antibiotics were administered following urine dipstick results alone, 368 women would have received antibiotics unnecessarily: an overprescription rate of 82% (368/449). If administration was based on urine culture findings plus urinary tract infection symptoms, 144 of 368 women with negative urine culture findings would have received antibiotics unnecessarily: an overprescription rate of 39.1% (144/368). The additional cost of urine culture was 0.48 euros per woman. Conclusion A high proportion of pregnant women with suspected urinary tract infections from refugee camps unnecessarily received antibiotics. Including urine culture in diagnosis, which is affordable in Lebanon, would greatly reduce antibiotic overprescription. Similar approaches could be adopted in other regions where microbiology laboratories are accessible.
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Affiliation(s)
- Christine Al Kady
- South Beirut Project, Lebanon Mission, Operational Center Brussels, Médecins Sans Frontières, Domtex Building, Fifth Floor, Hamra Main Street, Beirut, Lebanon
| | | | - Wafaa Chreif
- South Beirut Project, Lebanon Mission, Operational Center Brussels, Médecins Sans Frontières, Domtex Building, Fifth Floor, Hamra Main Street, Beirut, Lebanon
| | - Anna Farra
- Middle East Medical Unit, Médecins Sans Frontières, Beirut, Lebanon
| | | | - Heiman Wertheim
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Kingdom of the Netherlands
| | | | | | - Johanna Dibiasi
- South Beirut Project, Lebanon Mission, Operational Center Brussels, Médecins Sans Frontières, Domtex Building, Fifth Floor, Hamra Main Street, Beirut, Lebanon
| | - Annick Lenglet
- International Centre for Antimicrobial Resistance Solutions, Copenhagen, Denmark
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Tian Z, Zhang X, Yao G, Jin J, Zhang T, Sun C, Wang Z, Zhang Q. Intestinal flora and pregnancy complications: Current insights and future prospects. IMETA 2024; 3:e167. [PMID: 38882493 PMCID: PMC11170975 DOI: 10.1002/imt2.167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/27/2023] [Accepted: 12/22/2023] [Indexed: 06/18/2024]
Abstract
Numerous studies have demonstrated the pivotal roles of intestinal microbiota in many physiopathological processes through complex interactions with the host. As a unique period in a woman's lifespan, pregnancy is characterized by changes in hormones, immunity, and metabolism. The gut microbiota also changes during this period and plays a crucial role in maintaining a healthy pregnancy. Consequently, anomalies in the composition and function of the gut microbiota, namely, gut microbiota dysbiosis, can predispose individuals to various pregnancy complications, posing substantial risks to both maternal and neonatal health. However, there are still many controversies in this field, such as "sterile womb" versus "in utero colonization." Therefore, a thorough understanding of the roles and mechanisms of gut microbiota in pregnancy and its complications is essential to safeguard the health of both mother and child. This review provides a comprehensive overview of the changes in gut microbiota during pregnancy, its abnormalities in common pregnancy complications, and potential etiological implications. It also explores the potential of gut microbiota in diagnosing and treating pregnancy complications and examines the possibility of gut-derived bacteria residing in the uterus/placenta. Our aim is to expand knowledge in maternal and infant health from the gut microbiota perspective, aiding in developing new preventive and therapeutic strategies for pregnancy complications based on intestinal microecology.
