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Lan, R.

Publications and source records attributed to Lan, R..

At least 19 recordsLinked to original sources

Carnitine deficiency alters fuel metabolism and voluntary wheel running in mice

BackgroundCarnitine plays an obligatory role in energetics owing to its role in the translocation of long-chain fatty acids into the mitochondrion for oxidation. Here, we determined the metabolic and behavioral consequences of systemic carnitine deficiency (SCD) in mice. MethodsFemale C57BL/6J mice were randomized to receive normal drinking water (control, n = 8) or drinking water supplemented with mildronate 4g.L-1 (mildronate, n = 8) for 21 days. Body composition was assessed at baseline and post treatment. Metabolic and behavioral phenotyping was performed continuously over 72 hours following 14 days of control or mildronate treatment. Stable isotope were used to assess whole-body substrate oxidation. Carnitine subfractions were quantified in skeletal muscle and liver, as was mitochondrial respiratory function. Liver and muscle samples also underwent proteomic analysis. ResultsMildronate treatment depleted total carnitine in muscle and liver by [~]97% (P < 0.001) and [~]90% (P < 0.001), respectively. Carnitine depletion was accompanied by lower total energy expenditure (P = 0.01), attributable to lower voluntary wheel running (P = 0.01). Oxidation rates of palmitate (P < 0.01) but not octanoate were lower whereas rates of glucose oxidation were greater in carnitine depleted mice (P < 0.01). Mitochondrial respiratory capacity was unaltered by carnitine deficiency. Carnitine deficiency remodeled muscle and liver proteomes to support lipid oxidation and energy production. SummaryIn mice, carnitine deficiency is characterized by decreased long-chain fatty acid oxidation despite preserved mitochondrial respiratory capacity. Carnitine deficiency resulted in lower voluntary exercise and a concomitant reduction in energy expenditure.

physiology↗

Stage-adaptive integration of polydopamine promotes hPSC-derived alveolar organoids differentiation and maturation

Human pluripotent stem cell (hPSC)-derived alveolar organoids (ALOs) have emerged as a powerful tool for modeling human lung development and disease, and accelerating respiratory drug discovery. However, achieving the functional maturation of ALOs remains challenging. Polydopamine (PDA) is a mussel-inspired polyphenolic biomaterial with antioxidant and adhesive properties that can be deployed as surface coatings and nanoparticles (NPs) in cell culture systems. Here, we integrate PDA coatings and NPs sequentially in a stage-adaptive manner throughout the hPSC-derived ALOs differentiation system and study their contributions to ALOs maturation. Our results demonstrated PDA coating yielded more anterior foregut endoderm (AFE) spheroids by strengthening the interaction between Matrigel and substrate. Bulk RNA-seq revealed enrichment of cell-cell and cell-extracellular matrix interactions by PDA. The subsequent incorporation of PDA NPs in Matrigel at lung progenitor cells (LPCs) stage significantly mitigated reactive oxygen species (ROS) accumulation and enhanced LPCs generation. Functionally, AT2 cells in ALOs exhibit characteristic lysosome-to-lamellar body (LB) maturation due to the traffic of internalized PDA NPs to endolysosome. Transcriptomics further indicated enrichment of endocytic-phagosome and epithelium development pathways by PDA treatment. Together, our study establishes a stage-adaptive-integrated PDA strategy throughout hPSC-to-ALOs differentiation and demonstrates that PDA robustly enhances ALOs maturation and secretory function. Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=178 SRC="FIGDIR/small/708928v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@88208dorg.highwire.dtl.DTLVardef@1111590org.highwire.dtl.DTLVardef@9ea9b0org.highwire.dtl.DTLVardef@969fad_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

Defining Aeromonas species boundaries with large-scale average nucleotide identity analyses and genomic phylogeny

