Hello Andreea,
sorry about the late reply, I was on holidays. In the end,we had to resort to several measures, including using Sucuri, as well as changing hosting company, as the hackers were most likely to infect our VPS installation and the hosting company did not manage to solve this.
Luckily no vital files were compromised, but they abused our server to send spam.
In the end, using Sucuri was what fixed our issues for good. It's 300 Euros per year, and saves lots of headache!
Kind regards,
Daniel