Association Between Minimum Inhibitory Concentration, Beta-lactamase Genes and Mortality for Patients Treated With Piperacillin/Tazobactam or Meropenem From the MERINO Study.

INTRODUCTION: This study aims to assess the association of piperacillin/tazobactam and meropenem minimum inhibitory concentration (MIC) and beta-lactam resistance genes with mortality in the MERINO trial. METHODS: Blood culture isolates from enrolled patients were tested by broth microdilution and whole genome sequencing at a central laboratory. Multivariate logistic regression was performed to account for confounders. Absolute risk increase for 30-day mortality between treatment groups was calculated for the primary analysis (PA) and the microbiologic assessable (MA) populations. RESULTS: In total, 320 isolates from 379 enrolled patients were available with susceptibility to piperacillin/tazobactam 94% and meropenem 100%. The piperacillin/tazobactam nonsusceptible breakpoint (MIC >16 mg/L) best predicted 30-day mortality after accounting for confounders (odds ratio 14.9, 95% confidence interval [CI] 2.8-87.2). The absolute risk increase for 30-day mortality for patients treated with piperacillin/tazobactam compared with meropenem was 9% (95% CI 3%-15%) and 8% (95% CI 2%-15%) for the original PA population and the post hoc MA populations, which reduced to 5% (95% CI -1% to 10%) after excluding strains with piperacillin/tazobactam MIC values >16 mg/L. Isolates coharboring extended spectrum ß-lactamase (ESBL) and OXA-1 genes were associated with elevated piperacillin/tazobactam MICs and the highest risk increase in 30-day mortality of 14% (95% CI 2%-28%). CONCLUSIONS: After excluding nonsusceptible strains, the 30-day mortality difference from the MERINO trial was less pronounced for piperacillin/tazobactam. Poor reliability in susceptibility testing performance for piperacillin/tazobactam and the high prevalence of OXA coharboring ESBLs suggests that meropenem remains the preferred choice for definitive treatment of ceftriaxone nonsusceptible Escherichia coli and Klebsiella.

Geospatial epidemiology of Staphylococcus aureus in a tropical setting: an enabling digital surveillance platform.

Delivery of information to clinicians on evolving antimicrobial susceptibility needs to be accurate for the local needs, up-to-date and readily available at point of care. In northern Australia, bacterial infection rates are high but resistance to first- and second-line antibiotics is poorly described and currently-available datasets exclude primary healthcare data. We aimed to develop an online geospatial and interactive platform for aggregating, analysing and disseminating data on regional bacterial pathogen susceptibility. We report the epidemiology of Staphylococcus aureus as an example of the power of digital platforms to tackle the growing spread of antimicrobial resistance in a high-burden, geographically-sparse region and beyond. We developed an online geospatial platform called HOTspots that visualises antimicrobial susceptibility patterns and temporal trends. Data on clinically-important bacteria and their antibiotic susceptibility profiles were sought from retrospectively identified clinical specimens submitted to three participating pathology providers (96 unique tertiary and primary healthcare centres, n = 1,006,238 tests) between January 2008 and December 2017. Here we present data on S. aureus only. Data were available on specimen type, date and location of collection. Regions from the Australian Bureau of Statistics were used to provide spatial localisation. The online platform provides an engaging visual representation of spatial heterogeneity, demonstrating striking geographical variation in S. aureus susceptibility across northern Australia. Methicillin resistance rates vary from 46% in the west to 26% in the east. Plots generated by the platform show temporal trends in proportions of S. aureus resistant to methicillin and other antimicrobials across the three jurisdictions of northern Australia. A quarter of all, and up to 35% of methicillin-resistant S. aureus (MRSA) blood isolates in parts of the northern Australia were resistant to inducible-clindamycin. Clindamycin resistance rates in MRSA are worryingly high in regions of northern Australia and are a local impediment to empirical use of this agent for community MRSA. Visualising routinely collected laboratory data with digital platforms, allows clinicians, public health physicians and guideline developers to monitor and respond to antimicrobial resistance in a timely manner. Deployment of this platform into clinical practice supports national and global efforts to innovate traditional disease surveillance systems with the use of digital technology and to provide practical solutions to reducing the threat of antimicrobial resistance.

