Microbial Genomics最新文献

The hospital environment plays a critical role in the transmission of infectious diseases. Surveillance methods often rely on selective enrichment or deep metagenomic sequencing, which both have significant drawbacks in terms of community resolution and cost. Plate sweeps provide a practical moderate approach to cultivate a wide range of bacteria, capturing more diversity than a single colony pick without high sequencing costs. Here, we use this approach to characterize a newly built hospital intensive care unit (ICU) in Queensland, Australia. Between November 2023 and February 2024, we sampled 78 sites within an 8-bed private hospital ICU pre- and post-patient introduction to the environment. Samples were enriched on non-selective media before DNA was extracted from whole plate sweeps and sequenced using Illumina. We assessed species, antimicrobial resistance (AMR) genes, virulence genes and transmission across all samples and between the pre- and post-patient samples using Kraken2, AbritAMR and Tracs. While the rate of positive microbial growth within the ICU environment did not change significantly pre- and post-patient introduction, the post-patient microbiome consisted of largely different bacterial species; of 22 genera identified, only 3 genera were represented at both timepoints. Post-patient samples were enriched in AMR genes, including resistance to fosfomycin, quinolones and beta-lactams. Common genera identified post-patient were Pseudomonas, Delftia and Stenotrophomonas, often associated with areas of plumbing. Cluster analysis identified 17 possible transmission links from a single timepoint, highlighting several areas in the ICU (e.g. communal bathrooms) as key areas for transmission. We demonstrate the utility of plate sweeps as a means of economical non-selective environmental surveillance and highlight their ability to identify hotspots of transmission within a hospital ward that could be targeted by infection control prior to an outbreak of a more serious pathogen.

Escherichia coli resistant to third-generation cephalosporins (3GCs) is a WHO priority pathogen due to its antimicrobial resistance (AMR). In high-income countries, such as Australia, 3GC-resistant E. coli are a common cause of extra-intestinal infections in both healthcare and community settings. Long-term targeted surveillance efforts of AMR in E. coli routinely identify E. coli as a leading pathogen in bacteraemic infections. To date, there has been limited detailed genomic analysis of the drug-resistant E. coli circulating in Australian clinical settings. Here, we sought to explore the genomic diversity of 3GC-resistant isolates (mediated by extended-spectrum beta-lactamase or AmpC), collected from four hospital networks in Melbourne, Australia. We establish the population structure, identifying ten main lineages in addition to multiple other sequence types, demonstrating 3GC resistance has emerged in multiple genetic backgrounds. We show diversity of accessory genome features, including surface antigens, AMR and plasmid profiles. A total of 117 serotypes and 47 capsular loci were detected, with diversity observed within and between main lineages. We identified 17 unique 3GC resistance mechanisms disseminated across the E. coli population, which co-occurred in different combinations of AMR genes and plasmid replicons. We explored the use of genomic clustering as an approach to detect different population dynamics, identifying 99 clusters of which only 15 had more than 5 isolates. This study provides a comprehensive snapshot of these drug-resistant E. coli in Australia over this time period and will serve as a baseline for future studies of clinical and community drug-resistant isolates in Australia.

Streptococcus suis is a major pig pathogen with zoonotic potential, posing an occupational risk to farmers and meat handlers. We characterized 110 S. suis strains from diseased pigs in Ireland (2005-2022) using whole-genome sequencing to investigate population structure and phage-host dynamics. We identified 15 distinct serotypes, with serotypes 9 and 2 being the most dominant. In silico multi-locus sequence typing revealed high diversity within the collection, identifying several sequence types (STs), including 26 novel STs. Investigation of strain-level genomic clustering using PopPUNK against global S. suis genomes showed that the Irish isolates were phylogenetically dispersed across the broader global S. suis population rather than clustering in a single clonal group. The majority of Irish isolates fall within the ten established pathogenic lineages, including the highly virulent zoonotic lineage 1. A locally persistent clonal lineage was identified among Irish isolates, showing minimal genetic variation over a decade.Prophage analysis revealed novel viral taxa that were interspersed among known streptococcal phages, rather than clustering distinctly. Restriction-modification systems were the predominant anti-viral defence systems identified across genomes. CRISPR-Cas systems were present in limited strains but showed substantial targeting bias toward full-length prophages, indicating ongoing phage pressure. CRISPR spacers matched non-S. suis streptococcal phages, and phylogenomic analysis revealed that Vansinderenvirus phages clustered with S. suis rather than other Streptococcus thermophilus phages, suggesting evolutionary connections between phage lineages infecting different streptococci.This study presents the first comprehensive genomic characterization of S. suis in Ireland, revealing a diverse population with significant implications for animal and human health.

