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Am I right in suggesting that by close relatives the author meant closely related species, or did he have individual organisms in mind?
DETECTION OF HORIZONTAL GENE TRANSFER
There are several approaches to identify genetic changes due to HGT, including:
(1) experimental evidence, whereby a genetic marker is monitored for gene transfer to a recipient organism;
(2) phylogenetic analysisof gene sequences to identify topological inconsistencies between different gene families;
(3) nucleotide compositional analysis to identify any gene that has a nucleotide pattern that differs significantly from the overall genome; and
(4) evolutionary scenarios to explain the patchy appearance of a genetic signature, sequence or function that is not shared by close relatives.
(From "Risks from GMOs due to Horizontal Gene Transfer", by Paul Keese)
You are correct.
From the author's point of view there is not much difference, however. Phylogenetically speaking 'species' are kind of artificial distinctions that exist only as sets of individuals and don't usually convey information, so it makes sense to forget that species exist when talking about HGT. Hopefully that helps provide context for why such imprecise wording is so common.