Publications by authors named "Scott A Beatson"

131 Publications

Emergence and impact of oprD mutations in Pseudomonas aeruginosa strains in cystic fibrosis.

J Cyst Fibros 2021 Mar 25. Epub 2021 Mar 25.

QIMR Berghofer Medical Research Institute, Brisbane, Australia; Faculty of Medicine, The University of Queensland, Brisbane, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Australia; Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, Australia. Electronic address:

Background: Antimicrobial resistance in cystic fibrosis (CF) Pseudomonas aeruginosa airway infection is complex and often attributed to chromosomal mutations. How these mutations emerge in specific strains or whether particular gene mutations are clinically informative is unclear. This study focused on oprD, which encodes an outer membrane porin associated with carbapenem resistance when it is downregulated or inactivated.

Aim: Determine how mutations in oprD emerge in two prevalent Australian shared CF strains of P. aeruginosa and their clinical relevance.

Methods: The two most common shared CF strains in Queensland were investigated using whole genome sequencing and their oprD sequences and antimicrobial resistance phenotypes were established. P. aeruginosa mutants with the most common oprD variants were constructed and characterised. Clinical variables were compared between people with or without evidence of infection with strains harbouring these variants.

Results: Frequently found nonsense mutations arising from a 1-base pair substitution in oprD evolved independently in three sub-lineages, and are likely major contributors to the reduced carbapenem susceptibility observed in the clinical isolates. Lower baseline FEV %predicted was identified as a risk factor for infection with a sub-lineage (odds ratio=0.97; 95% confidence interval 0.96-0.99; p<0.001). However, acquiring these sub-lineage strains did not confer an accelerated decline in FEV nor increase the risk of death/lung transplantation.

Conclusions: Sub-lineages harbouring specific mutations in oprD have emerged and persisted in the shared strain populations. Infection with the sub-lineages was more likely in people with lower lung function, but this was not predictive of a worse clinical trajectory.
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http://dx.doi.org/10.1016/j.jcf.2021.03.007DOI Listing
March 2021

Genomic surveillance, characterization and intervention of a polymicrobial multidrug-resistant outbreak in critical care.

Microb Genom 2021 Mar 18;7(3). Epub 2021 Feb 18.

Pathology Queensland, Central Laboratory, Brisbane, QLD, Australia.

Infections caused by carbapenem-resistant (CR-Ab) have become increasingly prevalent in clinical settings and often result in significant morbidity and mortality due to their multidrug resistance (MDR). Here we present an integrated whole-genome sequencing (WGS) response to a persistent CR-Ab outbreak in a Brisbane hospital between 2016-2018.. and isolates were sequenced using the Illumina platform primarily to establish isolate relationships based on core-genome SNPs, MLST and antimicrobial resistance gene profiles. Representative isolates were selected for PacBio sequencing. Environmental metagenomic sequencing with Illumina was used to detect persistence of the outbreak strain in the hospital. In response to a suspected polymicrobial outbreak between May to August of 2016, 28 CR-Ab (and 21 other MDR Gram-negative bacilli) were collected from Intensive Care Unit and Burns Unit patients and sent for WGS with a 7 day turn-around time in clinical reporting. All CR-Ab were sequence type (ST)1050 (Pasteur ST2) and within 10 SNPs apart, indicative of an ongoing outbreak, and distinct from historical CR-Ab isolates from the same hospital. Possible transmission routes between patients were identified on the basis of CR-Ab and SNP profiles. Continued WGS surveillance between 2016 to 2018 enabled suspected outbreak cases to be refuted, but a resurgence of the outbreak CR-Ab mid-2018 in the Burns Unit prompted additional screening. Environmental metagenomic sequencing identified the hospital plumbing as a potential source. Replacement of the plumbing and routine drain maintenance resulted in rapid resolution of the secondary outbreak and significant risk reduction with no discernable transmission in the Burns Unit since. We implemented a comprehensive WGS and metagenomics investigation that resolved a persistent CR-Ab outbreak in a critical care setting.
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http://dx.doi.org/10.1099/mgen.0.000530DOI Listing
March 2021

Characterization of DtrJ as an IncC plasmid conjugative DNA transfer component.

Mol Microbiol 2021 Feb 10. Epub 2021 Feb 10.

School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.

Incompatibility group C (IncC) plasmids are large (50-400 kb), broad host range plasmids that drive the spread of genes conferring resistance to all classes of antibiotics, most notably the bla gene that confers resistance to last-line carbapenems and the mcr-3 gene that confers resistance to colistin. Several recent studies have improved our understanding of the basic biological mechanisms driving the success of IncC, in particular the identification of multiple novel IncC conjugation genes by transposon directed insertion-site sequencing. Here, one of these genes, dtrJ, was examined in further detail. The dtrJ gene is located in the DNA transfer locus on the IncC backbone, and quantitative reverse-transcriptase PCR analysis revealed it is transcribed in the same operon as the DNA transfer genes traI and traD (encoding the relaxase and coupling protein, respectively) and activated by the AcaDC regulatory complex. We confirmed that DtrJ is not required for pilus biogenesis or mate pair formation. Instead, DtrJ localizes to the membrane, where it interacts with the coupling protein TraD and functions as an IncC DNA transfer protein. Overall, this work has defined the role of DtrJ in DNA transfer of IncC plasmids during conjugation.
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http://dx.doi.org/10.1111/mmi.14697DOI Listing
February 2021

Repurposing a neurodegenerative disease drug to treat Gram-negative antibiotic-resistant bacterial sepsis.

Sci Transl Med 2020 11;12(570)

School of Chemistry and Molecular Biosciences and Australian Infectious Diseases Research Centre, The University of Queensland, Queensland 4072, Australia.

The emergence of polymyxin resistance in carbapenem-resistant and extended-spectrum β-lactamase (ESBL)-producing bacteria is a critical threat to human health, and alternative treatment strategies are urgently required. We investigated the ability of the hydroxyquinoline analog ionophore PBT2 to restore antibiotic sensitivity in polymyxin-resistant, ESBL-producing, carbapenem-resistant Gram-negative human pathogens. PBT2 resensitized , , , and to last-resort polymyxin class antibiotics, including the less toxic next-generation polymyxin derivative FADDI-287, in vitro. We were unable to select for mutants resistant to PBT2 + FADDI-287 in polymyxin-resistant containing a plasmid-borne gene or carrying a chromosomal mutation. Using a highly invasive strain engineered for polymyxin resistance through mutation, we successfully demonstrated the efficacy of PBT2 + polymyxin (colistin or FADDI-287) for the treatment of Gram-negative sepsis in immunocompetent mice. In comparison to polymyxin alone, the combination of PBT2 + polymyxin improved survival and reduced bacterial dissemination to the lungs and spleen of infected mice. These data present a treatment modality to break antibiotic resistance in high-priority polymyxin-resistant Gram-negative pathogens.
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http://dx.doi.org/10.1126/scitranslmed.abb3791DOI Listing
November 2020

Companion Animals Are Spillover Hosts of the Multidrug-Resistant Human Extraintestinal Pandemic Clones ST131 and ST1193.

