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Microbial Genomics May 2024In June 2023, UKHSA surveillance systems detected an outbreak of severe gastrointestinal symptoms caused by a rare serotype of Shiga toxin-producing , STEC O183:H18....
In June 2023, UKHSA surveillance systems detected an outbreak of severe gastrointestinal symptoms caused by a rare serotype of Shiga toxin-producing , STEC O183:H18. There were 26 cases aged 6 months to 74 years (42 % cases were aged 0-9 years), distributed across the UK with onset dates range between 22 May 2023 and 4 July 2023. The epidemiological and food chain investigations were inconclusive, although meat products made from beef mince were implicated as a potential vehicle. The outbreak strain belonged to sequence type (ST) 657 and harboured a Shiga toxin () subtype located on a prophage that was unique in the UKHSA -encoding bacteriophage database. Plasmid encoded, putative virulence genes , , , and were detected, however, the established STEC virulence genes involved in attachment to the gut mucosa ( and ) were absent. The acquisition of across the global population structure of ST657 appeared to correspond with the presence of , , , and . During the outbreak investigation, we used long read sequencing to characterise the plasmid and prophage content of this atypical STEC, to look for evidence to explain its recent emergence. Although we were unable to determine source and transmission route of the outbreak strain, the genomic analysis revealed potential clues as to how novel strains for STEC evolve. With the implementation of PCR capable of detecting all STEC, and genome sequencing for typing and virulence profiling, we have the tools to enable us to monitor the changing landscape of STEC. Improvements in the standardised collection of epidemiological data and trace-back strategies within the food industry, will ensure we have a surveillance system capable of alerting us to emerging threats to public health.
Topics: Shiga-Toxigenic Escherichia coli; Disease Outbreaks; Escherichia coli Infections; Humans; United Kingdom; Aged; Plasmids; Adult; Infant; Child, Preschool; Middle Aged; Child; Adolescent; Male; Virulence Factors; Female; Genomics; Prophages; Young Adult; Genome, Bacterial
PubMed: 38771013
DOI: 10.1099/mgen.0.001243 -
EcoSal Plus May 2024Toxin-antitoxin systems are ubiquitous in the prokaryotic world and widely distributed among chromosomes and mobile genetic elements. Several different toxin-antitoxin... (Review)
Review
Toxin-antitoxin systems are ubiquitous in the prokaryotic world and widely distributed among chromosomes and mobile genetic elements. Several different toxin-antitoxin system types exist, but what they all have in common is that toxin activity is prevented by the cognate antitoxin. In type I toxin-antitoxin systems, toxin production is controlled by an RNA antitoxin and by structural features inherent to the toxin messenger RNA. Most type I toxins are small membrane proteins that display a variety of cellular effects. While originally discovered as modules that stabilize plasmids, chromosomal type I toxin-antitoxin systems may also stabilize prophages, or serve important functions upon certain stress conditions and contribute to population-wide survival strategies. Here, we will describe the intricate RNA-based regulation of type I toxin-antitoxin systems and discuss their potential biological functions.
PubMed: 38767346
DOI: 10.1128/ecosalplus.esp-0025-2022 -
Virus Evolution 2024The transition between lytic and lysogenic life cycles is the most important feature of the life-history of temperate viruses. To explain this transition, an optimal...
The transition between lytic and lysogenic life cycles is the most important feature of the life-history of temperate viruses. To explain this transition, an optimal life-history model is offered based a discrete-time formulation of phage/bacteria population dynamics that features infection of bacteria by Poisson sampling of virions from the environment. The time step is the viral latency period. In this model, density-dependent viral absorption onto the bacterial surface produces virus/bacteria coexistence and density dependence in bacterial growth is not needed. The formula for the transition between lytic and lysogenic phases is termed the 'fitness switch'. According to the model, the virus switches from lytic to lysogenic when its population grows faster as prophage than as virions produced by lysis of the infected cells, and conversely for the switch from lysogenic to lytic. A prophage that benefits the bacterium it infects automatically incurs lower fitness upon exiting the bacterial genome, resulting in its becoming locked into the bacterial genome in what is termed here as a 'prophage lock'. The fitness switch qualitatively predicts the ecogeographic rule that environmental enrichment leads to microbialization with a concomitant increase in lysogeny, fluctuating environmental conditions promote virus-mediated horizontal gene transfer, and prophage-containing bacteria can integrate into the microbiome of a eukaryotic host forming a functionally integrated tripartite holobiont. These predictions accord more with the 'Piggyback-the-Winner' hypothesis than with the 'Kill-the-Winner' hypothesis in virus ecology.
