Epidemiology of β-Lactamase-Producing Pathogens

Clinical Microbiology Reviews, Год журнала: 2020, Номер 33(2)

Опубликована: Фев. 25, 2020

β-Lactam antibiotics have been widely used as therapeutic agents for the past 70 years, resulting in emergence of an abundance β-lactam-inactivating β-lactamases. Although penicillinases Staphylococcus aureus challenged initial uses penicillin, β-lactamases are most important Gram-negative bacteria, particularly enteric and nonfermentative pathogens, where collectively they confer resistance to all β-lactam-containing antibiotics.

Язык: Английский

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A Klebsiella pneumoniae ST307 outbreak clone from Germany demonstrates features of extensive drug resistance, hypermucoviscosity, and enhanced iron acquisition

Genome Medicine, Год журнала: 2020, Номер 12(1)

Опубликована: Дек. 1, 2020

Abstract Background Antibiotic-resistant Klebsiella pneumoniae are a major cause of hospital- and community-acquired infections, including sepsis, liver abscess, pneumonia, driven mainly by the emergence successful high-risk clonal lineages. The K. sequence type (ST) 307 lineage has appeared in several different parts world after first being described Europe 2008. From June to October 2019, we recorded an outbreak extensively drug-resistant ST307 four medical facilities north-eastern Germany. Methods Here, investigated these isolates those from subsequent cases same facilities. We performed whole-genome sequencing study phylogenetics, microevolution, plasmid transmission, as well phenotypic experiments growth curves, hypermucoviscosity, siderophore secretion, biofilm formation, desiccation resilience, serum survival, heavy metal resistance for in-depth characterization this clone. Results Phylogenetics suggest homogenous phylogram with sub-clades containing either only one patient or originating patients, suggesting inter-patient transmission. identified three large plasmids, carrying NDM-1, CTX-M-15, OXA-48, which likely donated other STs even bacterial species (e.g., Enterobacter cloacae ) within clinical settings. Several chromosomally plasmid-encoded, hypervirulence-associated virulence factors yersiniabactin, metabolite transporter, aerobactin, genes) were addition. While growth, comparable control strains, results secretion hypermucoviscosity revealed superiority clone, similar archetypical, hypervirulent strain (hvKP1). Conclusions combination extensive drug virulence, partly conferred through “mosaic” both antibiotic features, demonstrates serious public health implications.

Язык: Английский

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Systematic detection of horizontal gene transfer across genera among multidrug-resistant bacteria in a single hospital

eLife, Год журнала: 2020, Номер 9

Опубликована: Апрель 14, 2020

Multidrug-resistant bacteria pose a serious health threat, especially in hospitals. Horizontal gene transfer (HGT) of mobile genetic elements (MGEs) facilitates the spread antibiotic resistance, virulence, and environmental persistence genes between nosocomial pathogens. We screened genomes 2173 bacterial isolates from healthcare-associated infections single hospital over 18 months, identified identical nucleotide regions belonging to distinct genera. To further resolve these shared sequences, we performed long-read sequencing on subset generated highly contiguous genomes. then tracked appearance ten different plasmids all genomes, found evidence plasmid independent transmission. Finally, two instances likely within individual patients, including one that transferred second patient. This work expands our understanding HGT healthcare settings, can inform efforts limit drug-resistant pathogens

Язык: Английский

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Antimicrobial resistance in ICUs: an update in the light of the COVID-19 pandemic

Current Opinion in Critical Care, Год журнала: 2020, Номер 26(5), С. 433 - 441

Опубликована: Июль 28, 2020

To describe current antimicrobial resistance in ESKAPE Gram-negative microorganisms and their situation the ICUs, implication of so-called high-risk clones (HiRCs) involved spread as well relevance COVID-19 pandemic potential increase resistance.Extended-spectrum carbapenemase producing Enterobacterales multidrug extensive drug-resistant Pseudomonas aeruginosa Acinetobacter baumannii have increased worldwide. Sequence type (ST)131 Escherichia coli, ST258, ST11, ST10, ST147 ST307 Klebsiella pneumoniae, ST111, ST175, ST235 ST244 P. HiRCs are responsible for this some them implicated emergence mechanisms affecting new antimicrobials. A similar can be found with European clonal complex 1 2 A. baumannii. The high use antimicrobials during pandemic, particularly might a negative influence future trends resistance.The ICUs is mainly due to exemplified microorganisms. impact should monitored through specific surveillance studies ICUs.

