Biology subjects

Schembri, M. A.

Publications and source records attributed to Schembri, M. A..

16 recordsLinked to original sources

bioRxiv2026

Disruption of cAMP Signalling and RNA Regulation Confers Cefiderocol Resistance in Acinetobacter baumannii

Cefiderocol is a siderophore-conjugated cephalosporin used to treat severe multidrug-resistant Gram-negative infections. Its recent prioritisation for US national preparedness underscores its clinical importance, yet resistance can emerge despite apparent in vitro susceptibility. Here, we identify two regulatory routes to cefiderocol resistance in carbapenem-resistant Acinetobacter baumannii (CRAB): mutation of the cAMP-producing adenylate cyclase CavA and truncation of the glycine-rich RNA-binding domain of the post-transcriptional regulator Hfq. These variants occurred in contemporary clinical isolates, conferred resistance in a murine CRAB lung-infection model and imposed minimal fitness costs. In Escherichia coli, deletion of the CavA orthologue cyaA increased competitive fitness during sub-inhibitory cefiderocol exposure. Hfq-CLASH and integrated omics revealed Hfq-dependent regulation of Fur-associated iron homeostasis in A. baumannii. Under iron limitation, truncated-Hfq induced a defence-primed state that attenuated siderophore uptake and reduced cefiderocol activity. These findings identify bacterial regulatory state and iron availability as determinants of cefiderocol susceptibility, with implications for resistance surveillance and susceptibility testing.

microbiology↗

bioRxiv2026

Cross-species convergence of surface polysaccharides shapes the virulence of an atypical carbapenem resistant uropathogenic Escherichia coli clone

Carbapenem-resistant Escherichia coli (CREC) is an emerging global health threat associated with limited treatment options and increased mortality. Here, analysis of 20,331 E. coli genomes from urinary tract infection (UTI) and urine samples identifies phylogroup A sequence type 361 (ST361) as an emerging CREC clone associated with UTI. Phylogenetic and phylodynamic analyses reveal two dominant ST361 clades that emerged in Asia around 2006 and subsequently disseminated intercontinentally. ST361 exhibits near pan-drug resistance, with blaNDM-5 conferring carbapenem resistance. In silico capsule and O-antigen typing reveals a highly conserved Klebsiella-like surface polysaccharide serotype in 95.9% of ST361 genomes, which we show contributes to virulence in UTI and catheter-associated UTI mouse models. Analysis of the mobile genetic elements harbouring blaNDM-5 in ST361 and other CREC further reveals a dynamic interplay between plasmid transfer and insertion elements that contributes to blaNDM-5 dissemination. Together, these findings identify ST361 as an emerging UTI-associated CREC clone and reveal the convergence of clonal expansion, virulence-associated surface architecture and mobile genetic elements in its spread.

microbiology↗

bioRxiv2026

Paired in situ and molecular analyses identify mechanisms of pathogen persistence within environmental communities

Natural environments are a key reservoir for many opportunistic pathogens, yet mechanisms enabling persistence within complex microbial communities remain poorly defined. Current methods do not adequately link molecular and functional understanding of bacterial persistence to the activities of bacteria within their natural microbial community. Here we combine in situ culture-independent techniques, including metagenomics and metatranscriptomics, with isolate-level functional genomics and mutant studies to understand how opportunistic pathogens from the genera Escherichia, Klebsiella, and Enterococcus survive in urban-adjacent freshwater ecosystems. . Our results show that potential pathogens from each of these genera are both present and active within freshwater microbial communities. We further investigate a mouse-virulent isolate of the E. coli UPEC lineage ST73 isolated directly from this ecosystem, showing that this isolate persists in freshwater microcosms for at least one month. Paired transcriptomics and genome-scale fitness screening in creek water containing autochthonous microbiota identified E. coli genes required for persistence, including those involved in amino acid metabolism, nucleotide biosynthesis and biogenesis of curli. Isolate-resolved metatranscriptomics analysis supported these findings by revealing that many of these genes were highly expressed in situ. Deletion of curli structural genes resulted in reduced biofilm formation and a fitness defect specifically in the presence of freshwater microbiota, indicating that these structures promote environmental survival by improving E. coli competitiveness. Our study deepens our understanding of E. coli survival in waterways, while providing a broadly applicable framework for interrogating mechanisms of pathogen persistence in complex environments and communities.

