The Role of Phage in the Adaptation of Bacteria to New Environmental Niches

Casas, Veronica; Maloy, Stanley

doi:10.1007/978-3-319-69078-0_11

Cited by 8 publications

(7 citation statements)

References 231 publications

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“…In our study of the genomic diversity of our bla NDM-1 -harboring CREC isolates compared to other published genomes, we found that the specific features of the ST448 and ST131 isolates were different from various STs. In ST488 isolates, the prophage-encoding proteins may be associated with bacterial adaptation to the bacteriophages, 60 , 61 while non-fimbrial adhesin 1 is probably associated with cell attachment to abiotic surfaces and/or host cells, and the biofilm formation. 62 For the ST131 isolate, the FlhC, MntH, AlbA, and CsoR proteins are probably related to the production of flagellar, the transportation of divalent metal cation, the production of antilisterial bacteriocin subtilosin, and the expression of a copper-sensing repressor, which might be beneficial for bacterial evolution and pathogenicity.…”

Section: Discussionmentioning

confidence: 99%

In vitro Synergistic Activities of Fosfomycin in Combination with Other Antimicrobial Agents Against Carbapenem-Resistant Escherichia coli Harboring blaNDM-1 on the IncN2 Plasmid and a Study of the Genomic Characteristics of These Pathogens

Kaewnirat¹,

Chuaychob²,

Chukamnerd³

et al. 2022

IDR

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Purpose The spread of New Delhi metallo-β-lactamase (NDM) encoded by the bla NDM gene has been a global health crisis for many years. Most of bla NDM -harboring bacteria commonly carry various antimicrobial resistance (AMR) genes on their chromosomes or plasmids, leading to limited treatment options. Thus, we aimed to evaluate the synergistic effects of fosfomycin in combination with other antimicrobial agents against bla NDM -harboring carbapenem-resistant Escherichia coli (CREC) and to characterize the whole-genome and plasmid sequences of these pathogens. Methods Thirty-eight CREC isolates were collected from patients in the Medicine Ward, Songklanagarind Hospital, Thailand. The activity of fosfomycin in combination with other antimicrobial agents against CREC isolates harboring bla NDM on the plasmid was evaluated using the checkerboard method. In this method, the serial dilutions of two antibiotics were mixed with the cultured CREC, the mixtures were incubated, and FICI was calculated to interpret the synergistic activity of the combination. The whole-genome and particular plasmids of these pathogens were sequenced using next-generation sequencing. Sequence analysis, especially on antimicrobial resistance (AMR) genes, mobile-genetic elements (MGEs), and virulence genes was performed using many bioinformatics tools. Results Of the E. coli 38 isolates, only 3 isolates contained the bla NDM-1 gene, which is located on the IncN2 plasmid. The combinations of fosfomycin with aminoglycosides, colistin, tigecycline, sitafloxacin, and ciprofloxacin were synergies against bla NDM-1 -harboring CREC isolates. Genomic analysis revealed that these isolates harbored many β-lactam resistance genes and other AMR genes that may confer resistance to aminoglycoside, fluoroquinolone, rifampicin, trimethoprim, sulfonamide, tetracycline, and macrolide. Also, various MGEs, especially the bla NDM-1 -bearing IncN2 plasmid, were present in these isolates. Conclusion Our study demonstrated some synergistic effects of antimicrobial combination against CREC isolates harboring bla NDM-1 on the IncN2 plasmid. Also, our data on the whole-genome and plasmid sequences might be beneficial in the control of the spread of bla NDM-1 -harboring CREC isolates. The linkages between bla NDM-1 -carrying plasmid, patient information, and time of collection will be elucidated to track the horizontal gene transfer in the future.

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Section: Discussionmentioning

confidence: 99%

In vitro Synergistic Activities of Fosfomycin in Combination with Other Antimicrobial Agents Against Carbapenem-Resistant Escherichia coli Harboring blaNDM-1 on the IncN2 Plasmid and a Study of the Genomic Characteristics of These Pathogens

Kaewnirat¹,

Chuaychob²,

Chukamnerd³

et al. 2022

IDR

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“…Interactions between phages and bacterial hosts lead to dynamic co-evolution of the microbial community rather than to the simplest outcome of predation, infection, and lysis of susceptible hosts. This interplay is far more complex and may result in higher adaptation of hosts to environmental factors in a specific niche (Casas and Maloy, 2018). Selective pressure provided by predator-prey relationships can increase overall fitness of a bacterial population by enhancing reproduction rate among infected bacteria (Shapiro et al, 2016), promoting exchange of chromosomal and plasmid DNA (Thierauf et al, 2009) or by lysogenic conversion (Casas and Maloy, 2018).…”

Section: Presence Of Prophages and Crisprsmentioning

confidence: 99%

“…This interplay is far more complex and may result in higher adaptation of hosts to environmental factors in a specific niche (Casas and Maloy, 2018). Selective pressure provided by predator-prey relationships can increase overall fitness of a bacterial population by enhancing reproduction rate among infected bacteria (Shapiro et al, 2016), promoting exchange of chromosomal and plasmid DNA (Thierauf et al, 2009) or by lysogenic conversion (Casas and Maloy, 2018). Considering low temperatures in Antarctica negatively influence bacterial growth rate, a possible acceleration of reproduction rates caused by phage infection represents a notable advantage for the hosts.…”

Section: Presence Of Prophages and Crisprsmentioning

confidence: 99%

“…While only the P7388 T genome was predicted to contain one CRISPR array without cas-associated genes, the remaining analyzed genomes lack cas-associated genes as well as CRISPR arrays. This suggests that phage infection of these flavobacteria may be actually advantageous or if they developed defense mechanisms, these are likely associated with the surface receptors alterations, restriction/modification mechanisms or even immunity caused by already present prophages rather than with the Cas-system system (Casas and Maloy, 2018).…”

