In rapamycin-treated Ptpn2-KO macrophages, localisation of bacteria into lysosomes was indeed restored (figure 6A, colocalisation of mAIEC with LAMP1, subpanel viii), but there were still no pHRhodamine bright spots detectable on infection with pHRhodo particles, indicating that autophagy activation can restore the ability to transport bacteria into lysosomes in Ptpn2-KO cells, but that a defect in lysosomal acidification persists (figure 6A, subpanel iii). This evidence concerns the gene PTPN2 and infection.