Front Microbiol 2020 2;11:1968. Epub 2020 Sep 2.

Australian Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia.

sequence types 131 (ST131) and 1193 are multidrug-resistant extraintestinal pathogens that have recently spread epidemically among humans and are occasionally isolated from companion animals. This study characterized a nationwide collection of fluoroquinolone-resistant (FQ ) isolates from extraintestinal infections in Australian cats and dogs. For this, 59 cat and dog FQ clinical isolates (representing 6.9% of an 855-isolate collection) underwent PCR-based phylotyping and whole-genome sequencing (WGS). Isolates from commensal-associated phylogenetic groups A (14/59, 24%) and B1 (18/59, 31%) were dominant, with ST224 (10/59, 17%), and ST744 (8/59, 14%) predominating. Less prevalent were phylogenetic groups D (12/59, 20%), with ST38 (8/59, 14%) predominating, and virulence-associated phylogenetic group B2 (7/59, 12%), with ST131 predominating (6/7, 86%) and no ST1193 isolates identified. In a WGS-based comparison of 20 cat and dog-source ST131 isolates with 188 reference human and animal ST131 isolates, the cat and dog-source isolates were phylogenetically diverse. Although cat and dog-source ST131 isolates exhibited some minor sub-clustering, most were closely related to human-source ST131 strains. Furthermore, the prevalence of ST131 as a cause of FQ infections in Australian companion animals was relatively constant between this study and the 5-year-earlier study of Platell et al. (2010) (9/125 isolates, 7.2%). Thus, although the high degree of clonal commonality among FQ clinical isolates from humans vs. companion animals suggests the possibility of bi-directional between-species transmission, the much higher reported prevalence of ST131 and ST1193 among FQ clinical isolates from humans as compared to companion animals suggests that companion animals are spillover hosts rather than being a primary reservoir for these lineages.
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http://dx.doi.org/10.3389/fmicb.2020.01968DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7492567PMC
September 2020

Outbreak of multi-drug-resistant (MDR) Shigella flexneri in northern Australia due to an endemic regional clone acquiring an IncFII plasmid.

Eur J Clin Microbiol Infect Dis 2021 Feb 4;40(2):279-286. Epub 2020 Sep 4.

Public Health Microbiology, Queensland Health Forensic and Scientific Services, Brisbane, Australia.

Epidemiological surveillance of Shigella spp. in Australia is conducted to inform public health response. Multi-drug resistance has recently emerged as a contributing factor to sustained local transmission of Shigella spp. All data were collected as part of routine public health surveillance, and strains were whole-genome sequenced for further molecular characterisation. 108 patients with an endemic regional Shigella flexneri strain were identified between 2016 and 2019. The S. flexneri phylogroup 3 strain endemic to northern Australia acquired a multi-drug resistance conferring bla plasmid, which has an IncFII plasmid backbone with virulence and resistance elements typically found in IncR plasmids. This is the first report of multi-drug resistance in Shigella sp. in Australia that is not associated with men who have sex with men. This strain caused an outbreak of multi-drug-resistant S. flexneri in northern Australia that disproportionality affects Aboriginal and Torres Strait Islander children. Community controlled public health action is recommended.
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http://dx.doi.org/10.1007/s10096-020-04029-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7473701PMC
February 2021

Comprehensive analysis of IncC plasmid conjugation identifies a crucial role for the transcriptional regulator AcaB.

Nat Microbiol 2020 11 17;5(11):1340-1348. Epub 2020 Aug 17.

School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.

The IncC family of broad-host-range plasmids enables the spread of antibiotic resistance genes among human enteric pathogens. Although aspects of IncC plasmid conjugation have been well studied, many roles of conjugation genes have been assigned based solely on sequence similarity. We applied hypersaturated transposon mutagenesis and transposon-directed insertion-site sequencing to determine the set of genes required for IncC conjugation. We identified 27 conjugation genes, comprising 19 that were previously identified (including two regulatory genes, acaDC) and eight not previously associated with conjugation. We show that one previously unknown gene, acaB, encodes a transcriptional regulator that has a crucial role in the regulation of IncC conjugation. AcaB binds upstream of the acaDC promoter to increase acaDC transcription; in turn, AcaDC activates the transcription of IncC conjugation genes. We solved the crystal structure of AcaB at 2.9-Å resolution and used this to guide functional analyses that reveal how AcaB binds to DNA. This improved understanding of IncC conjugation provides a basis for the development of new approaches to reduce the spread of these multi-drug-resistance plasmids.
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http://dx.doi.org/10.1038/s41564-020-0775-0DOI Listing
November 2020

Fatal respiratory diphtheria caused by β-lactam-resistant Corynebacterium diphtheriae.

Clin Infect Dis 2020 Aug 9. Epub 2020 Aug 9.

School of Chemistry and Molecular Biosciences, University of Queensland, QLD, Australia.

Background: Diphtheria is a potentially fatal respiratory disease caused by toxigenic Corynebacterium diphtheriae. Although resistance to erythromycin has been recognised, β-lactam resistance in toxigenic diphtheria has not been described. Here, we report a case of fatal respiratory diphtheria caused by toxigenic C. diphtheriae resistant to penicillin and all other β-lactam antibiotics and describe a novel mechanism of inducible carbapenem resistance associated with the acquisition of a mobile resistance element.

Methods: Long-read whole genome sequencing was performed using Pacific Biosciences SMRT sequencing to determine the genome sequence of C. diphtheriae BQ11 and mechanism of β-lactam resistance. To investigate phenotypic inducibility of meropenem resistance, short read sequencing was performed using an Illumina NextSeq500 sequencer on the strain with and without exposure to meropenem.

