Determination of the eventual relationship between skin, nasal, throat, anorectal and urinary flora and infectious diseases in patients of the division of hematology and oncology

Febrile neutropenia, a treatment complication in pediatric haematology-oncology patients, increases the risk of hospital infection and increases morbidity and mortality rates. In these patients, we aimed to determine the possible relationships between potential pathogens that are part of the microbial flora and infectious diseases, considering the duration of hospitalisation and empirical treatments applied. Potential pathogen colonisation was characterised by throat, nose, skin swabs, anorectal and urine samples taken from 35 pediatric cancer patients with febrile neutropenia at three different times: on admission to the hospital, on the third day and at discharge. The presence of resistance and virulence genes in vancomycin-resistant (VREfm) isolates of E.faecium, the most frequently isolated species in our study, was investigated using PCR. The possible genetic relationships between 12 isolates from 4 patients from whom we were able to isolate VREfm in three time periods were analysed by MLST. It was observed that 62.85% (340/541) of the isolates were Gram-positive bacteria (GPB), GPB colonisation decreased at discharge, Gram-negative bacteria (GNB) followed a fluctuating course, and fungi decreased gradually. The McNemar test detected significant differences in the colonisation of E.faecium, Micrococcus luteus and C.albicans during hospitalisation. According to logistic regression analysis, anorectal (OR=15.4) and oropharyngeal regions (OR=4.48) were associated with an increased colonisation risk, while the risk decreased at discharge (OR=0.265). Carbapenem resistance was low in GNBs, except for S.maltophilia, 76.92% of which were resistant to meropenem, with a peak on day 3 and a subsequent decrease. All S.aureus isolates were resistant to methicillin, while vancomycin resistance was high and stable in E.faecium isolates. While 58.33% of VREfm isolates were positive for the vanA resistance gene, vanB was not detected in any isolate. Only esp (52.08%) and cylA (2.08%) were found to be positive among virulence genes. MLST revealed that new mutations emerged in the atpA, ddl, and pstS loci during hospitalisation. These findings, which indicate the coexistence of clonal persistence and adaptive evolution in the hospital environment, will provide essential data for surveillance studies of hospital infections.