The answer depends on what you plan to do with the partial fraction decomposition. To compute such decompositions requires only the the factors in the denominator be coprime (vs. powers of primes = irreducibles). For example, if $\rm\,(P,Q) = 1,\:$ i.e. $\rm\,P,Q\,$ are coprime, then
$$\rm \dfrac{A}{PQ} \,=\ \dfrac{B}P\, +\, \dfrac{C}Q \ \iff\ A\, =\, BQ + CP $$
Since $\rm\,(P,Q)=1,\,$ the latter equation can be solved for $\rm\,B,C\,$ using the extended gcd algorithm to compute the Bezout identity $\rm\ 1 = bQ + cP\,\ $ then multiplying it through by $\rm\,A.\:$ Then, if desired, one can decompose this further if the denominators decompose further. For example, if $\rm\:P = p^k\:$ is a prime power, and $\rm\:Q\:$ is a product of prime powers, then one can apply the above recusively, decomposing $\rm\:C/Q = C/P'Q',\:$ etc, till all the denominators are all prime powers. But many applications do not need such full decompositions into prime power denominators.
For example, let's consider Hermite's algorithm for integrating rational functions. It works as follows. By squarefree decomposing the denominator and partial fraction expanding, we reduce to integrating $\rm\:A/D^k\in \mathbb Q(x)\:,\:$ where $\rm\:\deg\:A < \deg\:D^k,\:$ and where $\rm\:D\:$ is squarefree, so $\rm\:\gcd(D,D') = 1\:.\:$ Thus by Bezout (extended Euclidean algorithm) there are $\rm\:B,C\in \mathbb Q[x]\:$ such that $\rm\ B\ D' + C\ D\ =\ A/(1-k)\:.\:$ Then a little algebra shows that
$$\rm\int \frac{A}{D^k}\ =\ \frac{B}{D^{k-1}}\ +\ \int \frac{(1-k)\ C - B'}{D^{k-1}} $$
Iterating the above rule we eventually reduce to the case $\rm\:k=1\:,\:$ i.e. squarefree denominator $\rm\:D\:.\:$
Thus using the above "quotient rule" and nothing deeper than Euclid's algorithm for polynomials (without requiring any factorization) one can mechanically compute the "rational part" of the integral of a rational function, i.e. the part of the integral not involving logarithms. This Hermite reduction rule is the basis of an algorithm due to Hermite (1872). It plays a fundamental role in the transcendental case of some integration algorithms.