Results: BQ11 demonstrated high-level resistance to penicillin (benzylpenicillin MIC ≥ 256 μg/ml), β-lactam/β-lactamase inhibitors and cephalosporins (amoxicillin/clavulanic acid MIC ≥ 256 μg/mL; ceftriaxone MIC ≥ 8 μg/L). Genomic analysis of BQ11 identified acquisition of a novel transposon carrying the penicillin binding protein Pbp2c, responsible for resistance to penicillin and cephalosporins. When strain BQ11 was exposed to meropenem, selective pressure drove amplification of the transposon in a tandem array and led to a corresponding change from a low level to high level meropenem resistant phenotype.

Conclusions: We have identified a novel mechanism of inducible antibiotic resistance whereby isolates that appear to be carbapenem susceptible on initial testing can develop in vivo resistance to carbapenems with repeated exposure. This phenomenon could have significant implications for treatment of C. diphtheriae infection and may lead to clinical failure.
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http://dx.doi.org/10.1093/cid/ciaa1147DOI Listing
August 2020

Antimicrobial Resistance in ESKAPE Pathogens.

Clin Microbiol Rev 2020 06 13;33(3). Epub 2020 May 13.

School of Chemistry and Molecular Biosciences, The University of Queensland, QLD, Australia

Antimicrobial-resistant ESKAPE ( , , , , , and species) pathogens represent a global threat to human health. The acquisition of antimicrobial resistance genes by ESKAPE pathogens has reduced the treatment options for serious infections, increased the burden of disease, and increased death rates due to treatment failure and requires a coordinated global response for antimicrobial resistance surveillance. This looming health threat has restimulated interest in the development of new antimicrobial therapies, has demanded the need for better patient care, and has facilitated heightened governance over stewardship practices.
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http://dx.doi.org/10.1128/CMR.00181-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7227449PMC
June 2020

Phase variation in latB associated with a fatal Pasteurella multocida outbreak in captive squirrel gliders.

Vet Microbiol 2020 Apr 14;243:108612. Epub 2020 Feb 14.

School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre, Australian Centre for Ecogenomics, University of Queensland, St. Lucia, Queensland, 4067, Australia. Electronic address:

A septicaemic disease outbreak caused by Pasteurella multocida at a zoo in Western Australia (Zoo A) occurred in a resident group of squirrel gliders (Petaurus norfolcensis) following the introduction of two squirrel gliders imported from another zoo (Zoo B). P. multocida isolates obtained from the affected animals and asymptomatic, cohabiting marsupials at both zoos were typed via lipopolysaccharide outer core biosynthesis locus (LPS) typing, repetitive extragenic palindromic PCR (Rep-PCR) typing, and multilocus sequence typing (ST). Investigation of isolate relatedness via whole genome sequencing (WGS) and phylogenomic analysis found that the outbreak isolates shared the same genetic profile as those obtained from the imported gliders and the positive marsupials at Zoo B. Phylogenomic analysis demonstrated that these isolates belonged to the same clone (named complex one), confirming that the outbreak strain originated at Zoo B. As well, the carriage of multiple different strains of this pathogen in a range of marsupials in a zoo setting has been demonstrated. Importantly, the genomic investigation identified a missense mutation in the latB, a structural LPS gene, resulting in introduction of an immediate stop codon in the isolates carried by asymptomatic squirrel gliders in Zoo B. The identified diversity in the latB gene of LPS outer core biosynthesis loci of these isolates is consistent with a novel phase variable mechanism for virulence in P. multocida. Our study demonstrates the benefit of WGS and bioinformatics analysis in epidemiological investigations of pasteurellosis and its potential to reveal unexpected insights into bacterial virulence.
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http://dx.doi.org/10.1016/j.vetmic.2020.108612DOI Listing
April 2020

Using genomics to understand inter- and intra- outbreak diversity of isolates associated with fowl cholera in meat chickens.

Microb Genom 2020 03;6(3)

Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Queensland, Australia.

Fowl cholera, caused by continues to be a challenge in meat-chicken-breeder operations and has emerged as a problem for free-range meat chickens. Here, using whole-genome sequencing (WGS) and phylogenomic analysis, we investigate isolate relatedness during outbreaks of fowl cholera on a free-range meat chicken farm over a 5-year period. Our genomic analysis revealed that while all outbreak isolates were sequence type (ST) 20, they could be separated into two distinct clades (clade 1 and clade 2) consistent with difference in their lipopolysaccharide (LPS) type. The isolates from the earlier outbreaks (clade 1) were carrying LPS type L3 while those from the more recent outbreaks (clade 2) were LPS type L1. Additionally, WGS data indicated high inter- and intra-chicken genetic diversity during a single outbreak. Furthermore, we demonstrate that while a killed autogenous vaccine carrying LPS type L3 had been successful in protecting against challenge from L3 isolates it might have driven the emergence of the closely related clade 2, against which the vaccine was ineffective. The genomic results also revealed a 14 bp deletion in the galactosyltransferase gene in LPS type L3 isolates, which would result in producing a semi-truncated LPS in those isolates. In conclusion, our study clearly demonstrates the advantages of genomic analysis over the conventional PCR-based approaches in providing clear insights in terms of linkage of isolate within and between outbreaks. More importantly, it provides more detailed information than the multiplex PCR on the possible structure of outer LPS, which is very important in the case of strain selection for killed autogenous vaccines.
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http://dx.doi.org/10.1099/mgen.0.000346DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7200057PMC
March 2020

Genomic Investigation Reveals Contaminated Detergent as the Source of an Extended-Spectrum-β-Lactamase-Producing Klebsiella michiganensis Outbreak in a Neonatal Unit.

J Clin Microbiol 2020 04 23;58(5). Epub 2020 Apr 23.

