Genomic Characteristics of NDM-Producing Enterobacteriaceae Isolates in Australia and Their blaNDM Genetic Contexts.

blaNDM has been reported in different Enterobacteriaceae species and on numerous plasmid replicon types (Inc). Plasmid replicon typing, in combination with genomic characteristics of the bacterial host (e.g., sequence typing), is used to infer the spread of antimicrobial resistance determinants between genetically unrelated bacterial hosts. The genetic context of blaNDM is heterogeneous. In this study, we genomically characterized 12 NDM-producing Enterobacteriaceae isolated in Australia between 2012 and 2014: Escherichia coli (n = 6), Klebsiella pneumoniae (n = 3), Enterobacter cloacae (n = 2) and Providencia rettgeri (n = 1). We describe their blaNDM genetic contexts within Tn125, providing insights into the acquisition of blaNDM into Enterobacteriaceae. IncFII-type (n = 7) and IncX3 (n = 4) plasmids were the most common plasmid types found. The IncHI1B (n = 1) plasmid was also identified. Five different blaNDM genetic contexts were identified, indicating four particular plasmids with specific blaNDM genetic contexts (NGCs), three of which were IncFII plasmids (FII-A to -C). Of note, the blaNDM genetic context of P. rettgeri was not conjugative. Epidemiological links between our NDM-producing Enterobacteriaceae were established by their acquisition of these five particular plasmid types. The combination of different molecular and genetic characterization methods allowed us to provide insight into the spread of plasmids transmitting blaNDM.

In vitro susceptibility testing of imipenem-relebactam and tedizolid against 102 Mycobacterium abscessus isolates.

OBJECTIVES: Mycobacterium abscessus is an emerging infection in people living with lung diseases, including cystic fibrosis (CF) and bronchiectasis, and it has limited treatment options and low cure rates. The off-label use of novel antibiotics developed for other bacterial pathogens offers potential new therapeutic options. We aimed to describe the in vitro activity of imipenem, imipenem-relebactam and tedizolid against comparator antibiotics in M. abscessus isolates from Australian patients with and without CF. METHODS: We performed susceptibility testing for imipenem-relebactam, tedizolid and comparator antibiotics by Clinical and Laboratory Standards Institute (CLSI) criteria against 102 clinical M. abscessus isolates, including 46 from people with CF. RESULTS: In this study, the minimum inhibitory concentration (MICs) of imipenem-relebactam was one-fold dilution less than of imipenem alone. The MIC50 and MIC90 of imipenem-relebactam were 8 and 16 mg/L, respectively, whereas for imipenem they were 16 and 32 mg/L. Tedizolid had an MIC50 and MIC90 of 2 and 4 mg/L, respectively. Forty non-CF isolates had linezolid susceptibility performed, with MIC50 and MIC90 values of 16 and 32 mg/L, respectively, measured. CONCLUSIONS: This study shows lower MICs for imipenem-relebactam and tedizolid compared to other more commonly used antibiotics and supports their consideration in clinical trials for M. abscessus treatment.

A systematic review of antimicrobial susceptibility testing as a tool in clinical trials assessing antimicrobials against infections due to gram-negative pathogens.

BACKGROUND: Antimicrobial susceptibility testing (AST) is the standard of care for treating bacterial infections. In randomized clinical trials of new antimicrobials, AST might not be performed or reported in real time. OBJECTIVES: To determine local, real-time laboratory AST performance, its usage in the trial flow, quality control (QC) of the local testing, central AST performance and the effect of using AST categorization on the trials' primary outcomes. DATA SOURCES: We systematically searched PubMed, Embase, PsychINFO and Web of Science. ELIGIBILITY CRITERIA: We included registered randomized controlled trials published in journals between January 2015 and December 2019. PARTICIPANTS AND INTERVENTIONS: We included trials comparing different antibiotics for the treatment of infections caused predominantly by Gram-negative bacteria. METHODS: Primary outcomes for different trial populations were extracted and differences between trial arms were compared for patients with infections caused by susceptible versus non-susceptible bacteria. Results are described narratively. RESULTS: Of 32 randomized trials, 25 trials reported that local AST was performed, 1312 reported the local laboratory AST methods, no trial reported QC, but post-hoc referral for AST at a reference laboratory was common. Patients' outcomes were superior when patients with infections due to susceptible and non-susceptible pathogens were compared post hoc (median difference 14%, interquartile range 8%-24%) in trials allowing this comparison (seven antimicrobials), except for colistin, where 14-day mortality was 9% higher when patients were treated with colistin for colistin-susceptible versus colistin-resistant carbapenem-resistant Acinetobacter baumannii. When excluding patients with pathogens that were non-susceptible to either antimicrobial in the trials, the difference in the primary outcome between the trial arms was reduced in five out of six trials. CONCLUSIONS: Trials should perform AST to guide patient inclusion or exclusion from the study and consider the impact of the central laboratory susceptibility results on the study outcomes when using post-hoc reference testing.

Self-collection: An appropriate alternative during the SARS-CoV-2 pandemic.

