Let $P(t, r_t, T)$ be the bond price at time $t$, where $0 \leq t \leq T$. Then, by Ito's formula,
\begin{align*}
&\ P(t, r_t, T) \\
=& P(0, r_0, T) + \int_0^t\partial_s P(s, r_s, T) ds + \int_0^t\partial_r P(s, r_{s-}, T) dr_s + \frac{1}{2}\sigma^2 \int_0^t r_s\partial_{rr} P(s, r_s, T)ds\\
& \quad +\sum_{s \leq t}\big[P(s, r_s, T) - P(s, r_{s-}, T) - \partial_r P(s, r_{s-}, T)\Delta r_s\big] \quad (\mbox{where } \Delta r_s=r_s - r_{s-})\\
=& P(0, r_0, T) + \int_0^t\partial_s P(s, r_s, T) ds + \int_0^t\partial_r P(s, r_s, T) dr_s^c + \frac{1}{2}\sigma^2 \int_0^t r_s\partial_{rr} P(s, r_s, T)ds\\
& \quad +\sum_{s \leq t}\big[P(s, r_s, T) - P(s, r_{s-}, T) \big] \quad (\mbox{where } dr_t^c = \kappa(\theta - r_t)dt + \sigma \sqrt{r_t} d W_t)\\
=& P(0, r_0, T) + \int_0^t\partial_s P(s, r_s, T) ds + \int_0^t\partial_r P(s, r_s, T) dr_s^c + \frac{1}{2}\sigma^2 \int_0^t r_s\partial_{rr} P(s, r_s, T)ds\\
& \quad +\int_0^t \int_{\mathbb{R}}\big[ P(s, r_{s-}+y, T) - P(s, r_{s-}, T)\big]\mu(ds, dy) \quad (\mbox{where } \mu = \sum_{i=1}^{\infty} \delta_{\tau_i, J_i})\\
=& P(0, r_0, T) + \int_0^t\partial_s P(s, r_s, T) ds + \int_0^t\partial_r P(s, r_s, T) dr_s^c + \frac{1}{2}\sigma^2 \int_0^t r_s\partial_{rr} P(s, r_s, T)ds\\
&\quad +\int_0^t \int_{\mathbb{R}}\big[P(s, r_{s-}+y, T) - P(s, r_{s-}, T)\big](\mu(ds, dy) - ds v(dy)) \\
&\quad +\int_0^t ds\int_{\mathbb{R}}\big[ P(s, r_s+y, T) - P(s, r_s, T)\big]\lambda f_J(y)dy,
\end{align*}
where $v(dy) = \lambda f_J(y)dy$. Here
\begin{align*}
M_t = \int_0^t \int_{\mathbb{R}}\big[ u(X_{s-} + y, s) - u(X_{s-}, s))\big](\mu(ds, dy) - ds v(dy))
\end{align*}
is a martingale. Since $P(t, r_t, T) e^{-\int_0^t r_s ds}$ is a martingale, and
\begin{align*}
d\Big(P(t, r_t, T) e^{-\int_0^t r_s ds}\Big) &= e^{-\int_0^t r_s ds}\big[-r_t P(t, r_t, T) dt + dP(t, r_t, T)\big],
\end{align*}
we obtain that
\begin{align*}
&-r_t P(t, r_t, T) + \partial_t P(t, r_t, T) + \kappa(\theta-r_t)\partial_r P(t, r_t, T)
+ \frac{1}{2}\sigma^2 r_t\partial_{rr} P(t, r_t, T) \\
& \qquad\qquad + \int_{\mathbb{R}}\big[ P(t, r_t+y, T) - P(t, r_t, T\big]\lambda f_J(y)dy = 0.
\end{align*}
That is,
\begin{align*}
& \partial_t P(t, r_t, T) + \kappa(\theta-r_t)\partial_r P(t, r_t, T)
+ \frac{1}{2}\sigma^2 r_t\partial_{rr} P(t, r_t, T) -(r_t+\lambda)P(t, r_t, T)\\
& \qquad\qquad + \lambda \int_{\mathbb{R}} P(t, r_t+y, T) f_J(y)dy = 0.
\end{align*}