SHIP: identifying antimicrobial resistance gene transfer between plasmids

Teixeira, Marco; Pillay, Stephanie; Urhan, Aysun; Abeel, Thomas

doi:10.1093/bioinformatics/btad612

Cited by 5 publications

(1 citation statement)

References 48 publications

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“…A schematic diagram of representative ARGs and MGEs is shown in Figure 6. Presence of IncX3 and IncP-6 Plasmid Replicon Types Plasmids have the ability to transfer AMR genes to other bacteria, which can speed up the spread and evolution of bacterial pathogens (Teixeira et al, 2023). Antimicrobial resistance genes in P. aeruginosa and other Gramnegative bacteria are largely transferred by the IncP-6 and IncX3 plasmids.…”

Section: Presence Of Insertion Sequence (Is) and Transposonmentioning

confidence: 99%

“Identification of potential high-risk clones of Carbapenem-ResistantPseudomonas aeruginosaco-producing, KPC-2, VIM-2 and OXA-74 from tertiary hospitals in Metro Manila, Philippines”

Tesalona,

Abulencia,

Pineda-Cortel

et al. 2024

Preprint

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Carbapenem-resistantPseudomonas aeruginosa(CRPA) is an opportunistic human pathogen and a global public health concern due to the limited treatment options available for infections by this pathogen. Identification of antimicrobial resistance (AMR) determinants at an early phase is crucial to administer the appropriate treatment in a timely manner, thereby alleviating the transmission and enhancing the outcomes of patients infected with these pathogens. This study investigated the whole genome sequence (WGS) of 35 CRPA isolates obtained from three hospitals in Metro Manila, Philippines, collected from August 2022 to January 2023. The investigation revealed that a high proportion of isolates obtained from Hospital B and C contained acquired AMR determinants. The traditional multilocus sequence type (MLST) analysis using Pasteur nomenclature in the PubMLST database revealed six different known sequence types (STs), namely ST111, ST175, ST1822, ST357, ST3753 and ST389 and the highest number of unknown STs (27 singletons). Moreover, to delineate the unknown STs identified, the Pasteur nomenclature in the Pathogenwatch database was used, which led to the identification of novel STs. Notably, a novel ST4b1c was found to co-produce the metallo-beta-lactamase (MBL) NDM-7, extended-spectrum beta-lactamases (ESBLs) CTX-M-15 and TEM-2, as well as class D OXA-395. Furthermore, potential high-risk clones represented by ST389 and novel STs (ST95c6, STf555, and STab6a) were identified, all of which co-produced carbapenemases KPC-2, VIM-2, and OXA-74. This study represents the first report in the Philippines on the co-production of ESBL KPC-2, MBL VIM-2 and Class D OXA-74 hosted by potential high-risk clones and novel STs. It underscores the need for continuous surveillance and monitoring of other problematic strains.

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Section: Presence Of Insertion Sequence (Is) and Transposonmentioning

confidence: 99%

“Identification of potential high-risk clones of Carbapenem-ResistantPseudomonas aeruginosaco-producing, KPC-2, VIM-2 and OXA-74 from tertiary hospitals in Metro Manila, Philippines”

Tesalona,

Abulencia,

Pineda-Cortel

et al. 2024

Preprint

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Genomic analysis of extensively drug resistant (XDR) Klebsiella pneumoniae high-risk clone ST14 co-harboring blaNDM and blaOXA-48 recovered from Saudi Arabia

Al-Zahrani,

Aljabri,

Alhazmi

et al. 2024

Journal of Infection and Public Health

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Identification of a novel mycovirus belonging to the “flexivirus”-related family with icosahedral virion

Wu,

Okada,

Neri

et al. 2024

Preprint

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The orderTymoviralescurrently comprises five viral families with positive-sense RNA ((+)RNA) genomes that infect plants, fungi, and insects. Virion morphologies within the orderTymoviralesdiffer between families, with icosahedral virions in theTymoviridaeand filamentous virions in the other ″flexi″viridaefamilies. Despite their different morphologies, these viruses are placed in the same order based on phylogenetic analyses of replicase-associated polyproteins. However, one of the families in theTymovirales,Deltaflexiviridae, is considered to be capsidless because there have been no published reports of virion isolation. Here we report that a new ″flexivirus″-related (+)RNA virus, prospectively named Fusarium oxysporum icosahedral virus 1 (FoIV1), is icosahedral, and that most deltaflexiviruses may have icosahedral virions. Phylogenetic analyses based on replicase-associated polyproteins indicated that FoIV1 forms a distinct group in theTymoviraleswith some viruses originally assigned to theDeltaflexiviridae. Electron microscopy, protein analysis, and protein structure predictions indicate that FoIV1 ORF4 encodes a single jelly-roll (SJR)-like coat protein (CP) that constitutes the icosahedral virions. Results of clustering analyses based on amino acid sequences and predicted CP structures suggested that most of the deltaflexiviruses have icosahedral virions composed of SJR-like CPs as in FoIV1, rather than having filamentous virions or capsidless. These results challenge the conventional understanding of viruses in the orderTymovirales, with important implications for revising its taxonomic framework and providing insights into the evolutionary relationships within this diverse and broad host range group of (+)RNA viruses.

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SHIP: identifying antimicrobial resistance gene transfer between plasmids

Cited by 5 publications

References 48 publications

“Identification of potential high-risk clones of Carbapenem-ResistantPseudomonas aeruginosaco-producing, KPC-2, VIM-2 and OXA-74 from tertiary hospitals in Metro Manila, Philippines”

“Identification of potential high-risk clones of Carbapenem-ResistantPseudomonas aeruginosaco-producing, KPC-2, VIM-2 and OXA-74 from tertiary hospitals in Metro Manila, Philippines”

Genomic analysis of extensively drug resistant (XDR) Klebsiella pneumoniae high-risk clone ST14 co-harboring blaNDM and blaOXA-48 recovered from Saudi Arabia

Identification of a novel mycovirus belonging to the “flexivirus”-related family with icosahedral virion

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