OBJECTIVES: To evaluate the reliability of self-collection for SARS-CoV-2 and other respiratory viruses because swab collections for SARS-CoV-2 put health workers at risk of infection and require use of personal protective equipment (PPE). METHODS: In a prospective study, patients from two states in Australia attending dedicated COVID-19 collection clinics were offered the option to first self-collect (SC) nasal and throat swabs (SCNT) prior to health worker collect (HC) using throat and nasal swabs (Site 1) or throat and nasopharyngeal swabs (Site 2). Samples were analysed for SARS-CoV-2 as well as common respiratory viruses. Concordance of results between methods was assessed using Cohen's kappa (κ) and Cycle threshold (Ct) values were recorded for all positive results as a surrogate measure for viral load. RESULTS: Of 236 patients sampled by HC and SC, 25 had SARS-CoV-2 (24 by HC and 25 by SC) and 63 had other respiratory viruses (56 by HC and 58 by SC). SC was highly concordant with HC (κ = 0.890) for all viruses including SARS-CoV-2 and more concordant than HC to positive results by any method (κ = 0.959 vs 0.933). Mean SARS-CoV-2 E-gene and N-gene, rhinovirus and parainfluenza Ct values did not differ between HC and SCNT. CONCLUSIONS: Self-collection of nasal and throat swabs offers a reliable alternative to health worker collection for the diagnosis of SARS-CoV-2 and other respiratory viruses and provides patients with easier access to testing, reduces exposure of the community and health workers to those being tested and reduces requirement for PPE.

First case report of human infection with Mycobacterium stomatepiae.

INTRODUCTION: We describe the first detailed case report of human infection with Mycobacterium stomatepiae. Infection with non-tuberculous mycobacteria (NTM) related to M. stomatepiae is well described, despite the lack of previous confirmed reports of M. stomatepiae-related human disease. Localised cervical lymphadenitis is the most common NTM disease in children, with species closely related to M. stomatepiae, such as Mycobacterium triplex and Mycobacterium florentinum, having been shown to be rare causative agents. CASE PRESENTATION: A 19-month-old girl presented with persistent unilateral neck lumps which developed following a facial laceration. Both lumps were fluctuant with overlying erythema and no fistulae present. Incision and drainage with curettage was performed. The operative sample of purulent fluid revealed pleomorphic bacilli on Ziehl-Neelsen staining. The isolate cultured was referred for further genotypic identification via 16S rRNA gene sequencing, identifying the organism as M. stomatepiae. CONCLUSION: We describe the first detailed case report of human infection with M. stomatepiae. This organism can now be added to the growing list of NTM that are opportunistic human pathogens, though it is likely to remain a very rare causative agent of this clinical syndrome. Early diagnosis relies on clinical suspicion by the treating doctor, flagging potential cases to the microbiology laboratory and hence allowing correct specimen set-up. Laboratory diagnosis requires incubation of cultures at lower temperatures, and definitive identification is best performed by sequencing methods, including 16S rRNA gene sequencing. The description of novel species of NTM causing human disease is likely to increase with further advancements in diagnostic methods.

Even high-dose extended infusions may not yield desired concentrations of ß-lactams: the value of therapeutic drug monitoring.

A 35-year-old patient in intensive care with severe burn injury developed episodes of sepsis. Blood culture yielded a multidrug-resistant Pseudomonas aeruginosa and treatment was commenced with amikacin (minimum inhibitory concentration (MIC) 2-4 mg/L, dose 20 mg/kg adjusted body weight 24-hourly) and meropenem (MIC 8 mg/L, dose 2 g IV 8-hourly and later 6-hourly). Despite the use of extended infusions with ß-lactam therapeutic drug monitoring and doses that were more than 2.5 times higher than standard meropenem doses, resistance emerged. This case report describes the application of therapeutic drug monitoring to optimize ß-lactam therapy in a difficult-to-treat critically ill patient.

Risk factors for urinary catheter associated bloodstream infection.

OBJECTIVES: Urinary catheter associated bloodstream infection (UCABSI) causes significant morbidity, mortality and healthcare costs. We aimed to define the risk factors for UCABSI. METHODS: A case-control study was conducted at two Australian tertiary hospitals. Patients with urinary source bloodstream infection associated with an indwelling urinary catheter (IDC) were compared to controls with an IDC who did not develop urinary source bloodstream infection. RESULTS: There were 491 controls and 67 cases included in the analysis. Independent statistically significant risk factors for the development of UCABSI included insertion of the catheter in operating theatre, chronic kidney disease, age-adjusted Charlson comorbidity index, accurate urinary measurements as reason for IDC insertion and dementia. IDCs were inserted for valid reasons in nearly all patients, however an appropriate indication at 48 h post-insertion was found in only 44% of patients. Initial empiric antibiotics were deemed inappropriate in 23 patients (34%). CONCLUSION: To our knowledge, this is the first study to look specifically at the risk factors for bloodstream infection in urinary catheterised patients. Several risk factors were identified. IDC management and empiric management of UCABSI could be improved and is likely to result in a decreased incidence of infection and its complications.