Section: Presence Of Prophages and Crisprsmentioning

confidence: 99%

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Flavobacterium flabelliforme sp. nov. and Flavobacterium geliluteum sp. nov., Two Multidrug-Resistant Psychrotrophic Species Isolated From Antarctica

et al. 2021

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Despite unfavorable Antarctic conditions, such as cold temperatures, freeze-thaw cycles, high ultraviolet radiation, dryness and lack of nutrients, microorganisms were able to adapt and surprisingly thrive in this environment. In this study, eight cold-adapted Flavobacterium strains isolated from a remote Antarctic island, James Ross Island, were studied using a polyphasic taxonomic approach to determine their taxonomic position. Phylogenetic analyses based on the 16S rRNA gene and 92 core genes clearly showed that these strains formed two distinct phylogenetic clusters comprising three and five strains, with average nucleotide identities significantly below 90% between both proposed species as well as between their closest phylogenetic relatives. Phenotyping revealed a unique pattern of biochemical and physiological characteristics enabling differentiation from the closest phylogenetically related Flavobacterium spp. Chemotaxonomic analyses showed that type strains P4023T and P7388T were characterized by the major polyamine sym-homospermidine and a quinone system containing predominantly menaquinone MK-6. In the polar lipid profile phosphatidylethanolamine, an ornithine lipid and two unidentified lipids lacking a functional group were detected as major lipids. These characteristics along with fatty acid profiles confirmed that these species belong to the genus Flavobacterium. Thorough genomic analysis revealed the presence of numerous cold-inducible or cold-adaptation associated genes, such as cold-shock proteins, proteorhodopsin, carotenoid biosynthetic genes or oxidative-stress response genes. Genomes of type strains surprisingly harbored multiple prophages, with many of them predicted to be active. Genome-mining identified biosynthetic gene clusters in type strain genomes with a majority not matching any known clusters which supports further exploratory research possibilities involving these psychrotrophic bacteria. Antibiotic susceptibility testing revealed a pattern of multidrug-resistant phenotypes that were correlated with in silico antibiotic resistance prediction. Interestingly, while typical resistance finder tools failed to detect genes responsible for antibiotic resistance, genomic prediction confirmed a multidrug-resistant profile and suggested even broader resistance than tested. Results of this study confirmed and thoroughly characterized two novel psychrotrophic Flavobacterium species, for which the names Flavobacterium flabelliforme sp. nov. and Flavobacterium geliluteum sp. nov. are proposed.

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“…The environmental adaptation of bacteria, in particular, is affected by bacteriophages (aka phages) [ 20 ], viruses that infect bacteria. Cyanobacterial phages (cyanophages) contribute to the evolution of cyanobacteria and can be considered a reservoir of genes important for the ecological adaptation of cyanobacteria [ 21 ].…”

Section: Introductionmentioning

confidence: 99%

Tychonema sp. BBK16 Characterisation: Lifestyle, Phylogeny and Related Phages

Evseev

Тихонова

Krasnopeev

et al. 2023

Viruses

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Cyanobacterial expansion is harmful to the environment, the ecology of Lake Baikal and the economy of nearby regions and can be dangerous to people and animals. Since 2011, the process of colonisation of the lake with potentially toxic cyanobacteria belonging to the genus Tychonema has continued. An understanding of the mechanism of successful expansion of Tychonema requires scrutiny of biological and genomic features. Tychonema sp. BBK16 was isolated from the coastal zone of Lake Baikal. The morphology of BBK16 biofilm was studied with light, scanning electron and confocal microscopy. The biofilm is based on filaments of cyanobacteria, which are intertwined like felt; there are also dense fascicles of rope-like twisted filaments that impart heterogeneity to the surface of the biofilm. Genome sequencing, intergenomic comparisons and phylogenetic analyses indicated that Tychonema sp. BBK16 represent a new species related to planktic cyanobacterium Tychonema bourrellyi, isolated from Alpine lentic freshwater. Genome investigation revealed the genes possibly responsible for the mixotrophic lifestyle. The presence of CRISPR-Cas and restriction modification defence mechanisms allowed to suggest the existence of phages infecting Tychonema sp. BBK16. Analysis of CRISPR spacers and prophage-derived regions allowed to suggest related cyanophages. Genomic analysis supported the assumption that mobile elements and horizontal transfer participate in shaping the Tychonema sp. BBK16 genome. The findings of the current research suggest that the aptitude of Tychonema sp. BBK16 for biofilm formation and, possibly, its mixotrophic lifestyle provide adaptation advantages that lead to the successful expansion of this cyanobacterium in the Baikal’s conditions of freshwater lake environments.

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The Role of Phage in the Adaptation of Bacteria to New Environmental Niches

Cited by 8 publications

References 231 publications

In vitro Synergistic Activities of Fosfomycin in Combination with Other Antimicrobial Agents Against Carbapenem-Resistant Escherichia coli Harboring blaNDM-1 on the IncN2 Plasmid and a Study of the Genomic Characteristics of These Pathogens

In vitro Synergistic Activities of Fosfomycin in Combination with Other Antimicrobial Agents Against Carbapenem-Resistant Escherichia coli Harboring blaNDM-1 on the IncN2 Plasmid and a Study of the Genomic Characteristics of These Pathogens

Flavobacterium flabelliforme sp. nov. and Flavobacterium geliluteum sp. nov., Two Multidrug-Resistant Psychrotrophic Species Isolated From Antarctica

Tychonema sp. BBK16 Characterisation: Lifestyle, Phylogeny and Related Phages

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