Detection of bacteria and fungi

A method of diagnosing the organism responsible for an infection, or a disease associated with the presence of a bacterial cell in a sample obtained from a mammalian subject comprising:

• (a) treating the sample under conditions sufficient to lyse bacterial cells;
• (b) after step (a), treating the sample under high pH conditions that inhibit the mammalian background from ATP-dependent ligase but which do not affect microbial NAD-dependent ligases released during the lysis of step (a);
• (c) contacting the sample with a nucleic acid molecule which acts as a substrate for NAD-dependent ligase activity in the sample;
• (d) incubating the thus contacted sample under conditions suitable for NAD-dependent ligase activity;
• and
• (e) determining the presence, amount, or both of a ligated nucleic acid molecule resulting from the action of the NAD-dependent ligase on the substrate nucleic acid molecule to indicate the presence of of a bacterial cell causing the infection.