Genetic Diversity and Hospital Circulation of Opportunistic Pathogens in COVID-19 ICUs: Whole-Genome Sequencing Data.

Svetlana S Smirnova, Dmitry D Avdyunin, Yulia S Stagilskaya, Anastasia A Kameneva, Tatiana A Platonova, Nikolai N Zhuikov, Tarek M Itani, Aleksandr V Semenov

Abstract read

PubMed Full text at PMC Publisher

In one paragraph

Article in Pathogens (Basel, Switzerland), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it

0cells of the map it votes in

0citing papers in PubMed

–field-weighted citation impact

1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors.

Svetlana S SmirnovaFederal Scientific Research Institute of Viral Infections «Virome» Rospotrebnadzor, Letnyaya Street, 23, 620030 Yekaterinburg, Russia.ORCID 0000-0002-9749-4611

Dmitry D AvdyuninFederal Scientific Research Institute of Viral Infections «Virome» Rospotrebnadzor, Letnyaya Street, 23, 620030 Yekaterinburg, Russia.ORCID 0009-0005-3660-2251

Yulia S StagilskayaFederal Scientific Research Institute of Viral Infections «Virome» Rospotrebnadzor, Letnyaya Street, 23, 620030 Yekaterinburg, Russia.ORCID 0009-0000-9261-5624

Anastasia A KamenevaFederal Scientific Research Institute of Viral Infections «Virome» Rospotrebnadzor, Letnyaya Street, 23, 620030 Yekaterinburg, Russia.

Tatiana A PlatonovaFederal Scientific Research Institute of Viral Infections «Virome» Rospotrebnadzor, Letnyaya Street, 23, 620030 Yekaterinburg, Russia.

Nikolai N ZhuikovFederal Scientific Research Institute of Viral Infections «Virome» Rospotrebnadzor, Letnyaya Street, 23, 620030 Yekaterinburg, Russia.

Tarek M ItaniFederal Scientific Research Institute of Viral Infections «Virome» Rospotrebnadzor, Letnyaya Street, 23, 620030 Yekaterinburg, Russia.ORCID 0000-0002-2113-6543

Aleksandr V SemenovFederal Scientific Research Institute of Viral Infections «Virome» Rospotrebnadzor, Letnyaya Street, 23, 620030 Yekaterinburg, Russia.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The COVID-19 pandemic led to a dramatic increase in healthcare-associated infections and antimicrobial resistance, particularly in intensive care units (ICUs). The aim of this study was to provide a comprehensive genomic characterisation of all clinically significant opportunistic pathogens (OPs) isolated from patients and the hospital environment in COVID-19 ICUs, and to use these data to reconstruct transmission pathways, identify reservoirs, and assess the molecular mechanisms of antimicrobial resistance and virulence. Whole-genome sequencing (WGS) was performed on 175 isolates isolated from patients and the hospital environment (including personal protective equipment, PPE) between 2021 and 2023. The species collection included nine OP species. Bioinformatic analysis included multilocus sequence typing, core genome single-nucleotide polymorphism analysis, phylogenetic reconstruction, and in silico detection of resistance and virulence genes and plasmid replicons. High-risk multidrug-resistant (MDR) clones were identified among

Indexed as

BacteriaCOVID-19Cross InfectionGenetic VariationIntensive Care UnitsOpportunistic InfectionsDrug Resistance, Multiple, BacterialGenome, BacterialHumansMultilocus Sequence TypingPhylogenyPolymorphism, Single NucleotideSARS-CoV-2Whole Genome Sequencingantimicrobial resistancecore genome SNP analysishealthcare-associated infectionsintensive care unitopportunistic pathogenspersonal protective equipmentplasmidswhole-genome sequencing

Identifiers

PMID42654782

DOI10.3390/pathogens15080845

PMCPMC13516873

What OpenQuestion holds

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.