Microbiology Department, Central Laboratory, Pathology Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia

species are problematic pathogens in neonatal units and may cause outbreaks, for which the sources of transmission may be challenging to elucidate. We describe the use of whole-genome sequencing (WGS) to investigate environmental sources of transmission during an outbreak of extended-spectrum-β-lactamase (ESBL)-producing colonizing neonates. Ceftriaxone-resistant spp. isolated from neonates (or their mothers) and the hospital environment were included. Short-read sequencing (Illumina) and long-read sequencing (MinION; Oxford Nanopore Technologies) were used to confirm species taxonomy, to identify antimicrobial resistance genes, and to determine phylogenetic relationships using single-nucleotide polymorphism profiling. A total of 21 organisms (10 patient-derived isolates and 11 environmental isolates) were sequenced. Standard laboratory methods identified the outbreak strain as an ESBL-producing , but taxonomic assignment from WGS data suggested closer identity to Strains isolated from multiple detergent-dispensing bottles were either identical or closely related by single-nucleotide polymorphism comparison. Detergent bottles contaminated by had been used for washing milk expression equipment. No new cases were identified once the detergent bottles were removed. Environmental reservoirs may be an important source in outbreaks of multidrug-resistant organisms. WGS, in conjunction with traditional epidemiological investigation, can be instrumental in revealing routes of transmission and guiding infection control responses.
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http://dx.doi.org/10.1128/JCM.01980-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7180233PMC
April 2020

Predicting nitroimidazole antibiotic resistance mutations in Mycobacterium tuberculosis with protein engineering.

PLoS Pathog 2020 02 7;16(2):e1008287. Epub 2020 Feb 7.

Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia.

Our inability to predict which mutations could result in antibiotic resistance has made it difficult to rapidly identify the emergence of resistance, identify pre-existing resistant populations, and manage our use of antibiotics to effectively treat patients and prevent or slow the spread of resistance. Here we investigated the potential for resistance against the new antitubercular nitroimidazole prodrugs pretomanid and delamanid to emerge in Mycobacterium tuberculosis, the causative agent of tuberculosis (TB). Deazaflavin-dependent nitroreductase (Ddn) is the only identified enzyme within M. tuberculosis that activates these prodrugs, via an F420H2-dependent reaction. We show that the native menaquinone-reductase activity of Ddn is essential for emergence from hypoxia, which suggests that for resistance to spread and pose a threat to human health, the native activity of Ddn must be at least partially retained. We tested 75 unique mutations, including all known sequence polymorphisms identified among ~15,000 sequenced M. tuberculosis genomes. Several mutations abolished pretomanid and delamanid activation in vitro, without causing complete loss of the native activity. We confirmed that a transmissible M. tuberculosis isolate from the hypervirulent Beijing family already possesses one such mutation and is resistant to pretomanid, before being exposed to the drug. Notably, delamanid was still effective against this strain, which is consistent with structural analysis that indicates delamanid and pretomanid bind to Ddn differently. We suggest that the mutations identified in this work be monitored for informed use of delamanid and pretomanid treatment and to slow the emergence of resistance.
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http://dx.doi.org/10.1371/journal.ppat.1008287DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7032734PMC
February 2020

Integrating multiple genomic technologies to investigate an outbreak of carbapenemase-producing Enterobacter hormaechei.

Nat Commun 2020 01 24;11(1):466. Epub 2020 Jan 24.

School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.

Carbapenem-resistant Enterobacteriaceae (CRE) represent an urgent threat to human health. Here we report the application of several complementary whole-genome sequencing (WGS) technologies to characterise a hospital outbreak of bla carbapenemase-producing E. hormaechei. Using Illumina sequencing, we determined that all outbreak strains were sequence type 90 (ST90) and near-identical. Comparison to publicly available data linked all outbreak isolates to a 2013 isolate from the same ward, suggesting an environmental source in the hospital. Using Pacific Biosciences sequencing, we resolved the complete context of the bla gene on a large IncHI2 plasmid carried by all IMP-4-producing strains across different hospitals. Shotgun metagenomic sequencing of environmental samples also found evidence of ST90 E. hormaechei and the IncHI2 plasmid within the hospital plumbing. Finally, Oxford Nanopore sequencing rapidly resolved the true relationship of subsequent isolates to the initial outbreak. Overall, our strategic application of three WGS technologies provided an in-depth analysis of the outbreak.
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http://dx.doi.org/10.1038/s41467-019-14139-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6981164PMC
January 2020

Genomic analysis of carbapenemase-producing in Queensland reveals widespread transmission of on an IncHI2 plasmid.

Microb Genom 2020 01 19;6(1). Epub 2019 Dec 19.

Central Microbiology, Pathology Queensland, QLD, Australia.

Carbapenemase-producing (CPE) are an increasingly common cause of healthcare-associated infections and may occasionally be identified in patients without extensive healthcare exposure. is the most frequently detected carbapenemase gene in within Australia, but little is known about the mechanisms behind its persistence. Here we used whole genome sequencing (WGS) to investigate the molecular epidemiology of in Queensland, Australia. In total, 107 CPE were collected between 2014 and 2017 and sent for WGS on an Illumina NextSeq500. Resistance genes and plasmid types were detected using a combination of read mapping and nucleotide comparison of assemblies. Six isolates were additionally sequenced using Oxford Nanopore MinION to generate long-reads and fully characterize the context of the gene. Of 107 CPE, 93 carried the gene; 74/107 also carried an IncHI2 plasmid, suggesting carriage of the gene on an IncHI2 plasmid. Comparison of these isolates to a previously characterized IncHI2 plasmid pMS7884A (isolated from an strain in Brisbane) suggested that all isolates carried a similar plasmid. Five of six representative isolates sequenced using Nanopore long-read technology carried IncHI2 plasmids harbouring the gene. While the vast majority of isolates represented , several other species were also found to carry the IncHI2 plasmid, including species, and species. Several clonal groups of were also identified, suggesting that persistence of is driven by both presence on a common plasmid and clonal spread of certain lineages.
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http://dx.doi.org/10.1099/mgen.0.000321DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7067041PMC
January 2020

Complex Multilevel Control of Hemolysin Production by Uropathogenic Escherichia coli.

mBio 2019 10 1;10(5). Epub 2019 Oct 1.