Aeromonas taxonomy has long been complicated by overlapping phenotypic, biochemical, and protein profiles. Here, we establish a robust genome-based framework for Aeromonas genomic species delineation. We analysed average nucleotide identity (ANI) across 4,366 available Aeromonas genomes and demonstrated that at 96% ANI threshold, skANI and fastANI generated too many clusters (65 and 57 respectively) and these clusters were not supported by core genome phylogeny. We identified 95.4% skANI (equivalent to 95.6% fastANI) as an operational threshold for the delineating Aeromonas genomic species. Using the 95.4% skANI threshold, we identified 44 ANI clusters among the 4,366 genomes, of which 43 clusters were genomic species supported by the core-genome phylogeny. Thirty-four of the 43 genomic species corresponded to existing taxonomic species, whilst the remaining nine are currently not recognised as taxonomic species. All recognised taxonomic species represented in the dataset retained their existing species designation except Aeromonas mytilicola, which was not separated from Aeromonas rivipollensis in both ANI clusters and the core-genome phylogeny. The digital DNA-DNA hybridisation (dDDH) values between the genomic species were below 70%, further supporting genomic species delineation. We further developed AeromonasGStyper, a genomic species typing tool that assigns query genomes based on ANI similarity to medoid genomes. In conclusion, this study establishes a genomic species framework for genome-based classification of Aeromonas and provides a practical approach for future genomic surveillance. Impact StatementAeromonas species have gained increased attention as emerging human enteric pathogens. Aeromonas taxonomy has long been complicated by overlapping phenotypic, biochemical, and protein profiles. Although a 96% average nucleotide identity (ANI) threshold was proposed previously for Aeromonas species delineation, analysis of 4,366 Aeromonas genomes demonstrated that this threshold generated excessive genomic clusters that were not supported by the core-genome phylogeny. We identified 95.4% skANI (equivalent to 95.6% fastANI) as an operational threshold for delineating Aeromonas genomic species, supported by core-genome phylogeny and digital DNA-DNA hybridisation (dDDH). The framework identified 43 genomic species, including 34 corresponding to recognised taxonomic species and nine genomic species that do not correspond to currently recognised taxonomic species. In addition, our data showed that Aeromonas mytilicola was not separated from Aeromonas rivipollensis by ANI clustering and core-genome phylogeny, supporting further taxonomic reassessment of the distinction between these two species.

microbiology↗

Multilevel HierCC typing scheme for global genomic epidemiology and antimicrobial resistance surveillance of Campylobacter jejuni

Campylobacter jejuni is the most common bacterial cause of human gastroenteritis around the world. The disease burden and financial cost associated with C. jejuni pose significant challenges to the global public health system. A stable, scalable and standardised typing scheme is essential for epidemiological and AMR surveillance for prevention and control of C. jejuni infections. We curated and assembled a C. jejuni global whole genome sequencing (WGS) dataset of 63,012 publicly available Illumina short-read genomes. A C. jejuni global cgMLST scheme with 1161 core loci was developed using a representative subset of 2,587 genomes. HierCC clustering of the cgMLST profiles was performed for all levels and suitable HierCC levels were selected to enable epidemiological analysis. Antimicrobial resistance (AMR) prediction was performed using AbritAMR. A HierCC cluster was classified as a resistant cluster if [&ge;]80% of the isolates were resistant to at least one antibiotic.We selected 9 HierCC levels (HC2, HC4, HC6, HC12, HC19, HC55, HC100, HC167 and HC264) to form the multilevel HierCC scheme. The multilevel design allowed natural and genetically discrete clusters to be described consistently at both global and local scale. We showcased the utility of the scheme with identification of country and continent specific clusters at HC264 to HC19 levels and differentiation of animal host specific (specialist) from human infection (generalist) clusters at HC264 to HC55 levels. In the USA dataset from 2016 to 2022, a total of 276 resistant clusters were identified with 22 resistant clusters increasing in frequence in recent years. An increased prevalence of C. jejuni carrying 50S_L22 mutations in the USA was observed from 2016 to 2022, suggesting continuing selection pressure from macrolide use in the farm animals. We developed a novel multilevel HierCC typing scheme to standardise AMR surveillance and provide flexible typing resolution for both short- and long-term epidemiological investigations of C. jejuni at global and local levels.

