ABSTRACT
Despite the reported elimination of measles virus in Australia, importation of cases from endemic countries continues to lead to secondary local transmission and outbreaks. Rapid laboratory confirmation of measles is paramount for individual patient management and outbreak responses. Further, it is important to rapidly distinguish infection from wild-type virus or vaccine strains to guide public health responses. We developed a high throughput, TaqMan-based multiplex reverse-transcription-polymerase chain reaction (PCR) assay using the BD MAX platform (Becton Dickinson) that simultaneously detects measles virus and differentiates between wild-type and vaccine strains without the need for sequencing.
Subject(s)
Measles Vaccine/immunology , Measles virus/immunology , Measles/prevention & control , RNA, Viral/genetics , Australia , Disease Outbreaks , Genotype , Humans , Multiplex Polymerase Chain Reaction/methodsABSTRACT
Background: VRE are prevalent among patients in ICUs. Non-typeable vanA VRE, due to loss of one of the genes used for MLST (pstS), have increased in Australia, suggestive of a new, hospital-acquired lineage. Objectives: To understand the significance of this lineage and its transmission using WGS of strains isolated from patients in ICUs across New South Wales, Australia. Methods: A total of 240 Enterococcus faecium isolates collected between February and May 2016, and identified by conventional PCR as vanA positive, were sequenced. Isolates originated from 12 ICUs in New South Wales, grouped according to six local health districts, and represented both rectal screening swab (n = 229) and clinical (n = 11) isolates. Results: ST analysis revealed the absence of the pstS gene in 84.2% (202 of 240) of vanA isolates. Two different non-typeable STs were present based on different allelic backbone patterns. Loss of the pstS gene appeared to be the result of multiple recombination events across this region. Evidence for pstS-negative lineage spread across all six local health districts was observed suggestive of inter-hospital transmission. In addition, multiple outbreaks were detected, some of which were protracted and lasted for the duration of the study. Conclusions: These findings confirmed the evolution, emergence and dissemination of non-typeable vanA E. faecium. This study has highlighted the utility of WGS when attempting to describe accurately the hospital-based pathogen epidemiology, which in turn will continue to inform optimal infection control measures necessary to halt the spread of this important nosocomial organism.
Subject(s)
Bacterial Proteins/genetics , Cross Infection/transmission , Enterococcus faecium/genetics , Genome, Bacterial , Gram-Positive Bacterial Infections/epidemiology , Vancomycin-Resistant Enterococci/genetics , Anti-Bacterial Agents/therapeutic use , Australia/epidemiology , Bacterial Typing Techniques , Cross Infection/epidemiology , Cross Infection/microbiology , Disease Outbreaks , Enterococcus faecium/classification , Enterococcus faecium/drug effects , Gram-Positive Bacterial Infections/transmission , Humans , Intensive Care Units/statistics & numerical data , New South Wales/epidemiology , Polymerase Chain Reaction , Vancomycin/pharmacology , Vancomycin-Resistant Enterococci/isolation & purification , Whole Genome SequencingABSTRACT
We identified discrete importation events of the mcr-1 gene on incompatibility group IncI2 plasmids in Escherichia coli isolated from patients in New South Wales, Australia, in 2011 and 2013. mcr-1 is present in a small minority of colistin-resistant Enterobacteriaceae and appears not to be established locally.
Subject(s)
Escherichia coli Infections/epidemiology , Escherichia coli Infections/microbiology , Escherichia coli Proteins/genetics , Escherichia coli/genetics , Anti-Bacterial Agents/pharmacology , Australia/epidemiology , Base Sequence , Binding Sites , Colistin/pharmacology , Drug Resistance, Bacterial , Escherichia coli/drug effects , Escherichia coli/isolation & purification , Escherichia coli Infections/history , Food Microbiology , History, 21st Century , Humans , Microbial Sensitivity Tests , Plasmids/genetics , Promoter Regions, Genetic , Ribosomes/metabolismABSTRACT
The BD Max StaphSR assay is an automated qualitative in vitro diagnostic test for the direct detection and differentiation of methicillin-susceptible Staphylococcus aureus (MSSA) and methicillin-resistant S. aureus (MRSA). A total of 460 specimens were tested, and the results were compared with standard culture-based identification. MRSA was detected in 48 samples (sensitivity of 100%; positive predictive value [PPV] of 100%). MSSA was detected in 112 samples (sensitivity of 99.1%; PPV of 100%), and 299 samples containing coagulase-negative staphylococcus and nonstaphylococcal species were negative by the BD Max StaphSR assay (specificity of 100%; negative predictive value [NPV] of 99.7 to 100%).
Subject(s)
Bacteremia/diagnosis , Bacteriological Techniques/methods , Diagnostic Tests, Routine/methods , Staphylococcal Infections/diagnosis , Staphylococcus aureus/isolation & purification , Automation, Laboratory/methods , Humans , Sensitivity and Specificity , Time FactorsABSTRACT
pJIE143 (34 kb), from an Escherichia coli ST131 isolate, carries bla(CTX-M-15) but could not be typed using the standard PCR-based replicon-typing primer set. Complete sequencing revealed a backbone with similarity to IncX plasmids, including a pir-like gene encoding a π-like replication protein and iterons related to those of other IncX plasmids. The 2.971-kb ISEcp1-bla(CTX-M-15)-orf477Δ transposition unit often found within Tn2 is inserted just beyond the end of pir, flanked by 5-bp direct repeats.
