I want to use DESEQ to look for differential abundant genes between my patient groups. For my samples, I have 6 patients, with each patient having 3 timepoints (baseline, infection, resolution). I want to look for DAGs with the following contrasts; Baseline vs infection, infection vs resolution.

This is what I have done so far:

dds<-DESeqDataSetFromMatrix(countData = counts, colData = metadata, design = ~ Pathology)
keep=rowSums(counts(dds)) >=10
dds=dds[keep,]
dds<-DESeq(dds)
basevsinf=results(dds, contrast = c("Pathology", "Baseline", "Infection"))

I am finding several DAGs however when I look at their individual abundance I see that they are really only present in 1 or 2 samples. I thought maybe this is an issue with my DESEQ design as I am not taking into consideration that the time points are continuous from each patient. (For example I am testing differences between the baselines of patients 1 to 6 and the infection point of patients 1 to 6). How do I include the fact that there is some within patient sampling within the design?

You might not have enough power to detect changes in the tissues you sequenced. Adding Patient to the design might help, but might not do much.

I am finding several DAGs however when I look at their individual abundance I see that they are really only present in 1 or 2 samples.

You might want to filter those genes away, with something like

keep <- rowSums(counts(dds) >= 10) >= 3