i would design your table like this:
addendum:
as response to edited question and comments below. it is based on guessing, what yo like to have:

for table environment is used threeparttable
, for multi line cells are used makecell
s:
\documentclass{amsart}
\usepackage{booktabs, makecell, threeparttable}
\renewcommand\theadfont{\normalsize}
\renewcommand\theadgape{}
\newcommand\mcm[1]{\multicolumn{1}{c}{\makecell[tl]{#1}}}
\newcommand\mcl[1]{\multicolumn{2}{l}{#1}}
\usepackage{siunitx}
\begin{document}
\begin{threeparttable}
\centering
{Pathogen Occurrence in Honey Bee Colonies with and
without Colony Collapse Disorder}
\medskip
\begin{tabular}{l l *{2}{S[table-format=2.0,
table-space-text-post={\;\%},
table-column-width=24mm]<{\,\%}} }
\toprule
& & \mcl{\thead{Percentage of colonies\\
affected by pathogen}} \\
\midrule
\mcl{Viruses} & \mcl{} \\
& IAPV & 83 & 5 \cr
& KBV & 100 & 76 \cr
\midrule
\mcl{Pathogen} & \mcm{Colonies with \\
colony collapse\\
disorder}
& \mcm{Colonies without\\
colony collapse \\
disorder} \\
\midrule
\mcl{Fungi} & \mcl{} \\
& \textit{Nosema apis} & 90 & 48 \cr
& \textit{Nosema ceranae} & 100 & 81 \cr
\midrule
\mcl{All Four Pathogens} & 83 & 0 \cr
\bottomrule
\end{tabular}
\end{threeparttable}
\end{document}
edit:
after last edit of question, it seems that you like to have the following looks of table (with consideration my taste what is good looking table):

(red lines indicate page layout).
note:
- demand, that can be used only
tabular
table environments is the very same as required to drill holes with square drill bit ...
- so, i suggest to use packages, which can make your life more relaxing and help you to design professional looks of table.
- differences between above table and previous propositions are minimal.
\documentclass{amsart}
\usepackage{caption}
\usepackage{booktabs, makecell, threeparttable}
\renewcommand\theadfont{\small}
\renewcommand\theadgape{}
\newcommand\mcm[1]{\multicolumn{1}{c}{\thead[tl]{#1}}}
\newcommand\mcl[1]{\multicolumn{2}{l}{\textbf{#1}}}
\usepackage{siunitx}
%-------------------------------- show page layout, only for test
\usepackage{showframe}
\renewcommand\ShowFrameLinethickness{0.15pt}
\renewcommand*\ShowFrameColor{\color{red}}
%---------------------------------------------------------------%
\begin{document}
\begin{center}
\begin{threeparttable}
\captionsetup{skip=1ex, margin=11mm, justification=centering}
\caption*{Pathogen Occurrence in Honey Bee Colonies with and
without Colony Collapse Disorder}
\begin{tabular}{l l *{2}{S[table-format=2.0,
table-space-text-post={\;\%},
table-column-width=24mm]<{\,\%}} }
\toprule
\mcl{Pathogen} & \mcm{Percentage affected in \\
colonies with colony \\
collapse disorder}
& \mcm{Percentage affected in \\
colonies without colony\\
collapse disorder} \\
\midrule
\mcl{Viruses} & \mcl{} \\
& IAPV & 83 & 5 \cr
& KBV & 100 & 76 \cr
\midrule
\mcl{Fungi} & \mcl{} \\
& \textit{Nosema apis} & 90 & 48 \cr
& \textit{Nosema ceranae} & 100 & 81 \cr
\midrule
\mcl{All Four Pathogens} & 83 & 0 \cr
\bottomrule
\end{tabular}
\end{threeparttable}
\end{center}
\end{document}
- if you like to have table with vertical lines -- what i strongly dissuade -- than just add
|
in column specification, where you like to have them, remove package booktabs
from preamble and replace \toprule
, \midrule
and \bottomrule
with \hline
and after some tweaks obtain:

\documentclass{amsart}
\usepackage{caption}
\usepackage{threeparttable}
\newcommand\mcl[1]{\multicolumn{2}{l|}{\textbf{#1}}}
\usepackage{siunitx}
%-------------------------------- show page layout, only for test
\usepackage{showframe}
\renewcommand\ShowFrameLinethickness{0.15pt}
\renewcommand*\ShowFrameColor{\color{red}}
%---------------------------------------------------------------%
\begin{document}
\begin{center}
\begin{threeparttable}
\captionsetup{skip=1ex, margin=11mm, justification=centering}
\sisetup{table-format=2.0,
table-space-text-post={\;\%},
table-column-width=24mm
}
\renewcommand\arraystretch{1.2}
\caption*{Pathogen Occurrence in Honey Bee Colonies with and
without Colony Collapse Disorder}
\begin{tabular}{l l | S<{\,\%} | S<{\,\%} }
\hline
\mcl{Pathogen} & \multicolumn{1}{p{33mm}|}{\centering
Percentage affected in
colonies with colony
collapse disorder}
& \multicolumn{1}{p{33mm}}{\centering
Percentage affected in
colonies without colony
collapse disorder} \\
\hline
\mcl{Viruses} & \multicolumn{1}{c|}{}
& \multicolumn{1}{c}{} \\
& IAPV & 83 & 5 \cr
& KBV & 100 & 76 \cr
\hline
\mcl{Fungi} & \multicolumn{1}{c|}{}
& \multicolumn{1}{c}{} \\
& \textit{Nosema apis} & 90 & 48 \cr
& \textit{Nosema ceranae} & 100 & 81 \cr
\hline
\mcl{All Four Pathogens} & 83 & 0 \cr
\end{tabular}
\end{threeparttable}
\end{center}
\end{document}