To do that, you must declare repository as a service and inject services which you need into it.

cities_repository:
        class: MY\EntityBundle\Entity\CitiesRepository
        arguments: [MYEntityBundle:Cities]
        factory_service: doctrine.orm.entity_manager
        factory_method: getRepository
        calls:
            - [ setCanonicalizer, [ @util.canonicalizer ] ]

The repository class:

namespace MY\EntityBundle\Entity;

use Doctrine\ORM\EntityRepository;
use FOS\UserBundle\Util\CanonicalizerInterface;

/**
 * CitiesRepository
 */
class CitiesRepository extends EntityRepository
{
    /**
     * @var CanonicalizerInterface $canonicalizer
     */
    protected $canonicalizer;

    public function setCanonicalizer(CanonicalizerInterface $canonicalizer)
    {
        $this->canonicalizer = $canonicalizer;
    }

    public function getCanonicalizer()
    {
        return $this->canonicalizer;
    }

    public function saveFromString($cityName, Countries $country)
    {
        $city = $this->findOneBy(
            array('name' => $this->canonicalizer->canonicalize($cityName))
        );
        if (!$city) {
            $city = new Cities();
            $city->setName($cityName);
            $city->setCountry($country);
            $this->_em->persist($city);
            $this->_em->flush();
        }

        return $city;
    }
}

Usage

$city = $this->get('cities_repository')->saveFromString(
            'Ho Chi Minh',
            new Countries('VN', 'Vietnam')
        );