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Background  Third-generation cephalosporin-resistant Gram-negatives (3GCR-GN) and vancomycin-resistant enterococci (VRE) are common causes of multi-drug resistant healthcare-associated infections, for which gut colonisation is considered a prerequisite. However, there remains a key knowledge gap about colonisation and infection dynamics in high-risk settings such as the intensive care unit (ICU), thus hampering infection prevention efforts.    Methods  We performed a three-month prospective genomic survey of infecting and gut-colonising 3GCR-GN and VRE among patients admitted to an Australian ICU. Bacteria were isolated from rectal swabs ( n  = 287 and  n  = 103 patients ≤2 and > 2 days from admission, respectively) and diagnostic clinical specimens between Dec 2013 and March 2014. Isolates were subjected to Illumina whole-genome sequencing ( n  = 127 3GCR-GN,  n  = 41 VRE). Multi-locus sequence types (STs) and antimicrobial resistance determinants were identified from de novo assemblies. Twenty-three isolates were selected for sequencing on the Oxford Nanopore MinION device to generate completed reference genomes (one for each ST isolated from ≥2 patients). Single nucleotide variants (SNVs) were identified by read mapping and variant calling against these references.    Results  Among 287 patients screened on admission, 17.4 and 8.4% were colonised by 3GCR-GN and VRE, respectively.  Escherichia coli  was the most common species ( n  = 36 episodes, 58.1%) and the most common cause of 3GCR-GN infection. Only two VRE infections were identified. The rate of infection among patients colonised with  E. coli  was low, but higher than those who were not colonised on admission ( n  = 2/33, 6% vs  n  = 4/254, 2%, respectively,  p  = 0.3). While few patients were colonised with 3GCR-  Klebsiella pneumoniae  or  Pseudomonas aeruginosa  on admission ( n  = 4), all such patients developed infections with the colonising strain. Genomic analyses revealed 10 putative nosocomial transmission clusters (≤20 SNVs for 3GCR-GN, ≤3 SNVs for VRE): four VRE, six 3GCR-GN ,  with epidemiologically linked clusters accounting for 21 and 6% of episodes, respectively (OR 4.3,  p  = 0.02).    Conclusions  3GCR- E. coli  and VRE were the most common gut colonisers.  E. coli  was the most common cause of 3GCR-GN infection, but other 3GCR-GN species showed greater risk for infection in colonised patients. Larger studies are warranted to elucidate the relative risks of different colonisers and guide the use of screening in ICU infection control.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12879-021-06386-z.

Genomic surveillance of antimicrobial resistant bacterial colonisation and infection in intensive care patients