Bacterial strain nomenclature in the genomic era: Life Identification Numbers using a gene-by-gene approach DOI Creative Commons
Féderica Palma, Mélanie Hennart, Keith A. Jolley

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Март 12, 2024

Abstract Unified strain taxonomies are crucial for fostering international communication in microbiological research and the epidemiological surveillance of bacterial pathogens. While multilocus sequence typing (MLST) has served as a foundation taxonomy two decades, whole genome sequencing enables more precise classifications significantly improves discriminatory resolution. The core genome-wide extension MLST (known cgMLST) thus holds great promise genotyping classification, but its implementation faces challenges that include missing data, potential instability cluster-based nomenclatures, necessity to ensure backwards compatibility with identifiers. Life Identification Number (LIN) codes offer solution by providing multi-level classification groups inherently stable. Here, we present, consolidate, extend cgMLST-based LIN code approach. We first develop nicknaming system prefixes, which flexible human-readable nomenclatures. Using Klebsiella pneumoniae (Kp) an example, nicknames were attributed inheritance from identifiers, perpetuating legacy nomenclatures genomic era. show while 7-gene sometimes conflates unrelated sublineages into same ST, highly concordant phylogenetic relationships. implement this novel code-based nomenclature BIGSdb platform, illustrate, Pathogenwatch, how it can also be used other epidemiology platforms. Finally, demonstrate value tracking diversity within high-risk internationally disseminated clonal Kp protracted outbreaks. Given stability, precision, flexibility, recommend adoption taxonomic approach suggest is widely applicable

Язык: Английский

International and regional spread of carbapenem-resistant Klebsiella pneumoniae in Europe DOI Creative Commons

Mabel Budia-Silva,

Tomislav Kostyanev,

Stefany Ayala-Montaño

и другие.

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Июнь 14, 2024

Abstract Carbapenem-resistant Klebsiella pneumoniae (CRKP) are of particular concern due to the spread antibiotic resistance genes associated with mobile genetic elements. In this study, we collected 687 carbapenem-resistant strains recovered among clinical samples from 41 hospitals in nine Southern European countries (2016-2018). We identified 11 major clonal lineages, most isolates belonging high-risk clones ST258/512, ST101, ST11, and ST307. bla KPC-like was prevalent carbapenemase-encoding gene (46%), OXA-48 present 39% isolates. Through combination comparison EURECA collection previous EuSCAPE (2013-2014), investigated circulating Europe exhibiting regional differences. particularly found ST258/512 Greece, Italy, Spain, ST101 Serbia Romania, NDM ST11 OXA-48-like ST14 Türkiye. Genomic surveillance across thus provides crucial insights for local risk mapping informs necessary adaptions implementation control strategies.

Язык: Английский

Процитировано

21
The pivotal role of IncFIB(Mar) plasmid in the emergence and spread of hypervirulent carbapenem-resistant Klebsiella pneumoniae DOI Creative Commons
Zhewei Sun, Jianfeng Zhang, Chuning Wang

и другие.

Science Advances, Год журнала: 2025, Номер 11(5)

Опубликована: Янв. 31, 2025

The hypervirulent carbapenem-resistant Klebsiella pneumoniae (hv-CRKP) poses a substantial challenge to the global health care. However, mechanism behind its evolution and transmission remain elusive. Here, four virulence plasmid types were identified from 310 hv-CRKP isolates collected nationwide during 2017–2018, based on their aerobactin ( iuc locus) lineage IncFIB replicons. Notably, pIUC1-IncFIB(K) 37 pIUC1-IncFIB(Mar), representing two epidemic plasmids in Asia Europe, respectively, accounted for >90% of episodes. Analysis 494 K. (376 2010–2013; 118 2017–2018) 2578 public genomes indicated notable role IncFIB(Mar) emergence spread. Conjugation assays showed helper could efficiently transfer into strain uniquely retromobilize with back CRKP. Thereafter, either lost rapidly or recombined , generating hybrid pIUC1-IncFIB(Mar) plasmid. Our findings elucidated formation, evolution, dissemination trajectories major strains different regions.

Язык: Английский

Процитировано

2
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

и другие.

