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Chan C, Coffey M, Murphy C, McKay I, Abdu J, Paida K, Tam RY, Wrigley-Carr H, Prentice B, Owens L, Belessis Y, Chuang S, Jaffe A, van Dorst J, Ooi CY. The Prevalence of Polyketide Synthase-Positive E. coli in Cystic Fibrosis. Microorganisms 2025; 13:681. [PMID: 40142573 PMCID: PMC11944406 DOI: 10.3390/microorganisms13030681] [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: 01/29/2025] [Revised: 03/14/2025] [Accepted: 03/14/2025] [Indexed: 03/28/2025] Open
Abstract
Cystic fibrosis (CF) patients experience higher risks of colorectal cancer but the pathogenesis is unclear. In the general population, polyketide synthase-positive (pks+) E. coli is implicated in intestinal carcinogenesis via the production of colibactin; however, the relevance in CF is unknown. In this study, we investigate pks+E. coli prevalence in CF and potential associations between pks+E. coli, gastrointestinal inflammation, and microbiome dynamics with fecal calprotectin and 16SrRNA gene taxonomic data. Cross-sectional analysis demonstrated no difference in pks+E. coli carriage between CF patients and healthy controls, 21/55 (38%) vs. 26/55 (47%), p = 0.32. Pks+E. coli was not associated with significant differences in mean (SD) calprotectin concentration (124 (154) vs. 158 (268) mg/kg; p = 0.60), microbial richness (159 (76.5) vs. 147 (70.4); p = 0.50) or Shannon diversity index (2.78 (0.77) vs. 2.65 (0.74); p = 0.50) in CF. Additionally, there was no association with exocrine pancreatic status (p = 0.2) or overall antibiotic use (p = 0.6). Longitudinally, CF subjects demonstrated intra-individual variation in pks+E. coli presence but no significant difference in overall prevalence. Future investigation into the effects of repeat exposure on risk profile and analysis of older CF cohorts is necessary to identify if associations with colorectal cancer exist.
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Affiliation(s)
- Christopher Chan
- School of Clinical Medicine, Discipline of Paediatrics & Child Health, UNSW Medicine & Health, University of New South Wales, Sydney, NSW 2031, Australia; (C.C.); (M.C.); (C.M.); (I.M.); (J.A.); (H.W.-C.); (B.P.); (S.C.); (A.J.); (C.Y.O.)
| | - Michael Coffey
- School of Clinical Medicine, Discipline of Paediatrics & Child Health, UNSW Medicine & Health, University of New South Wales, Sydney, NSW 2031, Australia; (C.C.); (M.C.); (C.M.); (I.M.); (J.A.); (H.W.-C.); (B.P.); (S.C.); (A.J.); (C.Y.O.)
- Department of Gastroenterology, Sydney Children’s Hospital, Randwick, NSW 2031, Australia
| | - Caitlin Murphy
- School of Clinical Medicine, Discipline of Paediatrics & Child Health, UNSW Medicine & Health, University of New South Wales, Sydney, NSW 2031, Australia; (C.C.); (M.C.); (C.M.); (I.M.); (J.A.); (H.W.-C.); (B.P.); (S.C.); (A.J.); (C.Y.O.)
| | - Isabelle McKay
- School of Clinical Medicine, Discipline of Paediatrics & Child Health, UNSW Medicine & Health, University of New South Wales, Sydney, NSW 2031, Australia; (C.C.); (M.C.); (C.M.); (I.M.); (J.A.); (H.W.-C.); (B.P.); (S.C.); (A.J.); (C.Y.O.)
| | - Jumaana Abdu
- School of Clinical Medicine, Discipline of Paediatrics & Child Health, UNSW Medicine & Health, University of New South Wales, Sydney, NSW 2031, Australia; (C.C.); (M.C.); (C.M.); (I.M.); (J.A.); (H.W.-C.); (B.P.); (S.C.); (A.J.); (C.Y.O.)
| | - Keerti Paida
- School of Clinical Medicine, Discipline of Paediatrics & Child Health, UNSW Medicine & Health, University of New South Wales, Sydney, NSW 2031, Australia; (C.C.); (M.C.); (C.M.); (I.M.); (J.A.); (H.W.-C.); (B.P.); (S.C.); (A.J.); (C.Y.O.)