Shiga toxin (Stx)-producing Escherichia coli (STEC) is a major cause of serious gastrointestinal illness, including diarrhoea, haemorrhagic colitis and life-threatening haemolytic-uraemic syndrome. Although O157:H7 STEC strains are the most prevalent, the incidence of STEC infections caused by several other serotypes has recently increased. O103:H2 STEC is one of these major non-O157 STEC strains, but systematic whole-genome sequence (WGS) analyses have not yet been conducted. To gain a global phylogenetic overview of O103:H2 STEC based on WGSs, we analysed 2,701 WGSs of O103:H2 strains, including 193 sequenced in this study. Sequence type (ST)-based classification divided the O103:H2 strains into three distinct E. coli lineages. As the virulence marker genes of typical STECs (stx, eae and ehxA) were found only in the major O103:H2 lineage (n=2,658) comprising ST17 and its single- and double-locus variants, we performed a global phylogenetic analysis of the major lineage. This analysis revealed that this lineage was divided into five clades (C1-C5) and that C1 was the ancestral clade, C2 and C3 emerged from C1 and C4 and C5 emerged from C3. While stx2 genes were sporadically distributed in limited STEC O103:H2 strains, stx1a, eae and ehxA were highly conserved throughout the entire STEC O103:H2 lineage. However, through a detailed comparison of seven closed genomes of STEC strains, covering the five clades and including four obtained in this study, we found marked variation in the genetic elements encoding the virulence genes (Stx1a phage, the locus of enterocyte effacement (LEE) and the virulence plasmid), such as rearrangement in the LEE accessory region, a shift in the integration sites of the Stx1a phage due to the replacement of the integrase gene-containing genomic segments, the replacement of the virulence plasmid and the gain and loss of virulence-related genes in the virulence plasmid. Overall, this study highlights the current global population structure of O103:H2 strains and provides evolutionary insights into the variation in virulence determinants within STEC O103:H2, which is relatively understudied among the major STEC lineages.

Insertion sequence (IS) elements are transposable regions of DNA present in a majority of bacterial genomes. It is hypothesized that differences in distributions of IS elements across bacterial strains and species reflect underlying differences in population biology. Therefore, shifts in IS element distributions between closely related strains may be proxies for and reflective of changes in population dynamics. Here, we investigate the presence and distribution of a subclass of IS5 elements throughout genomes of Pseudomonas syringae by querying complete genomes for the presence of InsH (the main transposase found within these IS5 elements). We report that this one subclass of IS5 elements appears to have recently undergone independent expansions in multiple P. syringae clades and find that a majority of IS5 insertion sites are not conserved across three closely related P. syringae pv. lachrymans genomes. We present further evidence, as has been shown for other members of the IS5 family in different taxa, that elements from this IS5 subclass can drive the expression of downstream genes in P. syringae. Taken together, our results highlight how dynamic IS5 elements can be within and across P. syringae genomes and point towards the potential for IS5 elements to rewire expression patterns across the P. syringae genome.

Non-tuberculous mycobacteria are emerging respiratory pathogens that can persist in treated water systems. In 2018, a cluster of Mycobacterium intracellulare lung infections was linked to a pool facility in Australia, prompting an epidemiological and genomic investigation. M. intracellulare was isolated from five sputum samples across four clinical cases and from fourteen pool water samples across a total of five collection time points. All cases were resolved following exclusion from the pool facility, with only one patient requiring short-term steroids; none of the patients required anti-mycobacterial treatment. To test if this was a point-source outbreak, whole-genome sequencing of mycobacteria recovered from patients and the pool was implemented. Initial analysis confirmed all patient and water isolates were M. intracellulare with sequence type 210. A complete, circular genome was constructed from one of the isolates linked to this cluster and was used as a reference genome for high-resolution core genome SNP analysis. This analysis showed tight clustering of M. intracellulare genomes from patient and pool water isolates that were distinct from other M. intracellulare. Thus, epidemiological and comparative genome analysis strongly implicated the pool as the origin of these infections.

Deep-sea polymetallic nodules, rich in cobalt, nickel and titanium, are valuable for electronics, aerospace and energy industries. However, the vertical distribution and ecological functions of prokaryotic communities in sediments beneath nodules from the Magellan seamounts, a unique microbial habitat characterized by ultra-slow sedimentation rates (0.4-4 mm ky^-1) and heterogeneous metal gradients, remain poorly characterized. In our research, 16S rRNA gene amplicon sequencing and metagenomic analyses of sediment cores (0-20 cm) from the western Pacific polymetallic nodule province revealed statistically significant decreases in prokaryotic diversity (Shannon index: 9.446 to 2.288; P<0.001). Proteobacteria, Crenarchaeota, Chloroflexi and Bacteroidota were the dominant taxa. The microbial co-occurrence network in the surface layer had a longer mean path length (2.11 vs 1 in the bottom layer) and a larger network diameter (11 vs 1), indicating a loose community structure and greater resistance to disturbance, while the bottom microbial network had a higher density (0.037 vs 0.01) and clustering coefficient (0.32 vs 1), suggesting tight microbial interactions. The concentrations of MnO (6.96-9.41 µg g^-1) and P₂O₅ (2.55-3.89 µg g^-1) gradually decreased with increasing depth. The concentrations of Co and Pb were relatively high in the surface sediments (0-8 cm) but decreased significantly below 8 cm. In contrast, the concentrations of Fe₂O₃ and As increased with depth. The environmental factors depth, MnO, Fe₂O₃ and heavy metals (Cr, Zn and Cu) were found to be the main drivers of the microbial community structure. We assembled 122 metagenome-assembled genomes from the metagenomic data. Gene abundance analysis revealed that sox genes (soxB/C/D/X/Y/Z) and assimilatory sulphate reduction genes (cysC and cysH) were highly abundant in the surface sediment, whereas the abundance of dissimilatory sulphate reduction genes (dsrA and dsrB) was enhanced in the bottom layer, reflecting a hierarchical adaptive strategy for sulphur metabolism. Our study expands current knowledge on the vertical variations of microbial diversity and microbially driven biogeochemical cycling in deep-sea settings underneath polymetallic nodules. Characterizing the microbial community underneath those nodules may provide insights into microbial resilience in extreme oligotrophic environments and valuable insights for future deep-sea mining activities.