Levels of Mycoplasma genitalium Antimicrobial Resistance Differ by Both Region and Gender in the State of Queensland, Australia: Implications for Treatment Guidelines.

Mycoplasma genitalium is frequently associated with urogenital and rectal infections, with the number of cases of macrolide-resistant and quinolone-resistant M. genitalium infection continuing to increase. In this study, we examined the levels of resistance to these two common antibiotic treatments in geographically distinct locations in Queensland, Australia. Samples were screened for macrolide resistance-associated mutations using a commercially available kit (ResistancePlus MG; SpeeDx), and quinolone resistance-associated mutations were identified by PCR and DNA sequencing. Comparisons between antibiotic resistance mutations and location/gender were performed. The levels of M. genitalium macrolide resistance were high across both locations (62%). Quinolone resistance mutations were found in ∼10% of all samples, with a number of samples harboring mutations conferring resistance to both macrolides and quinolones. Quinolone resistance was higher in southeast Queensland than in north Queensland, and this was consistent in both males and females (P = 0.007). The M. genitalium isolates in rectal swab samples from males harbored high levels of macrolide (75.9%) and quinolone (19%) resistance, with 15.5% harboring resistance to both classes of antibiotics. Overall, the lowest observed level of resistance was to quinolones in females from north Queensland (1.6%). These data highlight the high levels of antibiotic resistance in M. genitalium isolates within Queensland and the challenges faced by sexually transmitted infection clinicians in managing these infections. The data do, however, show that the levels of antibiotic resistance may differ between populations within the same state, which has implications for clinical management and treatment guidelines. These findings also support the need for ongoing antibiotic resistance surveillance and tailored treatment.

Genomic insights into the emergence and spread of international clones of healthcare-, community- and livestock-associated meticillin-resistant Staphylococcus aureus: Blurring of the traditional definitions.

The evolution of meticillin-resistant Staphylococcus aureus (MRSA) from meticillin-susceptible S. aureus has been a result of the accumulation of genetic elements under selection pressure from antibiotics. The traditional classification of MRSA into healthcare-associated MRSA (HA-MRSA) and community-associated MRSA (CA-MRSA) is no longer relevant as there is significant overlap of identical clones between these groups, with an increasing recognition of human infection caused by livestock-associated MRSA (LA-MRSA). Genomic studies have enabled us to model the epidemiology of MRSA along these lines. In this review, we discuss the clinical relevance of genomic studies, particularly whole-genome sequencing, in the investigation of outbreaks. We also discuss the blurring of each of the three epidemiological groups (HA-MRSA, CA-MRSA and LA-MRSA), demonstrating the limited relevance of this classification.

ST2249-MRSA-III: a second major recombinant methicillin-resistant Staphylococcus aureus clone causing healthcare infection in the 1970s.

Typing of healthcare-associated methicillin-resistant Staphylococcus aureus (MRSA) from Australia in the 1970s revealed a novel clone, ST2249-MRSA-III (CC45), present from 1973 to 1979. This clone was present before the Australian epidemic caused by the recombinant clone, ST239-MRSA-III. This study aimed to characterize the genome of ST2249-MRSA-III to establish its relationship to other MRSA clones. DNA microarray analysis was conducted and a draft genome sequence of ST2249 was obtained. The recombinant structure of the ST2249 genome was revealed by comparisons to publicly available ST239 and ST45 genomes. Microarray analysis of genomic DNA of 13 ST2249 isolates showed gross similarities with the ST239 chromosome in a segment around the origin of replication and with ST45 for the remainder of the chromosome. Recombination breakpoints were precisely determined by the changing pattern of nucleotide polymorphisms in the genome sequence of ST2249 isolate SK1585 compared with ST239 and ST45. One breakpoint was identified to the right of oriC, between sites 1014 and 1065 of the gene D484_00045. Another was identified to the left of oriC, between sites 1185 and 1248 of D484_01632. These results indicate that ST2249 inherited approximately 35.3% of its chromosome from an ST239-like parent and 64.7% from an ST45-like parent. ST2249-MRSA-III resulted from a major recombination between parents that resemble ST239 and ST45. Although only limited Australian archival material is available, the oldest extant isolate of ST2249 predates the oldest Australian isolate of ST239 by 3 years. It is therefore plausible that these two recombinant clones were introduced into Australia separately.