| | - Rachel Y. Tam
- School of Clinical Medicine, Discipline of Paediatrics & Child Health, UNSW Medicine & Health, University of New South Wales, Sydney, NSW 2031, Australia; (C.C.); (M.C.); (C.M.); (I.M.); (J.A.); (H.W.-C.); (B.P.); (S.C.); (A.J.); (C.Y.O.)
| | - Hannah Wrigley-Carr
- School of Clinical Medicine, Discipline of Paediatrics & Child Health, UNSW Medicine & Health, University of New South Wales, Sydney, NSW 2031, Australia; (C.C.); (M.C.); (C.M.); (I.M.); (J.A.); (H.W.-C.); (B.P.); (S.C.); (A.J.); (C.Y.O.)
| | - Bernadette Prentice
- School of Clinical Medicine, Discipline of Paediatrics & Child Health, UNSW Medicine & Health, University of New South Wales, Sydney, NSW 2031, Australia; (C.C.); (M.C.); (C.M.); (I.M.); (J.A.); (H.W.-C.); (B.P.); (S.C.); (A.J.); (C.Y.O.)
- Department of Respiratory Medicine, Sydney Children’s Hospital, Randwick, NSW 2031, Australia; (L.O.); (Y.B.)
| | - Louisa Owens
- Department of Respiratory Medicine, Sydney Children’s Hospital, Randwick, NSW 2031, Australia; (L.O.); (Y.B.)
| | - Yvonne Belessis
- Department of Respiratory Medicine, Sydney Children’s Hospital, Randwick, NSW 2031, Australia; (L.O.); (Y.B.)
| | - Sandra Chuang
- School of Clinical Medicine, Discipline of Paediatrics & Child Health, UNSW Medicine & Health, University of New South Wales, Sydney, NSW 2031, Australia; (C.C.); (M.C.); (C.M.); (I.M.); (J.A.); (H.W.-C.); (B.P.); (S.C.); (A.J.); (C.Y.O.)
- Department of Respiratory Medicine, Sydney Children’s Hospital, Randwick, NSW 2031, Australia; (L.O.); (Y.B.)
| | - Adam Jaffe
- School of Clinical Medicine, Discipline of Paediatrics & Child Health, UNSW Medicine & Health, University of New South Wales, Sydney, NSW 2031, Australia; (C.C.); (M.C.); (C.M.); (I.M.); (J.A.); (H.W.-C.); (B.P.); (S.C.); (A.J.); (C.Y.O.)
- Department of Respiratory Medicine, Sydney Children’s Hospital, Randwick, NSW 2031, Australia; (L.O.); (Y.B.)
| | - Josie van Dorst
- School of Clinical Medicine, Discipline of Paediatrics & Child Health, UNSW Medicine & Health, University of New South Wales, Sydney, NSW 2031, Australia; (C.C.); (M.C.); (C.M.); (I.M.); (J.A.); (H.W.-C.); (B.P.); (S.C.); (A.J.); (C.Y.O.)
| | - Chee Y. Ooi
- School of Clinical Medicine, Discipline of Paediatrics & Child Health, UNSW Medicine & Health, University of New South Wales, Sydney, NSW 2031, Australia; (C.C.); (M.C.); (C.M.); (I.M.); (J.A.); (H.W.-C.); (B.P.); (S.C.); (A.J.); (C.Y.O.)
