Let $\beta>0$, $x\ge 0$, $\alpha\in\mathbb{C}$. Compute $$\int_{-\infty}^\infty\dfrac{k^2+\beta^2+\beta}{(k^2+\alpha^2)(k^2+\beta^2)}\cos(kx)dk$$ Let $$f(k)=\dfrac{k^2+\beta^2+\beta}{(k^2+\alpha^2)(k^2+\beta^2)}$$ If $\alpha^2\in\mathbb{R}$, the integral equals $$\Re\left(\lim_{R\to\infty}\left(\int_Cf(k)e^{ikx}dk-\int_{C_R}f(k)e^{ikx}dk\right)\right)$$ where $C_R=\{|k|=R,\arg k\in(0,\pi)\}$ and $C=C_R\cup[-R,R]$. The integral over $C$ can be computed using Cauchy's residue theorem, with special cases $\alpha^2=\beta^2$ and $\alpha^2=\beta^2+\beta$. For all $k\in C_R$, $|e^{ikx}|\le 1$ since $\Im(k),x\ge 0$ and $|f(k)|=\Theta(R^{-2})$. $C_R$ has length $\pi R$, so the integral over $C_R$ has magnitude at most $\Theta(R^{-1})$, which tends to $0$ as $R\to\infty$, so $$\lim_{R\to\infty}\int_{C_R}f(k)e^{ikx}dk=0$$ so we can compute the integral when $\alpha^2\in\mathbb{R}$.
If $\alpha^2\not\in\mathbb{R}$, $f(k)\Re(e^{ikx})\neq \Re(f(k)e^{ikx})$, so this approach doesn't work. What do we do then?
This integral arises in the Fourier cosine transform solution to $y''-\alpha^2y=e^{-\beta x}$ for all $x\ge 0$ with $y'(0)=1$ and $y$ bounded as $x\to\infty$.
Your integral
$$I(x) = \int_{-\infty}^\infty\dfrac{k^2+\beta^2+\beta}{(k^2+\alpha^2)(k^2+\beta^2)}\cos(kx)dk$$
is very close to an Inverse Fourier Transform
$$\begin{align*}g(x) &= \dfrac{1}{2\pi}\int_{-\infty}^\infty\dfrac{k^2+\beta^2+\beta}{(k^2+\alpha^2)(k^2+\beta^2)}e^{ikx}dk \\ &= \mathscr{F}^{-1}\left\{\dfrac{k^2+\beta^2+\beta}{(k^2+\alpha^2)(k^2+\beta^2)}\right\}\\ &=\mathscr{F}^{-1}\left\{\dfrac{1- \frac{\beta}{\alpha^2-\beta^2}}{k^2+\alpha^2}\right\} +\mathscr{F}^{-1}\left\{\dfrac{\frac{\beta}{\alpha^2-\beta^2}}{k^2+\beta^2}\right\}\\ &=\dfrac{1- \frac{\beta}{\alpha^2-\beta^2}}{2\alpha}\mathscr{F}^{-1}\left\{\dfrac{2\alpha}{k^2+\alpha^2}\right\} +\dfrac{\frac{\beta}{\alpha^2-\beta^2}}{2\beta}\mathscr{F}^{-1}\left\{\dfrac{2\beta}{k^2+\beta^2}\right\}\\ g(x) &=\dfrac{1- \frac{\beta}{\alpha^2-\beta^2}}{2\alpha}e^{-\alpha|x|} +\dfrac{\frac{\beta}{\alpha^2-\beta^2}}{2\beta}e^{-\beta|x|} \\ \end{align*}$$
for $\Re[\alpha] > 0$
Since your integrand in $I(x)$ looks like an even function, I believe the sine part of the Inverse Fourier Transform makes no contribution, so we can get away with saying
$$\begin{align*}I(x) = 2\pi g(x) &=2\pi\dfrac{1- \frac{\beta}{\alpha^2-\beta^2}}{2\alpha}e^{-\alpha|x|} +2\pi\dfrac{\frac{\beta}{\alpha^2-\beta^2}}{2\beta}e^{-\beta|x|}\\ &=\pi\dfrac{\alpha^2-\beta-\beta^2}{\alpha^2-\beta^2}\dfrac{e^{-\alpha|x|}}{\alpha} +\pi\dfrac{\beta}{\alpha^2-\beta^2}\dfrac{e^{-\beta|x|}}{\beta}\\ \end{align*}$$
for $\Re[\alpha] > 0$