Carbapenemase-Producing Enterobacterales from Patients Arriving from Ukraine in Poland, March 2022–February 2023 DOI Creative Commons
Marta Biedrzycka, Radosław Izdebski, Waleria Hryniewicz

et al.

Infectious Diseases and Therapy, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 5, 2025

Despite a scarcity of data, before 2022 Ukraine was already considered high-prevalence country for carbapenemase-producing Enterobacterales (CPE), and the situation has dramatically worsened during full-scale war with Russia. The aim this study to analyse CPEs isolated in Poland from victims Ukraine. included 65 CPE isolates March till February 2023, recovered 36 Polish medical centres 57 patients arriving Ukraine, differing largely by age reason hospitalisation. All were sequenced MiSeq ten Klebsiella pneumoniae also MinION. Taxonomy, clonality resistomes analysed all CPEs, whereas phylogeny, serotypes, virulomes plasmids characterised K. pneumoniae, partially Escherichia coli ST131, using various bioinformatic tools. Multifactorial diversity reflected patients' clinical-epidemiological heterogeneity. represented six species. most prevalent 50 15 sequence types (STs), mainly ST395, ST307, ST11, ST147 ST23, producing NDM (-1/-5), OXA-48 (-48/-1242) or KPC (-2/-3)-like carbapenemases. Each STs produced groups loosely related isolates, clusters close relatives and/or unique correlating K serotypes Many these, especially NDM-1- OXA-48-producing ST395 Russian organisms. Others, example, NDM-1-producing clustered those Poland. Numerous had specific virulence genes, including aerobactin iuc, due spread pNDM-MAR plasmids, showing both resistance virulence. Two E. ST131 belonged clades B C1 KPC-3 NDM-1, respectively. Together similar studies Germany Netherlands, work documented broad dissemination driven number lineages circulating over large territory Eastern Europe.

Language: Английский

Clonal Candida auris and ESKAPE pathogens on the skin of residents of nursing homes DOI
Diana M. Proctor, Sarah Sansom, Clay Deming

et al.

Nature, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 26, 2025

Language: Английский

Citations

2
Rapid Genomic Characterization and Global Surveillance of Klebsiella Using Pathogenwatch DOI Creative Commons
Silvia Argimón, Sophia David, Anthony Underwood

et al.

Clinical Infectious Diseases, Journal Year: 2021, Volume and Issue: 73(Supplement_4), P. S325 - S335

Published: Sept. 30, 2021

Abstract Background Klebsiella species, including the notable pathogen K. pneumoniae, are increasingly associated with antimicrobial resistance (AMR). Genome-based surveillance can inform interventions aimed at controlling AMR. However, its widespread implementation requires tools to streamline bioinformatic analyses and public health reporting. Methods We developed web application Pathogenwatch, which implements analytics tailored species for integration visualization of genomic epidemiological data. populated Pathogenwatch 16 537 genomes enable contextualization user genomes. demonstrated features 1636 from 4 low- middle-income countries (LMICs) participating in NIHR Global Health Research Unit (GHRU) on Results Using we found that GHRU were dominated by a small number epidemic drug-resistant clones pneumoniae. differences their distribution observed (eg, ST258/512 Colombia, ST231 India, ST307 Nigeria, ST147 Philippines). Phylogenetic enabled retrospective monitoring spread. In particular, identified hospital outbreaks, detected introductions abroad, uncovered clonal expansions virulence genes. Assessment loci encoding O-antigens capsule represent possible vaccine candidates, showed 3 O-types (O1–O3) represented 88.9% all genomes, whereas types much more diverse. Conclusions provides free, accessible platform real-time analysis aid local, national, global levels. have improved representation participant countries, further facilitating ongoing surveillance.

Language: Английский

Citations

97
Analysis of Selection Methods to Develop Novel Phage Therapy Cocktails Against Antimicrobial Resistant Clinical Isolates of Bacteria DOI Creative Commons
Melissa E. K. Haines, Francesca E. Hodges, Janet Y. Nale

et al.

Frontiers in Microbiology, Journal Year: 2021, Volume and Issue: 12

Published: March 29, 2021

Antimicrobial resistance (AMR) is a major problem globally. The main bacterial organisms associated with urinary tract infection (UTI) sepsis are E. coli and Klebsiella along Enterobacter species. These all have AMR strains known as ESBL (Extended Spectrum Beta-Lactamase), which featured on the WHO priority pathogens list “critical” for research. Bacteriophages (phages), viruses that can infect kill bacteria, could provide an effective tool to tackle these strains. There currently no “gold standard” developing phage cocktail. Here we describe novel approach develop cocktail against set of ESBL-producing largely isolated from patients in United Kingdom hospitals. By comparing different measures efficacy, show most robust, suggest efficient screening cascade be used cocktails target other A panel 38 clinical urine samples was collated test efficacy. After initial 68 phages, six were identified tested determine their coverage killing efficiency. To achieve this, assessed four methods assess virulence across isolates. Direct Spot Test (DST), Efficiency Plating (EOP) assay, planktonic assay (PKA) biofilm assay. final phages effectively 23/38 (61%), 13/19 (68%) 10/19 (53%) based PKA data. collection had isolates prevalent UTI-associated ST131 sequence type, five targeted by Of virulence, data suggests PKAs much more time-consuming EOPs two assays correlates well. This good proxy should when combined index also allows “phage synergy” inform design.