School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia

Uropathogenic (UPEC) is the major cause of urinary tract infections. Nearly half of all UPEC strains secrete hemolysin, a cytotoxic pore-forming toxin. Here, we show that the prevalence of the hemolysin toxin gene () is highly variable among the most common 83 sequence types (STs) represented on the EnteroBase genome database. To explore this diversity in the context of a defined monophyletic lineage, we contextualized sequence variation of the operon within the genealogy of the globally disseminated multidrug-resistant ST131 clone. We show that sequence changes in and its newly defined 1.616-kb-long leader sequence correspond to phylogenetic designation, and that ST131 strains with the strongest hemolytic activity belong to the most extensive multidrug-resistant sublineage (clade C2). To define the set of genes involved in hemolysin production, the clade C2 strain S65EC was completely sequenced and subjected to a genome-wide screen by combining saturated transposon mutagenesis and transposon-directed insertion site sequencing with the capacity to lyse red blood cells. Using this approach, and subsequent targeted mutagenesis and complementation, 13 genes were confirmed to be specifically required for production of active hemolysin. New hemolysin-controlling elements included discrete sets of genes involved in lipopolysaccharide (LPS) inner core biosynthesis (, , , and ) and cytoplasmic chaperone activity ( and ), and we show these are required for hemolysin secretion. Overall, this work provides a unique description of hemolysin sequence diversity in a single clonal lineage and describes a complex multilevel system of regulatory control for this important toxin. Uropathogenic (UPEC) is the major cause of urinary tract infections and a frequent cause of sepsis. Nearly half of all UPEC strains produce the potent cytotoxin hemolysin, and its expression is associated with enhanced virulence. In this study, we explored hemolysin variation within the globally dominant UPEC ST131 clone, finding that strains from the ST131 sublineage with the greatest multidrug resistance also possess the strongest hemolytic activity. We also employed an innovative forward genetic screen to define the set of genes required for hemolysin production. Using this approach, and subsequent targeted mutagenesis and complementation, we identified new hemolysin-controlling elements involved in LPS inner core biosynthesis and cytoplasmic chaperone activity, and we show that mechanistically they are required for hemolysin secretion. These original discoveries substantially enhance our understanding of hemolysin regulation, secretion and function.
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http://dx.doi.org/10.1128/mBio.02248-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6775461PMC
October 2019

Whole-genome sequencing as an improved means of investigating Neisseria gonorrhoeae treatment failures.

Sex Health 2019 09;16(5):500-507

Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Qld 4072, Australia; and Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Qld 4072, Australia; and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld 4072, Australia; and Corresponding author: Email:

Background Although rare, Neisseria gonorrhoeae treatment failures associated with ceftriaxone have been reported. The World Health Organization (WHO) recommends standardised protocols to verify these cases. Two cases from Australia were previously investigated using N. gonorrhoeae multiantigen sequence typing (NG-MAST), which has been used extensively to assess treatment failures. Case 1 pharyngeal isolates were indistinguishable, whereas Case 2 pharyngeal isolates were distinguished based on an 18-bp deletion in the major outer membrane porin encoded by the porB gene, questioning the reliability of NG-MAST results. Here we used whole-genome sequencing (WGS) to reinvestigate Cases 1 and 2, with a view to examining WGS to assess treatment failures.

Methods: Pre- and post-treatment isolates for each case underwent Illumina sequencing, and the two post-treatment isolates underwent additional long-read sequencing using Pacific Biosciences. Sequence data were interrogated to identify differences at single nucleotide resolution.

Results: WGS identified variation in the pilin subunit encoded by the pilE locus for both cases and the specific 18-bp porB deletion in Case 2 was confirmed, but otherwise the isolates in each case were indistinguishable.

Conclusions: The WHO recommends standardised protocols for verifying N. gonorrhoeae treatment failures. Case 2 highlights the enhanced resolution of WGS over NG-MAST and emphasises the immediate effect that WGS can have in a direct clinical application for N. gonorrhoeae. Assessing the whole genome compared with two highly variable regions also provides a more confident predictor for determining treatment failure. Furthermore, WGS facilitates rapid comparisons of these cases in the future.
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http://dx.doi.org/10.1071/SH19012DOI Listing
September 2019

Population dynamics of an Escherichia coli ST131 lineage during recurrent urinary tract infection.

Nat Commun 2019 08 13;10(1):3643. Epub 2019 Aug 13.

School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Queensland, Australia.

Recurrent urinary tract infections (rUTIs) are extremely common, with ~ 25% of all women experiencing a recurrence within 1 year of their original infection. Escherichia coli ST131 is a globally dominant multidrug resistant clone associated with high rates of rUTI. Here, we show the dynamics of an ST131 population over a 5-year period from one elderly woman with rUTI since the 1970s. Using whole genome sequencing, we identify an indigenous clonal lineage (P1A) linked to rUTI and persistence in the fecal flora, providing compelling evidence of an intestinal reservoir of rUTI. We also show that the P1A lineage possesses substantial plasmid diversity, resulting in the coexistence of antibiotic resistant and sensitive intestinal isolates despite frequent treatment. Our longitudinal study provides a unique comprehensive genomic analysis of a clonal lineage within a single individual and suggests a population-wide resistance mechanism enabling rapid adaptation to fluctuating antibiotic exposure.
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http://dx.doi.org/10.1038/s41467-019-11571-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6692316PMC
August 2019

SMRT sequencing reveals differential patterns of methylation in two O111:H- STEC isolates from a hemolytic uremic syndrome outbreak in Australia.

Sci Rep 2019 07 1;9(1):9436. Epub 2019 Jul 1.

Australian Infectious Diseases Centre, The University of Queensland, Brisbane, QLD, Australia.

In 1995 a severe haemolytic-uremic syndrome (HUS) outbreak in Adelaide occurred. A recent genomic analysis of Shiga toxigenic Escherichia coli (STEC) O111:H- strains 95JB1 and 95NR1 from this outbreak found that the more virulent isolate, 95NR1, harboured two additional copies of the Shiga toxin 2 (Stx2) genes encoded within prophage regions. The structure of the Stx2-converting prophages could not be fully resolved using short-read sequence data alone and it was not clear if there were other genomic differences between 95JB1 and 95NR1. In this study we have used Pacific Biosciences (PacBio) single molecule real-time (SMRT) sequencing to characterise the genome and methylome of 95JB1 and 95NR1. We completely resolved the structure of all prophages including two, tandemly inserted, Stx2-converting prophages in 95NR1 that were absent from 95JB1. Furthermore we defined all insertion sequences and found an additional IS1203 element in the chromosome of 95JB1. Our analysis of the methylome of 95NR1 and 95JB1 identified hemi-methylation of a novel motif (5'-CTGCAG-3') in more than 4000 sites in the 95NR1 genome. These sites were entirely unmethylated in the 95JB1 genome, and included at least 177 potential promoter regions that could contribute to regulatory differences between the strains. IS1203 mediated deactivation of a novel type IIG methyltransferase in 95JB1 is the likely cause of the observed differential patterns of methylation between 95NR1 and 95JB1. This study demonstrates the capability of PacBio SMRT sequencing to resolve complex prophage regions and reveal the genetic and epigenetic heterogeneity within a clonal population of bacteria.
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http://dx.doi.org/10.1038/s41598-019-45760-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602927PMC
July 2019

Control of Bacterial Sulfite Detoxification by Conserved and Species-Specific Regulatory Circuits.