The Lancet Microbe, Год журнала: 2022, Номер 3(3), С. e224 - e234

Опубликована: Фев. 5, 2022

Язык: Английский

Процитировано

68
Global spread and evolutionary convergence of multidrug-resistant and hypervirulent Klebsiella pneumoniae high-risk clones DOI Creative Commons
Gabriele Arcari, Alessandra Carattoli

Pathogens and Global Health, Год журнала: 2022, Номер 117(4), С. 328 - 341

Опубликована: Сен. 11, 2022

For people living in developed countries life span is growing at a faster pace than ever. One of the main reasons for such success attributable to introduction and extensive use clinical practice antibiotics over course last seven decades. In hospital settings, Klebsiella pneumoniae represents well-known commonly described opportunistic pathogen, typically characterized by resistance several antibiotic classes. On other hand, broad wedge population Low and/or Middle Income Countries increasing rapidly, allowing spread commensal bacteria which are transmitted via human contact. Community transmission has been original milieu K. isolates an outstanding virulence (hypervirulent). These two characteristics, also defined as "pathotypes", originally emerged different pathways evolutionary history pneumoniae. long time, Sequence Type (ST), combination alleles 7 housekeeping genes Multi-Locus Typing, reliable marker pathotype: multidrug-resistant clones (e.g. ST258, ST147, ST101) Western world hypervirulent ST23, ST65, ST86) Eastern. Currently, boundaries separating pathotypes fading away due factors, we witnessing worrisome convergence certain high-risk clones. Here review evidence available on confluence multidrug-resistance hypervirulence specific

Язык: Английский

Процитировано

54
Genomic surveillance for multidrug-resistant or hypervirulent Klebsiella pneumoniae among United States bloodstream isolates DOI Creative Commons
Travis J. Kochan, Sophia Nozick,

Rachel Medernach

и другие.

BMC Infectious Diseases, Год журнала: 2022, Номер 22(1)

Опубликована: Июль 7, 2022

Klebsiella pneumoniae strains have been divided into two major categories: classical K. pneumoniae, which are frequently multidrug-resistant and cause hospital-acquired infections in patients with impaired defenses, hypervirulent severe community-acquired disseminated normal hosts. Both types of may lead to bacteremia associated significant morbidity mortality. The relative burden these among bloodstream isolates within the United States is not well understood.

Язык: Английский

Процитировано

48
Klebsiella pneumoniae clinical isolates with features of both multidrug-resistance and hypervirulence have unexpectedly low virulence DOI Creative Commons
Travis J. Kochan, Sophia Nozick,

Aliki Valdes

и другие.

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Дек. 2, 2023

Abstract Klebsiella pneumoniae has been classified into two types, classical K. (cKP) and hypervirulent (hvKP). cKP isolates are highly diverse important causes of nosocomial infections; they include globally disseminated antibiotic-resistant clones. hvKP sensitive to most antibiotics but virulent, causing community-acquired infections in healthy individuals. The virulence phenotype is associated with pathogenicity loci responsible for siderophore hypermucoid capsule production. Recently, convergent strains , which possess features both hvKP, have emerged cause much concern. Here, we screen the genomes 2,608 multidrug-resistant from United States identify 47 isolates. We perform phenotypic genomic characterization 12 representative These contain a variety antimicrobial resistance plasmids plasmids. Most aerobactin biosynthesis genes produce more siderophores than not capsule. Unexpectedly, only 1 tested level consistent murine pneumonia model. findings suggest that additional studies should be performed clarify whether indeed virulent mouse human infections.

Язык: Английский

Процитировано

35
Presence of hypervirulence-associated determinants in Klebsiella pneumoniae from hospitalised patients in Germany DOI Creative Commons

Anika Wahl,

Martin A. Fischer,

Kathleen Klaper

и другие.

