Mapping the ‘hospital microbiome’ and the spread of antimicrobial resistance and biofilm on the intensive care units from different regions

MR Khalid Johani1,2, Dr Dayane  Costa1,3, Dr Honghua  Hu1, Dr Stephanie  Dancer4, Dr Dulcelene  Meloc3, Dr Lillian  Kelly Lopes3, Dr Anaclara  Tipple3, Dr Anand  Deva1, Dr Iain  Gosbell5, Dr Slade  Jensen5, Dr Gregory  Whiteley6, Dr Karen  Vickery1

1Macquarie University, Sydney, Australia,

2Prince Sultan Military Medical City, Riyadh, Saudi Arabia,

3Federal University of Goias, Goiania, Brazil ,

4NHS Lanarkshire, Glasgow, United Kingdom,

5Western Sydney University, Sydney, Australia,

6Whiteley Corporation, Nth Sydney, Australia


Healthcare associated infections are a significant burden on health service providers, in terms of cost, morbidity and mortality. Organisms causing these infections can be sourced from the inanimate environment around patients. Could the difficulty of eradicating these organisms be because they reside in surface biofilms?


Following environmental cleaning and disinfection, samples from Brazil (n=40), Australia (n=44), Scotland (n=8) and Saudi Arabia (n=20) were obtained by aseptically cutting fragments from hospital furnishings and equipment. Samples were transported to Australia for biofilm analysis. Bacterial load/cm2 was determined by quantitative PCR of the 16S rRNA gene using eubacterial universal primers. The metagenomic sequencing was performed at the Australian Centre for Ecogenomics. Culturable MDRO were detected by sonication in tryptic soya broth followed by culture on HBA plates and specific methicillin-resistant Staphylococcus aureus(MRSA), vancomycin-resistant enterococci(VRE) and extended spectrum beta-lactamase(ESBL) agar plates. Biofilm presence was visually confirmed by live/dead BacLight staining combined with confocal laser scanning microscopy or scanning electron microscopy.


Sequencing of 16S rRNA genes identified Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes as the most abundant bacterial phyla, with 48 different genera across the samples.

the mean of the microbial load, as determined by PCR, being 4.4×103, 5.5×105, 2.6×104 and 3.4×104/cm2 for Brazilian, Australian, Scottish and Saudi hospitals respectively. Overall 59% of the 112 samples were still culture positive when they reached Australia for analysis. MDRO were isolated from 4/26 (15%), 13/23 (57%), 2/4 (50%) culture positive samples from Brazilian, Australian and Scottish hospitals respectively, MDRO were not isolated from Saudi samples.


Khalid is a Doctor of Philosophy(PhD) in Australian School of Advanced Medicine, Macaque university, Australia.

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