First, put $u=xt$ to get
$$E_1(x)=\int_x^\infty \frac{e^{-u}}{u}\, du\, ,$$
and then integrate by parts. This gives
$$E_1(x)=-\log(x) e^{-x} +\int_x^\infty \log(u) e^{-u}\, du$$
Since $\log(u)e^{-u}$ is integrable on $(0,\infty)$, the integral in the right-hand side tends to $c=\int_0^\infty \log(u) e^{-u} du$ as $x\to 0$. Moreover, integrating by parts again we get
\begin{eqnarray}
\int_x^\infty \log(u)e^{-u}du-c&=&\int_0^x \log(u)e^{-u} du\\
&=&(x\log(x)-x)e^{-x}+\int_0^x (u\log(u)-u)e^{-u}du\\
&=&O(x\log(x))\, ,
\end{eqnarray}
so that $\int_x^\infty \log(u)e^{-u}du=c+O(x\log(x))$. Finally, since $e^{-x}=1+O(x)$ we also have $\log(x)e^{-x}=\log(x)+O(x\log(x))$. Altogether, this gives
$$E_1(x)=-\log(x)+c +O(x\log(x))\, ,$$
with $c=\int_0^\infty \log(u) e^{-u} du $.