microbiology↗

bioRxiv2025

Extracellular loops of the β-barrel domain catalyze rapid folding for function of self-associating autotransporters

Bacterial aggregation is a phenotype associated with disease pathogenesis. Aggregate formation enhances biofilm development, host colonization, and resistance to antibiotics and host defenses. Antigen 43 (Ag43) is a surface-located autotransporter produced by pathogenic Escherichia coli that mediates cell aggregation in biofilms. Two Ag43 molecules, each from neighboring bacterial cells, fold into elongated {beta}-helical passenger domains that associate in a head-to-tail manner while being anchored to the cell surface by their outer membrane-embedded {beta}-barrels. In this study, we conduct mutational analyses on Ag43 to show that the {beta}-hairpin structure of the fourth and fifth extracellular loops of the {beta}-barrel domain have a crucial role for passenger domain folding and subsequent formation of bacterial aggregates. This work provides mechanistic insight into the role of the autotransporter {beta}-barrel domain to nucleate the rapid folding of the passenger domain into the {beta}-helix that enables bacterial interactions during infection.

biochemistry↗

bioRxiv2024

Discovery and characterisation of new phage targeting uropathogenic Escherichia coli

Antimicrobial resistance (AMR) is increasing at an escalating rate with few new therapeutic options in the pipeline. Urinary tract infections (UTIs) are one of the most prevalent bacterial infections globally and are particularly prone to becoming recurrent and antibiotic resistant. The aim of this study was to discover and characterise new bacterial viruses (phage) against uropathogenic Escherichia coli (UPEC), which is the leading cause of UTIs. Six phages from the Autographiviridae family and Guernseyvirinae sub-family were isolated from wastewater and sequenced. The length of the isolated phage genomes was between 39,471 bp and 45,233 bp, with a GC content between 45.0% and 51.0%, and 57 to 84 predicted coding sequences (CDS) per genome. These phages were found to infect between 25 - 75% of the twelve UPEC strains tested. Using sequence comparison and predicted structural alignments, we show a similarity between the C-terminal domain of the tail fiber proteins of two phage that correlates with their host range. In vitro characterisation of phage cocktails against a single bacterial strain did not perform better than the best-performing phage, but did show synergistic improvement against a mixed UPEC strain population. Lastly, we measured the effectiveness of treatment with phage with different lytic kinetics in a sequential treatment and found it was improved over single phage treatment.

microbiology↗

bioRxiv2023

Molecular mechanisms of re-emerging chloramphenicol susceptibility in extended-spectrum beta-lactamase producing Enterobacterales

Infections with Enterobacterales (E) are increasingly difficult to treat due to antimicrobial resistance. After ceftriaxone replaced chloramphenicol (CHL) as empiric therapy for suspected sepsis in Malawi in 2004, ESBL-E rapidly emerged. Concurrently, resistance to CHL in Escherichia coli and Klebsiella spp. decreased, raising the possibility of CHL re-introduction. However, many phenotypically susceptible isolates still carry CHL acetyltransferase (CAT) genes. We used a combination of genomics, phenotypic susceptibility assays, experimental evolution and functional assays for CAT activity to understand the molecular mechanisms and stability of this re-emerging CHL susceptibility. Of 840 Malawian isolates, 31% had discordant CHL susceptibility genotype-phenotype, and we selected 42 isolates for in-depth analysis. Stable degradation of cat genes by insertion sequences led to re-emergence of CHL susceptibility. Our study suggests CHL could be reintroduced as reserve agent for critically ill patients with ESBL-E infections in Malawi and similar settings and highlights the ongoing challenges in inferring antimicrobial resistance from sequence data.

microbiology↗

bioRxiv2022

Chemical structures of cyclic ADP ribose (cADPR) isomers and the molecular basis of their production and signaling

