Genomic analysis of bacterial pathogens in the Hunter

<p dir="ltr">The antimicrobial resistance (AMR) crisis is one of the most challenging public health problems encountered by countries all over the world. Many sectors are severely affected by this issue including human health, food, plant and animal production. Hospitals are at the forefront of this problem, with an increasing number of infections in healthcare settings caused by multi-resistant organisms (MROs). These organisms can be passed between patients, the environment and occasionally on the hands of healthcare workers. Understanding the prevalence and transmission patterns of specific MROs within hospital settings is essential for developing targeted infection prevention and control strategies.</p><p dir="ltr">This study examined bacterial isolates that were collected in 2022 at John Hunter Hospital (JHH) in New South Wales, Australia. It aimed to investigate the carriage of vancomycin-resistant enterococci (VRE), carbapenemase-producing organisms (CPOs), including carbapenemase-producing Enterobacterales (CPE), and extended-spectrum beta-lactamase (ESBL)-producing organisms among adult inpatients at JHH. Environmental samples were also collected to assess potential transmission between patients and the hospital environment.</p><p dir="ltr">Antibiotic susceptibility testing was performed on all isolates of P. aeruginosa, Enterococcus spp. and isolates from the order of Enterobacterales. Many of these isolates were subjected to whole genome sequencing, which allowed us to detect clonality among the isolates, comment on their virulence and resistance patterns and identify any mobile genetic elements that could be facilitating the spread of resistance genes.</p><p dir="ltr">The study discovered clonal strains of vancomycin-susceptible (VSE) and vancomycin-resistant Enterococcus faecium (VREfm) in the patient and environmental samples, suggesting that transmission had been occurring between patients and the environment. Current and historical MLST data showed that these lineages have been present in JHH for over 8 years. A large putative recombination event was also discovered between VSE and VRE isolates which led to the transfer of the vancomycin resistance locus and an allele used in multi-locus sequence typing, demonstrating challenges in the use of this typing approach for tracking the spread of E. faecium clones. Additionally, two patients were found to be carrying carbapenemase-producing P. aeruginosa, which was the only Gram-negative MRO detected among the patient samples. In contrast, many Gram-negative species were isolated from the hospital environmental samples, including P. aeruginosa, multiple CPE species and Stenotrophomonas maltophilia. Carbapenemase genes were detected among the patient P. aeruginosa isolates and the environmental CPE isolates, and these were found to be associated with class 1 integrons.</p><p dir="ltr">Overall, the study demonstrated the critical need for enhanced surveillance and infection control measures to address the growing threat of AMR in hospital settings. The study highlights the significant role of the hospital environment in the transmission of MROs and that more stringent and targeted cleaning measures need to be put in place. Addressing this challenge is essential for reducing the burden of AMR in healthcare facilities.</p>