- Department of Gastroenterology, Sydney Children’s Hospital, Randwick, NSW 2031, Australia
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Traini I, Chan SY, Menzies J, Hughes J, Coffey MJ, McKay IR, Ooi CY, Leach ST, Krishnan U. Intestinal dysbiosis and inflammation in children with repaired esophageal atresia. J Pediatr Gastroenterol Nutr 2024; 78:43-51. [PMID: 38291693 DOI: 10.1002/jpn3.12053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 09/23/2023] [Accepted: 09/26/2023] [Indexed: 02/01/2024]
Abstract
OBJECTIVES This study aims to compare the intestinal microbiota and intestinal inflammation of children with esophageal atresia (EA) to matched healthy controls, and to investigate the relationship between these factors and clinical outcomes. METHODS A cross-sectional study of 35 children with EA and 35 matched healthy controls (HC) from a single tertiary pediatric hospital in Australia was conducted. Demographic and dietary data were collected using surveys. Stool samples were analyzed using 16S rRNA sequencing, and fecal calprotectin measurements were used to measure intestinal inflammation. Comparisons were made between the groups, and correlations between the microbiota and clinical factors were investigated in the EA cohort. RESULTS Compared to HC, children with EA had similar alpha diversity, but beta diversity analysis revealed clustering of EA and HC cohorts. Children with EA had a significantly higher relative abundance of the order Lactobacillales, and a lower abundance of the genus uncultured Bacteroidales S24-7. Fecal calprotectin was significantly higher in children with EA compared to HC. In the EA cohort, children taking proton pump inhibitors (PPI's) had lower alpha diversity and higher calprotectin levels compared to those not taking PPI's. There was a negative correlation between calprotectin and length/height-for-age z scores, and children with higher calprotectin levels had a greater burden of gastrointestinal symptoms. CONCLUSIONS Children with EA have an altered intestinal microbiota compared to HC, which is likely related to PPI use, and may be impacting on growth and quality of life. It is important to rationalize PPI use in this cohort.
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Affiliation(s)
- Isabelle Traini
- Discipline of Pediatrics, School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Randwick, New South Wales, Australia
| | - Sin Y Chan
- Discipline of Pediatrics, School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Randwick, New South Wales, Australia
| | - Jessica Menzies
- Department of Nutrition and Dietetics, Sydney Children's Hospital, Randwick, New South Wales, Australia
| | - Jennifer Hughes
- Department of Speech Pathology, Sydney Children's Hospital, Randwick, New South Wales, Australia
| | - Michael J Coffey
- Discipline of Pediatrics, School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Randwick, New South Wales, Australia
| | - Isabelle R McKay
- Discipline of Pediatrics, School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Randwick, New South Wales, Australia
| | - Chee Y Ooi
- Discipline of Pediatrics, School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Randwick, New South Wales, Australia
- Department of Gastroenterology, Sydney Children's Hospital, Randwick, New South Wales, Australia
| | - Steven T Leach
- Discipline of Pediatrics, School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Randwick, New South Wales, Australia
| | - Usha Krishnan
- Discipline of Pediatrics, School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Randwick, New South Wales, Australia
- Department of Gastroenterology, Sydney Children's Hospital, Randwick, New South Wales, Australia
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Wang X, Shao Z, Zhu M, Li B, You M, Chen X. The correlation of the intestinal with pharyngeal microbiota in early neonates. Front Microbiol 2023; 14:1225352. [PMID: 37601350 PMCID: PMC10434775 DOI: 10.3389/fmicb.2023.1225352] [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] [Received: 05/19/2023] [Accepted: 07/11/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction The gut-lung axis has long been recognized as an important mechanism affecting intestinal and lung immunity. Still, few studies have examined the correlation between the intestinal and pharyngeal microbiota in early neonates, especially when feeding patterns are one of the main drivers of microbiota development. Methods To explore the composition and function of intestinal and pharyngeal microbiota and to analyze the effect of limited formula feeding on the initial microbiota colonization in early full-term neonates, we characterized the stool and oropharyngeal microbiota of 20 healthy full-term newborns sampled on days 0 and 5-7 after birth using 16S rRNA gene sequencing. Based on the sequencing results, a comparison was made of the compositions and functions of the intestinal and oropharyngeal microbiota for analysis. Results and discussion At the phylum level, Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes were the most abundant in both niches. At the genus level, the species of pioneer bacteria were rich in the intestine and oropharynx but low in abundance on day 0. On days 5-7, Bifidobacterium (25.40%) and Escherichia-Shigella (22.16%) were dominant in the intestine, while Streptococcus (38.40%) and Staphylococcus (23.13%) were dominant in the oropharynx. There were eight core bacteria genera in the intestine and oropharynx on days 5-7, which were Bifidobacterium, Escherichia-Shigella, Staphylococcus, Streptococcus, Bacteroides, Parabacteroides, Rothia, and Acinetobacter. As indicated by PICRUSt analysis, on days 5-7, the intestinal microbiota was more predictive than the oropharyngeal microbiota in transcription, metabolism, cell motility, cellular processes and signaling, and organismal system function in the KEGG pathway. Compared to exclusive breastfeeding, limited formula feeding (40-60%) had no significant effect on the neonatal intestinal and oropharyngeal microbiota composition during the initial colonization period. Our results suggest that the initial colonization of microbiota is closely related to the ecological niche environment in the intestine and oropharynx, with their core microbiota being closely correlated. We found that early limited formula feeding could not significantly affect the initial colonization of microbiota in the intestine and oropharynx.
