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Journal of Global Antimicrobial... May 2024The emergence and outbreak of carbapenem-resistant Pseudomonas aeruginosa are a major global public threat. In this study we aimed to characterize the genome of...
OBJECTIVES
The emergence and outbreak of carbapenem-resistant Pseudomonas aeruginosa are a major global public threat. In this study we aimed to characterize the genome of drug-resistant and virulent genes in an extremely drug-resistant (XDR) P. aeruginosa strain to understand its antimicrobial resistance trends and pathogenicity.
METHODS
An XDR P. aeruginosa strain was isolated in China from a patient with severe pneumonia. Antimicrobial susceptibility testing, genome sequencing, and phylogenetic analysis were performed. Predictions were fulfilled using curated bioinformatics tools.
RESULTS
Assembly of the strain (CRPA190) comprised 76 contigs with a total length of 7 009 318 bp. CRPA190 belongs to sequence type 1971 (ST1971) and the O11 serogroup. Nine prophage regions, three CRISPR arrays, and two Cas clusters were identified. However, no plasmids were predicted. Antibiotic susceptibility tests showed that CRPA190 was resistant to all the tested antibiotics, including carbapenem, polymyxin B, and ceftazidime-avibactam. Forty antimicrobial resistance genes were predicted in CRPA190, including several carbapenemase genes such as bla, bla, bla, and bla. The isolate was predicted to be pathogenic and possess strong biofilm-forming ability. It harbours virulence genes that are associated with an arsenal of virulence determinants involved in adherence, motility, exotoxins, exoenzymes, immune modulation, biofilms, nutritional/metabolic factors, and effector delivery systems.
CONCLUSIONS
These findings enhance our understanding of the resistance and pathogenicity of the ST1971 P. aeruginosa strain that is unique in China and provide a broader perspective on the global epidemiological landscape, suggesting the emergence of P. aeruginosa ST1971, which requires control measures to limit its dissemination.
PubMed: 38734235
DOI: 10.1016/j.jgar.2024.04.002 -
International Journal of Molecular... Apr 2024Goose erysipelas is a serious problem in waterfowl breeding in Poland. However, knowledge of the characteristics of strains causing this disease is limited. In this...
Goose erysipelas is a serious problem in waterfowl breeding in Poland. However, knowledge of the characteristics of strains causing this disease is limited. In this study, the antimicrobial susceptibility and serotypes of four strains from domestic geese were determined, and their whole-genome sequences (WGSs) were analyzed to detect resistance genes, integrative and conjugative elements (ICEs), and prophage DNA. Sequence type and the presence of resistance genes and transposons were compared with 363 publicly available strains, as well as 13 strains of other species. Four strains tested represented serotypes 2 and 5 and the MLST groups ST 4, 32, 242, and 243. Their assembled circular genomes ranged from 1.8 to 1.9 kb with a GC content of 36-37%; a small plasmid was detected in strain 1023. Strains 1023 and 267 were multidrug-resistant. The resistance genes detected in the genome of strain 1023 were , , and s cluster, while strain 267 contained the and genes. Mutations in the gene were detected in both strains. The gene was embedded in a Tn-like transposon, which in strain 1023, together with the other resistance genes, was located on a large integrative and conjugative-like element of 130 kb designated as ICEEr1023. A minor integrative element of 74 kb was identified in strain 1012 (ICEEr1012). This work contributes to knowledge about the characteristics of bacteria and, for the first time, reveals the occurrence of and resistance genes in strains of this species. Phage infection appears to be responsible for the introduction of the gene into the genome of strain 267, while ICEs most likely play a key role in the spread of the other resistance genes identified in
Topics: Animals; Geese; Poland; Erysipelothrix; Prophages; Anti-Bacterial Agents; Erysipelothrix Infections; Poultry Diseases; Whole Genome Sequencing; Genome, Bacterial; DNA Transposable Elements; Drug Resistance, Bacterial; Conjugation, Genetic; Plasmids
PubMed: 38731857
DOI: 10.3390/ijms25094638 -
FEBS Open Bio Jun 2024The development of the Escherichia coli K-12 laboratory strains JM83, JM109 and XL1-Blue was instrumental in early gene technology. We report the comprehensive genome... (Comparative Study)
Comparative Study
The development of the Escherichia coli K-12 laboratory strains JM83, JM109 and XL1-Blue was instrumental in early gene technology. We report the comprehensive genome sequence analysis of JM83 and XL1-Blue using Illumina and Oxford Nanopore technologies and a comparison with both the wild-type sequence (MG1655) and the genome of JM109 deposited at GenBank. Our investigation provides insight into the way how the genomic background that allows blue/white colony selection-by complementing a functionally inactive ω-fragment of β-galactosidase (LacZ) with its α-peptide encoded on the cloning vector-has been implemented independently in these three strains using classical bacterial genetics. In fact, their comparative analysis reveals recurrent motifs: (i) inactivation of the native enzyme via large deletions of chromosomal regions encompassing the lac locus, or a chemically induced frameshift deletion at the beginning of the lacZ cistron, and (ii) utilization of a defective prophage (ϕ80), or an F'-plasmid, to provide the lacZ∆M15 allele encoding its ω-fragment. While the genetic manipulations of the E. coli strains involved repeated use of mobile genetic elements as well as harsh chemical or physical mutagenesis, the individual modified traits appear remarkably stable as they can be found even in distantly related laboratory strains, beyond those investigated here. Our detailed characterization at the genome sequence level not only offers clues about the mechanisms of classical gene transduction and transposition but should also guide the future fine-tuning of E. coli strains for gene cloning and protein expression, including phage display techniques, utilizing advanced tools for site-specific genome engineering.