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Affiliation(s)
- Zhenyu Tian
- National Key Laboratory for Innovation and Transformation of Luobing Theory; The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences; Department of Cardiology Qilu Hospital of Shandong University Jinan China
| | - Xinjie Zhang
- Department of Biology University College London London UK
| | - Guixiang Yao
- National Key Laboratory for Innovation and Transformation of Luobing Theory; The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences; Department of Cardiology Qilu Hospital of Shandong University Jinan China
| | - Jiajia Jin
- National Key Laboratory for Innovation and Transformation of Luobing Theory; The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences; Department of Cardiology Qilu Hospital of Shandong University Jinan China
| | - Tongxue Zhang
- National Key Laboratory for Innovation and Transformation of Luobing Theory; The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences; Department of Cardiology Qilu Hospital of Shandong University Jinan China
| | - Chunhua Sun
- Department of Health Management Center, Qilu Hospital, Cheeloo College of Medicine Shandong University Jinan China
| | - Zhe Wang
- Department of Geriatrics Shandong Provincial Hospital Affiliated to Shandong First Medical University Jinan China
| | - Qunye Zhang
- National Key Laboratory for Innovation and Transformation of Luobing Theory; The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences; Department of Cardiology Qilu Hospital of Shandong University Jinan China
- Cardiovascular Disease Research Center of Shandong First Medical University Central Hospital Affiliated to Shandong First Medical University Jinan China
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Marti DT, Bratosin F, Rosca O, Folescu R, Citu C, Ratiu A, Popa ZL. Impact of Genital Infections and Antibiotic Use on Incidence of Preterm Birth: A Retrospective Observational Study. Antibiotics (Basel) 2024; 13:240. [PMID: 38534675 DOI: 10.3390/antibiotics13030240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/02/2024] [Accepted: 03/05/2024] [Indexed: 03/28/2024] Open
Abstract
This study investigates the complex interplay among genital infections, antibiotic usage, and preterm birth. This study aims to identify common genital pathogens associated with preterm births, assess the impact of various antibiotic treatments on pregnancy outcomes, and understand antibiotic resistance patterns among these pathogens. This study included 71 pregnant women who experienced preterm birth and 94 women with genital infections who delivered at term. Various maternal characteristics, medical history, signs and symptoms, gestational weight, gestational age, type of birth, vaginal pH, Nugent scores, and vaginal flora were analyzed. Antibiotic resistance patterns of isolated microorganisms were also examined. The prevalence of sexually transmitted diseases (STDs) and genital herpes was significantly higher in the preterm group. Preterm births were associated with fever, pelvic pain, vaginal spotting, and fatigue. Vaginal pH levels and Nugent scores were significantly higher in the preterm group, indicating disturbed vaginal flora. The presence of Extended-Spectrum Beta-Lactamases (ESBLs) was a particularly strong risk factor, increasing by more than four times the odds of preterm birth (OR = 4.45, p = 0.001). Vancomycin-Resistant Enterococci (VRE) presence was another critical factor, with a four-fold increase in the odds of preterm birth (OR = 4.01, p = 0.034). The overall presence of Multidrug-Resistant (MDR) organisms significantly increased the odds of preterm birth (OR = 3.73, p = 0.001). Specific pathogens like Chlamydia trachomatis (OR = 3.12, p = 0.020) and Mycoplasma hominis (OR = 3.64, p = 0.006) were also identified as significant risk factors. Ureaplasma urealyticum also showed a significantly higher risk of preterm birth (OR = 2.76, p = 0.009). This study highlights the importance of screening for and treating genital infections during pregnancy, especially STDs and genital herpes, as they can significantly increase the risk of preterm birth. Additionally, the presence of specific microorganisms and antibiotic resistance patterns plays an essential role in preterm birth risk. Early detection and targeted antibiotic treatment may help mitigate this risk and improve pregnancy outcomes.
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Affiliation(s)
- Daniela Teodora Marti
- Clinical Analysis Laboratory, Emergency Clinical Hospital of Arad County, 310037 Arad, Romania
- Department of Biology and Life Sciences, Vasile Goldis University of Medicine, 310048 Arad, Romania
| | - Felix Bratosin
- Department of Infectious Diseases, "Victor Babes" University of Medicine and Pharmacy Timisoara, 300041 Timisoara, Romania
- Doctoral School, "Victor Babes" University of Medicine and Pharmacy Timisoara, 300041 Timisoara, Romania
- Methodological and Infectious Diseases Research Center, Department of Infectious Diseases, "Victor Babes" University of Medicine and Pharmacy Timisoara, 300041 Timisoara, Romania
| | - Ovidiu Rosca
- Department of Infectious Diseases, "Victor Babes" University of Medicine and Pharmacy Timisoara, 300041 Timisoara, Romania