Language: Английский

Citations

67
Resistome and virulome accretion in an NDM-1-producing ST147 sublineage of Klebsiella pneumoniae associated with an outbreak in Tuscany, Italy: a genotypic and phenotypic characterisation DOI
Vincenzo Di Pilato, Lucia Henrici De Angelis, Noemi Aiezza

et al.

The Lancet Microbe, Journal Year: 2022, Volume and Issue: 3(3), P. e224 - e234

Published: Feb. 5, 2022

Language: Английский

Citations

65
Genomic Epidemiology of Global Carbapenemase-Producing Escherichia coli, 2015–2017 DOI Creative Commons

Gisele Peirano,

Liang Chen, Diego B. Nóbrega

et al.

Emerging infectious diseases, Journal Year: 2022, Volume and Issue: 28(5)

Published: May 1, 2022

We describe the global molecular epidemiology of 229 carbapenemase-producing Escherichia coli in 36 countries during 2015-2017. Common carbapenemases were oxacillinase (OXA) 181 (23%), New Delhi metallo-β-lactamase (NDM) 5 (20%), OXA-48 (17%), Klebsiella pneumoniae carbapenemase 2 (15%), and NDM-1 (10%). identified dominant sequence types (STs); 4 (ST410, ST131, ST167, ST405), 1 (ST1284) was limited to Turkey. OXA-181 frequent Jordan (because ST410-B4/H24RxC subclade) Turkey ST1284). found nearly identical IncX3-blaOXA-181 plasmids among 11 STs from 12 countries. NDM-5 Egypt, Thailand (linked with ST167-B subclades), Vietnam ST448). common ST11260). Global K. linked ST131 C1/H30 subclade various STs. The E. population is dominated by diverse different characteristics varied geographic distributions, requiring ongoing genomic surveillance.

Language: Английский

Citations

59
Genomic evolution of the globally disseminated multidrug-resistant Klebsiella pneumoniae clonal group 147 DOI Creative Commons
Carla Rodrigues, Siddhi Desai,

Virginie Passet

et al.

Microbial Genomics, Journal Year: 2022, Volume and Issue: 8(1)

Published: Jan. 12, 2022

The rapid emergence of multidrug-resistant Klebsiella pneumoniae is being driven largely by the spread specific clonal groups (CGs). Of these, CG147 includes 7-gene multilocus sequence typing (MLST) types (STs) ST147, ST273 and ST392. has caused nosocomial outbreaks across world, but its global population dynamics remain unknown. Here, we report a pandrug-resistant ST147 clinical isolate from India (strain DJ) define evolution CG147. Antimicrobial-susceptibility testing following European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines genome sequencing (Illumina Oxford Nanopore Technologies, Unicycler assembly) were performed strain DJ. Additionally, collated 217 publicly available genomes [National Center for Biotechnology Information (NCBI), May 2019]. was inferred within temporal phylogenetic framework (beast) based recombination-free alignment (Roary/Gubbins). Comparative genomic analyses focused resistance virulence genes other genetic elements (BIGSdb, Kleborate, PlasmidFinder, phaster, ICEfinder CRISPRCasFinder). Strain DJ had pandrug-resistance phenotype. Its comprised chromosome, seven plasmids one linear phage-plasmid. Four carbapenemase detected: blaNDM-5 two copies blaOXA-181 in second copy an 84 kb IncFII plasmid. carried mean 13 acquired or mutations; 63 % gene 83 harboured blaCTX-M. All presented GyrA ParC mutations common subtype I-E CRISPR-Cas system. ST392 emerged 2005 1995, respectively. most represented branch, itself divided into main clades with distinct capsular loci: KL64 (74 %, included, 1994 disseminated worldwide, carbapenemases varying among world regions) KL10 (20 2002, predominantly found Asian countries, associated NDM OXA-48-like). Furthermore, subclades ST147-KL64 differed at yersiniabactin locus, OmpK35/K36 mutations, plasmid replicons prophages. absence IncF some possible activity K. comprises extensively resistant isolates, carries multiple diverse mobile elements, including chromosomal blaNDM-5. several marked their own features temporo-spatial dynamics. These findings highlight need precision surveillance strategies to limit particularly concerning subsets.

Language: Английский

Citations

47
Genomic analysis of the international high-risk clonal lineage Klebsiella pneumoniae sequence type 395 DOI Creative Commons
Elvira Shaidullina, Michael Schwabe, Thomas D. Rohde

et al.

Genome Medicine, Journal Year: 2023, Volume and Issue: 15(1)

Published: Feb. 13, 2023

Klebsiella pneumoniae, which is frequently associated with hospital- and community-acquired infections, contains multidrug-resistant (MDR), hypervirulent (hv), non-MDR/non-hv as well convergent representatives. It known that mostly international high-risk clonal lineages including sequence types (ST) 11, 147, 258, 307 drive their global spread. ST395, was first reported in the context of a carbapenemase-associated outbreak France 2010, less well-characterized, yet emerging lineage.