Cyclic ADP ribose (cADPR) isomers are important signaling molecules produced by bacterial and plant Toll/interleukin-1 receptor (TIR) domains via NAD+ hydrolysis, yet their chemical structures are unknown. We show that v-cADPR (2cADPR) and v2-cADPR (3cADPR) isomers are cyclized by O-glycosidic bond formation between the ribose moieties in ADPR. Structures of v-cADPR (2cADPR)-producing TIR domains reveal that conformational changes are required for the formation of the active assembly that resembles those of Toll-like receptor adaptor TIR domains, and mutagenesis data demonstrate that a conserved tryptophan is essential for cyclization. We show that v2-cADPR (3cADPR) is a potent activator of ThsA effector proteins from Thoeris anti-phage defence systems and is responsible for suppression of plant immunity by the effector HopAM1. Collectively, our results define new enzymatic activities of TIR domains, reveal the molecular basis of cADPR isomer production, and establish v2-cADPR (3cADPR) as an antiviral signaling molecule and an effector-mediated signaling molecule for plant immunity suppression. One-Sentence SummaryThe chemical structures of two O-glycosidic bond-containing cyclic ADP ribose isomers, the molecular basis of their production, and their function in antiviral and plant immunity suppression by bacteria are reported.

biochemistry↗

bioRxiv2021

Modified defence peptides from horseshoe crab target and kill bacteria inside host cells

Bacteria that occupy an intracellular niche can evade extracellular host immune responses and antimicrobial molecules. In addition to classic intracellular pathogens, other bacteria including uropathogenic Escherichia coli (UPEC) can adopt both extracellular and intracellular lifestyles. UPEC intracellular survival and replication complicates treatment, as many therapeutic molecules do not effectively reach all components of the infection cycle. In this study, we explored cell penetrating antimicrobial peptides from distinct structural classes as alternative molecules for targeting bacteria. We identified two {beta}-hairpin peptides from the horseshoe crab, tachyplesin I and polyphemusin I, with broad antimicrobial activity toward a panel of pathogenic and non-pathogenic bacteria in planktonic form. Peptide analogues [I11A]tachyplesin I and [I11S]tachyplesin I maintained activity toward bacteria, but were less toxic to mammalian cells than native tachyplesin I. This important increase in therapeutic window allowed treatment with higher concentrations of [I11A]tachyplesin I and [I11S]tachyplesin I, to significantly reduce intramacrophage survival of UPEC in an in vitro infection model. Mechanistic studies using bacterial cells, model membranes and cell membrane extracts, suggest that tachyplesin I and polyphemusin I peptides kill UPEC by selectively binding and disrupting bacterial cell membranes. Moreover, treatment of UPEC with sublethal peptide concentrations increased zinc toxicity and enhanced innate macrophage antimicrobial pathways. In summary, our combined data show that cell penetrating peptides are attractive alternatives to traditional small molecule antibiotics for treating UPEC infection, and that optimization of native peptide sequences can deliver effective antimicrobials for targeting bacteria in extracellular and intracellular environments.

microbiology↗

bioRxiv2021

Fine tuning the mechanism of Antigen 43 self-association to modulate aggregation levels of Escherichia coli pathogens

Bacterial aggregates and biofilms allow bacteria to colonise a diverse array of surfaces that can ultimately lead to infections, where the protection they afford permits bacteria to resist anti-microbials and host immune factors. Despite these advantages there is a trade-off, whereby bacterial spread is reduced. As such, biofilm development needs to be regulated appropriately to suit the required niche. Here we investigate members from one of largest groups of bacterial adhesins, the autotransporters, for their critical role in the formation of bacterial aggregates and biofilms. We describe the structural and functional characterisation of autotransporter Ag43 homologues from diverse pathogenic Escherichia strains. We reveal a common mode of trans-association that leads to cell clumping and show that subtle variations in these interactions governs their aggregation kinetics. Our in depth investigation reveals an underlying molecular basis for the tuning of bacterial aggregation.

biochemistry↗

bioRxiv2021

MicroPIPE: An end-to-end solution for high-quality complete bacterial genome construction

Oxford Nanopore Technology (ONT) long-read sequencing has become a popular platform for microbial researchers; however, easy and automated construction of high-quality bacterial genomes remains challenging. Here we present MicroPIPE: a reproducible end-to-end bacterial genome assembly pipeline for ONT and Illumina sequencing. To construct MicroPIPE, we evaluated the performance of several tools for genome reconstruction and assessed overall genome accuracy using ONT both natively and with Illumina. Further validation of MicroPIPE was carried out using 11 sequence type (ST)131 Escherichia coli and eight publicly available Gram-negative and Gram-positive bacterial isolates. MicroPIPE uses Singularity containers and the workflow manager Nextflow and is available at https://github.com/BeatsonLab-MicrobialGenomics/micropipe.

bioinformatics↗

bioRxiv2020

Strain and lineage-level methylome heterogeneity in the multi-drug resistant pathogenic Escherichia coli ST101 clone

