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e bla NDM 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 bla NDM 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 bla NDM genetic contexts within Tn125, providing insights into the acquisition of bla NDM 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 bla NDM genetic contexts were identified, indicating four particular plasmids with specific bla NDM genetic contexts (NGCs), three of which were IncFII plasmids (FII-A to -C). Of note, the bla NDM 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 bla NDM .

SUMMARYCulture-independent diagnostic techniques are increasingly used in clinical laboratories. They have improved turnaround times and are generally more sensitive than culture.Their relative ease of use may increase the numbers of patients being tested.These tests allow detection of organisms that are currently difficult or impossible to culture.The main non-culture methods are immunoassays, which detect antibody or microbial antigen, and nucleic acid amplification testing, which detects microbial RNA or DNA.For some infections, culture may need to be combined with these tests to determine antibiotic susceptibility.important ancillary information about the likelihood of clinical infection, such as the presence, nature and differential of inflammatory cells in a specimen. Microscopy can also be highly specific for some infections, and it is the diagnostic gold standard for detecting parasitic pathogens of the blood (e.g. malaria) or gastrointestinal tract (e.g. giardiasis).Microscopy has several clear drawbacks. Even for parasitic enteropathogens the sensitivity of a single specimen is poor, 1 and for most common bacterial and fungal infections it is neither sensitive nor specific.Microscopy is labour intensive and requires highly skilled scientists for optimal diagnostic performance. For most pathogens, microscopy is best used as an adjunct to traditional culture or molecular methods. ImmunoassaysImmunoassays use antibodies to detect either antibody or antigen in a patient's sample (usually serum but also nasopharyngeal swabs, throat swabs and urine). Testing for antibodiesAntibody immunoassays -usually referred to as serology -have the particular advantage over other non-culture diagnostic methods in their ability to retrospectively diagnose infection long after viable microorganisms or recoverable nucleic acid have disappeared. Other advantages include a high degree of specificity where seroconversion has occurred, fast turnaround times and improved safety compared to culture methods for some organisms (e.g. Coxiella burnetii). They can also rule out acute infection based on serological evidence of previous exposure and immunity. IntroductionTraditional methods for diagnosing infection have relied largely on clinical microbiology laboratories selecting, isolating and then identifying pathogenic organisms via culture. This can be very time consuming. For some fastidious or slow-growing organisms, the delay to definitive microbiological diagnosis can stretch to weeks, while some organisms cannot be cultured at all. Other drawbacks with culture methods include problems with sensitivity, cost (resource intensive) and potential safety concerns with pathogenic organisms such as Mycobacterium tuberculosis or Coxiella burnetii (the causative organism of Q fever).Non-culture-based diagnostic methods (see Table) can have significant advantages over traditional culture methods. For example, nucleic acid amplification testing has drastically reduced turnaround times for many routine diagnostic tests and enabled high th...

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