Front Microbiol 2019 14;10:960. Epub 2019 May 14.

Centre for Metals in Biology, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia.

Although sulfite, a by-product of the degradation of many sulfur compounds, is highly reactive and can cause damage to DNA, proteins and lipids, comparatively little is known about the regulation of sulfite-oxidizing enzyme (SOEs) expression. Here we have investigated the regulation of SOE-encoding genes in two species of α-Proteobacteria, and , that degrade organo- and inorganic sulfur compounds, respectively, and contain unrelated types of SOEs that show different expression patterns. Our work revealed that in both cases, the molecular signal that triggers SOE gene expression is sulfite, and strong up-regulation depends on the presence of a sulfite-responsive, cognate Extracytoplasmic function (ECF) sigma factor, making sulfite oxidation a bacterial stress response. An additional RpoE1-like ECF sigma factor was also involved in the regulation, but was activated by different molecular signals, taurine (Sm) and tetrathionate (Sn), respectively, targeted different gene promoters, and also differed in the magnitude of the response generated. We therefore propose that RpoE1 is a secondary, species-specific regulator of SOE gene expression rather than a general, conserved regulatory circuit. Sulfite produced by major dissimilatory processes appeared to be the trigger for SOE gene expression in both species, as we were unable to find evidence for an increase of SOE activity in stationary growth phase. The basic regulation of bacterial sulfite oxidation by cognate ECF sigma factors is likely to be applicable to three groups of alpha and beta-Proteobacteria in which we identified similar SOE operon structures.
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http://dx.doi.org/10.3389/fmicb.2019.00960DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6527743PMC
May 2019

Novel insights into pasteurellosis in captive pinnipeds.

Vet Microbiol 2019 Apr 14;231:232-237. Epub 2019 Mar 14.

Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Queensland, Australia; School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre, Australian Centre for Ecogenomics, The University of Queensland, St Lucia, Queensland, Australia. Electronic address:

Pasteurella multocida is a heterogeneous bacterium, which has the capacity to cause disease in a wide range of host species and is also recognized as an important zoonotic pathogen. Two sequential deaths in captive fur seals occurred at Sea World, Australia during December 2017. A fibrinosuppurative bronchopneumonia in a Subantarctic fur seal (Arctocephalus tropicalis) resulted in death within 24 h of nonspecific signs of illness, whereas a septic peritonitis in a New Zealand fur seal (Arctocephalus forsteri) resulted in death within 12 h of clinical presentation. The cases happened within three days in two different pool locations, although both had previously been housed in the same area. A total of six Pasteurella multocida isolates were obtained from several internal organs at necropsy in both cases and were subjected to whole genome sequencing and phylogenomic analysis. In-silico typing of the isolates revealed that all belonged to Multi-Locus Sequence Type 7 and carried lipopolysaccharide outer core biosynthesis loci Type 3. Phylogenomic analysis of the isolates confirmed that the isolates were near identical at the core genome level, suggesting acquisition from a common source. The results also revealed the presence of within host and across animal diversity of P. multocida isolates for the first time even in a clearly connected outbreak.
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http://dx.doi.org/10.1016/j.vetmic.2019.03.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7117180PMC
April 2019

Variation in hemolysin A expression between uropathogenic isolates determines NLRP3-dependent -independent macrophage cell death and host colonization.

FASEB J 2019 06 14;33(6):7437-7450. Epub 2019 Mar 14.

Centre for Inflammation and Disease Research, Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Queensland, Australia.

Uropathogenic (UPEC) is the major cause of urinary tract infections (UTIs). The multidrug-resistant sequence type 131 (ST131) clone is a serious threat to human health, yet its effects on immune responses are not well understood. Here we screened a panel of ST131 isolates, finding that only strains expressing the toxin hemolysin A (HlyA) killed primary human macrophages and triggered maturation of the inflammasome-dependent cytokine IL-1β. Using a representative strain, the requirement for the gene in these responses was confirmed. We also observed considerable heterogeneity in levels of cell death initiated by different HlyA ST131 isolates, and this correlated with secreted HlyA levels. Investigation into the biological significance of this variation revealed that an ST131 strain producing low levels of HlyA initiated cell death that was partly dependent on the nod-like receptor family pyrin domain-containing 3 (NLRP3) inflammasome, with this response being associated with a host-protective role in a mouse UTI model. When the same ST131 strain was engineered to overexpress high HlyA levels, macrophage cell death occurred even when NLRP3 function was abrogated, and bladder colonization was significantly increased. Thus, variation in HlyA expression in UPEC affects mechanisms by which macrophages die, as well as host susceptibility resistance to colonization.-Murthy, A. M. V., Sullivan, M. J., Nhu, N. T. K., Lo, A. W., Phan, M.-D., Peters, K. M., Boucher, D., Schroder, K., Beatson, S. A., Ulett, G. C., Schembri, M. A., Sweet, M. J. Variation in hemolysin A expression between uropathogenic isolates determines NLRP3-dependent -independent macrophage cell death and host colonization.
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http://dx.doi.org/10.1096/fj.201802100RDOI Listing
June 2019

Detection of Epidemic Scarlet Fever Group A Streptococcus in Australia.

Clin Infect Dis 2019 09;69(7):1232-1234

Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia.

Sentinel hospital surveillance was instituted in Australia to detect the presence of pandemic group A Streptococcus strains causing scarlet fever. Genomic and phylogenetic analyses indicated the presence of an Australian GAS emm12 scarlet fever isolate related to United Kingdom outbreak strains. National surveillance to monitor this pandemic is recommended.
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http://dx.doi.org/10.1093/cid/ciz099DOI Listing
September 2019

Discovery of -Mediated Colistin Resistance in a Highly Virulent Escherichia coli Lineage.

mSphere 2018 10 10;3(5). Epub 2018 Oct 10.