microbiology↗

Phage-encoded sRNA counteracts xenogenic silencing in pathogenic E. coli

Horizontal gene transfer introduces foreign DNA that can disrupt cellular processes and is therefore subject to xenogenic silencing by nucleoid-associated proteins such as H-NS and Hha. In Enterohaemorrhagic Escherichia coli (EHEC), prophages make up a large fraction of the accessory genome and encode many virulence factors, yet to be expressed they must overcome this silencing. We identify a prophage-encoded small RNA (sRNA), HnrS, that functions as an anti-silencing factor by targeting the H-NS paralogue Hha. HnrS is a short (66-nt) sRNA present in multiple copies (up to nine) in EHEC and Enteropathogenic Escherichia coli (EPEC) genomes and is enriched in E. coli strains that carry the locus of enterocyte effacement (LEE). We show that HnrS directly base-pairs with the ribosome-binding site of the hha mRNA, repressing its translation and thereby reducing Hha-enhanced H-NS silencing. This counter-silencing de-represses the LEE type III secretion system and concomitantly represses motility. Transcriptomic profiling further revealed that HnrS indirectly activates genes involved in nitrate/nitrite respiration and nitric oxide resistance, metabolic pathways that contribute to survival in the inflamed gastrointestinal tract. Deletion of hnrS reduced expression of nitrate reductase genes and impaired actin pedestal formation on host epithelial cells. Our results indicate that prophage-encoded, multicopy hnrS provides a counter-silencing mechanism that reduces Hha-H-NS repression at specific virulence loci. This likely enables expression of horizontally acquired genes without broadly disrupting the core H-NS regulon. HnrS illustrates how mobile genetic elements deploy sRNAs to counteract xenogenic silencing and promote virulence gene expression, enhancing colonisation of the host. Importance statementHorizontally acquired genes are often silenced to protect bacterial genomes, but this defence also limits the expression of new traits. We identify a prophage-encoded small RNA, HnrS, that counteracts this restriction by repressing the xenogenic silencer Hha, lifting Hha-H-NS-mediated repression of virulence and metabolic genes. HnrS activates the locus of enterocyte effacement, nitrate/nitrite respiration, and nitric oxide resistance--pathways that help E. coli survive and colonise the inflamed gut. Our findings reveal an RNA-based counter-silencing mechanism encoded by mobile genetic elements, showing how phages can reprogram bacterial regulatory networks to promote adaptation and pathogenicity.

microbiology↗

Genomic analysis identifies Campylobacter concisus genomospecies 2 as a novel species and proposes the name Campylobacter oralis

Campylobacter concisus comprises two distinct genomospecies (GS) based on core genome analysis. Here we conducted further analysis and demonstrated that C. concisus GS2 strains belong to a novel Campylobacter species. A total of 245 C. concisus genomes including 85 GS1 and 160 GS2 strains were analysed. DNA-DNA hybridization (DDH) values between strains of GS1 and GS2 C. concisus were from 42.8% to 66%. Average Nucleotide Identity (ANI) between GS1 and GS2 C. concisus strains were from 87.8% to 89.7%. The average GC contents of GS1 and GS2 C. concisus strains were 37.3% and 39.2% respectively. GS1 and GS2 specific genes have been identified. GS1 and GS2 C. concisus strains can also be differentiated based on core genome, 23S rRNA polymorphisms and protein profiles. Their morphology appears different under certain conditions. In conclusion, ANI and DDH values clearly support that C. concisus GS2 as a novel Campylobacter species, for which we propose the name Campylobacter oralis. The identification of C. concisus and C. oralis specific genes, along with differences in their protein profiles, morphology, core genome and 23S rRNA phylogeny, further support this classification.