- Doctoral School, "Victor Babes" University of Medicine and Pharmacy Timisoara, 300041 Timisoara, Romania
- Methodological and Infectious Diseases Research Center, Department of Infectious Diseases, "Victor Babes" University of Medicine and Pharmacy Timisoara, 300041 Timisoara, Romania
| | - Roxana Folescu
- Department of Family Medicine, "Victor Babes" University of Medicine and Pharmacy Timisoara, 300041 Timisoara, Romania
| | - Cosmin Citu
- Department of Obstetrics and Gynecology, "Victor Babes" University of Medicine and Pharmacy Timisoara, 300041 Timisoara, Romania
| | - Adrian Ratiu
- Department of Obstetrics and Gynecology, "Victor Babes" University of Medicine and Pharmacy Timisoara, 300041 Timisoara, Romania
| | - Zoran Laurentiu Popa
- Department of Obstetrics and Gynecology, "Victor Babes" University of Medicine and Pharmacy Timisoara, 300041 Timisoara, Romania
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Bernabeu M, Cabello-Yeves E, Flores E, Samarra A, Kimberley Summers J, Marina A, Collado MC. Role of vertical and horizontal microbial transmission of antimicrobial resistance genes in early life: insights from maternal-infant dyads. Curr Opin Microbiol 2024; 77:102424. [PMID: 38237429 DOI: 10.1016/j.mib.2023.102424] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 02/12/2024]
Abstract
Early life represents a critical window for metabolic, cognitive and immune system development, which is influenced by the maternal microbiome as well as the infant gut microbiome. Antibiotic exposure, mode of delivery and breastfeeding practices modulate the gut microbiome and the reservoir of antibiotic resistance genes (ARGs). Vertical and horizontal microbial gene transfer during early life and the mechanisms behind these transfers are being uncovered. In this review, we aim to provide an overview of the current knowledge on the transfer of antibiotic resistance in the mother-infant dyad through vertical and horizontal transmission and to highlight the main gaps and challenges in this area.
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Affiliation(s)
- Manuel Bernabeu
- Institute of Agrochemistry and Food Technology - National Research Council (IATA-CSIC), 46980 Valencia, Spain.
| | - Elena Cabello-Yeves
- Instituto de Biomedicina de Valencia-Consejo de Investigaciones Científicas (IBV-CSIC), CIBER de Enfermedades Raras (CIBERER), 46010 Valencia, Spain.
| | - Eduard Flores
- Institute of Agrochemistry and Food Technology - National Research Council (IATA-CSIC), 46980 Valencia, Spain
| | - Anna Samarra
- Institute of Agrochemistry and Food Technology - National Research Council (IATA-CSIC), 46980 Valencia, Spain
| | - Joanna Kimberley Summers
- Wellington Lab, School of Life Sciences, University of Warwick, CV4 7AL Coventry, United Kingdom
| | - Alberto Marina
- Instituto de Biomedicina de Valencia-Consejo de Investigaciones Científicas (IBV-CSIC), CIBER de Enfermedades Raras (CIBERER), 46010 Valencia, Spain
| | - M Carmen Collado
- Institute of Agrochemistry and Food Technology - National Research Council (IATA-CSIC), 46980 Valencia, Spain
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Allert M, Ferretti P, Johnson KE, Heisel T, Gonia S, Knights D, Fields DA, Albert FW, Demerath EW, Gale CA, Blekhman R. Assembly, stability, and dynamics of the infant gut microbiome are linked to bacterial strains and functions in mother's milk. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.28.577594. [PMID: 38328166 PMCID: PMC10849666 DOI: 10.1101/2024.01.28.577594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
The establishment of the gut microbiome in early life is critical for healthy infant development. Although human milk is recommended as the sole source of nutrition for the human infant, little is known about how variation in milk composition, and especially the milk microbiome, shapes the microbial communities in the infant gut. Here, we quantified the similarity between the maternal milk and the infant gut microbiome using 507 metagenomic samples collected from 195 mother-infant pairs at one, three, and six months postpartum. We found that the microbial taxonomic overlap between milk and the infant gut was driven by bifidobacteria, in particular by B. longum. Infant stool samples dominated by B. longum also showed higher temporal stability compared to samples dominated by other species. We identified two instances of strain sharing between maternal milk and the infant gut, one involving a commensal (B. longum) and one a pathobiont (K. pneumoniae). In addition, strain sharing between unrelated infants was higher among infants born at the same hospital compared to infants born in different hospitals, suggesting a potential role of the hospital environment in shaping the infant gut microbiome composition. The infant gut microbiome at one month compared to six months of age was enriched in metabolic pathways associated with de-novo molecule biosynthesis, suggesting that early colonisers might be more versatile and metabolically independent compared to later colonizers. Lastly, we found a significant overlap in antimicrobial resistance genes carriage between the mother's milk and their infant's gut microbiome. Taken together, our results suggest that the human milk microbiome has an important role in the assembly, composition, and stability of the infant gut microbiome.
