The Emerging Nosocomial Pathogen Klebsiella michiganensis
            <i>:</i>
            Genetic Analysis of a KPC-3 Producing Strain Isolated from Venus Clam

Simoni, Serena; Leoni, Francesca; Veschetti, Laura; Malerba, Giovanni; Carelli, Maria; Lleò, Maria M.; Brenciani, Andrea; Morroni, Gianluca; Giovanetti, Eleonora; Rocchegiani, Elena; Barchiesi, Francesca; Vignaroli, Carla

doi:10.1128/spectrum.04235-22

“…Our findings to this point established that swaps of several tra/trb genes yielded chimeric machines functional at least for DNA transfer. The potential for chimeric T4SSs to assemble in natural settings is medically important in view of recent evidence that enterobacterial clinical isolates can carry two or more F-like plasmids [ 76 – 78 ]. Here, we surveyed the COMPASS database [ 76 ] for strains carrying one or more F plasmids, and determined that indeed an appreciable fraction of sequenced strains (~15%) harbor two or more F plasmids ( Fig 7Ai ), Recently, it was also reported ~25% of ‘classical’ F plasmids (those designated as group A) lack one or more genes required for F transfer [ 26 ].…”

Section: Resultsmentioning

confidence: 99%

Chimeric systems composed of swapped Tra subunits between distantly-related F plasmids reveal striking plasticity among type IV secretion machines

Kishida,

Li,

Ogawa-Kishida

et al. 2024

View full text Add to dashboard Cite

Bacterial type IV secretion systems (T4SSs) are a versatile family of macromolecular translocators, collectively able to recruit diverse DNA and protein substrates and deliver them to a wide range of cell types. Presently, there is little understanding of how T4SSs recognize substrate repertoires and form productive contacts with specific target cells. Although T4SSs are composed of a number of conserved subunits and adopt certain conserved structural features, they also display considerable compositional and structural diversity. Here, we explored the structural bases underlying the functional versatility of T4SSs through systematic deletion and subunit swapping between two conjugation systems encoded by the distantly-related IncF plasmids, pED208 and F. We identified several regions of intrinsic flexibility among the encoded T4SSs, as evidenced by partial or complete functionality of chimeric machines. Swapping of VirD4-like TraD type IV coupling proteins (T4CPs) yielded functional chimeras, indicative of relaxed specificity at the substrate—TraD and TraD—T4SS interfaces. Through mutational analyses, we further delineated domains of the TraD T4CPs contributing to recruitment of cognate vs heterologous DNA substrates. Remarkably, swaps of components comprising the outer membrane core complexes, a few F-specific subunits, or the TraA pilins supported DNA transfer in the absence of detectable pilus production. Among sequenced enterobacterial species in the NCBI database, we identified many strains that harbor two or more F-like plasmids and many F plasmids lacking one or more T4SS components required for self-transfer. We confirmed that host cells carrying co-resident, non-selftransmissible variants of pED208 and F elaborate chimeric T4SSs, as evidenced by transmission of both plasmids. We propose that T4SS plasticity enables the facile assembly of functional chimeras, and this intrinsic flexibility at the structural level can account for functional diversification of this superfamily over evolutionary time and, on a more immediate time-scale, to proliferation of transfer-defective MGEs in nature.

show abstract

“…Our findings to this point established that swaps of several tra/trb genes yielded chimeric machines functional at least for DNA transfer. The potential for chimeric T4SSs to assemble in natural settings is medically important in view of recent evidence that enterobacterial clinical isolates can carry two or more F-like plasmids [70][71][72]. Here, we surveyed the COMPASS database [70] for strains carrying one or more F plasmids, and determined that indeed an appreciable fraction of sequenced strains (~15%) harbored two or more F plasmids (Fig.…”

Section: Discussionmentioning

confidence: 99%

Chimeric systems composed of swapped Tra subunits between distantly-related F plasmids reveal striking plasticity among type IV secretion machines