microbiology↗

Global genomic dissection of antimicrobial resistance in Salmonella Typhimurium

Salmonella Typhimurium (STm) is a globally prevalent pathogen. We compiled a dataset comprising [~]65,000 publicly available STm isolates and analysed the predicted-resistance to 15 key antibiotics. Additionally, we typed all isolates using a standardized typing method, multilevel genome typing (MGT), and characterised the resistance profiles by MGT sequence types (ST). We identified 407 MGT STs wherein at least 80% of the isolates were non-susceptible to at least one antibiotic. For the key antibiotics prescribed for severe salmonellosis, we identified three ciprofloxacin non-susceptible MGT STs, and eight cefotaxime non-susceptible MGT STs in the last two years of the dataset (2021-2022). While the ciprofloxacin non-susceptible MGT STs comprised isolates predominantly from the UK; only one cefotaxime non-susceptible MGT ST comprised isolates predominantly from UK and associated with swine, with others from USA, and associated with cattle and poultry. Integration of AMR predictions with MGT strain typing provides sharable, standardised, and specific identification and tracking of resistant isolates. This integrated analysis presents a unique approach for the global surveillance of antimicrobial resistance and resistant strains.

microbiology↗

Characterising Staphylococcus aureus genomic epidemiology with Multilevel Genome Typing.

Staphylococcus aureus is a major source of both hospital and community acquired infections, and is the leading source of skin and soft tissue infections worldwide. Advances in whole genome sequencing (WGS) technologies have recently generated large volumes of S. aureus WGS data. The timely classification of S. aureus WGS data with genomic typing technologies has the potential to describe detailed genomic epidemiology at large and small scales. In this study, a multilevel genome typing (MGT) scheme comprised of 8 levels of multilocus sequence typing schemes of increasing resolution was developed for S. aureus and used to analyse 50,481 publicly available genomes. Application of MGT to S. aureus epidemiology was showcased in three case studies. Firstly, the population structure of the globally disseminated sequence type ST8 were described by MGT2, which was compared with Spa typing. Secondly, MGT was used to characterise MLST ST8 - PFGE USA300 isolates that colonised multiple body sites of the same patient. Unique STs from multiple MGT levels were able to group isolates of the same patient, and the highest resolution MGT8 separated isolates within a patient that varied in predicted antimicrobial resistance. Lastly, MGT was used to describe the transmission of MLST ST239 - SCCmec III throughout a single hospital. MGT STs were able to describe both isolates that had spread between wards and also isolates that had colonised different reservoirs within a ward. The S. aureus MGT describes large- and small-scale S. aureus genomic epidemiology with scalable resolutions using stable and standardised ST assignments. The S. aureus MGT database is online (https://mgtdb.unsw.edu.au/staphylococcus) and is capable of tracking new and existing clones to facilitate the design of new strategies to reduce the global burden of S. aureus related diseases.

microbiology↗

Intercellular Signaling Pathways as Therapeutic Targets for Vascular Dementia Repair

Vascular dementia (VaD) is a white matter ischemic disease and the second-leading cause of dementia, with no direct therapy. Within the lesion site, cell-cell interactions dictate the trajectory towards disease progression or repair. To elucidate the underlying intercellular signaling pathways, a VaD mouse model was developed for transcriptomic and functional studies. The mouse VaD transcriptome was integrated with a human VaD snRNA-Seq dataset. A custom-made database encompassing 4053 human and 2032 mouse ligand-receptor (L-R) interactions identified significantly altered pathways shared between human and mouse VaD. Two intercellular L-R systems, Serpine2-Lrp1 and CD39-A3AR, were selected for mechanistic study as both the ligand and receptor were dysregulated in VaD. Decreased Seprine2 expression enhances OPC differentiation in VaD repair. A clinically relevant drug that reverses the loss of CD39-A3AR function promotes tissue and behavioral recovery in the VaD model. This study presents novel intercellular signaling targets and may open new avenues for VaD therapies.