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Affiliation(s)
- Mattea Allert
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Pamela Ferretti
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Kelsey E Johnson
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Timothy Heisel
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Sara Gonia
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Dan Knights
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - David A Fields
- Department of Pediatrics, the University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Frank W Albert
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Ellen W Demerath
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Cheryl A Gale
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Ran Blekhman
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
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Inchingolo F, Inchingolo AD, Palumbo I, Trilli I, Guglielmo M, Mancini A, Palermo A, Inchingolo AM, Dipalma G. The Impact of Cesarean Section Delivery on Intestinal Microbiota: Mechanisms, Consequences, and Perspectives-A Systematic Review. Int J Mol Sci 2024; 25:1055. [PMID: 38256127 PMCID: PMC10816971 DOI: 10.3390/ijms25021055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 12/31/2023] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
The relationship between cesarean section (CS) delivery and intestinal microbiota is increasingly studied. CS-born infants display distinct gut microbial compositions due to the absence of maternal birth canal microorganisms. These alterations potentially link to long-term health implications like immune-related disorders and allergies. This correlation underscores the intricate connection between birth mode and the establishment of diverse intestinal microbiota. A systematic literature review was conducted on the PubMed, Scopus, and Web of Science databases by analyzing the articles and examining the intricate interactions between CS delivery and the infant's intestinal microbiota. The analysis, based on a wide-ranging selection of studies, elucidates the multifaceted dynamics involved in CS-associated shifts in the establishment of fetal microbiota. We also explore the potential ramifications of these microbial changes on neonatal health and development, providing a comprehensive overview for clinicians and researchers. By synthesizing current findings, this review contributes to a deeper understanding of the interplay between delivery mode and early microbial colonization, paving the way for informed clinical decisions and future investigations in the field of perinatal medicine.
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Affiliation(s)
- Francesco Inchingolo
- Department of Interdisciplinary Medicine, School of Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.D.I.); (I.P.); (I.T.); (M.G.); (A.M.); (A.M.I.); (G.D.)
| | - Alessio Danilo Inchingolo
- Department of Interdisciplinary Medicine, School of Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.D.I.); (I.P.); (I.T.); (M.G.); (A.M.); (A.M.I.); (G.D.)
| | - Irene Palumbo
- Department of Interdisciplinary Medicine, School of Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.D.I.); (I.P.); (I.T.); (M.G.); (A.M.); (A.M.I.); (G.D.)
| | - Irma Trilli
- Department of Interdisciplinary Medicine, School of Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.D.I.); (I.P.); (I.T.); (M.G.); (A.M.); (A.M.I.); (G.D.)
| | - Mariafrancesca Guglielmo
- Department of Interdisciplinary Medicine, School of Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.D.I.); (I.P.); (I.T.); (M.G.); (A.M.); (A.M.I.); (G.D.)
| | - Antonio Mancini
- Department of Interdisciplinary Medicine, School of Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.D.I.); (I.P.); (I.T.); (M.G.); (A.M.); (A.M.I.); (G.D.)
| | - Andrea Palermo
- College of Medicine and Dentistry, Birmingham B4 6BN, UK;
| | - Angelo Michele Inchingolo
- Department of Interdisciplinary Medicine, School of Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.D.I.); (I.P.); (I.T.); (M.G.); (A.M.); (A.M.I.); (G.D.)
| | - Gianna Dipalma
- Department of Interdisciplinary Medicine, School of Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.D.I.); (I.P.); (I.T.); (M.G.); (A.M.); (A.M.I.); (G.D.)