Topics: Genome, Bacterial; Escherichia coli; beta-Galactosidase; Cloning, Molecular; Genomics
PubMed: 38726771
DOI: 10.1002/2211-5463.13812 -
Microbiome May 2024The rumen microbiome enables ruminants to digest otherwise indigestible feedstuffs, thereby facilitating the production of high-quality protein, albeit with suboptimal...
BACKGROUND
The rumen microbiome enables ruminants to digest otherwise indigestible feedstuffs, thereby facilitating the production of high-quality protein, albeit with suboptimal efficiency and producing methane. Despite extensive research delineating associations between the rumen microbiome and ruminant production traits, the functional roles of the pervasive and diverse rumen virome remain to be determined.
RESULTS
Leveraging a recent comprehensive rumen virome database, this study analyzes virus-microbe linkages, at both species and strain levels, across 551 rumen metagenomes, elucidating patterns of microbial and viral diversity, co-occurrence, and virus-microbe interactions. Additionally, this study assesses the potential role of rumen viruses in microbial diversification by analyzing prophages found in rumen metagenome-assembled genomes. Employing CRISPR-Cas spacer-based matching and virus-microbe co-occurrence network analysis, this study suggests that the viruses in the rumen may regulate microbes at strain and community levels through both antagonistic and mutualistic interactions. Moreover, this study establishes that the rumen virome demonstrates responsiveness to dietary shifts and associations with key animal production traits, including feed efficiency, lactation performance, weight gain, and methane emissions.
CONCLUSIONS
These findings provide a substantive framework for further investigations to unravel the functional roles of the virome in the rumen in shaping the microbiome and influencing overall animal production performance. Video Abstract.
Topics: Rumen; Animals; Viruses; Metagenome; Gastrointestinal Microbiome; Virome; Ruminants; Methane; Animal Feed; Bacteria
PubMed: 38725064
DOI: 10.1186/s40168-024-01791-3 -
BMC Microbiology May 2024The Hyphomicrobiales bacterial order (previously Rhizobiales) exhibits a wide range of lifestyle characteristics, including free-living, plant-association,... (Comparative Study)
Comparative Study
The Hyphomicrobiales bacterial order (previously Rhizobiales) exhibits a wide range of lifestyle characteristics, including free-living, plant-association, nitrogen-fixing, and association with animals (Bartonella and Brucella). This study explores the diversity and evolutionary strategies of bacteriophages within the Hyphomicrobiales order, comparing animal-associated (AAB) with non-animal-associated bacteria (NAAB). We curated 560 high-quality complete genomes of 58 genera from this order and used the PHASTER server for prophage annotation and classification. For 19 genera with representative genomes, we curated 96 genomes and used the Defense-Finder server to summarize the type of anti-phage systems (APS) found in this order. We analyzed the genetic repertoire and length distributions of prophages, estimating evolutionary rates and comparing intact, questionable, and incomplete prophages in both groups. Analyses of best-fit parameters and bootstrap sensitivity were used to understand the evolutionary processes driving prophage gene content. A total of 1860 prophages distributed in Hyphomicrobiales were found, 695 in AAB and 1165 in the NAAB genera. The results revealed a similar number of prophages per genome in AAB and NAAB and a similar length distribution, suggesting shared mechanisms of genetic acquisition of prophage genes. Changes in the frequency of specific gene classes were observed between incomplete and intact prophages, indicating preferential loss or enrichment in both groups. The analysis of best-fit parameters and bootstrap sensitivity tests indicated a higher selection coefficient, induction rate, and turnover in NAAB genomes. We found 68 types of APS in Hyphomicrobiales; restriction modification (RM) and abortive infection (Abi) were the most frequent APS found for all Hyphomicrobiales, and within the AAB group. This classification of APS showed that NAAB genomes have a greater diversity of defense systems compared to AAB, which could be related to the higher rates of prophage induction and turnover in the latter group. Our study provides insights into the distributions of both prophages and APS in Hyphomicrobiales genomes, demonstrating that NAAB carry more defense systems against phages, while AAB show increased prophage stability and an increased number of incomplete prophages. These results suggest a greater role for domesticated prophages within animal-associated bacteria in Hyphomicrobiales.