Comparison of test specificities of commercial antigen-based assays and in-house PCR methods for detection of rotavirus in stool specimens.

Seven commercial rotavirus antigen assays were compared with in-house PCR methods for detecting rotavirus in stool specimens. The assay sensitivities were 80% to 100%, while the specificities were 54.3% for one commercial immunochromatographic (ICT) method and 99.4% to 100% for other assays. Thus, except for one commercial ICT, all the assays were generally reliable for rotavirus detection.

Staphylococcus aureus 'Down Under': contemporary epidemiology of S. aureus in Australia, New Zealand, and the South West Pacific.

The clinical and molecular epidemiology of Staphylococcus aureus disease has changed considerably over the past two decades, particularly with the emergence and spread of community-associated methicillin-resistant S. aureus (CA-MRSA) clones. Indeed, some of the first global descriptions of CA-MRSA were from remote indigenous communities in Western Australia, and from Pacific Peoples in New Zealand. The epidemiology of S. aureus infections in the South West Pacific has several unique features, largely because of the relative geographical isolation and unique indigenous communities residing in this region. In particular, a number of distinct CA-MRSA clones circulate in Australia and New Zealand, such as sequence type (ST) 93 methicillin-resistant S. aureus (MRSA) (Queensland clone) and clonal complex 75 S. aureus (Staphylococcus argenteus) in Australia, and ST30 MRSA (Southwest Pacific clone) in New Zealand. In addition, there is a disproportionate burden of S. aureus disease in indigenous paediatric populations, particularly in remote Aboriginal communities in Australia, and in Pacific Peoples and Maori in New Zealand. In this review, we provide a contemporary overview of the clinical and molecular epidemiology of S. aureus disease in the South West Pacific region, with a particular focus on features distinct to this region.

Molecular investigation of bacterial communities on the inner and outer surfaces of peripheral venous catheters.

Peripheral venous catheters (PVCs) are some of the most widely used medical devices in hospitals worldwide. PVC-related infections increase morbidity and treatment costs. The inner surfaces of PVCs are rarely examined for the population structure of bacteria, as it is generally believed that bacteria at this niche are similar to those on the external surface of PVCs. We primarily test this hypothesis and also study the effect of antibiotic treatment on bacterial communities from PVC surfaces. The inner and outer surfaces of PVCs from 15 patients were examined by 454 GS FLX Titanium 16S rRNA sequencing and the culture method. None of the PVCs were colonised according to the culture method and none of the patients had a bacteraemia. From a total of 127,536 high-quality sequence reads, 14 bacterial phyla and 268 diverse bacterial genera were detected. The number of operational taxonomic units for each sample was in the range of 86-157, even though 60 % of patients had received antibiotic treatment. Stenotrophomonas maltophilia was the predominant bacterial species in all the examined PVC samples. There were noticeable but not statistically significant differences between the inner and outer surfaces of PVCs in terms of the distribution of the taxonomic groups. In addition, the bacterial communities on PVCs from antibiotic-treated patients were significantly different from untreated patients. In conclusion, the surfaces of PVCs display complex bacterial communities. Although their significance has yet to be determined, these findings alter our perception of PVC-related infections.

Vancomycin in the treatment of meticillin-resistant Staphylococcus aureus (MRSA) infection: End of an era?

Infection with meticillin-resistant Staphylococcus aureus (MRSA) continues to have significant morbidity and mortality. Vancomycin, which has been the mainstay of treatment of invasive MRSA infections, has several drawbacks related to its pharmacological properties as well as varying degrees of emerging resistance. These resistant subpopulations are difficult to detect, making therapy with vancomycin less reliable. The newer agents such as linezolid, daptomycin, ceftaroline, and the newer glycopeptides telavancin and oritavancin are useful alternatives that could potentially replace vancomycin in the treatment of certain conditions. By summarising the discussions that took place at the III MRSA Consensus Conference in relation to the current place of vancomycin in therapy and the potential of the newer agents to replace vancomycin, this review focuses on the challenges faced by the laboratory and by clinicians in the diagnosis and treatment of MRSA infections.