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Samarra A, Cabrera-Rubio R, Martínez-Costa C, Collado MC. The role of Bifidobacterium genus in modulating the neonate microbiota: implications for antibiotic resistance acquisition in early life. Gut Microbes 2024; 16:2357176. [PMID: 38798019 PMCID: PMC11135851 DOI: 10.1080/19490976.2024.2357176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 05/15/2024] [Indexed: 05/29/2024] Open
Abstract
Resistance to antibiotics in newborns is a huge concern as their immune system is still developing, and infections and resistance acquisition in early life have short- and long-term consequences for their health. Bifidobacterium species are important commensals capable of dominating the infant gut microbiome and are known to be less prone to possess antimicrobial resistance genes than other taxa that may colonize infants. We aimed to study the association between Bifidobacterium-dominated infant gut microbiota and the antibiotic resistant gene load in neonates, and to ascertain the perinatal factors that may contribute to the antibiotic resistance acquisition. Two hundred infant fecal samples at 7 days and 1 month of age from the MAMI birth cohort were included in the study and for whom maternal-neonatal clinical records were available. Microbiota profiling was carried out by 16S rRNA amplicon sequencing, and targeted antibiotic resistance genes (ARGs) including tetM, tetW, tetO, blaTEM, blaSHV and ermB were quantified by qPCR. Infant microbiota clustered into two distinct groups according to their Bifidobacterium genus abundance: high and low. The main separation of groups or clusters at each time point was performed with an unsupervised non-linear algorithm of k-means partitioning to cluster data by time points based on Bifidobacterium genus relative abundance. Microbiota composition differed significantly between both groups, and specific bifidobacterial species were enriched in each cluster. Lower abundance of Bifidobacterium in the infant gut was associated with a higher load of antibiotic resistance genes. Our results highlight the relevance of Bifidobacterium genus in the early acquisition and establishment of antibiotic resistance in the gut. Further studies are needed to develop strategies to promote a healthy early colonization and fight against the spread of antibiotic resistances.
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Affiliation(s)
- Anna Samarra
- Department of Biotechnology, Institute of Agrochemistry and Food Technology- National Research Council (IATA-CSIC), Paterna, Valencia, Spain
| | - Raúl Cabrera-Rubio
- Department of Biotechnology, Institute of Agrochemistry and Food Technology- National Research Council (IATA-CSIC), Paterna, Valencia, Spain
| | - Cecilia Martínez-Costa
- Department of Pediatrics, School of Medicine, University of Valencia, Valencia, Spain
- Pediatric Gastroenterology and Nutrition Section, Hospital Clínico Universitario Valencia, Valencia, Spain
| | - Maria Carmen Collado
- Department of Biotechnology, Institute of Agrochemistry and Food Technology- National Research Council (IATA-CSIC), Paterna, Valencia, Spain
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11
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Samarra A, Flores E, Bernabeu M, Cabrera-Rubio R, Bäuerl C, Selma-Royo M, Collado MC. Shaping Microbiota During the First 1000 Days of Life. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1449:1-28. [PMID: 39060728 DOI: 10.1007/978-3-031-58572-2_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/28/2024]
Abstract
Given that the host-microbe interaction is shaped by the immune system response, it is important to understand the key immune system-microbiota relationship during the period from conception to the first years of life. The present work summarizes the available evidence concerning human reproductive microbiota, and also, the microbial colonization during early life, focusing on the potential impact on infant development and health outcomes. Furthermore, we conclude that some dietary strategies including specific probiotics and other-biotics could become potentially valuable tools to modulate the maternal-neonatal microbiota during this early critical window of opportunity for targeted health outcomes throughout the entire lifespan.
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Affiliation(s)
- Anna Samarra
- Department of Biotechnology, Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Paterna-Valencia, Spain
| | - Eduard Flores
- Department of Biotechnology, Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Paterna-Valencia, Spain
| | - Manuel Bernabeu
- Department of Biotechnology, Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Paterna-Valencia, Spain
| | - Raul Cabrera-Rubio
- Department of Biotechnology, Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Paterna-Valencia, Spain
| | - Christine Bäuerl
- Department of Biotechnology, Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Paterna-Valencia, Spain
| | - Marta Selma-Royo
- Department of Biotechnology, Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Paterna-Valencia, Spain
| | - Maria Carmen Collado
- Department of Biotechnology, Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Paterna-Valencia, Spain.