neuroscience↗

Proteomic comparison of epidemic Australian Bordetella pertussis biofilm cells

Bordetella pertussis causes whooping cough, a severe respiratory infectious disease. Studies have compared the currently dominant single nucleotide polymorphism (SNP) cluster I (pertussis toxin promoter allele, ptxP3) and previously dominant SNP cluster II (ptxP1) strains as planktonic cells. Since biofilm formation is linked with B. pertussis pathogenesis in vivo, this study compared the biofilm formation capabilities of representative strains of cluster I and cluster II. Confocal laser scanning microscopy found that the cluster I strain had a denser biofilm structure compared to the cluster II strain. Differences in protein expression of the biofilm cells were then compared using Tandem Mass Tagging (TMT) and high-resolution multiple reaction monitoring (MRM-hr). In total, 1453 proteins were identified of which 40 proteins had significant differential expression between the two strains in biofilm conditions. Of particular interest was a large increase in expression of energy metabolism proteins (cytochrome proteins PetABC and BP3650) in the cluster I strain. When the expression of these proteins was compared between 6 additional strains from each cluster, it was found that the protein expression varied between all strains. These findings suggest that there are large levels of individual proteomic diversity between B. pertussis strains in biofilm conditions despite the highly conserved genome of the species. Overall, this study revealed visual differences in biofilm structure between B. pertussis strains and highlighted strain specific variation in protein expression that dominate potential cluster specific changes that may be linked with the dominance of cluster I strains. ImportanceBordetella pertussis causes whooping cough. The currently circulating cluster I strains have taken over previously dominant cluster II strains. It is important to understand the reasons behind the evolution to develop new strategies against the pathogen. Recent studies have shown that B. pertussis can form biofilms during infection. This study compared the biofilm formation capabilities of a cluster I and a cluster II strain and identified visual differences in the biofilms. The protein expression between these strains grown in biofilms were compared and proteins identified with varied expression were measured with additional strains from each cluster. It was found that despite the highly conserved genetics of the species, there was varied protein expression between the additional strains. This study highlights that strain specific variation in protein expression during biofilm conditions that may dominate the cluster specific changes that may be linked to the dominance of cluster I strains.

microbiology↗

Neoadjuvant Therapy Differentially Remodels Carcinoma and Tumor Microenvironment in Pancreatic Ductal Adenocarcinoma: Insights from Spatially Resolved Transcriptomics

PurposeNeoadjuvant therapy (NAT) is increasingly being used for pancreatic ductal adenocarcinoma (PDAC) treatment. However, its distinct effects on carcinoma cells and the tumor microenvironment (TME) are not fully understood. This study employs spatial transcriptomics and single-cell RNA sequencing to investigate how NAT differentially remodels PDACs carcinoma cells and TME. Experimental DesignWe used spatial transcriptomics to compare gene expression profiles in carcinoma cells and the TME between NAT-treated and NAT-naive PDAC patients and correlated with their clinicopathologic features. Complementary single-nucleus RNA sequencing (snRNA-seq) analysis was conducted to validate our findings and identify cell types driving NAT-induced gene expression alterations. ResultsWe found NAT not only induces apoptosis and inhibits proliferation in carcinoma cells but also significantly remodels the TME. Notably, NAT induces a coordinated upregulation of multiple key complement genes (C3, C1S, C1R, C4B and C7) in the TME, making the complement pathway one of the most significantly affected pathways by NAT. Patients with higher TME complement expression following NAT exhibit improved overall survival; more immunomodulatory and neurotrophic cancer-associated fibroblasts (CAFs); more CD4+ T cells, monocytes and mast cells; and lower immune exhaustion gene expression. snRNA-seq analysis demonstrates C3 complement upregulation specifically in CAFs but not in other stroma cell types. ConclusionsOur findings indicate that NAT may reduce immunosuppression in PDAC by enhancing complement production and signaling within the TME. These findings suggest that local complement dynamics could serve as a novel biomarker for prognosis, evaluating treatment response and resistance, and guiding therapeutic strategies in NAT-treated PDAC patients. Translational RelevanceAs neoadjuvant therapy (NAT) increasingly becomes the preferred approach in treating resectable and borderline resectable pancreatic ductal adenocarcinoma (PDAC), there is a growing demand for novel biomarkers specifically tailored for post-NAT PDAC patients. Our study focused on how NAT differentially remodels the tumor cells and the tumor microenvironment (TME). We demonstrate that NAT can enhance local complement production and signaling in PDACs TME, which is associated with reduced immune exhaustion and improved overall survival. Our results highlight the importance of local complement dynamics in influencing treatment response, resistance, and overall clinical outcomes in PDAC. This new mechanism provides new opportunities in biomarker development which could facilitate more accurate prognostication and precise treatment stratification, particularly for patients undergoing NAT in PDAC.

