A metagenomic prospective cohort study on gut microbiome composition and clinical infection in small bowel transplantation

Figures & data

Table 1. Organisms cultured from clinical samples by participant.

Participant	Cultured organism causing infection	Sample type	Days post transplantation	Presumed organism origin
1	Candida glabrata	Abdominal drain fluid	22	Gut
2	Vancomycin resistant Enterococcus faecium Vancomycin resistant Enterococcus faecium Vancomycin resistant Enterococcus faecium Staphylococcus epidermidis Staphylococcus epidermidis Staphylococcus epidermidis Vancomycin resistant Enterococcus faecium Vancomycin resistant Enterococcus faecium Vancomycin resistant Enterococcus faecium*	Urine Blood Blood Blood Blood Blood Blood Line culture Blood	41 81 100 133 134 137 148 149 151	Gut Gut Gut Skin Skin Skin Gut Gut Gut
3	Aspergillus fumigatus Vancomycin resistant Enterococcus faecium* Pseudomonas spp. Aspergillus fumigatus	Sputum Abdominal body fluid Urine Bone biopsy	4 12 67 182	Lungs Gut Unclear Lungs
4	Vancomycin sensitive Enterococcus faecium Vancomycin resistant Enterococcus faecium Klebsiella michiganensis Klebsiella michiganensis* Vancomycin resistant Enterococcus faecium	Abdominal drain fluid Abdominal drain fluid Abdominal drain fluid Peritoneal fluid (surgical sample) Donor artery/vein (surgical sample)	7 13 13 15 15	Gut Gut Gut Gut Gut
5	None

*Bacterial isolates that underwent whole-genome sequencing.

Figure 1. Stacked bar charts representing the relative abundances (% of OTUs in sample) of five most prominent phyla by sampling timepoint.

Samples are arranged longitudinally by participant, beginning with the donor sample. Samples were assigned a unique alphanumeric identification comprising the participant’s unique number (1,2,3,4,5), followed by the transplantation visit (V1) or endoscopy number (E1-E6) and the sample type (ileal-I, colonic-C, donor-D.)

Figure 2. Shannon α-diversity index, at species level, of participant samples.

Samples are arranged longitudinally by participant. Timepoint 1 corresponds to the date of transplant and all subsequent timepoints show α-diversity at follow-up endoscopies.

Figure 3. Quantification of antimicrobial resistance genes (ARG) present in participant samples.

A) Cumulative number of ARGs in all patient samples at time point 1 (day of transplant,) time point 2 and 3 (1st and 2nd endoscopy follow up.) *Significant difference in number of ARGs between timepoints. B) ARG evolution in samples, over time, by participant. ARG are grouped by mechanism of resistance and annotated by antimicrobial drug class to which they confer resistance. If an AMR gene conferred resistance to $\ge$ 3 antimicrobial classes, the antimicrobial drug class was classified as ‘multidrug’ resistance.

Table 2. Clinical summary of participants.

Participant	Age	Transplanted organs	Past MDRO*	Antimicrobial treatment	Immunosuppressive maintenance	Toxo IgG status (D/R)	Pathogens	Sepsis or rejection episode?	Other infection related complications?	Survival at 1 year	Length of stay (days)
1	52	Small bowel, colon, pancreas	None	Meropenem Vancomycin Caspofungin	Tacrolimus Methylprednisolone Mycophenolate mofetil	-/-	Candida glabrata	Sepsis	None	Alive	53
2	29	Small bowel, stomach, colon, pancreas	None	Meropenem Metronidazole Ciprofloxacin Vancomycin Tigecycline Amikacin Cidofovir Anidulafungin	Tacrolimus Methylprednisolone Mycophenolate mofetil Thymoglobulin (rabbit anti-thymocyte globulin)	-/-	Enterococcus faecium	Sepsis & Rejection	Delirium: Fall with subdural hemorrhage.	Died	164
3	43	Jejunum, colon, pancreas, liver	Vancomycin resistant Enterococcus faecium	Daptomycin Metronidazole Gentamicin Vancomycin Ciprofloxacin Tigecycline Voriconazole Linezolid	Tacrolimus Methylprednislone Mycophenolate mofetil	-/-	Aspergillus fumigatus	Sepsis	Readmission with fungal discitis.	Alive	144
4	24	Small bowel, pancreas, liver	None	Vancomycin	Tacrolimus Methylprednislone	-/-	Enterococcus faecium Klebsiella michiganensis Enterococcus faecium	None	Intra-abdominal bleed: Mycotic breakdown of aortoconduit anastomosis.	Died	18
5	43	Intestine, pancreas, liver	None	Meropenem Fluconazole Ertapenem	Tacrolimus Methyprednisolone Mycopheolate mofetil	-/-	None	None	Abdominal collection and chyle leak. Pyrexia of Unknown Origin.	Alive	57

*MDRO- Multi-drug resistant organisms.

Figure 4. Multivariable association matrix depicting the top 50 functional pathway genes with significant alterations.

Metabolic gene abundances are represented in participants 1, 2, 3 and 4, in relation to participant 5. Participant 5 had the best post-op outcome: No sepsis or rejection episodes, survival at 1 year and short hospital in-patient stay. Red depicts significantly enriched metabolic pathway genes and blue depicts significantly depleted genes.

Figure 5. Principal coordinate analysis depicting the microbial composition of the three sample types: donor, recipient ileum and recipient colon.

Ellipses show a large overlap in the ileal and colonic microbial compositions in the transplant recipients.

Data availability statement

The authors confirm that the data supporting the findings of this study are available in the article and its supplementary materials. The microbial WMS reads for 40 patient samples and WGS reads for 3 bacterial isolates have been deposited in the NCBI Sequence Read Archive under BioProject accession PRJNA1004534.