USA300 abroad: global spread of a virulent strain of community-associated methicillin-resistant Staphylococcus aureus.

The epidemic of USA300-0114 methicillin-resistant Staphylococcus aureus (MRSA) in the USA has been remarkable for its virulence and for its ability to cause infections in both the community and healthcare settings. Although it has mainly been associated with skin and soft tissue infections, particularly furunculosis, it has also caused severe life-threatening conditions such as necrotizing pneumonia, osteomyelitis, and septic arthritis. This strain or a closely related Latin American variant has now spread to multiple countries on five continents, where associated clinical and epidemiological features have been in keeping with those seen in the USA. Furthermore, it has become the dominant community-associated MRSA strain in five countries. It is now a major international epidemic strain, but whether it will supplant established community-associated strains in other countries remains to be seen.

Increases in Australian cutaneous abscess hospitalisations: 1999-2008.

Staphylococcus aureus is the most common cause of skin and soft tissue infections (SSTIs). Such infections have increased in several countries recently and at a time when community-associated methicillin-resistant S. aureus (CA-MRSA) strains have emerged globally. We examined changes in Australian hospitalisations for the treatment of cutaneous abscesses between 1999 and 2008, a period when increased numbers of CA-MRSA infections were being reported. National hospitalisation data for cutaneous abscess treatment (1999-2008) were examined. Hospitalisation numbers were collated and age-specific admission rates calculated and examined for changes over time. Yearly admissions for the treatment of cutaneous abscesses increased by 48%, from 8,849 (1999-2000) to 13,126 (2007-2008). The crude annual hospitalisation rate per 100,000 population rose from 46 to 62 respectively. However, increases in admission rates were limited to the 10 to 54 years age range. Incidence rate ratios (IRRs) for final versus baseline year admission rates for these age groups ranged from 1.36 (95% confidence interval [CI] 1.04-1.78) for those aged 10-14 years to 1.64 (95% CI 1.26-2.12) for those aged 45-49 years; p<0.05. Increases in hospitalisation for cutaneous abscess treatment have occurred in Australia during the last decade. Research into the underlying causes and prevention of these infections is a public health priority.

Influenza-associated bacterial pathogens in patients with 2009 influenza A (H1N1) infection: impact of community-associated methicillin-resistant Staphylococcus aureus in Queensland, Australia.

BACKGROUND: Secondary bacterial pneumonia due to community onset methicillin-resistant Staphylococcus aureus (MRSA) has become a highly publicised cause of influenza-associated death. There is a risk that case reports of fatal outcomes with post-influenza MRSA pneumonia may unduly influence antibiotic prescribing. AIMS: The aim of this study was to demonstrate the incidence of community-onset MRSA pneumonia in 2009 H1N1 influenza patients. METHODS: The microbiology records of patients positive for influenza A (H1N1) in 2009 were reviewed for positive blood or respiratory tract cultures and urinary pneumococcal antigen results within a Queensland database. Patients with such positive results within 48 h of hospital admission and a positive H1N1 influenza result in the prior 6 weeks were included. RESULTS: In 2009, 4491 laboratory-confirmed pandemic influenza A (H1N1) infections were detected. Fifty patients (1.1% of the H1N1 cohort) who were hospitalised with H1N1 and who had a bacterial respiratory tract pathogen were identified. Streptococcus pneumoniae (16 patients; 32%), Staphylococcus aureus (13 patients; 26%) and Haemophilus influenzae (9 patients; 18%) were the most commonly cultured organisms. Of the cohort of 4491 patients, MRSA was detected in only two patients, both of whom were admitted to intensive care units and survived after prolonged admissions. CONCLUSIONS: Influenza-associated community-onset MRSA pneumonia was infrequently identified in the 2009 H1N1 season in Queensland, despite community-onset MRSA skin and soft tissue infections being very common. Although post-influenza MRSA pneumonia is of great concern, its influence on empiric-prescribing guidelines should take into account its incidence relative to other secondary bacterial pathogens.

Better clinical decision making and reducing diagnostic error.