Topics: Prophages; Animals; Evolution, Molecular; Genome, Bacterial; Phylogeny; Genome, Viral; Bacteria; Genetic Variation
PubMed: 38724926
DOI: 10.1186/s12866-024-03315-3 -
Cell Host & Microbe May 2024Bacterial genomes are littered with exogenous: competing DNA elements. Here, Sprenger et al. demonstrate that the Vibrio cholerae prophage VP882 modulates host...
Bacterial genomes are littered with exogenous: competing DNA elements. Here, Sprenger et al. demonstrate that the Vibrio cholerae prophage VP882 modulates host functions via production of regulatory sRNAs to promote phage development. Alternatively, host sRNAs inhibit the VP882 lytic phase by specifically regulating phage genes.
Topics: Vibrio cholerae; Prophages; RNA, Small Untranslated; Genome, Bacterial; Bacteriophages; Gene Expression Regulation, Bacterial; RNA, Bacterial
PubMed: 38723602
DOI: 10.1016/j.chom.2024.04.013 -
Nature May 2024Cobalamin (vitamin B, herein referred to as B) is an essential cofactor for most marine prokaryotes and eukaryotes. Synthesized by a limited number of prokaryotes, its...
Cobalamin (vitamin B, herein referred to as B) is an essential cofactor for most marine prokaryotes and eukaryotes. Synthesized by a limited number of prokaryotes, its scarcity affects microbial interactions and community dynamics. Here we show that two bacterial B auxotrophs can salvage different B building blocks and cooperate to synthesize B. A Colwellia sp. synthesizes and releases the activated lower ligand α-ribazole, which is used by another B auxotroph, a Roseovarius sp., to produce the corrin ring and synthesize B. Release of B by Roseovarius sp. happens only in co-culture with Colwellia sp. and only coincidently with the induction of a prophage encoded in Roseovarius sp. Subsequent growth of Colwellia sp. in these conditions may be due to the provision of B by lysed cells of Roseovarius sp. Further evidence is required to support a causative role for prophage induction in the release of B. These complex microbial interactions of ligand cross-feeding and joint B biosynthesis seem to be widespread in marine pelagic ecosystems. In the western and northern tropical Atlantic Ocean, bacteria predicted to be capable of salvaging cobinamide and synthesizing only the activated lower ligand outnumber B producers. These findings add new players to our understanding of B supply to auxotrophic microorganisms in the ocean and possibly in other ecosystems.
Topics: Atlantic Ocean; Coculture Techniques; Ligands; Microbial Interactions; Prophages; Vitamin B 12; Alteromonadaceae; Rhodobacteraceae; Ribonucleosides; Cobamides; Ecosystem
PubMed: 38720071
DOI: 10.1038/s41586-024-07396-y -
BMC Microbiology May 2024The in-depth understanding of the role of lateral genetic transfer (LGT) in phage-prophage interactions is essential to rationalizing phage applications for human and...
Genetic recombination-mediated evolutionary interactions between phages of potential industrial importance and prophages of their hosts within or across the domains of Escherichia, Listeria, Salmonella, Campylobacter, and Staphylococcus.
BACKGROUND
The in-depth understanding of the role of lateral genetic transfer (LGT) in phage-prophage interactions is essential to rationalizing phage applications for human and animal therapy, as well as for food and environmental safety. This in silico study aimed to detect LGT between phages of potential industrial importance and their hosts.
METHODS
A large array of genetic recombination detection algorithms, implemented in SplitsTree and RDP4, was applied to detect LGT between various Escherichia, Listeria, Salmonella, Campylobacter, Staphylococcus, Pseudomonas, and Vibrio phages and their hosts. PHASTER and RAST were employed respectively to identify prophages across the host genome and to annotate LGT-affected genes with unknown functions. PhageAI was used to gain deeper insights into the life cycle history of recombined phages.
