Molecular epidemiology and hospital spread of ceftriaxone non-susceptible enterobacterales in the Sunshine Coast region, Australia

Background: Extended spectrum beta‐lactamase (ESBL) and AmpC‐producing Enterobacterales are prevalent worldwide. Poor clinical outcomes, including death, are more common in patients both colonised and infected with these organisms1. Australia is thought to have a comparatively low prevalence of such organisms, however no clear continuous surveillance system exists2. Specific ESBL type has shown significant geographic variation, having different therapeutic and infection control implications for different regions3. Little is known about the prevalence, molecular type and spread of ESBL and AmpC‐producing Enterobacterales among hospitalised patients in the Sunshine Coast region. Aims: To (i) Determine the prevalence and molecular epidemiology of ESBL and AmpC‐producing Enterobacterales, (ii) Develop an in‐house multiplex polymerase chain reaction (PCR) assay to detect common ESBL genes, (iii) Compare our PCR assay to the double disc diffusion method for detection of ESBLs, and to (iv) Establish, with whole genome sequencing (WGS), whether transmission was occurring in our intensive care unit (ICU). Methods: Clinical specimens from adult and paediatric patients culturing Enterobacterales resistant to a third‐generation cephalosporin were collected prospectively from July 2017 to August 2018 at the Sunshine Coast University Hospital laboratory. Antibiotic susceptibility testing was determined using VITEK‐2®. A validated in‐house pentaplex PCR assay was developed and used to detect common beta‐lactamase genes (CTX‐1, CTX‐9, SHV, TEM, CMY). All isolates collected from patients admitted to the ICU were identified and underwent WGS analysis using the Illumina® platform. Results: 295 clinical specimens were identified. Escherichia coli (78.8%), Klebsiella pneumoniae (16.8%) with 1‐2% consisting of Enterobacter spp., Serratia marcescens and Citrobacter freundii. Specimens included urine (53.8%), rectal swab (39.4%), pus (3.0%) and blood (2.4%). Carbapenem resistance was observed in 3.3%. ICU patient specimens made up 18.2%. The majority (87.8%) of isolates had at least one gene identified on PCR testing of which 48.5% produced CTX‐1, 31.2% produced CTX‐9, 15.9% produced SHV, 12.5% produced CMY and 40.6% produced TEM. Approximately forty percent of isolates produced more than one ESBL with the most common being CTX‐1 and TEM coproduction. A small amount (<5%) of isolates were negative on PCR testing. Fourteen (4.7%) isolates that were negative on double disc diffusion had ESBL genes detected by our PCR assay. WGS of non‐identical ICU patient E. coli (n = 44) and K. pneumoniae (n = 10) isolates revealed no strong evidence for transmission of these organisms between patients during this time period, with the smallest single nucleotide polymorphism (SNP) difference being 300 SNPs. Conclusion: Multidrug resistant Gram‐negative organisms are present on the Sunshine Coast and cause significant morbidity. Our real‐time pentaplex PCR assay was able to successfully identify common beta‐lactamase genes, revealing a frequency distribution among our organisms similar to that noted in previous Australian studies (CTX‐1 group most commonly identified). We were not able to identify evidence of ICU transmission, which recognises the success of current infection control practices at our institution.