Supplement 3. Whole genome sequencing results WGS showed that the majority of Escherichia coli (97%) and Klebsiella spp. (100%) isolates were CTX-M positive (Supplementary file 3). Of the 32 ESBL-E. coli, 11 (34.4%) belonged to sequence type (ST) 131. One Citrobacter freundii carried an mcr-9 gene (with a colistin minimal inhibitory concentration (MIC) of 0.5 µg/mL as measured by Vitek2). While the Proteus spp. phenotypically showed ESBL activity, no betalactamase resistance genes were identified (Supplementary file 3). Prevalence of antimicrobial resistance genes among the different species as determined using the CARD web-interface (https://card.mcmaster.ca/). The analysis (restricted to perfect and strict hits only) was focused on different types of beta-lactamases and aminoglycoside modifying enzymes. *sequence types involved: E.coli ST131 (n=11), ST10/ST69 (n=4), ST405/ST744 (n=2), ST38/ST58/ST75/ST88/ST120/ST167/ST224/ST636/ST13164 (n=1); K. pneumoniae ST152/ST307/ST464/ST561 (n=1); S. aureus ST6 (n=1) Species # isolates OXA-1 OXA-10 blaZ SHV TEM CTX-M GES-1 SHV ACT CMY DHA EC AAC(3)-IId AAC(3)-IIe AAC(6')-Ib10 AAC(6')-Ib9 AAC(6')-Ib-cr6 aadA aadA2 aadA3 aadA5 ANT(2'')-Ia ANT(3'')-IIa APH(3')-Ia APH(3'')-Ib APH(6)-Id MCR-9.1 mecA Citrobacter freundii 2 500 0 0 050501000100500 0 0 0500 0 050 0500 0 0 0500 Enterobacter hormaechei 1 000000001000000000000000000000 Escherichia coli* 32 19 3.1 0 0 34 97 0 0 0 0 6.3 479.43.1 0 0 16 9.43.1 0 19 0 3.19.4 34 47 0 0 Klebsiella pneumoniae* 4 500 0501001000250 02505050250500 0 0 0 0 0 075750 0 Klebsiella aerogenes 1 0000010000000000000000000010010000 Proteus spp. 3 000000000000000000000000333300 Staphylococcus aureus* 1 00100000000000000000000000000100 0 10 20 30 40 50 60 70 80 90 100 percentage positive isolates Legend beta-lactamase ESBL type beta-lactamase ampC type beta-lactamase aminoglycoside modifying enzyme miscellaneous 2 95 Comparing universal screening and universal risk-assessment for MDRO
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