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https://www.readbyqxmd.com/read/27890457/the-role-of-whole-genome-sequencing-wgs-in-antimicrobial-susceptibility-testing-of-bacteria-report-from-the-eucast-subcommittee
#1
REVIEW
Matthew J Ellington, Oskar Ekelund, Frank M Aarestrup, Rafael Canton, Michel Doumith, Christian Giske, Hajo Grundman, Henrik Hasman, Matthew Holden, Katie L Hopkins, Jon Iredell, Gunnar Kahlmeter, Claudio U Köser, Alasdair MacGowan, Dik Mevius, Mike Mulvey, Thierry Naas, Tim Peto, Jean-Marc Rolain, Ørjan Samuelsen, Neil Woodford
Whole genome sequencing (WGS) offers the potential to predict antimicrobial susceptibility from a single assay. The European Committee on Antimicrobial Susceptibility Testing (EUCAST) established a subcommittee to review the current development status of WGS for bacterial antimicrobial susceptibility testing (AST). The published evidence for using WGS as a tool to infer antimicrobial susceptibility accurately is currently either poor or non-existent and the evidence / knowledge base requires significant expansion...
November 23, 2016: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/27773067/rapid-detection-of-carbapenemase-producing-enterobacteriaceae-using-maldi-tof-ms
#2
James Knox, Snehal Jadhav, Danielle Sevior, Alex Agyekum, Margaret Whipp, Lynette Waring, Jonathan Iredell, Enzo Palombo
No abstract text is available yet for this article.
February 2016: Pathology
https://www.readbyqxmd.com/read/27601224/problematic-dichotomization-of-risk-for-intensive-care-unit-icu-acquired-invasive-candidiasis-results-using-a-risk-predictive-model-to-categorize-3-levels-of-risk-from-a-multicenter-prospective-cohort-of-australian-icu-patients
#3
E Geoffrey Playford, Jeffrey Lipman, Michael Jones, Anna F Lau, Masrura Kabir, Sharon C-A Chen, Deborah J Marriott, Ian Seppelt, Thomas Gottlieb, Winston Cheung, Jonathan R Iredell, Emma S McBryde, Tania C Sorrell
BACKGROUND:  Delayed antifungal therapy for invasive candidiasis (IC) contributes to poor outcomes. Predictive risk models may allow targeted antifungal prophylaxis to those at greatest risk. METHODS:  A prospective cohort study of 6685 consecutive nonneutropenic patients admitted to 7 Australian intensive care units (ICUs) for ≥72 hours was performed. Clinical risk factors for IC occurring prior to and following ICU admission, colonization with Candida species on surveillance cultures from 3 sites assessed twice weekly, and the occurrence of IC ≥72 hours following ICU admission or ≤72 hours following ICU discharge were measured...
September 6, 2016: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/27120170/in-vitro-volatile-organic-compound-profiling-using-gc%C3%A3-gc-tofms-to-differentiate-bacteria-associated-with-lung-infections-a-proof-of-concept-study
#4
K D Nizio, K A Perrault, A N Troobnikoff, M Ueland, S Shoma, J R Iredell, P G Middleton, S L Forbes
Chronic pulmonary infections are the principal cause of morbidity and mortality in individuals with cystic fibrosis (CF). Due to the polymicrobial nature of these infections, the identification of the particular bacterial species responsible is an essential step in diagnosis and treatment. Current diagnostic procedures are time-consuming, and can also be expensive, invasive and unpleasant in the absence of spontaneously expectorated sputum. The development of a rapid, non-invasive methodology capable of diagnosing and monitoring early bacterial infection is desired...
June 2016: Journal of Breath Research
https://www.readbyqxmd.com/read/27073105/systemic-inflammatory-response-syndrome-based-severe-sepsis-screening-algorithms-in-emergency-department-patients-with-suspected-sepsis
#5
Amith L Shetty, Tristam Brown, Tarra Booth, Kim Linh Van, Daphna E Dor-Shiffer, Milan R Vaghasiya, Cassanne E Eccleston, Jonathan Iredell
OBJECTIVE: Systemic inflammatory response syndrome (SIRS)-based severe sepsis screening algorithms have been utilised in stratification and initiation of early broad spectrum antibiotics for patients presenting to EDs with suspected sepsis. We aimed to investigate the performance of some of these algorithms on a cohort of suspected sepsis patients. METHODS: We conducted a retrospective analysis on an ED-based prospective sepsis registry at a tertiary Sydney hospital, Australia...