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Tarek A, Abdalla S, Dokmak NA, Ahmed AA, El-Mahdy TS, Safwat NA. Bacterial Diversity and Antibiotic Resistance Patterns of Community-Acquired Urinary Tract Infections in Mega Size Clinical Samples of Egyptian Patients: A Cross-Sectional Study. Cureus 2024; 16:e51838. [PMID: 38327928 PMCID: PMC10849261 DOI: 10.7759/cureus.51838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2024] [Indexed: 02/09/2024] Open
Abstract
BACKGROUND Community-acquired urinary tract infection (UTI) is one of the most common infectious diseases nowadays. Alarming increased levels of antimicrobial resistance are developing globally which limit treatment options and may lead to life-threatening problems. AIM Our study aimed to collect surveillance data on non-hospitalized Egyptian UTI cases and to develop strategies against multidrug-resistant pathogens (MDR). According to our knowledge, this is the first study to screen this high number (15,252 urine samples) in a short period (three months), providing valuable data on resistance profiles in non-hospitalized Egyptian UTI patients. METHODS A total of 15,252 urine samples were collected from different patients. Positive cultures were identified using a semi-quantitative method. Kirby-Bauer's disc diffusion method was used for antibiotic susceptibility testing, the double disc diffusion method was used for extended-spectrum beta-lactamases-producing strains, and the Chi-square test was used for statistical data processing. RESULTS The results showed 61% positive cultures, females accounted for 67.5%. Infants and elderly patients showed the highest positive cultures (74.4% and 69.2%, respectively). Despite Escherichia coli being the most common uropathogen (47.19%), Klebsiella species(24.42%) were the most MDR and extended-spectrum β-lactamase (ESBL)-producing organisms. E. coli and Klebsiella spp. displayed increased resistance to cephalosporins (75% and 81%, respectively). In contrast, both organisms displayed high sensitivity to carbapenems. Unlike Klebsiella spp., E. coli was highly sensitive (92%) to first-line treatment (nitrofurantoin) for UTI. Moreover, trimethoprim/sulfamethoxazole showed higher sensitivity rates compared to other nations. CONCLUSION Despite Escherichia coli being the most often identified bacteria in our isolates Klebsiella spp. displayed higher resistance to the majority of tested antibiotics. Fortunately, trimethoprim/sulfamethoxazole significantly increased sensitivity, especially against E. coli. However, both species showed high rates of cephalosporin resistance. Moreover, It is important to promote Egypt's national action plan for antimicrobial resistance in collaboration with the World Health Organization, especially in the community to minimize the chance of bacterial resistance in the Egyptian community.
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Affiliation(s)
- Amr Tarek
- Microbiology and Immunology, Modern University for Technology and Information (MTI), Cairo, EGY
| | - Salah Abdalla
- Microbiology and Immunology, Suez-Canal University, Ismailia, EGY
| | - Nehal A Dokmak
- Microbiology and Immunology, Modern University for Technology and Information (MTI), Cairo, EGY
| | - Ali A Ahmed
- Microbiology and Immunology, Suez-Canal University, Ismailia, EGY
| | - Taghrid S El-Mahdy
- Microbiology and Immunology, Helwan University, Cairo, EGY
- Microbiology and Immunology, Modern University for Technology and Information (MTI), Cairo, EGY
| | - Nesreen A Safwat
- Microbiology and Immunology, Modern University for Technology and Information (MTI), Cairo, EGY
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Cheng L, Correia MSP, Higdon SM, Romero Garcia F, Tsiara I, Joffré E, Sjöling Å, Boulund F, Norin EL, Engstrand L, Globisch D, Du J. The protective role of commensal gut microbes and their metabolites against bacterial pathogens. Gut Microbes 2024; 16:2356275. [PMID: 38797999 PMCID: PMC11135852 DOI: 10.1080/19490976.2024.2356275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 05/13/2024] [Indexed: 05/29/2024] Open
Abstract
Multidrug-resistant microorganisms have become a major public health concern around the world. The gut microbiome is a gold mine for bioactive compounds that protect the human body from pathogens. We used a multi-omics approach that integrated whole-genome sequencing (WGS) of 74 commensal gut microbiome isolates with metabolome analysis to discover their metabolic interaction with Salmonella and other antibiotic-resistant pathogens. We evaluated differences in the functional potential of these selected isolates based on WGS annotation profiles. Furthermore, the top altered metabolites in co-culture supernatants of selected commensal gut microbiome isolates were identified including a series of dipeptides and examined for their ability to prevent the growth of various antibiotic-resistant bacteria. Our results provide compelling evidence that the gut microbiome produces metabolites, including the compound class of dipeptides that can potentially be applied for anti-infection medication, especially against antibiotic-resistant pathogens. Our established pipeline for the discovery and validation of bioactive metabolites from the gut microbiome as novel candidates for multidrug-resistant infections represents a new avenue for the discovery of antimicrobial lead structures.