genomics↗

Genomic epidemiology and multilevel genome typing of Bordetella pertussis

Bordetella pertussis is responsible for the respiratory infectious disease pertussis (or whooping cough), which causes one of the most severe diseases in infants, although it can be prevented by whole cell and acellular vaccines. The recent resurgence of pertussis is partially due to pathogen adaptation to vaccines as well as resistance to antimicrobials. Surveillance of current circulating and emerging strains is therefore vital to understand the risks they pose to public health. Although there is increased genomics based typing, a genomic nomenclature for this pathogen has not been well established. Here, we implemented the Multilevel Genome Typing (MGT) system for B. pertussis with five levels of resolution, which provide targeted typing of relevant lineages as well as discrimination of closely related strains at the finest scale. The low resolution levels can describe the distribution of alleles of major vaccine antigen genes such as ptxP, fim3, fhaB and prn as well as temporal and spatial trends within the B. pertussis global population. Mid-resolution levels enables typing of antibiotic resistant lineages and Prn deficient lineages within the ptxP3 clade. High resolution levels can capture small-scale epidemiology such as local transmission events and has comparable resolution to existing genomic methods of strain relatedness assessment. The scheme offers stable MGT type assignments aiding harmonisation of typing and communication between laboratories. The scheme is available at www.mgtdb.unsw.edu.au/pertussis/ is regularly updated from global data repositories and accepts public data submissions. The MGT scheme provides a comprehensive, robust, and scalable system for global surveillance of B. pertussis.

microbiology↗

SaLTy: a novel Staphylococcus aureus Lineage Typer

Staphylococcus aureus asymptomatically colonises 30% of humans and in 2017 was associated with 20,000 deaths in the USA alone. Dividing S. aureus into smaller sub-groups can reveal the emergence of distinct sub-populations with varying potential to cause infections. Despite multiple molecular typing methods categorising such sub-groups, they do not take full advantage of S. aureus WGS when describing the fundamental population structure of the species. In this study, we developed Staphylococcus aureus Lineage Typing (SaLTy), which rapidly divides the species into 61 phylogenetically congruent lineages. Alleles of three core genes were identified that uniquely define the 61 lineages and were used for SaLTy typing. SaLTy was validated on 5,000 genomes and 99.12% (4,956/5,000) of isolates were assigned the correct lineage. We compared SaLTy lineages to previously calculated clonal complexes (CCs) from BIGSdb (n=21,173). SALTy improves on CCs by grouping isolates congruently with phylogenetic structure. SaLTy lineages were further used to describe the carriage of Staphylococcal chromosomal cassette containing mecA (SCCmec) which is carried by methicillin-resistant S. aureus (MRSA). Most lineages had isolates lacking SCCmec and the four largest lineages varied in SCCmec over time. Classifying isolates into SaLTy lineages, which were further SCCmec typed, allowed SaLTy to describe high-level MRSA epidemiology We provide SALTy as a simple typing method that defines phylogenetic lineages (https://github.com/LanLab/SaLTy). SALTy is highly accurate and can quickly analyse large amounts of S. aureus WGS. SALTy will aid the characterisation of S. aureus populations and the ongoing surveillance of sub-groups that threaten human health.

microbiology↗

MGTdb: A web service and database for studying the global and local genomic epidemiology of bacterial pathogens