School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia

Resistance to last-line polymyxins mediated by the plasmid-borne mobile colistin resistance gene () represents a new threat to global human health. Here we present the complete genome sequence of an -positive multidrug-resistant strain (MS8345). We show that MS8345 belongs to serotype O2:K1:H4, has a large 241,164-bp IncHI2 plasmid that carries 15 other antibiotic resistance genes (including the extended-spectrum β-lactamase ) and 3 putative multidrug efflux systems, and contains 14 chromosomally encoded antibiotic resistance genes. MS8345 also carries a large ColV-like virulence plasmid that has been associated with bacteremia. Whole-genome phylogeny revealed that MS8345 clusters within a discrete clade in the sequence type 95 (ST95) lineage, and MS8345 is very closely related to the highly virulent O45:K1:H4 clone associated with neonatal meningitis. Overall, the acquisition of a plasmid carrying resistance to colistin and multiple other antibiotics in this virulent lineage is concerning and might herald an era where the empirical treatment of ST95 infections becomes increasingly more difficult. ST95 is a globally disseminated clone frequently associated with bloodstream infections and neonatal meningitis. However, the ST95 lineage is defined by low levels of drug resistance amongst clinical isolates, which normally provides for uncomplicated treatment options. Here, we provide the first detailed genomic analysis of an ST95 isolate that has both high virulence potential and resistance to multiple antibiotics. Using the genome, we predicted its virulence and antibiotic resistance mechanisms, which include resistance to last-line antibiotics mediated by the plasmid-borne gene. Finding an ST95 isolate resistant to nearly all antibiotics that also has a high virulence potential is of major clinical importance and underscores the need to monitor new and emerging trends in antibiotic resistance development in this important global lineage.
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http://dx.doi.org/10.1128/mSphere.00486-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6180223PMC
October 2018

Effect of Piperacillin-Tazobactam vs Meropenem on 30-Day Mortality for Patients With E coli or Klebsiella pneumoniae Bloodstream Infection and Ceftriaxone Resistance: A Randomized Clinical Trial.

JAMA 2018 09;320(10):984-994

University of Queensland, UQ Centre for Clinical Research, Brisbane, Queensland, Australia.

Importance: Extended-spectrum β-lactamases mediate resistance to third-generation cephalosporins (eg, ceftriaxone) in Escherichia coli and Klebsiella pneumoniae. Significant infections caused by these strains are usually treated with carbapenems, potentially selecting for carbapenem resistance. Piperacillin-tazobactam may be an effective "carbapenem-sparing" option to treat extended-spectrum β-lactamase producers.

Objectives: To determine whether definitive therapy with piperacillin-tazobactam is noninferior to meropenem (a carbapenem) in patients with bloodstream infection caused by ceftriaxone-nonsusceptible E coli or K pneumoniae.

Design, Setting, And Participants: Noninferiority, parallel group, randomized clinical trial included hospitalized patients enrolled from 26 sites in 9 countries from February 2014 to July 2017. Adult patients were eligible if they had at least 1 positive blood culture with E coli or Klebsiella spp testing nonsusceptible to ceftriaxone but susceptible to piperacillin-tazobactam. Of 1646 patients screened, 391 were included in the study.

Interventions: Patients were randomly assigned 1:1 to intravenous piperacillin-tazobactam, 4.5 g, every 6 hours (n = 188 participants) or meropenem, 1 g, every 8 hours (n = 191 participants) for a minimum of 4 days, up to a maximum of 14 days, with the total duration determined by the treating clinician.

Main Outcomes And Measures: The primary outcome was all-cause mortality at 30 days after randomization. A noninferiority margin of 5% was used.

Results: Among 379 patients (mean age, 66.5 years; 47.8% women) who were randomized appropriately, received at least 1 dose of study drug, and were included in the primary analysis population, 378 (99.7%) completed the trial and were assessed for the primary outcome. A total of 23 of 187 patients (12.3%) randomized to piperacillin-tazobactam met the primary outcome of mortality at 30 days compared with 7 of 191 (3.7%) randomized to meropenem (risk difference, 8.6% [1-sided 97.5% CI, -∞ to 14.5%]; P = .90 for noninferiority). Effects were consistent in an analysis of the per-protocol population. Nonfatal serious adverse events occurred in 5 of 188 patients (2.7%) in the piperacillin-tazobactam group and 3 of 191 (1.6%) in the meropenem group.

Conclusions And Relevance: Among patients with E coli or K pneumoniae bloodstream infection and ceftriaxone resistance, definitive treatment with piperacillin-tazobactam compared with meropenem did not result in a noninferior 30-day mortality. These findings do not support use of piperacillin-tazobactam in this setting.

Trial Registration: anzctr.org.au Identifiers: ACTRN12613000532707 and ACTRN12615000403538 and ClinicalTrials.gov Identifier: NCT02176122.
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http://dx.doi.org/10.1001/jama.2018.12163DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6143100PMC
September 2018

Whole genome sequencing reveals the emergence of a Pseudomonas aeruginosa shared strain sub-lineage among patients treated within a single cystic fibrosis centre.

BMC Genomics 2018 Aug 30;19(1):644. Epub 2018 Aug 30.

School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.

Background: Chronic lung infections caused by Pseudomonas aeruginosa are a significant cause of morbidity and mortality in people with cystic fibrosis (CF). Shared P. aeruginosa strains, that can be transmitted between patients, are of concern and in Australia the AUST-02 shared strain is predominant in individuals attending CF centres in Queensland and Western Australia. M3L7 is a multidrug resistant sub-type of AUST-02 that was recently identified in a Queensland CF centre and was shown to be associated with poorer clinical outcomes. The main aim of this study was to resolve the relationship of the emergent M3L7 sub-type within the AUST-02 group of strains using whole genome sequencing.

Results: A whole genome core phylogeny of 63 isolates indicated that M3L7 is a monophyletic sub-lineage within the context of the broader AUST-02 group. Relatively short branch lengths connected all of the M3L7 isolates. A phylogeny based on nucleotide polymorphisms present across the genome showed that the chronological estimation of the most recent common ancestor was around 2001 (± 3 years). SNP differences between sequential non-hypermutator M3L7 isolates collected 3-4 years apart from five patients suggested both continuous infection of the same strain and cross-infection of some M3L7 variants between patients. The majority of polymorphisms that were characteristic of M3L7 (i.e. acquired after divergence from all other AUST-02 isolates sequenced) were found to produce non-synonymous mutations in virulence and antibiotic resistance genes.

