Draft Genome Sequences of Six Multidrug-Resistant Clinical Strains of Acinetobacter baumannii, Isolated at Two Major Hospitals in Kuwait

Nasser, Kother; Mustafa, Abu Salim; Khan, Mohd Wasif; Purohit, Prashant; Al‐Obaid, Inaam; Dhar, Rita

doi:10.1128/genomea.00264-18

Cited by 6 publications

(5 citation statements)

References 9 publications

(9 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Analysis of patient isolates and strain relationships. Raw reads corresponding to genomes for outbreak isolates 29,[49][50][51] were downloaded and assembled using the Velvet assembler (v1.2.10) with parameters optimized by Velvet Optimiser (k-mer length: ranging from 81-127), scaffolded with OPERA-LG 74 (v1.4.1) and gap-filled with FinIS 75 (v0.3). Outbreak genomes from the same species were jointly analyzed with high-quality genomes from the hospital environment.…”

Section: © the Author(s) 2020mentioning

confidence: 99%

Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment

Li¹,

Bertrand²,

Kwah³

et al. 2020

Nat Med

157

View full text Add to dashboard Cite

Although disinfection is key to infection control, the colonization patterns and resistomes of hospital-environment microbes remain underexplored. We report the first extensive genomic characterization of microbiomes, pathogens and antibiotic resistance cassettes in a tertiary-care hospital, from repeated sampling (up to 1.5 years apart) of 179 sites associated with 45 beds. Deep shotgun metagenomics unveiled distinct ecological niches of microbes and antibiotic resistance genes characterized by biofilm-forming and human-microbiome-influenced environments with corresponding patterns of spatiotemporal divergence. Quasi-metagenomics with nanopore sequencing provided thousands of high-contiguity genomes, phage and plasmid sequences (>60% novel), enabling characterization of resistome and mobilome diversity and dynamic architectures in hospital environments. Phylogenetics identified multidrug-resistant strains as being widely distributed and stably colonizing across sites. Comparisons with clinical isolates indicated that such microbes can persist in hospitals for extended periods (>8 years), to opportunistically infect patients. These findings highlight the importance of characterizing antibiotic resistance reservoirs in hospitals and establish the feasibility of systematic surveys to target resources for preventing infections.

show abstract

Section: © the Author(s) 2020mentioning

confidence: 99%

Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment

Li¹,

Bertrand²,

Kwah³

et al. 2020

Nat Med

157

View full text Add to dashboard Cite

show abstract

“…Raw reads corresponding to genomes for outbreak isolates 38,55,57,86 were downloaded and assembled using the Velvet assembler 87…”

Section: Analysis Of Patient Isolates and Strain Relationshipsmentioning

confidence: 99%

Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment

Chng

Bertrand

et al. 2019

Preprint

View full text Add to dashboard Cite

There is growing attention surrounding hospital acquired infections (HAIs) due to high associated healthcare costs, compounded by the scourge of widespread multi-antibiotic resistance. Although hospital environment disinfection is well acknowledged to be key for infection control, an understanding of colonization patterns and resistome profiles of environment-dwelling microbes is currently lacking. We report the first extensive genomic characterization of microbiomes (355), common HAI-associated microbes (891) and transmissible drug resistance cassettes (1435) in a tertiary hospital environment based on a 2-timepoint sampling of 179 sites from 45 beds. Deep shotgun metagenomic sequencing unveiled two distinct ecological niches of microbes and antibiotic resistance genes characterized by biofilm-forming and human microbiome influenced environments that display corresponding patterns of divergence over space and time. To study common nosocomial pathogens that were typically present at low abundances, a combination of culture enrichment and long-read nanopore sequencing was used to obtain thousands of high contiguity genomes (2347) and closed plasmids (5910), a significant fraction of which (>58%) are not represented in current sequence databases. These high-quality assemblies and metadata enabled a rich characterization of resistance gene combinations, plasmid architectures, and the dynamic nature of hospital environment resistomes and their reservoirs. Phylogenetic analysis identified multidrug resistant clonal strains as being more widely disseminated and stably colonizing across hospital sites. Further genomic comparisons with clinical isolates across multiple species supports the hypothesis that multidrug resistant strains can persist in the hospital environment for extended periods (>8 years) to opportunistically infect patients. These findings highlight the importance of characterizing antibiotic resistance reservoirs in the hospital environment and establishes the feasibility of systematic genomic surveys to help target resources more efficiently for preventing HAIs.

show abstract

“…This finding fits well with a microbiological concept that A. baumannii is naturally resistant in any type of colonization sites. In clinical settings, A. baumannii is an emerging pathogen associated with hospital and community outbreaks [45][46][47]. It is clear that A. baumannii contains two main features of a successful nosocomial pathogen: sufficient antibiotic resistance elements as well as immense capacity for environmental colonization [48,49].…”

Section: Carbapenem-resistant Acinetobacter Baumanniimentioning

confidence: 99%

World Health Organization Report: Current Crisis of Antibiotic Resistance

et al. 2019

View full text Add to dashboard Cite

Antibiotic resistance is the most challenging clinical and public health problem. Despite of living in the era of novel technologies in biomedical research, many of untreatable infectious diseases are ranked as the main causes of human death worldwide. Increased antibiotic use in human and use in animal production are the two major causes of emergence of resistant bacteria in hospitals, human communities, and also animal farms. Current body of evidences is indicating that major factors that led to existing crisis on antibiotics worldwide are poor educational programs on hygiene and health, inappropriate prescription in addition to the overprescription in clinical settings (mainly in developing countries with easier access to the antibiotics) and lack of accurate diagnostic tools in laboratories in order to control the emergence of antibiotics against widely used drugs in community. It sounds using the antibodies against problematic bacteria in farms has more benefits than treating them with susceptible antibiotics. As best strategy, we pointed that the crisis of antibiotic resistance may be solved when all contributors be acknowledged to their responsibilities and duties to minimize this global problem threatening the human health. China and the USA as the two main antibiotics user in industrial scale should have taken new policy in meat industry. Currently, antibiotic resistance presents a growing health threat worldwide being the cause of many nosocomial and often deadly infections.

show abstract

Draft Genome Sequences of Six Multidrug-Resistant Clinical Strains of Acinetobacter baumannii, Isolated at Two Major Hospitals in Kuwait

Cited by 6 publications

References 9 publications

Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment

Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment

Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment

World Health Organization Report: Current Crisis of Antibiotic Resistance

Contact Info

Product

Resources

About