A major amount of our time working in clinical practice involves thinking and decision making. Perhaps it is because decision making is such a commonplace activity that it is assumed we can all make effective decisions. However, this is not the case and the example of diagnostic error supports this assertion. Until quite recently there has been a general nihilism about the ability to change the way that we think, but it is now becoming accepted that if we can think about, and understand, our thinking processes we can improve our decision making, including diagnosis. In this paper we review the dual process model of decision making and highlight ways in which decision making can be improved through the application of this model to our day-to-day practice and by the adoption of de-biasing strategies and critical thinking.

Comparison of a multiplexed MassARRAY system with real-time allele-specific PCR technology for genotyping of methicillin-resistant Staphylococcus aureus.

The Sequenom MassARRAY iPLEX single-nucleotide polymorphism (SNP) typing platform uses matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) coupled with single-base extension PCR for high-throughput multiplex SNP detection. In this study, we investigated the use of iPLEX MassARRAY technology for methicillin-resistant Staphylococcus aureus (MRSA) genotyping. A 16-plex MassARRAY iPLEX GOLD assay (MRSA-iPLEX) was developed that targets a set of informative SNPs and binary genes for MRSA characterization. The method was evaluated with 147 MRSA isolates, and the results were compared with those of an established SYBR Green-based real-time PCR system utilizing the same SNP-binary markers. A total of 2352 markers belonging to 44 SNP-binary profiles were analysed by both real-time PCR and MRSA-iPLEX. With real-time PCR as the reference standard, MRSA-iPLEX correctly assigned 2298 of the 2352 (97.7%) markers. Sequence variation in the MRSA-iPLEX primer targets accounted for the majority of MRSA-iPLEX erroneous results, highlighting the importance of primer target selection. MRSA-iPLEX provided optimal throughput for MRSA genotyping, and was, on a reagent basis, more cost-effective than the real-time PCR methods. The 16-plex MRSA-iPLEX is a suitable alternative to SYBR Green-based real-time PCR typing of major sequence types and clonal complexes of MRSA.

The role of surveillance cultures in the prediction of susceptibility patterns of Gram-negative bacilli in the intensive care unit.

Surveillance cultures may detect colonisation with drug-resistant Gram-negative bacteria and can be hypothesised to guide appropriate initial antibiotic treatment for intensive care unit (ICU) patients. We investigated the microbiological data of 228 episodes of nosocomial bloodstream infection (BSI) due to Gram-negative bacteria in an ICU in which piperacillin/tazobactam or meropenem was used empirically for serious infections, to evaluate the contribution of surveillance cultures to an appropriate choice of initial antibiotic therapy. Surveillance cultures were taken in advance of BSI in 218 (95.6%) of 228 episodes. Concordant organisms with identical identification and susceptibilities were found in prior surveillance cultures and subsequent blood cultures in 65 (29.8%) of 218 episodes. Surveillance cultures predicted resistance in 52.9% and 51.4% of BSIs caused by resistant pathogens to piperacillin/tazobactam and meropenem, respectively. The negative predictive value of surveillance cultures negative for a resistant organism also exceeded 90% for piperacillin/tazobactam and meropenem. Given that the overall resistant rates of BSI pathogens of our study were 11.3% to piperacillin/tazobactam and 16.4% to meropenem, surveillance cultures in our setting may provide important information on the probability of drug resistance of the causative pathogens and some utility in aiding empiric antibiotic therapy for ICU patients who subsequently develop BSI.

First outbreak of PVL-positive nonmultiresistant MRSA in a neonatal ICU in Australia: comparison of MALDI-TOF and SNP-plus-binary gene typing.

The purpose of this brief report is to describe the first outbreak of a community-associated nonmultiresistant and PVL-positive MRSA strain (CC30) in a neonatal intensive care unit in Australia. The utility of matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF-MS) for microbial typing is compared with single nucleotide polymorphism (SNP) plus binary gene analysis. The composite correlation index analysis of the MALDI-TOF-MS data demonstrated the similar inter-strain relatedness found with the SNP-plus-binary gene typing used to confirm the outbreak. The evolving spread of MRSA emphasizes the importance of surveillance, infection control vigilance and the ongoing investigation of rapid typing methods for MRSA.