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Affiliation(s)
- Liqin Cheng
- Centre for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Stockholm, Sweden
- The Department of Pathophysiology, School of Basic Medicine Science, Central South University, Changsha, China
| | - Mário S. P. Correia
- Department of Chemistry - BMC, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Shawn M. Higdon
- Centre for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Stockholm, Sweden
| | - Fabricio Romero Garcia
- Centre for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Stockholm, Sweden
| | - Ioanna Tsiara
- Department of Chemistry - BMC, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Enrique Joffré
- Centre for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Stockholm, Sweden
| | - Åsa Sjöling
- Centre for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Stockholm, Sweden
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden
| | - Fredrik Boulund
- Centre for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Stockholm, Sweden
| | - Elisabeth Lissa Norin
- Centre for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Stockholm, Sweden
| | - Lars Engstrand
- Centre for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Stockholm, Sweden
- Science for Life Laboratory, Stockholm, Sweden
| | - Daniel Globisch
- Centre for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Stockholm, Sweden
- Department of Chemistry - BMC, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Juan Du
- Centre for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Stockholm, Sweden
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Saturio S, Rey A, Samarra A, Collado MC, Suárez M, Mantecón L, Solís G, Gueimonde M, Arboleya S. Old Folks, Bad Boon: Antimicrobial Resistance in the Infant Gut Microbiome. Microorganisms 2023; 11:1907. [PMID: 37630467 PMCID: PMC10458625 DOI: 10.3390/microorganisms11081907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023] Open
Abstract
The development of the intestinal microbiome in the neonate starts, mainly, at birth, when the infant receives its founding microbial inoculum from the mother. This microbiome contains genes conferring resistance to antibiotics since these are found in some of the microorganisms present in the intestine. Similarly to microbiota composition, the possession of antibiotic resistance genes is affected by different perinatal factors. Moreover, antibiotics are the most used drugs in early life, and the use of antibiotics in pediatrics covers a wide variety of possibilities and treatment options. The disruption in the early microbiota caused by antibiotics may be of great relevance, not just because it may limit colonization by beneficial microorganisms and increase that of potential pathogens, but also because it may increase the levels of antibiotic resistance genes. The increase in antibiotic-resistant microorganisms is one of the major public health threats that humanity has to face and, therefore, understanding the factors that determine the development of the resistome in early life is of relevance. Recent advancements in sequencing technologies have enabled the study of the microbiota and the resistome at unprecedent levels. These aspects are discussed in this review as well as some potential interventions aimed at reducing the possession of resistance genes.
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Affiliation(s)
- Silvia Saturio
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), 33300 Villaviciosa, Spain; (S.S.); (A.R.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain; (M.S.); (L.M.); (G.S.)
| | - Alejandra Rey
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), 33300 Villaviciosa, Spain; (S.S.); (A.R.)
| | - Anna Samarra
- Institute of Agrochemistry and Food Technology (IATA-CSIC), 46980 Paterna, Spain; (A.S.); (M.C.C.)
| | - Maria Carmen Collado
- Institute of Agrochemistry and Food Technology (IATA-CSIC), 46980 Paterna, Spain; (A.S.); (M.C.C.)
| | - Marta Suárez
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain; (M.S.); (L.M.); (G.S.)
- Pediatrics Service, Central University Hospital of Asturias (HUCA-SESPA), 33011 Oviedo, Spain
| | - Laura Mantecón
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain; (M.S.); (L.M.); (G.S.)
- Pediatrics Service, Central University Hospital of Asturias (HUCA-SESPA), 33011 Oviedo, Spain
| | - Gonzalo Solís
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain; (M.S.); (L.M.); (G.S.)
- Pediatrics Service, Central University Hospital of Asturias (HUCA-SESPA), 33011 Oviedo, Spain
| | - Miguel Gueimonde
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), 33300 Villaviciosa, Spain; (S.S.); (A.R.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain; (M.S.); (L.M.); (G.S.)
| | - Silvia Arboleya
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), 33300 Villaviciosa, Spain; (S.S.); (A.R.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain; (M.S.); (L.M.); (G.S.)
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