RESULTS
The split decomposition inferences (bootstrap values: 91.3-100; fit: 91.433-100), coupled with the Phi (0.0-2.836E-12) and RDP4 (P being well below 0.05) statistics, provided strong evidence for LGT between certain Escherichia, Listeria, Salmonella, and Campylobacter virulent phages and prophages of their hosts. The LGT events entailed mainly the phage genes encoding for hypothetical proteins, while some of these genetic loci appeared to have been affected even by intergeneric recombination in specific E. coli and S. enterica virulent phages when interacting with their host prophages. Moreover, it is shown that certain L. monocytogenes virulent phages could serve at least as the donors of the gene loci, involved in encoding for the basal promoter specificity factor, for L. monocytogenes. In contrast, the large genetic clusters were determined to have been simultaneously exchanged by many S. aureus prophages and some Staphylococcus temperate phages proposed earlier as potential therapeutic candidates (in their native or modified state). The above genetic clusters were found to encompass multiple genes encoding for various proteins, such as e.g., phage tail proteins, the capsid and scaffold proteins, holins, and transcriptional terminator proteins.
CONCLUSIONS
It is suggested that phage-prophage interactions, mediated by LGT (including intergeneric recombination), can have a far-reaching impact on the co-evolutionary trajectories of industrial phages and their hosts especially when excessively present across microbially rich environments.
Topics: Prophages; Recombination, Genetic; Campylobacter; Staphylococcus; Gene Transfer, Horizontal; Bacteriophages; Listeria; Salmonella; Evolution, Molecular; Bacteria
PubMed: 38704526
DOI: 10.1186/s12866-024-03312-6 -
Emerging Microbes & Infections Dec 2024is a major bacterial pathogen in pigs and an emerging zoonotic pathogen. Different serotypes exhibit diverse characteristics in population structure and pathogenicity....
is a major bacterial pathogen in pigs and an emerging zoonotic pathogen. Different serotypes exhibit diverse characteristics in population structure and pathogenicity. Surveillance data highlight the significance of serotype 4 (SS4) in swine streptococcusis, a pathotype causing human infections. However, except for a few epidemiologic studies, the information on SS4 remains limited. In this study, we investigated the population structure, pathogenicity, and antimicrobial characteristics of SS4 based on 126 isolates, including one from a patient with septicemia. We discovered significant diversities within this population, clustering into six minimum core genome (MCG) groups (1, 2, 3, 4, 7-2, and 7-3) and five lineages. Two main clonal complexes (CCs), CC17 and CC94, belong to MCG groups 1 and 3, respectively. Numerous important putative virulence-associated genes are present in these two MCG groups, and 35.00% (7/20) of pig isolates from CC17, CC94, and CC839 (also belonging to MCG group 3) were highly virulent (mortality rate ≥ 80%) in zebrafish and mice, similar to the human isolate ID36054. Cytotoxicity assays showed that the human and pig isolates of SS4 strains exhibit significant cytotoxicity to human cells. Antimicrobial susceptibility testing showed that 95.83% of strains isolated from our labs were classified as multidrug-resistant. Prophages were identified as the primary vehicle for antibiotic resistance genes. Our study demonstrates the public health threat posed by SS4, expanding the understanding of SS4 population structure and pathogenicity characteristics and providing valuable information for its surveillance and prevention.
Topics: Streptococcus suis; Animals; Swine; Humans; Streptococcal Infections; Serogroup; Swine Diseases; Virulence; Mice; Genome, Bacterial; Zebrafish; Anti-Bacterial Agents; Phylogeny; Microbial Sensitivity Tests; Virulence Factors
PubMed: 38703011
DOI: 10.1080/22221751.2024.2352435 -
Frontiers in Cellular and Infection... 2024Diagnosing poses challenges, and it's unclear if its rare isolation is due to infrequent occurrence or its fastidious nutritional requirements.
INTRODUCTION
Diagnosing poses challenges, and it's unclear if its rare isolation is due to infrequent occurrence or its fastidious nutritional requirements.
METHODS
This study analyzes the complete genome sequence of , obtained directly from the pus of a sternum infection in a lung transplant patient using metagenomic sequencing.
RESULTS
Genome analysis revealed limited therapeutic options for the infection, primarily susceptibility to tetracyclines. Three classes of mobile genetic elements were identified: two new insertion sequences, a new prophage (phiUMCG-1), and a species-specific variant of a mycoplasma integrative and conjugative element (MICE). Additionally, a Type I Restriction-Modification system was identified, featuring 5'-terminally truncated pseudogenes with overlapping repeats, indicating the potential for forming alternative variants through recombination.
CONCLUSION
This study represents the first-ever acquisition of a complete circularized bacterial genome directly from a patient sample obtained from invasive infection of a primary sterile site using culture-independent, PCR-free clinical metagenomics.
Topics: Humans; Metagenomics; Genome, Bacterial; High-Throughput Nucleotide Sequencing; Mycoplasma; Mycoplasma Infections; Whole Genome Sequencing; Lung Transplantation; Prophages; Interspersed Repetitive Sequences; Anti-Bacterial Agents
PubMed: 38694516
DOI: 10.3389/fcimb.2024.1368923