Epidemiology of non-multiresistant methicillin-resistant Staphylococcus aureus infection in Queensland, Australia: associations with indigenous populations and Panton-Valentine leukocidin.

The purpose of this study was to determine the extent of the spread of epidemic clones of non-multiresistant methicillin-resistant Staphylococcus aureus (nmMRSA) and the epidemiology of resultant infections throughout the state of Queensland. We collected a sample of clinical isolates of nmMRSA from laboratories serving public hospitals and clinics throughout the state. Three hundred isolates were typed and tested for the presence of Panton-Valentine leukocidin (PVL) genes and demographic and clinical data were collected from associated cases. Fifteen percent of S. aureus isolates were nmMRSA and 69% of these belonged to PVL-positive clones, predominantly ST93 and CC30. Low numbers of USA300- and USA400-like isolates were also present. Infections due to PVL-positive strains were much less frequently acquired in hospital (3.4%) than those due to PVL-negative nmMRSA (23.7%). Thirty-seven percent of cases were in indigenous people who make up only 3.6% of the general population. The proportion of cases with PVL-positive, but non-negative isolates decreased progressively with age, suggesting that immunity to PVL might be an important determinant of protection. nmMRSA strains are present throughout Queensland and cause infections in both community and healthcare settings.

Increasing incidence of candidaemia: long-term epidemiological trends, Queensland, Australia, 1999-2008.

Given variability in the epidemiology of candidaemia and a relative paucity of contemporary longitudinal data, a passive laboratory-based surveillance study was performed to assess the epidemiology of candidaemia in all public healthcare facilities in Queensland, Australia over the period 1999-2008. Demographic and microbiological data on all candidaemia episodes, together with appropriate denominators (admissions and patient-days), were collected from laboratory and administrative information systems. From 1999 to 2008, 1137 episodes occurred (overall incidence-density: 0.45 per 10 000 patient-days) with a 3.5-fold increase in density (P<0.0001 for trend). Candidaemia episodes originating in traditional high-risk areas either decreased (haemato-oncology and paediatric wards) or remained stable (intensive care units). Episodes on adult medical/surgical wards increased significantly over time, accounting for 60% of the total by 2008. The relative proportion caused by Candida albicans decreased and Candida parapsilosis increased (both P<0.01). The proportion of fluconazole-resistant isolates did not change. The increasing occurrence of candidaemia outside traditional high-risk areas and the emergence of C. parapsilosis present new challenges for preventive and early intervention strategies.

Prevalence of Staphylococcus aureus strains in an Australian cohort, 1989-2003: evidence for the low prevalence of the toxic shock toxin and Panton-Valentine leukocidin genes.

The purpose of this paper is to determine the prevalence of the toxic shock toxin gene (tst) and to enumerate the circulating strains of methicillin-sensitive Staphylococcus aureus (MSSA) and methicillin-resistant S. aureus (MRSA) in Australian isolates collected over two decades. The aim was to subtype these strains using the binary genes pvl, cna, sdrE, pUB110 and pT181. Isolates were assayed using real-time polymerase chain reaction (PCR) for mecA, nuc, 16 S rRNA, eight single-nucleotide polymorphisms (SNPs) and for five binary genes. Two real-time PCR assays were developed for tst. The 90 MRSA isolates belonged to CC239 (39 in 1989, 38 in 1996 and ten in 2003), CC1 (two in 2003) and CC22 (one in 2003). The majority of the 210 MSSA isolates belonged to CC1 (26), CC5 (24) and CC78 (23). Only 18 isolates were tst-positive and only 15 were pvl-positive. Nine MSSA isolates belonged to five binary types of ST93, including two pvl-positive types. The proportion of tst-positive and pvl-positive isolates was low and no significant increase was demonstrated. Dominant MSSA clonal complexes were similar to those seen elsewhere, with the exception of CC78. CC239 MRSA (AUS-2/3) was the predominant MRSA but decreased significantly in prevalence, while CC22 (EMRSA-15) and CC1 (WA-1) emerged. Genetically diverse ST93 MSSA predated the emergence of ST93-MRSA (the Queensland clone).