Supplementary MaterialsSupplementary materials 1 mgen-6-321-s001

Supplementary MaterialsSupplementary materials 1 mgen-6-321-s001. treat, but have been historically rare in Australia. More recently, CPE have caused outbreaks within hospitals and are now a major infection control concern. Previous work has demonstrated complex, in association with a widespread IncHI2 plasmid. The majority of and other species such as or species. Other carbapenemase genes were infrequent and almost exclusively associated with healthcare exposure overseas. The persistence of lineages as well as a common IncHI2 transmissible plasmid. Introduction Carbapenemase-producing (CPE) are a growing burden worldwide, and attacks with these microorganisms are connected with significant morbidity and mortality [1 frequently, 2]. The grouped family members contains bacterial varieties such as for example as well as the complicated, which are in charge of nearly all infections due to gram-negative bacterias [3]. CPE typically carry a variety of antibiotic resistance genes, leaving few effective treatment options [4, 5]. CPE transmission occurs most frequently in clinical environments [6]; however, community-acquired CPE are increasingly recognized, posing a great threat to public health [6, 7]. CPE genes endemic to certain geographical locations have been described, such as are referred to the central laboratory in Brisbane for further analysis. Isolate selection and CPE detection Susceptibility testing was performed using Vitek 2 (bioMrieux), with minimum inhibitory concentrations (MICs) for meropenem also determined using MIC gradient tests (Etest; bioMrieux). Carbapenemase production was detected using colorimetric methods (RAPIDEC CARBA-NP; bioMrieux; or CARBA; Bio-Rad) and chromogenic N-563 agar (chromID CARBA SMART Agar; bioMrieux). Any with a meropenem MIC >0.25?mg l?1 by Vitek2 or 0.125?mg l?1 by N-563 Etest [15], a positive colorimetric test for carbapenemase or growth on chromID CARBA SMART agar was submitted for molecular confirmation of CPE status using a multiplex PCR assay targeting NDM, IMP-4-like, VIM, KPC and OXA-48-like carbapenemase genes [16C19]. Any isolated between January 2014 and May 2017 with PCR confirmation of carbapenemase genes, or suspected carbapenemase production by phenotypic methods, was characterized further by WGS. Only a single Rabbit Polyclonal to CARD6 CPE isolate per patient was included in the WGS analysis. However, additional CPE sequences were included if a different CPE species was subsequently isolated or PCR demonstrated the presence of a different carbapenemase gene as compared with the initial organism. Clinical data Clinical variables of patients with CPE were collected from the electronic medical record. This included ward of admission at the time of CPE detection, admitting clinical service, body site of initial specimen with CPE, the Charlson Comorbidity score [20] at N-563 admission, and other significant risk factors for infection (end-stage renal failure requiring dialysis, solid organ or haemopoietic stem cell transplant, cytotoxic chemotherapy, monoclonal antibody therapy or other immunosuppression). The following were recorded if present within 12?months prior to CPE detection: any history of travel or healthcare exposure overseas, prior admission to hospital or regular healthcare exposure (e.g. haemodialysis), intensive care unit (ICU) admission, previous colonization or infection with an extended-spectrum -lactamase (ESBL)-producing (MRSA) or vancomycin resistant enterococci (VRE). The presence of any of the following was recorded if present within 1?month prior to CPE detection: surgical procedures, endoscopy, any episode of neutropenia and antibiotic exposure. Any directed antibiotic therapy for the CPE and its duration was recorded, as was the outcome (died or survived) up to hospital discharge. DNA extraction and sequencing DNA was extracted from pure bacterial colonies after overnight incubation.