PubMed: 38756985
DOI: 10.1093/ve/veae028 -
Frontiers in Microbiology 2024In natural microbiomes, microorganisms interact with each other and exhibit diverse functions. Microbiome engineering, which enables bacterial knockdown, is a promising...
In natural microbiomes, microorganisms interact with each other and exhibit diverse functions. Microbiome engineering, which enables bacterial knockdown, is a promising method to elucidate the functions of targeted bacteria in microbiomes. However, few methods to selectively kill target microorganisms in the microbiome without affecting the growth of nontarget microorganisms are available. In this study, we focused on the host-specific lytic ability of virulent phages and validated their potency for precise microbiome engineering. In an artificial microbiome consisting of , , , and , the addition of bacteriophages infecting their respective host strains specifically reduced the number of these bacteria more than 10 orders. Remarkably, the reduction in target bacteria did not affect the growth of nontarget bacteria, indicating that bacteriophages were effective tools for precise microbiome engineering. Moreover, a virulent derivative of the λ phage was synthesized from prophage DNA in the genome of λ lysogen by DNA assembly and phage-rebooting techniques, and -targeted microbiome engineering was achieved. These results propose a novel approach for precise microbiome engineering using bacteriophages, in which virulent phages are synthesized from prophage DNA in lysogenic strains without isolating phages from environmental samples.
PubMed: 38756723
DOI: 10.3389/fmicb.2024.1403903 -
Communications Biology May 2024Long-chain fatty acids with antimicrobial properties are abundant on the skin and mucosal surfaces, where they are essential to restrict the proliferation of...
Long-chain fatty acids with antimicrobial properties are abundant on the skin and mucosal surfaces, where they are essential to restrict the proliferation of opportunistic pathogens such as Staphylococcus aureus. These antimicrobial fatty acids (AFAs) elicit bacterial adaptation strategies, which have yet to be fully elucidated. Characterizing the pervasive mechanisms used by S. aureus to resist AFAs could open new avenues to prevent pathogen colonization. Here, we identify the S. aureus lipase Lip2 as a novel resistance factor against AFAs. Lip2 detoxifies AFAs via esterification with cholesterol. This is reminiscent of the activity of the fatty acid-modifying enzyme (FAME), whose identity has remained elusive for over three decades. In vitro, Lip2-dependent AFA-detoxification was apparent during planktonic growth and biofilm formation. Our genomic analysis revealed that prophage-mediated inactivation of Lip2 was rare in blood, nose, and skin strains, suggesting a particularly important role of Lip2 for host - microbe interactions. In a mouse model of S. aureus skin colonization, bacteria were protected from sapienic acid (a human-specific AFA) in a cholesterol- and lipase-dependent manner. These results suggest Lip2 is the long-sought FAME that exquisitely manipulates environmental lipids to promote bacterial growth in otherwise inhospitable niches.
Topics: Staphylococcus aureus; Fatty Acids; Animals; Mice; Lipase; Humans; Staphylococcal Infections; Bacterial Proteins; Biofilms; Female; Staphylococcal Skin Infections
PubMed: 38750133
DOI: 10.1038/s42003-024-06278-3 -
Nature Communications May 2024Evidence from the International Space Station suggests microbial populations are rapidly adapting to the spacecraft environment; however, the mechanism of this...