Escherichia coli Sequence Type (ST)101 is an emerging, multi-drug resistant lineage associated with carbapenem resistance. We recently completed a comprehensive genomics study on mobile genetic elements (MGEs) and their role in blaNDM-1 dissemination within the ST101 lineage. DNA methyltransferases (MTases) are also frequently associated with MGEs, with DNA methylation guiding numerous biological processes including genomic defence against foreign DNA and regulation of gene expression. The availability of Pacific Biosciences Single Molecule Real Time Sequencing data for seven ST101 strains enabled us to investigate the role of DNA methylation on a genome-wide scale (methylome). We defined the methylome of two complete (MS6192 and MS6193) and five draft (MS6194, MS6201, MS6203, MS6204, MS6207) ST101 genomes. Our analysis identified 14 putative MTases and eight N6-methyladenine DNA recognition sites, with one site that has not been described previously. Furthermore, we identified a Type I MTase encoded within a Transposon 7-like Transposon and show its acquisition leads to differences in the methylome between two almost identical isolates. Genomic comparisons with 13 previously published ST101 draft genomes identified variations in MTase distribution, consistent with MGE differences between genomes, highlighting the diversity of active MTases within strains of a single E. coli lineage. It is well established that MGEs can contribute to the evolution of E. coli due to their virulence and resistance gene repertoires. This study emphasises the potential for mobile genetic elements to also enable highly similar bacterial strains to rapidly acquire genome-wide functional differences via changes to the methylome. Impact StatementEscherichia coli ST101 is an emerging human pathogen frequently associated with carbapenem resistance. E. coli ST101 strains carry numerous mobile genetic elements that encode virulence determinants, antimicrobial resistance, and DNA methyltransferases (MTases). In this study we provide the first comprehensive analysis of the genome-wide complement of DNA methylation (methylome) in seven E. coli ST101 genomes. We identified a Transposon carrying a Type I restriction modification system that may lead to functional differences between two almost identical genomes and showed how small recombination events at a single genomic region can lead to global methylome changes across the lineage. We also showed that the distribution of MTases throughout the ST101 lineage was consistent with the presence or absence of mobile genetic elements on which they are encoded. This study shows the diversity of MTases within a single bacterial lineage and shows how strain and lineage-specific methylomes may drive host adaptation. Data SummarySequence data including reads, assemblies and motif summaries have previously been submitted to the National Center for Biotechnology Information (https://www.ncbi.nlm.nih.gov) under the BioProject Accessions: PRJNA580334, PRJNA580336, PRJNA580337, PRJNA580338, PRJNA580339, PRJNA580341 and PRJNA580340 for MS6192, MS6193, MS6194, MS6201, MS6203, MS6204 and MS6207 respectively. All supporting data, code, accessions, and protocols have been provided within the article or through supplementary data files.

genomics↗

bioRxiv2019

Genomic characterisation and context of the blaNDM-1 carbapenemase in Escherichia coli ST101.

Carbapenems are last-resort antibiotics; however, the spread of plasmid-encoded carbapenemases such as the New Delhi metallo-{beta}-lactamase 1 (NDM-1) challenges their effectiveness. The rise of NDM-1 has coincided with the emergence of extensively multidrug resistant (MDR) lineages such as Escherichia coli ST101. Here we present a comprehensive genomic analysis of seven E. coli ST101 isolates that carry the blaNDM-1 gene. We determined the complete genomes of two isolates and the draft genomes of five isolates, enabling complete resolution of the plasmid context of blaNDM-1. Comparisons with thirteen previously published ST101 genomes revealed a monophyletic lineage within the B1 phylogroup forming two clades (designated Clade 1 and Clade 2). Most Clade 1 strains are MDR, encoding resistance to at least 9 different antimicrobial classes, including extended spectrum cephalosporins. Additionally, we characterised different pathways for blaNDM-1 carriage and persistence in the ST101 lineage. For IncC plasmids, carriage was associated with recombination and local transposition events within the antibiotic resistance island. In contrast, we revealed recent transfer of a large blaNDM-1 resistance island between F-type plasmids. The complex acquisition pathways characterised here highlight the benefits of long-read Single Molecule Real Time sequencing in revealing evolutionary events that would not be apparent by short-read sequencing alone. These high-quality E. coli ST101 genomes will provide an important reference for further analysis of the role of mobile genetic elements in this emerging multidrug resistant lineage. ImportanceCarbapenem resistant Escherichia coli are urgent priority organisms as they are resistant to our drugs of last resort. E. coli ST101 have been reported as carriers of the New Delhi Metallo-beta-Lactamase 1 gene (blaNDM-1), conferring resistance to carbapenems, however there is limited genomic information available for this lineage. In this study we used long-read genome sequencing to characterise the complete genomes of two E. coli ST101 strains and determine the carriage of blaNDM-1 in a collection of E. coli ST101 strains. We showed that carriage of blaNDM-1 and resistance determinants to eight other antimicrobial classes was confined to a single clade. We also showed two different pathways for the carriage of blaNDM-1, which was dependent on the type of plasmid. Long-read sequencing allowed us to show the full complexities of these resistance regions and highlighted how strains from an emerging E. coli lineage have become resistant to nearly all available antimicrobials.