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Affiliation(s)
- Xuejuan Wang
- Department of Neonatal, Shanghai Pudong New Area Health Maternal and Child Health Hospital, Shanghai, China
- Department of Pediatric, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zhiying Shao
- Department of Neonatal, Shanghai Pudong New Area Health Maternal and Child Health Hospital, Shanghai, China
| | - Minrong Zhu
- Department of Neonatal, Shanghai Pudong New Area Health Maternal and Child Health Hospital, Shanghai, China
| | - Bingjie Li
- Department of Pediatric, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Mingyu You
- Department of Pediatric, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaoqing Chen
- Department of Pediatric, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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McKay I, van Dorst J, Katz T, Doumit M, Prentice B, Owens L, Belessis Y, Chuang S, Jaffe A, Thomas T, Coffey M, Ooi CY. Diet and the gut-lung axis in cystic fibrosis - direct & indirect links. Gut Microbes 2023; 15:2156254. [PMID: 36573804 PMCID: PMC9809969 DOI: 10.1080/19490976.2022.2156254] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 12/02/2022] [Indexed: 12/28/2022] Open
Abstract
Cystic fibrosis (CF) is a multisystem, autosomal, recessive disease primarily affecting the lungs, pancreas, gastrointestinal tract, and liver. Whilst there is increasing evidence of a microbial 'gut-lung axis' in chronic respiratory conditions, there has been limited analysis of such a concept in CF. We performed a comprehensive dietary and microbiota analysis to explore the interactions between diet, gastrointestinal microbiota, respiratory microbiota, and clinical outcomes in children with CF. Our results demonstrate significant alterations in intestinal inflammation and respiratory and gastrointestinal microbiota when compared to age and gender matched children without CF. We identified correlations between the gastrointestinal and respiratory microbiota, lung function, CF pulmonary exacerbations and anthropometrics, supporting the concept of an altered gut-lung axis in children with CF. We also identified significant differences in dietary quality with CF children consuming greater relative proportions of total, saturated and trans fats, and less relative proportions of carbohydrates, wholegrains, fiber, insoluble fiber, starch, and resistant starch. Our findings position the CF diet as a potential modulator in gastrointestinal inflammation and the proposed gut-lung axial relationship in CF. The dietary intake of wholegrains, fiber and resistant starch may be protective against intestinal inflammation and should be explored as potential therapeutic adjuvants for children with CF.