Multilevel genome typing (MGT) enables the genomic characterization of bacterial isolates and the relationships among them. The MGT system describes an isolate using multiple multilocus sequence typing (MLST) schemes, referred to as levels. Thus, for a new isolate, sequence types (STs) assigned at multiple precisely defined levels can be used to type isolates at multiple resolutions. The MGT designation for isolates is stable, and assignment is faster than existing approaches. MGTs utility has been demonstrated in multiple species. This paper presents a publicly accessible web service called MGTdb, which enables the assignment of MGT sequence types to isolates, along with their storage, retrieval and analysis. The MGTdb web service enables upload of genome data as sequence reads or alleles, which are processed and assigned MGT identifiers. Additionally, any newly sequenced isolates deposited in NCBI Sequence Read Archive are also regularly retrieved (currently daily), processed, assigned MGT and made publicly available in MGTdb. Interactive visualisation tools are presented to assist analysis, along with capabilities to download publicly available isolates and assignments for use with external software. MGTdb is currently available for Salmonella enterica serovars Typhimurium and Enteritidis, and Vibrio cholerae. We demonstrate the usability of MGTdb through three case studies to study the long-term national surveillance of S. Typhimurium, and the local epidemiology and outbreaks of S. Typhimurium, and the global epidemiology of V. cholerae. Thus, MGTdb enables epidemiological and microbiological investigations at multiple levels of resolution for all publicly available isolates of these pathogens. Database URLhttps://mgtdb.unsw.edu.au

bioinformatics↗

Integrating proteomic data with metabolic modelling provides insight into key pathways of Bordetella pertussis biofilms

Pertussis, commonly known as whooping cough is a severe respiratory disease caused by the bacterium, Bordetella pertussis. Despite widespread vaccination, pertussis resurgence has been observed globally. The development of the current acellular vaccine (ACV) has been based on planktonic studies. However, recent studies have shown that B. pertussis readily forms biofilms. A better understanding of B. pertussis biofilms is important for developing novel vaccines that can target all aspects of B. pertussis infection. This study compared the proteomic expression of biofilm and planktonic B. pertussis cells to identify key changes between the conditions. Major differences were identified in virulence factors including an upregulation of toxins (adenylate cyclase toxin and dermonecrotic toxin) and downregulation of pertactin and type III secretion system proteins in biofilm cells. To further dissect metabolic pathways that are altered during the biofilm lifestyle, the proteomic data was then incorporated into a genome scale metabolic model using the integrative metabolic analysis tool (iMAT). The analysis revealed that planktonic cells utilised the glyoxylate shunt while biofilm cells completed the full tricarboxylic acid cycle. Differences in processing aspartate, arginine and alanine were identified as well as unique export of valine out of biofilm cells which may have a role in inter-bacterial communication and regulation. Finally, increased polyhydroxybutyrate accumulation and superoxide dismutase activity in biofilm cells may contribute to increased persistence during infection. Taken together, this study modelled major proteomic and metabolic changes that occur in biofilm cells which helps lay the groundwork for further understanding B. pertussis pathogenesis.

microbiology↗

Genomic epidemiology and multilevel genome typing of Australian Salmonella enterica serovar Enteritidis