genomics↗

bioRxiv2019

Multiple evolutionary trajectories for non-O157 Shiga toxigenic Escherichia coli

BackgroundShiga toxigenic Escherichia coli (STEC) is an emerging global pathogen and remains a major cause of food-borne illness with more severe symptoms including hemorrhagic colitis and hemolytic-uremic syndrome. Since the characterization of the archetypal STEC serotype, E. coli O157:H7, more than 250 STEC serotypes have been defined. Many of these non-O157 STEC are associated with clinical cases of equal severity as O157. In this study, we utilize whole genome sequencing of 44 STEC strains from eight serogroups associated with human infection to establish their evolutionary relationships and contrast this with their virulence gene profiles and established typing methods. ResultsOur phylogenomic analysis delineated these STEC strains into seven distinct lineages, each with a characteristic repertoire of virulence factors. Some lineages included commensal or other E. coli pathotypes. Multiple independent acquisitions of the Locus for Enterocyte Effacement were identified, each associated with a distinct repertoire of effector genes. Lineages were inconsistent with O-antigen typing in several instances, consistent with lateral gene transfer within the O-antigen locus. STEC lineages could be defined by the conservation of clustered regularly interspaced short palindromic repeats (CRISPRs), however, no CRISPR profile could differentiate STEC from other E. coli strains. Six genomic regions (ranging from 500 bp - 10 kbp) were found to be conserved across all STEC in this dataset and may dictate interactions with Stx phage lysogeny. ConclusionsThe genomic analyses reported here present non-O157 STEC as a diverse group of pathogenic E. coli emerging from multiple lineages that independently acquired mobile genetic elements that promote pathogenesis.

microbiology↗

bioRxiv2018

Identification and characterization of a phase-variable element that regulates the autotransporter UpaE in uropathogenic Escherichia coli

Uropathogenic Escherichia coli (UPEC) are the most common etiological agent of uncomplicated urinary tract infection (UTI). An important mechanism of gene regulation in UPEC is phase variation that involves inversion of a promoter-containing DNA element via enzymatic activity of tyrosine recombinases, resulting in biphasic, ON or OFF expression of target genes. The UPEC reference strain CFT073 has five tyrosine site-specific recombinases that function at two previously characterized promoter inversion systems, fimS and hyxS. Three of the five recombinases are located proximally to their cognate target elements, which is typical of promoter inversion systems. The genes for the other two recombinases, IpuA and IpuB are located distal from these sites. Here, we identified and characterized a third phase variable invertible element in CFT073, ipuS located proximal to ipuA and ipuB. The inversion of ipuS is catalyzed by four of the five CFT073 recombinases. Orientation of the element drives transcription of a two-gene operon containing ipuR, a predicted LuxR-type regulator, and upaE, a predicted autotransporter. We show that the predicted autotransporter UpaE is surface-located and facilitates biofilm formation as well as adhesion to extracellular matrix proteins in a K-12 recombinant background. Consistent with this phenotype, the ipuS ON condition in CFT073 results in defective swimming motility, increased adherence to human kidney epithelial cells, and a positive competitive kidney colonization advantage in experimental mouse UTI infections. Overall, the identification of a third phase-switch in UPEC that is regulated by a shared set of recombinases describes a complex phase-variable virulence network in UPEC.\n\nImportanceUropathogenic Escherichia coli (UPEC) is the most common cause of urinary tract infection (UTI). ON versus OFF phase-switching by inversion of small DNA elements at two chromosome sites in UPEC regulates the expression of important virulence factors, including the type 1 fimbriae adhesion organelle. In this report, we describe a third invertible element, ipuS, in the UPEC reference strain CFT073. The inversion of ipuS controls the phase variable expression of upaE, an autotransporter gene that encodes a surface protein involved in adherence to extracellular matrix proteins and colonization of the kidneys in a murine model of UTI.