June 2016: Emergency Medicine Australasia: EMA
https://www.readbyqxmd.com/read/26912748/predictability-of-phenotype-in-relation-to-common-%C3%AE-lactam-resistance-mechanisms-in-escherichia-coli-and-klebsiella-pneumoniae
#6
Alex Agyekum, Alicia Fajardo-Lubián, Xiaoman Ai, Andrew N Ginn, Zhiyong Zong, Xuejun Guo, John Turnidge, Sally R Partridge, Jonathan R Iredell
The minimal concentration of antibiotic required to inhibit the growth of different isolates of a given species with no acquired resistance mechanisms has a normal distribution. We have previously shown that the presence or absence of transmissible antibiotic resistance genes has excellent predictive power for phenotype. In this study, we analyzed the distribution of six β-lactam antibiotic susceptibility phenotypes associated with commonly acquired resistance genes in Enterobacteriaceae in Sydney, Australia...
May 2016: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/26858245/antibiotic-resistance-in-enterobacteriaceae-mechanisms-and-clinical-implications
#7
REVIEW
Jon Iredell, Jeremy Brown, Kaitlin Tagg
Resistance of the Enterobacteriaceae to antibiotics, especially of the β lactam type, is increasingly dominated by the mobilization of continuously expressed single genes that encode efficient drug modifying enzymes. Strong and ubiquitous selection pressure has seemingly been accompanied by a shift from "natural" resistance, such as inducible chromosomal enzymes, membrane impermeability, and drug efflux, to the modern paradigm of mobile gene pools that largely determine the epidemiology of modern antibiotic resistance...
February 8, 2016: BMJ: British Medical Journal
https://www.readbyqxmd.com/read/26830052/blactx-m-15-carried-by-incf-type-plasmids-is-the-dominant-esbl-gene-in-escherichia-coli-and-klebsiella-pneumoniae-at-a-hospital-in-ghana
#8
Alex Agyekum, Alicia Fajardo-Lubián, Daniel Ansong, Sally R Partridge, Tsiri Agbenyega, Jonathan R Iredell
Escherichia coli and Klebsiella pneumoniae producing extended-spectrum β-lactamases (ESBLs) are among the most multidrug-resistant pathogens in hospitals and are spreading worldwide. Horizontal gene transfer and spread of high-risk clones are involved in ESBL dissemination. Investigation of the resistance phenotypes of 101 consecutive clinical E. coli (n=58) and K. pneumoniae (n=43) isolated at the Komfo Anokye Teaching Hospital in Ghana over 3 months revealed 63 (62%) with an ESBL phenotype. All 63 had a blaCTX-M gene, and sequence analysis showed that 62 of these were blaCTX-M-15...
April 2016: Diagnostic Microbiology and Infectious Disease
https://www.readbyqxmd.com/read/26588228/maldi-tof-mass-spectrometry-for-multilocus-sequence-typing-of-escherichia-coli-reveals-diversity-among-isolates-carrying-blacmy%C3%A2-%C3%A2-like-genes
#9
Kaitlin A Tagg, Andrew N Ginn, Sally R Partridge, Jonathan R Iredell
Effective surveillance and management of pathogenic Escherichia coli relies on robust and reproducible typing methods such as multilocus sequence typing (MLST). Typing of E. coli by MLST enables tracking of pathogenic clones that are known to carry virulence factors or spread resistance, such as the globally-prevalent ST131 lineage. Standard MLST for E. coli requires sequencing of seven alleles, or a whole genome, and can take several days. Here, we have developed and validated a nucleic-acid-based MALDI-TOF mass spectrometry (MS) method for MLST as a rapid alternative to sequencing that requires minimal operator expertise...