Salmonella enterica serovar Enteritidis is one of the leading causes of salmonellosis in Australia. However, the majority of S. Enteritidis cases in Australia are travel-related with a small proportion being locally acquired. This study aimed to characterise the genomic features of Australian S. Enteritidis and compare them with international strains using multilevel genome typing (MGT). A total of 568 S. Enteritidis isolates from two Australian states across two consecutive years were analysed using the S. Enteritidis MGT scheme and database (MGTdb) - which contained 40,390 publicly available genomes from 99 countries. The Australian S. Enteritidis strains were divided into three phylogenetic clades (A, B and C). Clades A and C represented 16.4% and 3.5% of the total isolates, respectively, and were of local origin. Clade B accounted for 80.1% of the isolates which belonged to seven previously defined lineages but was dominated by the global epidemic lineage (MGT4-CC1). At MGT5 level, three out of five top sequence types (STs) in Australia were also top STs in Asia, suggesting that a fair proportion of Australian S. Enteritidis cases may be epidemiologically linked with Asian strains. In 2018, a large egg-associated local outbreak was caused by a recently defined clade B lineage prevalent in Europe and was closely related, but not directly linked, to three isolates from Europe. Additionally, antimicrobial-resistance genes were only found in Australian clade B isolates, with a predicted multidrug resistance (MDR) rate of 11.7%. Over half (54.8%) of the MDR isolates belonged to 10 MDR-associated MGT-STs, which were also frequent in Asian S. Enteritidis. IncX1 plasmids were frequently present in the Australian MDR isolates. Overall, this study investigated the genomic epidemiology of S. Enteritidis in Australia, including the first large local outbreak, using MGT. The open MGT platform enables a standardised and sharable nomenclature that can be effectively applied to public health for unified surveillance of S. Enteritidis nationally and globally. ImportanceSalmonella enterica serovar Enteritidis is a leading cause of foodborne infections. We previously developed a genomic typing database - MGTdb for S. Enteritidis to facilitate global surveillance of this pathogen. In this study we examined the genomic features of Australian S. Enteritidis using the MGTdb and found that Australian S. Enteritidis is mainly epidemiologically linked with Asian strains (especially strains carrying antimicrobial resistance genes) followed by European strains. The first large-scale egg-associated local outbreak in Australia was caused by a recently defined lineage prevalent in Europe, and three European isolates in the MGTdb were closely related but not directly linked to this outbreak. In summary, the S. Enteritidis MGTdb open platform is shown to be a potential powerful tool for national and global public health surveillance of this pathogen.

genomics↗

Genomic dissection of the microevolution of Australian epidemic Bordetella pertussis

Whooping cough (pertussis) is a highly contagious respiratory disease caused by the bacterium Bordetella pertussis. Despite high vaccine coverage, pertussis has re-emerged in many countries and caused two large epidemics in Australia since 2007. Here, we undertook a genomic and phylogeographic study of 385 Australian B. pertussis isolates collected from 2008 to 2017. The Australian B. pertussis population was found to be composed of mostly ptxP3 strains carrying different fim3 alleles, with ptxP3-fim3A genotype expanded far more than ptxP3-fim3B. Within the former, there were six co-circulating epidemic lineages (EL1 to EL6). The multiple ELs emerged, expanded, and then declined at different time points over the two epidemics, likely driven by immune selection from pertussis vaccination and natural infection in addition to local and global transmission events. Both hard and soft selective sweeps through vaccine selection pressures determined the current B. pertussis population dynamics. Relative risk analysis found that once a new B. pertussis lineage emerged, it was more likely to spread locally within the first 1.5 years. However, after 1.5 years, any new lineage was likely to expand to a wider region and became no longer spatially structured across the country. Phylogenetic analysis revealed the expansion of ptxP3 strains was also associated with replacement of the type III secretion system allele bscI1 with bscI3. This study advanced our understanding of the epidemic population structure and spatial and temporal dynamics of B. pertussis in a highly immunised population.

microbiology↗

Lasting effects of low-calorie sweeteners on glucose regulation, sugar intake, and memory

Low-calorie sweetener (LCS) consumption in children has increased due to widespread LCS presence in the food environment and efforts to mitigate obesity through sugar replacement. However, mechanistic studies on the impact of early-life LCS consumption are lacking. Therefore, we developed a rodent model to evaluate the effects of daily LCS consumption (acesulfame potassium, saccharin, or stevia) during adolescence on adult metabolic, gut microbiome, neural, and behavioral outcomes. Results reveal that habitual early-life LCS consumption disrupts post-oral glucose tolerance and impairs hippocampal-dependent memory in the absence of weight gain. Furthermore, LCS consumption reduces lingual sweet taste receptor expression and alters sugar-motivated appetitive and consummatory responses. RNA sequencing analyses reveal that LCS also impacts collagen- and synaptic signaling-related gene pathways in the hippocampus and nucleus accumbens, respectively, in a sex-dependent manner. Collectively, these results suggest that regular early-life LCS consumption yields long-lasting impairments in metabolism, sugar-motivated behavior, and hippocampal-dependent memory.

neuroscience↗