microbiology↗

bioRxiv2017

Dominance of ST131 Escherichia coli carrying blaCTX-M in patients with bloodstream infections caused by cephalosporin-resistant strains in Australia, New Zealand and Singapore: whole genome analysis of isolates from a randomised trial

Synopsis/AbstractO_ST_ABSObjectivesC_ST_ABSTo characterise multi-drug resistant Escherichia coli isolated from patients in Australia, New Zealand and Singapore with bloodstream infection (BSI).\n\nMethodsWe prospectively collected third-generation cephalosporin resistant (3GC-R) E. coli from blood cultures obtained from patients enrolled in a randomised controlled trial. Whole genome sequencing was used to characterise antibiotic resistance genes, sequence types (STs), plasmids and phylogenetic relationships. Antibiotic susceptibility was determined using disk diffusion and Etest.\n\nResultsA total of 70 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 [IQR 64-81]). The median Pitt bacteraemia score at presentation was 1 (IQR 0-2, range 0-3) and ICU admission was infrequent (3.1%). ST131 possessed significantly more acquired resistance genes than non-ST131 (p=0.003). Clade C1/C2 ST131 predominated (30.2% and 53.5% of all ST131 respectively) and these were all resistant to ciprofloxacin. All clade A ST131 were community-associated. The predominant ESBL types were blaCTX-M (78.6% of isolates) and were strongly associated with ST131, 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 (p-AmpC) genes (mainly blaCMY-2) were also frequent (17.1%) but were more common with non-ST131 strains (p< 0.001). The majority of plasmid replicon types were IncF.\n\nConclusionsIn a prospective collection of 3GC-R E. coli causing BSI in the Australasian region, community-associated Clade C1/C2 ST131 predominate in association with blaCTX-M ESBLs, although a significant proportion of non-ST131 strains carried blaCMY-2.

microbiology↗

bioRxiv2017

Genomic investigation of an outbreak of carbapenemase-producing Enterobacter cloacae: long-read sequencing reveals the context of blaIMP4 on a widely distributed IncHI2 plasmid

Carbapenem-resistant Enterobacteriaceae (CRE) represent one of the most urgent threats to human health posed by antibiotic resistant bacteria. Enterobacter hormaechei and other members of the Enterobacter cloacae complex are the most commonly encountered Enterobacter spp. within clinical settings, responsible for numerous outbreaks and ultimately poorer patient outcomes. Here we applied three complementary whole genome sequencing (WGS) technologies to characterise a hospital cluster of blaIMP-4 carbapenemase-producing E. hormaechei.\n\nIn response to a suspected CRE outbreak in 2015 within an Intensive Care Unit (ICU)/Burns Unit in a Brisbane tertiary referral hospital we used Illumina sequencing to determine that all outbreak isolates were sequence type (ST)90 and near-identical at the core genome level. Comparison to publicly available data unequivocally linked all 10 isolates to a 2013 isolate from the same ward, confirming the hospital environment as the most likely original source of infection in the 2015 cases. No clonal relationship was found to IMP-4-producing isolates identified from other local hospitals. However, using Pacific Biosciences long-read sequencing we were able to resolve the complete context of the blaIMP-4 gene, which was found to be on a large IncHI2 plasmid carried by all IMP-4-producing isolates. Continued surveillance of the hospital environment was carried out using Oxford Nanopore long-read sequencing, which was able to rapidly resolve the true relationship of subsequent isolates to the initial outbreak. Shotgun metagenomic sequencing of environmental samples also found evidence of ST90 E. hormaechei and the IncHI2 plasmid within the hospital plumbing.\n\nOverall, our strategic application of three WGS technologies provided an in-depth analysis of the outbreak, including the transmission dynamics of a carbapenemase-producing E. hormaechei cluster, identification of possible hospital reservoirs and the full context of blaIMP-4 on a multidrug resistant IncHI2 plasmid that appears to be widely distributed in Australia.

genomics↗