Evidence from the International Space Station suggests microbial populations are rapidly adapting to the spacecraft environment; however, the mechanism of this adaptation is not understood. Bacteriophages are prolific mediators of bacterial adaptation on Earth. Here we survey 245 genomes sequenced from bacterial strains isolated on the International Space Station for dormant (lysogenic) bacteriophages. Our analysis indicates phage-associated genes are significantly different between spaceflight strains and their terrestrial counterparts. In addition, we identify 283 complete prophages, those that could initiate bacterial lysis and infect additional hosts, of which 21% are novel. These prophage regions encode functions that correlate with increased persistence in extreme environments, such as spaceflight, to include antimicrobial resistance and virulence, DNA damage repair, and dormancy. Our results correlate microbial adaptation in spaceflight to bacteriophage-encoded functions that may impact human health in spaceflight.
Topics: Space Flight; Bacteria; Bacteriophages; Adaptation, Physiological; Prophages; Humans; Virulence; Genome, Bacterial
PubMed: 38750067
DOI: 10.1038/s41467-023-42104-w -
Journal of Chemotherapy (Florence,... May 2024Two isolates harbouring three carbapenemase genes each, were isolated from two patients from different ICUs at University Hospital Centre Zagreb, Croatia, which is to...
Two isolates harbouring three carbapenemase genes each, were isolated from two patients from different ICUs at University Hospital Centre Zagreb, Croatia, which is to our knowledge, the first report of triple carbapenemase (, , and co-existence in strains and also among Enterobacterales members in Croatia. Antimicrobial susceptibility testing showed susceptibility only to colistin and amikacin. The production of carbapenemases was phenotypically tested by immunochromatographic assay and confirmed by PCR. Detailed analysis by Whole Genome Sequencing (WGS) of short reads by Illumina and long reads by Oxford Nanopore Technologies (ONT) was additionally performed and showed that both isolates belonged to ST200. They were separated by 98 Single Nucleotide Polymorphisms (SNPs) having variations in the number of genes on the chromosome, the number of genes on the plasmid, non-identical plasmids, different plasmid content in general, and only one isolate carried a 94 kb prophage.
PubMed: 38741515
DOI: 10.1080/1120009X.2024.2354107 -
The ISME Journal Jan 2024Temperate phages can interact with bacterial hosts through lytic and lysogenic cycles via different mechanisms. Lysogeny has been identified as the major form of...
Temperate phages can interact with bacterial hosts through lytic and lysogenic cycles via different mechanisms. Lysogeny has been identified as the major form of bacteria-phage interaction in the coral-associated microbiome. However, the lysogenic-to-lytic switch of temperate phages in ecologically important coral-associated bacteria and its ecological impact have not been extensively investigated. By studying the prophages in coral-associated Halomonas meridiana, we found that two prophages, Phm1 and Phm3, are inducible by the DNA-damaging agent mitomycin C and that Phm3 is spontaneously activated under normal cultivation conditions. Furthermore, Phm3 undergoes an atypical lytic pathway that can amplify and package adjacent host DNA, potentially resulting in lateral transduction. The induction of Phm3 triggered a process of cell lysis accompanied by the formation of outer membrane vesicles (OMVs) and Phm3 attached to OMVs. This unique cell-lysis process was controlled by a four-gene lytic module within Phm3. Further analysis of the Tara Ocean dataset revealed that Phm3 represents a new group of temperate phages that are widely distributed and transcriptionally active in the ocean. Therefore, the combination of lateral transduction mediated by temperate phages and OMV transmission offers a versatile strategy for host-phage coevolution in marine ecosystems.
Topics: Halomonas; Anthozoa; Prophages; Animals; Lysogeny; Transduction, Genetic; Mitomycin
PubMed: 38739683
DOI: 10.1093/ismejo/wrae085 -
The Lancet Regional Health. Europe Jun 2024Invasive pneumococcal disease due to serotype 3 (S3-IPD) is associated with high mortality rates and long-term adverse effects. The introduction of the 13-valent...