Kishida,

Li,

Ogawa-Kishida

et al. 2023

Preprint

0

View full text Add to dashboard Cite

Bacterial type IV secretion systems (T4SSs) are a versatile family of macromolecular translocators, collectively able to recruit diverse DNA and protein substrates and deliver them to a wide range of cell types. Presently, there is little understanding of how T4SSs recognize substrate repertoires and form productive contacts with specific target cells. Although T4SSs are composed of a number of conserved subunits and adopt certain conserved structural features, they also display considerable compositional and structural diversity. Here, we explored the structural bases underlying the functional versatility of T4SSs through systematic deletion and subunit swapping between two conjugation systems encoded by the distantly-related IncF plasmids, pED208 and F. We identified several regions of intrinsic flexibility among the encoded T4SSs, as evidenced by partial or complete functionality of chimeric machines. Swapping of VirD4-like TraD type IV coupling proteins (T4CPs) yielded functional chimeras, indicative of relaxed specificity at the substrate - TraD and TraD - T4SS interfaces. Through mutational analyses, we further delineated domains of the TraD T4CPs contributing to recruitment of cognate vs heterologous DNA substrates. Remarkably, swaps of components comprising the outer membrane core complexes, a few F-specific subunits, or the TraA pilins supported DNA transfer in the absence of detectable pilus production. Among sequenced enterobacterial species in the NCBI database, we identified many strains that harbor two or more F-like plasmids and many F plasmids lacking one or more T4SS components required for self-transfer. We confirmed that host cells carrying co-resident, non-selftransmissible variants of pED208 and F elaborate chimeric T4SSs, as evidenced by transmission of both plasmids. We propose that T4SS plasticity enables the facile assembly of functional chimeras, and this intrinsic flexibility at the structural level can account for functional diversification of this superfamily over evolutionary time and, on a more immediate time-scale, to proliferation of transfer-defective MGEs in nature.AUTHOR SUMMARYMobile genetic elements (MGEs) comprise a diverse group of extrachromosomal plasmids or integrated DNA fragments that are widely distributed among many bacterial species. MGEs typically encode conjugation systems dedicated to their transmission to other bacteria, and also code for resistance to antibiotics or virulence or other fitness traits. The conjugation systems, along with an equally medically important group of translocators devoted to the interkingdom delivery of protein effectors by pathogenic species, comprise the superfamily of type IV secretion systems (T4SSs). Recent studies have defined many mechanistic and structural features of the T4SSs, yet there remains little understanding of how T4SSs recruit specific DNA or protein substrates, elaborate functional channels, and in some cases build attachment organelles termed conjugative pili. We explored the mechanics of T4SS machine function by systematically exchanging individual components between two distinct conjugation systems functioning in enterobacterial species. Through construction of chimeric machines, and further mutational analyses, we identified subunits or protein domains of conjugation machines specifying recruitment of distinct DNA substrates or selectively contributing to assembly of translocation channels or conjugative pili. Such features of T4SSs are prime targets for development of inhibitory strategies aimed at blocking T4SS functions for therapeutic intervention.

show abstract

“…Furthermore, Enterobacteriaceae regroups important seafood-borne pathogens, and include genera like Escherichia [ 23 , 24 ], Shigella which was reported in Japan [ 25 ], Salmonella [ 26 , 27 , 28 , 29 , 30 , 31 ] and Klebsiella in Portugal [ 32 ], Tunisia [ 33 ] and Italy [ 34 ], which have drawn attention to their health threats and their contribution to the spread of antibiotic resistance in the environment ( Figure 1 and Supplementary Table S1 ).…”

Section: Shellfish May Be Contaminated By a Large Diversity Of Pathogensmentioning

confidence: 99%

A Comprehensive Review for the Surveillance of Human Pathogenic Microorganisms in Shellfish

Desdouits,

Reynaud,

Philippe

et al. 2023

View full text Add to dashboard Cite

Bivalve molluscan shellfish have been consumed for centuries. Being filter feeders, they may bioaccumulate some microorganisms present in coastal water, either naturally or through the discharge of human or animal sewage. Despite regulations set up to avoid microbiological contamination in shellfish, human outbreaks still occur. After providing an overview showing their implication in disease, this review aims to highlight the diversity of the bacteria or enteric viruses detected in shellfish species, including emerging pathogens. After a critical discussion of the available methods and their limitations, we address the interest of technological developments using genomics to anticipate the emergence of pathogens. In the coming years, further research needs to be performed and methods need to be developed in order to design the future of surveillance and to help risk assessment studies, with the ultimate objective of protecting consumers and enhancing the microbial safety of bivalve molluscan shellfish as a healthy food.

show abstract

The Emerging Nosocomial Pathogen Klebsiella michiganensis : Genetic Analysis of a KPC-3 Producing Strain Isolated from Venus Clam

Cited by 8 publications

References 30 publications

Chimeric systems composed of swapped Tra subunits between distantly-related F plasmids reveal striking plasticity among type IV secretion machines

Chimeric systems composed of swapped Tra subunits between distantly-related F plasmids reveal striking plasticity among type IV secretion machines

Chimeric systems composed of swapped Tra subunits between distantly-related F plasmids reveal striking plasticity among type IV secretion machines

A Comprehensive Review for the Surveillance of Human Pathogenic Microorganisms in Shellfish

Contact Info

Product

Resources

About