Biology subjects

Tanaka, M. M.

Publications and source records attributed to Tanaka, M. M..

5 recordsLinked to original sources

bioRxiv2022

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↗

bioRxiv2022

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↗

bioRxiv2021

Tracing boundaries in Eastern Antarctica: Multi-scale drivers of soil microbial communities across the hyperarid Vestfold Hills

Microorganisms are key to sustaining core ecosystem processes across terrestrial Antarctica but they are rarely considered in conservation frameworks. Whilst greater advocacy has been made towards the inclusion of microbial data in this context, there is still a need for better tools to quantify multispecies responses to environmental change. Here, we extend the scope of Gradient Forest modelling beyond macroorganisms and small datasets to the comprehensive polar soil microbiome encompassing >17, 000 sequence variants for bacteria, micro-eukarya and archaea throughout the hyperarid Vestfold Hills of Eastern Antarctica. Quantification of microbial diversity against 79 physiochemical variables revealed that whilst rank-order importance differed, predictors were broadly consistent between domains, with greatest sharing occurring between bacteria and micro-eukarya. Moisture was identified as the most robust predictor for shaping the regional soil microbiome, with highest compositional turnover or "splits" occurring within the 10 - 12 % moisture content range. Often the most responsive taxa were rarer lineages of bacteria and micro-eukarya with phototrophic and nutrient-cycling capacities such as Cyanobacteria (up to 61.81 % predictive capacity), Chlorophyta (62.17 %) and Ochrophyta (57.81 %). These taxa groups are thus at greater risk of biodiversity loss or gain to projected climate trajectories, which will inevitably disturb current ecosystem dynamics. Better understanding of these threshold tipping points will positively aid conservation efforts across Eastern Antarctica. Furthermore, the successful implementation of an improved Gradient Forest model also presents an exciting opportunity to broaden its use on microbial systems globally.

microbiology↗

bioRxiv2020

Elucidation of global and local epidemiology of Salmonella Enteritidis through multilevel genome typing

Salmonella enterica serovar Enteritidis is a major cause of foodborne Salmonella infections and outbreaks in humans. Effective surveillance and timely outbreak detection are essential for public health control. Multilevel genome typing (MGT) with multiple levels of resolution has been previously demonstrated as a promising tool for this purpose. In this study, we developed MGT with nine levels for S. Enteritidis and characterised the genomic epidemiology of S. Enteritidis in detail. We examined 26,670 publicly available S. Enteritidis genome sequences from isolates spanning 101 years from 86 countries to reveal their spatial and temporal distributions. Using the lower resolution MGT levels, globally prevalent and regionally restricted sequence types (STs) were identified; avian associated MGT4-STs were found that were common in human cases in the USA were identified; temporal trends were observed in the UK with MGT5-STs from 2014 to 2018, revealing both long lived endemic STs and the rapid expansion of new STs. Using MGT3 to MGT6, we identified MDR associated STs at various MGT levels, which improves precision of detection and global tracking of MDR clones. We also found that the majority of the global S. Enteritidis population fell within two predominant lineages, which had significantly different propensity of causing large scale outbreaks. An online open MGT database has been established for unified international surveillance of S. Enteritidis. We demonstrated that MGT provides a flexible and high-resolution genome typing tool for S. Enteritidis surveillance and outbreak detection. Impact statementSalmonella enterica serovar Enteritidis is a common foodborne pathogen that can cause large outbreaks. Surveillance and high-resolution typing are essential for outbreak prevention and control. Genome sequencing offers unprecedented power for these purposes and a standardised method or platform for the interpretation, comparison and communication of genomic typing data is highly desirable. In this work, we developed a genomic typing scheme called Multilevel Genome Typing (MGT) for S. Enteritidis. We analysed 26,670 publicly available genomes of S. Enteritidis using MGT. We characterised the geographic and temporal distribution of S. Enteritidis MGT types as well as their association with multidrug resistance (MDR) and virulence genes. A publicly available MGT database for S. Enteritidis was established, which has the potential facilitate the unified global public health surveillance for this pathogen. Data SummaryO_LIThe MGT database for S. Enteritidis is available at https://mgtdb.unsw.edu.au/enteritidis/. C_LIO_LIAll accession numbers of the public available genomes were available in the MGT database and Data Set S1, Tab 1. And there were no newly sequenced data in this study. C_LIO_LISupplementary material: Supplementary Fig. S1 to S7, supplementary methods and supporting results about the evaluation of potential repeat sequencing bias. C_LIO_LIData Set S1: Supporting tables of the main results. C_LIO_LIData Set S2. Supporting tables of the repeat sequencing bias evaluation by removing the potential repeat sequencing isolates. Note outbreak isolates may also be removed. C_LI

genomics↗

bioRxiv2019

Extreme niche partitioning promotes a remarkably high diversity of soil microbiomes across eastern Antarctica.

Terrestrial Antarctica, a predominantly microbial realm, encompasses some of the most unique environments on Earth where resident soil microbiota play key roles in the sustainability and evolution of the ecosystem. Yet the fundamental ecological processes that govern the assemblage of these natural communities remain unclear. Here, we combined multivariate analyses, co-occurrence networks and fitted species abundance distributions of amplicon sequencing data to disentangle community assemblage patterns of polar soil microbiomes across two ice-free deserts (Windmill Islands and Vestfold Hills) situated along the coastline of eastern Antarctica. Our findings report that communities were predominantly structured by non-neutral processes, with niche partitioning being particularly strong for bacterial communities at the Windmill Islands. In contrast, both eukaryotic and archaeal communities exhibited multimodal distributions, indicating the potential emergence of neutrality. Between the three microbial domains, polar soil bacterial communities consistently demonstrated the greatest taxonomic diversity, estimated richness, network connectivity and linear response to contemporary environmental soil parameters. We propose that reduced niche overlap promotes greater phylogenetic diversity enabling more bacterial species to co-exist and essentially thrive under adversity. However, irrespective of overall relative abundance, consistent and robust associations between co-existing community members from all three domains of life highlights the key roles that diverse taxa play in ecosystem dynamics. SignificanceIn the face of a warming Antarctica, contemporary dynamics between polar soil microbial communities will inevitably change due to the climate-induced expansion of new ice-free areas. Increasing concern about disturbance and rapid biodiversity loss has intensified the need to better understand microbial community structure and function in high-latitude soils. We have taken an integrated approach to elucidate domain-level assemblage patterns across east Antarctic soil microbiomes. These assemblage patterns will be available to feed into policy management and conservation planning frameworks to potentially mitigate future biodiversity loss.

microbiology↗