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Affiliation(s)
- Isabelle McKay
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, UNSW Medicine and Health, Univeristy of New South Wales, Randwick, Australia
| | - Josie van Dorst
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, UNSW Medicine and Health, Univeristy of New South Wales, Randwick, Australia
| | - Tamarah Katz
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, UNSW Medicine and Health, Univeristy of New South Wales, Randwick, Australia
- Department of Nutrition and Dietetics, Sydney Children’s Hospital Randwick, Randwick, Australia
| | - Michael Doumit
- Department of Physiotherapy, Sydney Children’s Hospital Randwick, Randwick, Australia
| | - Bernadette Prentice
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, UNSW Medicine and Health, Univeristy of New South Wales, Randwick, Australia
- Molecular and Integrative Cystic Fibrosis (miCF) Research Centre, University of New South Wales, Randwick, Australia
- Department of Respiratory Medicine, Sydney Childrens Hospital, Randwick, Australia
| | - Louisa Owens
- Department of Respiratory Medicine, Sydney Childrens Hospital, Randwick, Australia
| | - Yvonne Belessis
- Department of Respiratory Medicine, Sydney Childrens Hospital, Randwick, Australia
| | - Sandra Chuang
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, UNSW Medicine and Health, Univeristy of New South Wales, Randwick, Australia
- Department of Respiratory Medicine, Sydney Childrens Hospital, Randwick, Australia
| | - Adam Jaffe
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, UNSW Medicine and Health, Univeristy of New South Wales, Randwick, Australia
- Molecular and Integrative Cystic Fibrosis (miCF) Research Centre, University of New South Wales, Randwick, Australia
- Department of Respiratory Medicine, Sydney Childrens Hospital, Randwick, Australia
| | - Torsten Thomas
- Biological, Earth and Environmental Sciences, University of New South Wales, Randwick, Australia
- University of New South Wales, Centre for Marine Science and Innovation, Randwick, Australia
| | - Michael Coffey
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, UNSW Medicine and Health, Univeristy of New South Wales, Randwick, Australia
- Department of Gastroenterology, Sydney Children’s Hospital, Randwick, Australia
| | - Chee Y. Ooi
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, UNSW Medicine and Health, Univeristy of New South Wales, Randwick, Australia
- Molecular and Integrative Cystic Fibrosis (miCF) Research Centre, University of New South Wales, Randwick, Australia
- Department of Gastroenterology, Sydney Children’s Hospital, Randwick, Australia
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Traini I, Chan SY, Menzies J, Hughes J, Coffey MJ, Katz T, McKay IR, Ooi CY, Leach ST, Krishnan U. Evaluating the Dietary Intake of Children With Esophageal Atresia: A Prospective, Controlled, Observational Study. J Pediatr Gastroenterol Nutr 2022; 75:221-226. [PMID: 35653431 DOI: 10.1097/mpg.0000000000003498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
OBJECTIVES Children with esophageal atresia (EA) often have feeding difficulties and dysphagia, which may compromise their nutritional status. This study aimed to compare dietary intake between children with EA and matched healthy controls (HC) and to investigate the relationship between dietary factors, growth, dysphagia, and feeding difficulties in the EA cohort. METHODS This cross-sectional cohort study recruited children with EA and HC aged 2-17 years from a tertiary pediatric hospital in Australia. Growth parameters were measured. Dietary intake was assessed using the validated Australian Child and Adolescent Eating Survey. Dysphagia and feeding difficulties were assessed using objective questionnaires. RESULTS Twenty-one children with EA were matched for age and sex with 21 HC. Compared to HC, children with EA had lower mean z scores for height-for-age, but mean weight-for-age and body mass index-for-age z scores were similar. Energy intake was similar between the groups. The diet of children with EA consisted of a higher proportion of fats and lower proportion of carbohydrates compared to matched HC. Dysphagia severity in children with EA positively correlated with proportion of energy from fats and saturated fats. CONCLUSIONS Children with EA have similar energy intake and growth parameters to HC, but their diet consists of a higher proportion of fats and lower proportion of carbohydrates compared to HC. Targeted dietary interventions and parental education are necessary.
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Affiliation(s)
- Isabelle Traini
- From the School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Randwick, NSW, Australia
| | - Sin Yee Chan
- From the School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Randwick, NSW, Australia
| | - Jessica Menzies
- the Department of Nutrition and Dietetics, Sydney Children's Hospital, Randwick, NSW, Australiathe
| | - Jennifer Hughes
- the Department of Speech Pathology, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Michael J Coffey
- From the School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Randwick, NSW, Australia
| | - Tamarah Katz
- the Department of Nutrition and Dietetics, Sydney Children's Hospital, Randwick, NSW, Australiathe
| | - Isabelle R McKay
- From the School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Randwick, NSW, Australia
| | - Chee Y Ooi
- From the School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Randwick, NSW, Australia
- the Department of Gastroenterology, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Steven T Leach
- From the School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Randwick, NSW, Australia
| | - Usha Krishnan
- From the School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Randwick, NSW, Australia
- the Department of Gastroenterology, Sydney Children's Hospital, Randwick, NSW, Australia
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