scholarly journals Investigation of a Carbapenemase-producing Acinetobacter baumannii outbreak using whole genome sequencing versus a standard epidemiologic investigation

2018 ◽  
Vol 7 (1) ◽  
Author(s):  
Chloe Bogaty ◽  
Laura Mataseje ◽  
Andrew Gray ◽  
Brigitte Lefebvre ◽  
Simon Lévesque ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Acinetobacter Baumannii ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Epidemiologic Investigation

scholarly journals Whole-Genome Sequencing for Investigating a Health Care-Associated Outbreak of Carbapenem-Resistant Acinetobacter baumannii

Diagnostics ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 201
Author(s):  
Sang Mee Hwang ◽  
Hee Won Cho ◽  
Tae Yeul Kim ◽  
Jeong Su Park ◽  
Jongtak Jung ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Acinetobacter Baumannii ◽  
Genome Sequencing ◽  
Snp Analysis ◽  
Whole Genome ◽  
Phylogenetic Tree Analysis ◽  
Web Based ◽  
Hospital Outbreak ◽  
Carbapenem Resistant ◽  
Bioinformatics Tools

Carbapenem-resistant Acinetobacter baumannii (CRAB) outbreaks in hospital settings challenge the treatment of patients and infection control. Understanding the relatedness of clinical isolates is important in distinguishing outbreak isolates from sporadic cases. This study investigated 11 CRAB isolates from a hospital outbreak by whole-genome sequencing (WGS), utilizing various bioinformatics tools for outbreak analysis. The results of multilocus sequence typing (MLST), single nucleotide polymorphism (SNP) analysis, and phylogenetic tree analysis by WGS through web-based tools were compared, and repetitive element polymerase chain reaction (rep-PCR) typing was performed. Through the WGS of 11 A. baumannii isolates, three clonal lineages were identified from the outbreak. The coexistence of blaOXA-23, blaOXA-66, blaADC-25, and armA with additional aminoglycoside-inactivating enzymes, predicted to confer multidrug resistance, was identified in all isolates. The MLST Oxford scheme identified three types (ST191, ST369, and ST451), and, through whole-genome MLST and whole-genome SNP analyses, different clones were found to exist within the MLST types. wgSNP showed the highest discriminatory power with the lowest similarities among the isolates. Using the various bioinformatics tools for WGS, CRAB outbreak analysis was applicable and identified three discrete clusters differentiating the separate epidemiologic relationships among the isolates.

Extensively drug-resistant Acinetobacter baumannii isolated from intensive care units in northern Italy: a genomic approach to characterize new sequence types

2019 ◽  
Vol 14 (15) ◽  
pp. 1281-1292 ◽  
Author(s):  
Giovanni Lorenzin ◽  
Erika Scaltriti ◽  
Franco Gargiulo ◽  
Francesca Caccuri ◽  
Giorgio Piccinelli ◽  
...  
Keyword(s):  
Intensive Care ◽  
Whole Genome Sequencing ◽  
Acinetobacter Baumannii ◽  
Intensive Care Units ◽  
Genome Sequencing ◽  
Multilocus Sequence Typing ◽  
Whole Genome ◽  
Drug Resistant ◽  
Extensively Drug Resistant ◽  
Sequence Types

Aim: This study aims to characterize clinical strains of Acinetobacter baumannii with an extensively drug-resistant phenotype. Methods: VITEK® 2, Etest® method and broth microdilution method for colistin were used. PCR analysis and multilocus sequence typing Pasteur scheme were performed to identify bla-OXA genes and genetic relatedness, respectively. Whole-genome sequencing analysis was used to characterize three isolates. Results: All the isolates were susceptible only to polymyxins. blaOXA-23-like gene was the only acquired carbapenemase gene in 88.2% of the isolates. Multilocus sequence typing identified various sequence types: ST2, ST19, ST195, ST577 and ST632. Two new sequence types, namely, ST1279 and ST1280, were detected by whole-genome sequencing. Conclusion: This study showed that carbapenem-resistant A. baumannii isolates causing infections in intensive care units almost exclusively produce OXA-23, underlining their frequent spread in Italy.

Whole-genome sequencing of NDM-1-producing ST85 Acinetobacter baumannii isolates from Tunisia

2018 ◽  
Vol 52 (6) ◽  
pp. 916-921 ◽  
Author(s):  
Nadia Jaidane ◽  
Thierry Naas ◽  
Saoussen Oueslati ◽  
Sandrine Bernabeu ◽  
Noureddine Boujaafar ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Acinetobacter Baumannii ◽  
Genome Sequencing ◽  
Whole Genome

69 Outbreak of Carbapenem-polymyxin-quat-resistant Acinetobacter Baumannii Associated with Mafenide Acetate Shortages: An Interdisciplinary Approach to Eradication

2020 ◽  
Vol 41 (Supplement_1) ◽  
pp. S45-S45
Author(s):  
Irma D Fleming ◽  
Carla Tang ◽  
Lois Remington ◽  
Giavonni Lewis
Keyword(s):  
Infection Control ◽  
Whole Genome Sequencing ◽  
Acinetobacter Baumannii ◽  
Genome Sequencing ◽  
Interdisciplinary Approach ◽  
Environmental Services ◽  
Whole Genome ◽  
Traumatic Injuries ◽  
Department Of Health ◽  
Surgical Suite