BACKGROUND
Invasive pneumococcal disease due to serotype 3 (S3-IPD) is associated with high mortality rates and long-term adverse effects. The introduction of the 13-valent pneumococcal conjugate vaccine (PCV13) into the Spanish paediatric immunisation programme has not led to a decrease in the adult S3-IPD. We aimed to analyse the incidence, clinical characteristics and genomics of S3-IPD in adults in Spain.
METHODS
Adult IPD episodes hospitalized in a Southern Barcelona hospital were prospectively collected (1994-2020). For genomic comparison, S3-IPD isolates from six Spanish hospitals (2008-2020) and historical isolates (1989-1993) were analysed by WGS (Illumina and/or MinION).
FINDINGS
From 1994 to 2020, 270 S3-IPD episodes were detected. When comparing pre-PCV (1994-2001) and late-PCV13 (2016-2020) periods, only modest changes in S3-IPD were observed (from 1.58 to 1.28 episodes per 100,000 inhabitants year). In this period, the incidence of the two main lineages shifted from 0.38 to 0.67 (CC180-GPSC12) and from 1.18 to 0.55 (CC260-GPSC83). The overall 30-day mortality remained high (24.1%), though a decrease was observed between the pre-PCV (32.4%; 95.0% CI, 22.0-45.0) and the late-PCV13 period (16.7%; 95.0% CI, 7.5-32.0) (p = 0.06). At the same time, comorbidities increased from 77.3% (95.0% CI, 65.0-86.0) to 85.7% (95.0% CI, 71.0-94.0) (p = 0.69). There were no differences in clinical characteristics or 30-day mortality between the two S3 lineages. Although both lineages were genetically homogeneous, the CC180-GPSC12 lineage presented a higher SNP density, a more open pan-genome, and a major presence of prophages and mobile genetic elements carrying resistance genes.
INTERPRETATION
Adult S3-IPD remained stable in our area over the study period despite PCV13 introduction in children. However, a clonal shift was observed. The decrease in mortality rates and the increase in comorbidities suggest a change in clinical management and overall population characteristics. The low genetic variability and absence of clinical differences between lineages highlight the role of the S3 capsule in the disease severity.
FUNDING
This study has been funded by Instituto de Salud Carlos III (ISCIII) "PI18/00339", "PI21/01000", "INT22/00096", "FI22/00279", CIBER "CIBERES-CB06/06/0037", "CIBERINFEC-CB21/13/00009" and MSD grant "IISP 60168".
PubMed: 38737571
DOI: 10.1016/j.lanepe.2024.100913 -
Marine Genomics Jun 2024Rossellomorea sp. y25, a putative new species of yellow pigment-producing, aerobic and chemoheterotrophic bacterium belonging to the family Bacillaceae, was isolated...
Rossellomorea sp. y25, a putative new species of yellow pigment-producing, aerobic and chemoheterotrophic bacterium belonging to the family Bacillaceae, was isolated from the sediments at the depth of 1829 m in the South China Sea. In this study, we present the complete genome sequences of strain y25, which consisted of only one circular chromosome with 4,633,006 bp and the content of G + C was 41.76%. A total of 4466 CDSs, 106 tRNA, 33 rRNA, and 101 sRNA genes were obtained. Genomic analysis of strain y25 showed that it has the ability to produce antioxidant carotenoids and a large number of heavy metal resistance genes, such as arsenic, cadmium and zinc. In addition, strain y25 contains a prophage that may contribute to host protection against lysis by related Bacillus-like phages. This is the first report of genome-wide information on a bacterium of the genus Rossellomorea isolated from the deep sea, providing insights into how microorganisms of this genus adapt to deep-sea environments.
Topics: Genome, Bacterial; Geologic Sediments; China; Bacillaceae; Whole Genome Sequencing; Seawater
PubMed: 38735673
DOI: 10.1016/j.margen.2024.101110