Язык: Английский

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Whole-Genome Sequencing Surveillance and Machine Learning of the Electronic Health Record for Enhanced Healthcare Outbreak Detection

Clinical Infectious Diseases, Год журнала: 2021, Номер 75(3), С. 476 - 482

Опубликована: Ноя. 5, 2021

Most hospitals use traditional infection prevention (IP) methods for outbreak detection. We developed the Enhanced Detection System Healthcare-Associated Transmission (EDS-HAT), which combines whole-genome sequencing (WGS) surveillance and machine learning (ML) of electronic health record (EHR) to identify undetected outbreaks responsible transmission routes, respectively.We performed WGS healthcare-associated bacterial pathogens from November 2016 2018. EHR ML was used routes WGS-detected outbreaks, were investigated by an IP expert. Potential infections prevented estimated compared with practice during same period.Of 3165 isolates, there 2752 unique patient isolates in 99 clusters involving 297 (10.8%) identified WGS; ranged 2-14 patients. At least 1 route detected 65.7% clusters. During time, investigation prompted 15 suspected 133 patients, events 5 (3.8%). If EDS-HAT had been running real 25-63 transmissions could have prevented. found be cost-saving more effective than practice, overall savings $192 408-$692 532.EDS-HAT multiple not using methods, correctly most would save hospital substantial costs. Traditional misidentified did occur. combined has potential costs enhance safety.

Язык: Английский

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Genomic surveillance for multidrug-resistant or hypervirulent Klebsiella pneumoniae among United States bloodstream isolates

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

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Genomic dissection of endemic carbapenem resistance reveals metallo-beta-lactamase dissemination through clonal, plasmid and integron transfer

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

Опубликована: Авг. 8, 2023

Abstract Infections caused by metallo-beta-lactamase-producing organisms (MBLs) are a global health threat. Our understanding of transmission dynamics and how MBLs establish endemicity remains limited. We analysed two decades bla IMP-4 evolution in hospital using sequence data from 270 clinical environmental isolates (including 169 completed genomes) identified the gene across 7 Gram-negative genera, 68 bacterial strains distinct plasmid types. showed an initial multi-species outbreak conserved IncC plasmids (95 genomes 37 strains) allowed to be established through ability disseminate successful strain-genetic setting pairs we termed propagators, particular Serratia marcescens Enterobacter hormaechei . From this reservoir, persisted diversification genetic settings that resulted transfer between hosts integron carrying plasmids. findings provide framework for spread may have broader applicability other carbapenemase-producing organisms.

Язык: Английский

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Assessing computational predictions of antimicrobial resistance phenotypes from microbial genomes

Briefings in Bioinformatics, Год журнала: 2024, Номер 25(3)

Опубликована: Март 27, 2024

Abstract The advent of rapid whole-genome sequencing has created new opportunities for computational prediction antimicrobial resistance (AMR) phenotypes from genomic data. Both rule-based and machine learning (ML) approaches have been explored this task, but systematic benchmarking is still needed. Here, we evaluated four state-of-the-art ML methods (Kover, PhenotypeSeeker, Seq2Geno2Pheno Aytan-Aktug), an baseline the ResFinder by training testing each them across 78 species–antibiotic datasets, using a rigorous workflow that integrates three evaluation approaches, paired with distinct sample splitting methods. Our analysis revealed considerable variation in performance techniques datasets. Whereas generally excelled closely related strains, handling divergent genomes. Overall, Kover most frequently ranked top among followed PhenotypeSeeker Seq2Geno2Pheno. AMR antibiotic classes such as macrolides sulfonamides were predicted highest accuracies. quality predictions varied substantially combinations, particularly beta-lactams; species, phenotyping beta-lactams compound, aztreonam, amoxicillin/clavulanic acid, cefoxitin, ceftazidime piperacillin/tazobactam, alongside tetracyclines demonstrated more variable than other benchmarked antibiotics. By organism, Campylobacter jejuni Enterococcus faecium robustly those Escherichia coli, Staphylococcus aureus, Salmonella enterica, Neisseria gonorrhoeae, Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii, Streptococcus pneumoniae Mycobacterium tuberculosis. In addition, our study provides software recommendations combination. It furthermore highlights need optimization robust clinical applications, strains diverge used training.

Язык: Английский

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Genomic surveillance as a scalable framework for precision phage therapy against antibiotic-resistant pathogens

Cell, Год журнала: 2024, Номер unknown

Опубликована: Сен. 1, 2024

Язык: Английский

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Anatomy of an extensively drug-resistant Klebsiella pneumoniae outbreak in Tuscany, Italy

Proceedings of the National Academy of Sciences, Год журнала: 2021, Номер 118(48)

Опубликована: Ноя. 24, 2021

Significance Carbapenem-resistant Klebsiella pneumoniae belongs to the “critical-priority” tier of bacterial pathogens as identified by World Health Organization. Emerging “high-risk” lineages are responsible for difficult-to-treat, hospital-acquired infections and outbreaks around globe. By integrating genomic epidemiological data isolates collected over 20 mo, this study revealed both high, regional prevalence rapid spread, within a single hospital, K. ST-147 in Italy. Besides resistance nearly all antibiotics, lineage carried hybrid plasmid harboring set biomarker genes previously linked hypervirulence. Convergence virulence determinants is major concern these findings highlight need robust, global surveillance monitor emergence high-risk .

Язык: Английский

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