2015: PloS One
https://www.readbyqxmd.com/read/26489012/use-of-an-innovative-personality-mindset-profiling-tool-to-guide-culture-change-strategies-among-different-healthcare-worker-groups
#10
COMPARATIVE STUDY
M Lindsay Grayson, Nenad Macesic, G Khai Huang, Katherine Bond, Jason Fletcher, Gwendolyn L Gilbert, David L Gordon, Jane F Hellsten, Jonathan Iredell, Caitlin Keighley, Rhonda L Stuart, Charles S Xuereb, Marilyn Cruickshank
INTRODUCTION: Important culture-change initiatives (e.g. improving hand hygiene compliance) are frequently associated with variable uptake among different healthcare worker (HCW) categories. Inherent personality differences between these groups may explain change uptake and help improve future intervention design. MATERIALS AND METHODS: We used an innovative personality-profiling tool (ColourGrid®) to assess personality differences among standard HCW categories at five large Australian hospitals using two data sources (HCW participant surveys [PS] and generic institution-wide human resource [HR] data) to: a) compare the relative accuracy of these two sources; b) identify differences between HCW groups and c) use the observed profiles to guide design strategies to improve uptake of three clinically-important initiatives (improved hand hygiene, antimicrobial stewardship and isolation procedure adherence)...
2015: PloS One
https://www.readbyqxmd.com/read/26388864/applying-the-emergency-risk-management-process-to-tackle-the-crisis-of-antibiotic-resistance
#11
Dale Dominey-Howes, Beata Bajorek, Carolyn A Michael, Brittany Betteridge, Jonathan Iredell, Maurizio Labbate
We advocate that antibiotic resistance be reframed as a disaster risk management problem. Antibiotic-resistant infections represent a risk to life as significant as other commonly occurring natural disasters (e.g., earthquakes). Despite efforts by global health authorities, antibiotic resistance continues to escalate. Therefore, new approaches and expertise are needed to manage the issue. In this perspective we: (1) make a call for the emergency management community to recognize the antibiotic resistance risk and join in addressing this problem; (2) suggest using the risk management process to help tackle antibiotic resistance; (3) show why this approach has value and why it is different to existing approaches; and (4) identify public perception of antibiotic resistance as an important issue that warrants exploration...
2015: Frontiers in Microbiology
https://www.readbyqxmd.com/read/26126049/evaluation-of-point-of-care-testing-in-critically-unwell-patients-comparison-with-clinical-laboratory-analysers-and-applicability-to-patients-with-ebolavirus-infection
#12
COMPARATIVE STUDY
Jen Kok, Jimmy Ng, Stephen C Li, John Giannoutsos, Vineet Nayyar, Jonathan R Iredell, Dominic E Dwyer, Sharon C-A Chen
Data on the performance of point-of-care (POC) or near-patient devices in the management of critically unwell patients are limited, meaning that there are demands for confirming POC test results in the routine clinical laboratory and so potentially leading to delay in treatment provision. We evaluated the performance of the i-STAT CHEM 8+ and CG4+, Hemochron Signature Elite, HemoCue Hb 201+ and WBC Diff Systems on whole blood collected from medical and surgical patients admitted to the intensive care unit at an Australian tertiary care hospital...
August 2015: Pathology
https://www.readbyqxmd.com/read/26099646/distribution-of-acquired-ampc-%C3%AE-lactamase-genes-in-sydney-australia
#13
Kaitlin A Tagg, Andrew N Ginn, Xiuhong Jiang, Justin Ellem, Sally R Partridge, Jonathan R Iredell
Investigation of plasmid-borne AmpC β-lactamase genes in Escherichia coli and Klebsiella spp. revealed blaCMY-2-like genes predominantly in E. coli and blaDHA genes equally distributed between both species. This distribution remained stable over time, but blaACT/MIR-like genes, initially common in Klebsiella spp., were not identified in more recent isolates.
September 2015: Diagnostic Microbiology and Infectious Disease
https://www.readbyqxmd.com/read/26055385/relative-strengths-of-promoters-provided-by-common-mobile-genetic-elements-associated-with-resistance-gene-expression-in-gram-negative-bacteria
#14
Muhammad Kamruzzaman, Jason D Patterson, Shereen Shoma, Andrew N Ginn, Sally R Partridge, Jonathan R Iredell
Comparison of green fluorescent protein expression from outward-facing promoters (POUT) of ISAba1, ISEcp1, and ISAba125 revealed approximate equivalence in strength, intermediate between PCS (strong) and PCWTGN-10 (weak) class 1 integron promoter variants, >30-fold stronger than POUT of ISCR1, and >5 times stronger than Ptac. Consistent with its usual role, PCWTGN-10 produces more mRNA from a "downstream" gfp gene transcriptionally linked to a "usual" PCWTGN-10-associated gene cassette than does POUT of ISAba1...