Conclusions: M3L7 has recently diverged from a common ancestor, indicating descent from a single carrier at a CF treatment centre in Australia. Both adaptation to the lung and transmission of M3L7 between adults attending this centre may have contributed to its rapid dissemination. Further genomic investigations are required on multiple intra-sample isolates of this sub-type to decipher potential mechanisms which facilitates its epidemiological success.
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http://dx.doi.org/10.1186/s12864-018-5018-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6117919PMC
August 2018

Discovery of New Genes Involved in Curli Production by a Uropathogenic Escherichia coli Strain from the Highly Virulent O45:K1:H7 Lineage.

mBio 2018 08 21;9(4). Epub 2018 Aug 21.

School of Chemistry and Molecular Biosciences, the University of Queensland, Brisbane, Queensland, Australia

Curli are bacterial surface-associated amyloid fibers that bind to the dye Congo red (CR) and facilitate uropathogenic (UPEC) biofilm formation and protection against host innate defenses. Here we sequenced the genome of the curli-producing UPEC pyelonephritis strain MS7163 and showed it belongs to the highly virulent O45:K1:H7 neonatal meningitis-associated clone. MS7163 produced curli at human physiological temperature, and this correlated with biofilm growth, resistance of sessile cells to the human cationic peptide cathelicidin, and enhanced colonization of the mouse bladder. We devised a forward genetic screen using CR staining as a proxy for curli production and identified 41 genes that were required for optimal CR binding, of which 19 genes were essential for curli synthesis. Ten of these genes were novel or poorly characterized with respect to curli synthesis and included genes involved in purine biosynthesis, a regulator that controls the Rcs phosphorelay system, and a novel repressor of curli production (referred to as ). The involvement of these genes in curli production was confirmed by the construction of defined mutants and their complementation. The mutants did not express the curli major subunit CsgA and failed to produce curli based on CR binding. Mutation of (the first gene in the purine biosynthesis pathway) and also led to attenuated colonization of the mouse bladder. Overall, this work has provided new insight into the regulation of curli and the role of these amyloid fibers in UPEC biofilm formation and pathogenesis. Uropathogenic (UPEC) strains are the most common cause of urinary tract infection, a disease increasingly associated with escalating antibiotic resistance. UPEC strains possess multiple surface-associated factors that enable their colonization of the urinary tract, including fimbriae, curli, and autotransporters. Curli are extracellular amyloid fibers that enhance UPEC virulence and promote biofilm formation. Here we examined the function and regulation of curli in a UPEC pyelonephritis strain belonging to the highly virulent O45:K1:H7 neonatal meningitis-associated clone. Curli expression at human physiological temperature led to increased biofilm formation, resistance of sessile cells to the human cationic peptide LL-37, and enhanced bladder colonization. Using a comprehensive genetic screen, we identified multiple genes involved in curli production, including several that were novel or poorly characterized with respect to curli synthesis. In total, this study demonstrates an important role for curli as a UPEC virulence factor that promotes biofilm formation, resistance, and pathogenesis.
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http://dx.doi.org/10.1128/mBio.01462-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6106082PMC
August 2018

Use of whole genome sequencing to investigate an increase in Neisseria gonorrhoeae infection among women in urban areas of Australia.

Sci Rep 2018 01 24;8(1):1503. Epub 2018 Jan 24.

The University of Queensland, UQ Centre for Clinical Research, Herston, Queensland, 4029, Australia.

Increasing rates of gonorrhoea have been observed among women within the Australian state of New South Wales. Here, we applied whole genome sequencing (WGS) to better understand the associated networks and transmission dynamics. Ninety-four isolates of a particular N. gonorrhoeae genotype (G122) associated with women (years 2012 to 2014) underwent phylogenetic analysis using core single nucleotide polymorphisms. WGS data revealed five main clusters, all of which were heterogeneous in terms of patient age and site of infection. The relatively high cervical/vaginal infections in each cluster was indicative of transmission in the general heterosexual population, noting that there is typically high rates of condom use for vaginal sex among local commercial sex workers. WGS also enabled the identification of groups of individuals belonging to tighter transmission chains within clusters, and hence may present a new tool for targeting public health interventions. The enhanced resolution of WGS provides a ready means of confirming suspected changes in N. gonorrhoeae epidemiology, but also enables key features to be identified or new questions to be raised regarding the composition of the associated sexual networks.
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http://dx.doi.org/10.1038/s41598-018-20015-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5784116PMC
January 2018

Whole genome analysis of cephalosporin-resistant Escherichia coli from bloodstream infections in Australia, New Zealand and Singapore: high prevalence of CMY-2 producers and ST131 carrying blaCTX-M-15 and blaCTX-M-27.

J Antimicrob Chemother 2018 03;73(3):634-642

University of Queensland, UQ Centre for Clinical Research, Royal Brisbane & Women's Hospital, Queensland, Australia.

Objectives: To characterize MDR Escherichia coli from bloodstream infections (BSIs) in Australia, New Zealand and Singapore.

Methods: We collected third-generation cephalosporin-resistant (3GC-R) E. coli from blood cultures in patients enrolled in a randomized controlled trial from February 2014 to August 2015. WGS was used to characterize antibiotic resistance genes, MLST, plasmids and phylogenetic relationships. Antibiotic susceptibility was determined using disc diffusion and Etest.

Results: A total of 70 3GC-R E. coli were included, of which the majority were ST131 (61.4%). BSI was most frequently from a urinary source (69.6%), community associated (62.9%) and in older patients (median age 71 years). The median Pitt score was 1 and ICU admission was infrequent (3.1%). ST131 possessed more acquired resistance genes than non-ST131 (P = 0.003). Clade C1/C2 ST131 predominated (30.2% and 53.5% of ST131, respectively) and these were all ciprofloxacin resistant. All clade A ST131 (n = 6) were community associated. The predominant ESBL types were blaCTX-M (80.0%) and were strongly associated with ST131 (95% carried blaCTX-M), with the majority blaCTX-M-15. Clade C1 was associated with blaCTX-M-14 and blaCTX-M-27, whereas blaCTX-M-15 predominated in clade C2. Plasmid-mediated AmpC genes (mainly blaCMY-2) were frequent (17.1%) but were more common in non-ST131 (P < 0.001) isolates from Singapore and Brisbane. Two strains carried both blaCMY-2 and blaCTX-M. The majority of plasmid replicon types were IncF.

Conclusions: In a prospective collection of 3GC-R E. coli causing BSI, community-associated Clade C1/C2 ST131 predominate in association with blaCTX-M ESBLs, although a significant proportion of non-ST131 strains carried blaCMY-2.
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http://dx.doi.org/10.1093/jac/dkx466DOI Listing
March 2018