In humans, adenoviruses (AdVs) are frequently associated with respiratory illnesses, posing risks to children with developing immune systems and immunocompromised individuals. Outbreaks and epidemics are generally centred in close-contact settings, such as childcare facilities, and transmission occurs through faecal-oral and airborne pathways. AdVs have coevolved across the primate lineage, but very little is known about whether the early-life dynamics in non-human primates mirror those in humans. Here, we leverage longitudinal data collected on a population of geladas (Theropithecus gelada) in the Simien Mountains National Park, Ethiopia, to evaluate AdV dynamics across the gelada lifespan. We identified ten coding-complete AdV genomes representing seven unique simian adenovirus (SAdV) types, four of which are adequately different from the known ones to establish new species. We assessed behavioural and seasonal drivers of SAdV presence and richness across repeated faecal samples from known individuals. Contrary to our expectation that the highest risk would occur after the initiation of play behaviour in infancy (~6 months of age), when peer-to-peer transmission risk is expected to increase, SAdV likelihood was highest in infants under 6 months of age. Risk and richness declined over the lifespan, with very few adults infected, and higher minimum temperatures were weakly but significantly negatively associated with richness. Our results suggest that, unlike in humans, SAdV exposure occurs prior to the initiation of close-contact play behaviours and likely results from the close spatial proximity of conspecifics throughout the dependent period. Like AdVs in humans, SAdVs in geladas maintain low levels in adulthood, with early infections potentially conferring life-long immunity.

Streptococcus pneumoniae (Sp) is an opportunistic pathogen that colonizes the mucosal surfaces of the human upper respiratory tract. While transcriptomic studies of Sp have become more common, most have focused on laboratory-adapted strains such as D39 or TIGR4. These strains, though widely used in research, may not fully capture the biology of clinical isolates, particularly the hypervirulent serotype 1 (S1). S1 is clinically significant due to its association with invasive disease, epidemic outbreaks and a distinct global distribution, particularly in regions with a high pneumococcal disease burden. Unlike many other serotypes, S1 is frequently linked to hypervirulence and a propensity for rapid spread, making it a high-priority target for understanding the molecular mechanisms underpinning pneumococcal pathogenesis. In this study, we conducted a comprehensive in vitro transcriptomic analyses of Sp S1 strains, positioning this work as a valuable resource for the pneumococcal research community. Using a straightforward approach, we cultured three distinct S1 strains - ST306, ST217 and ST615, representing European, African and South American S1 lineages, respectively - in Brain Heart Infusion medium and compared transcriptomic profiles during exponential growth to those of the well-characterized laboratory-adapted D39 strain. Our analysis revealed significant differential expression of 292 genes in all three S1 isolates compared to D39. Among these, 151 genes had higher expression, including those involved in competence pathways and purine metabolism, while 141 genes exhibited lower expression, particularly those linked to lactose metabolism and iron/amino acid transport. These findings underscore the distinct molecular features of S1 strains, which likely contribute to the unique pathogenic properties of this serotype. The identification of the distinct transcriptional signatures of hypervirulent S1 strains paves the way for future efforts to design targeted therapeutics against pneumococcal S1 infections.

Homing, a biological phenomenon involving enzyme-mediated genetic exchange by homologous recombination, has been highlighted as a potential driver of phage genome evolution. In the current study, 18 lactococcal phages, belonging to the Skunavirus genus, were isolated from Dutch dairy facilities, and their genomes were sequenced. Together with 71 phages from previous studies involving Dutch dairy fermentation facilities, a total of 89 Skunavirus genomes were analysed, revealing a strong correlation between phage diversity and the applied starter culture. These analysed Skunavirus genomes were predicted to encode a total of 212 intact HNH endonucleases (HNHEs), which were classified into families based on structural homology and their insertion locations on the genome. Members of the I-HmuI-like HNHE family were observed to be present among most analysed genomes, though they varied in individual Skunavirus phages in both their number and genomic locations. Phylogenetic analysis revealed that these I-HmuI-like HNHEs cluster together according to their insertion locations and the corresponding starter cultures. Furthermore, the so-called genetic marker exclusion activity of particular expressed HNHEs against Skunavirus sk1 infection was observed, indicative of their role in phage genome evolution and associated adaptation processes.