International Journal of Medical Microbiology, Год журнала: 2024, Номер 314, С. 151601 - 151601

Опубликована: Фев. 8, 2024

Klebsiella (K.) pneumoniae is a ubiquitous Gram-negative bacterium and common coloniser of animals humans. Today, K. one the most persistent nosocomial pathogens worldwide poses severe threat/burden to public health by causing urinary tract infections, pneumonia bloodstream infections. Affected infections are mainly immunocompromised individuals hospitalised patients. In recent years, new type has emerged associated with community-acquired such as pyogenic liver abscess in otherwise healthy therefore termed hypervirulent (hvKp). The aim this study was characterisation isolates properties hypervirulence from Germany. A set 62 potentially human patients compiled. Inclusion criteria were presence at least determinant that been previously hypervirulence: (I) clinical manifestation, (II) positive string test marker for hypermucoviscosity, (III) virulence genes rmpA and/or rmpA2 magA. Phenotypic included antimicrobial resistance testing broth microdilution. Whole genome sequencing (WGS) performed using Illumina® MiSeq, NextSeq investigate genetic repertoire multi-locus sequence types (ST), capsule (K), further collected isolates. For selected long-read applied plasmid sequences determinants compared. WGS analyses confirmed several signature hvKp. Among them, prevalent siderophore loci iuc ybt regulator rmpA2. dominant ST among hvKp ST395 K2 K5; both have described our data multidrug-resistant (MDR) ST23 K1 second abundant study; commonly hypervirulence. general, beta-lactams caused production extended-spectrum beta-lactamases (ESBL) carbapenemases observed frequently isolates, confirming threatening rise MDR-hvKp strains. Our results show strains carry present many years detection carbapenemase on same highly problematic requires intensified screening molecular surveillance. However, non-uniform definition complicates their detection. Testing hypermucoviscosity alone not specific enough identify Thus, we suggest classification should be only fulfil phenotypical (severe manifestations, hypermucoviscosity) but also two e.g. ybt,

Язык: Английский

Процитировано

10
Vaccines and Monoclonal Antibodies as Alternative Strategies to Antibiotics to Fight Antimicrobial Resistance DOI Open Access
Chiara La Guidara, Roberto Adamo, Claudia Sala

и другие.

International Journal of Molecular Sciences, Год журнала: 2024, Номер 25(10), С. 5487 - 5487

Опубликована: Май 17, 2024

Antimicrobial resistance (AMR) is one of the most critical threats to global public health in 21st century, causing a large number deaths every year both high-income and low- middle-income countries. Vaccines monoclonal antibodies can be exploited prevent treat diseases caused by AMR pathogens, thereby reducing antibiotic use decreasing selective pressure that favors emergence resistant strains. Here, differences mechanism action vaccines compared antibiotics are discussed. The state art for vaccine technologies reviewed, with particular focus on approaches validated clinical studies. By underscoring scope limitations different emerging technologies, this review points out complementary fighting AMR. Gaps antigen discovery some as well challenges associated development these therapies against highlighted.

Язык: Английский

Процитировано

9
Extensively Drug-Resistant Klebsiella pneumoniae Counteracts Fitness and Virulence Costs That Accompanied Ceftazidime-Avibactam Resistance Acquisition DOI
Elias Eger, Michael Schwabe, Lukas Schulig

и другие.

Microbiology Spectrum, Год журнала: 2022, Номер 10(3)

Опубликована: Апрель 18, 2022

Extensively drug-resistant Klebsiella pneumoniae causing major outbreaks and severe infections has become a significant challenge for health care systems worldwide. Rapid resistance development against last-resort therapeutics like ceftazidime-avibactam is driver the accelerated emergence of such pathogens.

Язык: Английский

Процитировано

32
A panel of diverse Klebsiella pneumoniae clinical isolates for research and development DOI Creative Commons
Melissa J. Martin, William Stribling,

Ana C. Ong

и другие.

Microbial Genomics, Год журнала: 2023, Номер 9(5)

Опубликована: Май 4, 2023

are a leading cause of healthcare-associated infections worldwide. In particular, strains expressing extended-spectrum β-lactamases (ESBLs) and carbapenemases pose serious treatment challenges, the World Health Organization (WHO) to designate ESBL carbapenem-resistant Enterobacteriaceae as 'critical' threats human health. Research efforts combat these pathogens can be supported by accessibility diverse clinically relevant isolates for testing novel therapeutics. Here, we describe panel 100

Язык: Английский

Процитировано

20