Language: Английский

Citations

37
ESKAPE and Beyond: The Burden of Coinfections in the COVID-19 Pandemic DOI Creative Commons
Miguel Ángel Loyola-Cruz, Luis Uriel Gonzalez-Avila, Arturo Martínez-Trejo

et al.

Pathogens, Journal Year: 2023, Volume and Issue: 12(5), P. 743 - 743

Published: May 22, 2023

The ESKAPE group constitute a threat to public health, since these microorganisms are associated with severe infections in hospitals and have direct relationship high mortality rates. presence of bacteria had impact on the incidence healthcare-associated coinfections SARS-CoV-2 pandemic. In recent years, pathogens shown resistance multiple antibiotic families. high-risk clones within this contributes spread mechanisms worldwide. pandemic, were implicated severely ill COVID-19 patients. aim review is describe main involved patients, addressing mainly antimicrobial mechanisms, epidemiology, clones.

Language: Английский

Citations

32
The Significance of Epidemic Plasmids in the Success of Multidrug-Resistant Drug Pandemic Extraintestinal Pathogenic Escherichia coli DOI Creative Commons
Johann Pitout, Liang Chen

Infectious Diseases and Therapy, Journal Year: 2023, Volume and Issue: 12(4), P. 1029 - 1041

Published: March 22, 2023

Epidemic IncF plasmids have been pivotal in the selective advantage of multidrug-resistant (MDR) extraintestinal pathogenic Escherichia coli (ExPEC). These offered several advantages to their hosts that allowed them coevolve with bacterial host genomes and played an integral role success ExPEC. are large, mosaic, often contain various types antimicrobial resistance (AMR) virulence associated factor (VAF) genes. The presence AMR, VAF genes, addition/restriction systems combined truncated transfer regions, led fixation certain ExPEC MDR clones, such as ST131 ST410. entered ancestral lineage mid 1900s different clade/CTX-M plasmid combinations coevolved over time. IncF_CTX-M-15/ST131-C2 subclade combination emerged during early 2000s, spread rapidly across globe, is one greatest clone/plasmid successes millennium. ST410-B3 containing blaCTX-M-15 incorporated NDM-5 carbapenemase gene into existing platforms, providing additional positive included carbapenems. A "plasmid-replacement" clade scenario occurred histories ST410 subclades gained AMR genes on platforms. use agents will generate selection pressures enhance risks for continuous emergence clone/IncF combinations. reasons clade/IncF replacements associations between clades specific unknown. Such information aid designing management prevention strategies combat AMR.

Language: Английский

Citations

27
Prevalence and clonal diversity of carbapenem-resistant Klebsiella pneumoniae causing neonatal infections: A systematic review of 128 articles across 30 countries DOI Creative Commons
Ya Hu,

Yongqiang Yang,

Yu Feng

et al.

PLoS Medicine, Journal Year: 2023, Volume and Issue: 20(6), P. e1004233 - e1004233

Published: June 20, 2023

Background Klebsiella pneumoniae is the most common pathogen causing neonatal infections, leading to high mortality worldwide. Along with increasing antimicrobial use in neonates, carbapenem-resistant K . (CRKP) has emerged as a severe challenge for infection control and treatment. However, no comprehensive systematic review available describe global epidemiology of CRKP infections. We therefore performed data worldwide combined genome-based analysis address prevalence, clonal diversity, carbapenem resistance genes Methods findings studies reporting population-based infections caused by combination all publicly genomes origins. searched multiple databases (PubMed, Web Science, Embase, Ovid MEDLINE, Cochrane, bioRxiv, medRxiv) identify that have reported up June 30, 2022. included addressing prevalence colonization neonates but excluded lacking numbers geographical location, or independent on isolates. used narrative synthesis pooling JMP statistical software. identified 8,558 articles excluding those did not meet inclusion criteria. 128 studies, none which were preprints, comprising 127,583 30 countries including 21 low- middle-income (LMICs) analysis. found bloodstream type data. estimated pooled hospitalized was 0.3% (95% confidence interval [CI], 0.2% 0.3%). Based patient outcomes, we 22.9% CI, 13.0% 32.9%). A total 535 from GenBank Sequence Read Archive, 204 linked any publications. incorporated literature understanding species distribution, carbapenemase types. 146 sequence types (STs) strains ST17, ST11, ST15 3 lineages. In particular, ST17 been seen 8 across 4 continents. The vast majority (75.3%) 1,592 analyzing encoding metallo-β-lactamases NDM (New Delhi metallo-β-lactamase) appeared be (64.3%). main limitation this study absence scarcity North America, South Oceania. Conclusions contributes considerable number leads significant mortality. Neonatal are highly diverse, while globally prevalent merits early detection treatment prevention. dominance bla imposes challenges therapeutic options supports continued inhibitor-related drug discovery.

Language: Английский

Citations

23