August 2015: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/25977400/non-susceptibility-to-ceftaroline-in-healthcare-associated-multiresistant-mrsa-in-eastern-australia
#15
LETTER
Nasmiya Mubarak, Indy Sandaradura, Lupeoletalalelei Isaia, Matthew O'Sullivan, Fei Zhou, Deborah Marriott, Jon R Iredell, John Harkness, David Andresen
No abstract text is available yet for this article.
August 2015: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/25952328/inci-shufflons-assembly-issues-in-the-next-generation-sequencing-era
#16
Michael S M Brouwer, Kaitlin A Tagg, Dik J Mevius, Jonathan R Iredell, Alex Bossers, Hilde E Smith, Sally R Partridge
The shufflon is a site-specific recombination system first identified in the IncI1 plasmid R64. The R64 shufflon consists of four segments, separated by short repeats, which are rearranged and inverted by the recombinase protein Rci, generating diversity in the C-terminal end of the PilV protein. PilV is the tip adhesin of the thin pilus structure involved in bacterial conjugation and may play a role in determining recipient cell specificity during liquid mating. The variable arrangements of the shufflon region would be expected to make plasmid assembly difficult, particularly with short-read sequencing technology, but this is not usually mentioned in recent publications reporting IncI plasmid sequences...
July 2015: Plasmid
https://www.readbyqxmd.com/read/25929173/different-inci1-plasmids-from-escherichia-coli-carry-isecp1-blactx-m-15-associated-with-different-tn2-derived-elements
#17
Zhiyong Zong, Andrew N Ginn, Hana Dobiasova, Jonathan R Iredell, Sally R Partridge
The bla(CTX-M-15) gene, encoding the globally dominant CTX-M-15 extended-spectrum β-lactamase, has generally been found in a 2.971-kb ISEcp1-bla(CTX-M-15)-orf477Δ transposition unit, with ISEcp1 providing a promoter. In available IncF plasmid sequences from Escherichia coli, this transposition unit interrupts a truncated copy of transposon Tn2 that lies within larger multiresistance regions. In E. coli, bla(CTX-M-15) is also commonly associated with IncI1 plasmids and here three such plasmids from E. coli clinical isolates from western Sydney 2006-2007 have been sequenced...
July 2015: Plasmid
https://www.readbyqxmd.com/read/25827513/delusional-infestation-an-australian-multicentre-study-of-23-consecutive-cases
#18
MULTICENTER STUDY
M M A Tran, J R Iredell, D R Packham, M V N O'Sullivan, B J Hudson
Delusional infestation remains a debilitating condition that is therapeutically challenging for clinicians. This case series identifies 23 patients with delusional infestation in an Australian setting. The majority of patients are women and unlikely to have a psychiatric comorbid background. The use of unnecessary anti-parasitic medication is prevalent.
April 2015: Internal Medicine Journal
https://www.readbyqxmd.com/read/25714588/rapid-identification-of-pathogens-using-molecular-techniques
#19
REVIEW
Theo P Sloots, Michael D Nissen, Andrew N Ginn, Jonathan R Iredell
Real-time PCR is the traditional face of nucleic acid detection in the diagnostic microbiology laboratory and is now generally regarded as robust enough to be widely adopted. Methods based on nucleic acid detection of this type are bringing increased accuracy to diagnosis in areas where culture is difficult and/or expensive, and these methods are often effective partners to other rapid molecular diagnostic tools such as matrix-assisted laser desorption ionisation-time of flight mass spectrometry (MALDI-TOF MS)...
April 2015: Pathology
https://www.readbyqxmd.com/read/25673797/candida-colonization-as-a-risk-marker-for-invasive-candidiasis-in-mixed-medical-surgical-intensive-care-units-development-and-evaluation-of-a-simple-standard-protocol
#20
Anna F Lau, Masrura Kabir, Sharon C-A Chen, E Geoffrey Playford, Deborah J Marriott, Michael Jones, Jeffrey Lipman, Emma McBryde, Thomas Gottlieb, Winston Cheung, Ian Seppelt, Jonathan Iredell, Tania C Sorrell
Colonization with Candida species is an independent risk factor for invasive candidiasis (IC), but the minimum and most practicable parameters for prediction of IC have not been optimized. We evaluated Candida colonization in a prospective cohort of 6,015 nonneutropenic, critically ill patients. Throat, perineum, and urine were sampled 72 h post-intensive care unit (ICU) admission and twice weekly until discharge or death. Specimens were cultured onto chromogenic agar, and a subset underwent molecular characterization...
April 2015: Journal of Clinical Microbiology
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