Abstract Introduction In the wake of Hurricane Maria, many US hospitals experienced massive drug shortages requiring substitution with alternative therapies. Our regional center experienced an increased incidence of Carbapenem-Polymyxin-Quat-Resistant Acinetobacter baumannii(CPQRA) infections, compared to a previous year of no infections. Here we describe a successful interdisciplinary approach to its eradication. Methods We conducted a retrospective review of CPQRA outbreaks for November and December 2018 in the burn ICU. De-identified data was collected and analyzed. In collaboration with the state’s department of health and epidemiology section, whole-genome sequencing was carried out on bacterial isolates. In addition, we instituted adenosine triphosphate (ATP) monitoring on all surfaces, a process of rapidly measuring actively growing microorganisms. Results Resistant Acinetobacter was isolated from five ICU patients, two of whom died with CPQRA bacteremia, producing a case-fatality rate of 40%. The two cases that died both suffered traumatic injuries with multiple fractures in addition to an average TBSA of 58%.Non-fatal cases suffered no other traumatic injuries and had an average TBSA of 51%.During this period, genitourinary irrigant (neomycin-Polymyxin B) and polymyxin ointment were the primary topical agents for wound care. Whole genome sequencing revealed a qacEdelta1 positive strain and identified the primary source as a patient that returned from a long-term care facility carrying the converted A. Baumannii infection. ATP testing also showed increased levels in patient rooms and surgical suite. Conclusions As a result of these findings, we achieved eradication by developing new and reinforcing traditional practices of infection control. This included UV light therapy to all ICU rooms and surgical suite, oversight of environmental services procedures, rigorous enforcement of hospital infection control procedures, auditing hand hygiene, increased efforts in antibiotic stewardshipand discontinuing Polymyxin containing topicals. By January 2019 there were no new cases of CPQRA in the ICU. This study shows that the resistance and rapid spread of CPQRA can be controlled with the cooperation of hospital staff, environmental services, infection control, pharmacy and the state’s department of health. With the coordinated efforts of all parties, we were able to successfully eradicate a virulent and fatal resistant A. baumannii strain. Applicability of Research to Practice Describe an approach to eradicating resistant organisms and provide a roadmap to characterize the source, implement control measures to terminate an outbreak, and institute preventive measures.

Whole genome analysis of extensively drug-resistant Acinetobacter bau-mannii clinical isolates in Thailand

2020 ◽  
Vol 20 ◽  
Author(s):  
Peechanika Chopjitt ◽  
Anusak Kerdsin ◽  
Dan Takeuchi ◽  
Rujirat Hatrongjit ◽  
Parichart Boueroy ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Acinetobacter Baumannii ◽  
Genome Sequencing ◽  
Efflux Pump ◽  
Multidrug Resistant ◽  
Whole Genome ◽  
Drug Resistant ◽  
Resistant Genes ◽  
Extensively Drug Resistant ◽  
Antibiotic Efflux

Background:: Acinetobacter baumannii is recognized as a majority opportunistic nosocomial pathogen and caus-ing hospital-acquired infection worldwide. The increasing prevalence of extensively drug-resistant Acinetobacter baumannii (XDRAB) has become a rising concern in healthcare facilities and has impeded public health due to limitation of therapeutic options and are associated with high morbidity and mortality as well as longer hospitalization. Whole-genome sequencing of highly multidrug resistant A. baumannii will increase understanding of resistant mechanisms, the emergence of novel re-sistance, genetic relationships among the isolates, source tracking, and treatment decisions in selected patients. Objective:: This study revealed the genomic analysis to explore blaOXA-23 harboring XDRAB isolates in Thailand. Methods:: Whole-genome sequencing of the two XDRAB isolates was carried out on a HiSeq2000 Illumina platform and susceptibility on antimicrobials was conducted. Results:: Both isolates revealed sequence types of international, clone II-carrying, multiple antimicrobial-resistant genes—ST195 and ST451. They were resistant to antimicrobial agents in all drug classes tested for Acinetobacter spp. They carried 18 antimicrobial-resistant genes comprising of 4 -lactamase genes (blaOXA-23, blaOXA-66, blaTEM-1D, blaADC-25), 4 aminogly-coside-resistant genes (armA, aph(3')-Ia, aph(3'')-Ib, aph(6)-Id), 3 macrolide-resistant genes (amvA, mphE, msrE), 1 sulfon-amide-resistant gene (sul-2), 2 tetracycline-resistant genes (tetB, tetR), 1 resistant-nodulation-cell division (RND) antibiotic efflux pump gene cluster, 2 major facilitator superfamily (MFS) antibiotic efflux pump genes (abaF, abaQ), and 1 small multidrug-resistant (SMR) antibiotic efflux pump gene (abeS). Mutation of gyrA (S81L) occurred in both isolates. Conclusions:: Whole-genome sequencing revealed both blaOXA-23 harboring XDRAB isolates were clustered under interna-tional clone II with difference STs and carrying multiple antimicrobial-resistant genes conferred their resistance to antimi-crobial agents. Inactivation of antimicrobials and target modification by enzymes, and pumping antibiotics by efflux pump are mainly resistance mechanism of the XDRAB in this study.

scholarly journals Complete Genome Sequence of Acinetobacter sp. Strain NCu2D-2 Isolated from a Mouse

2017 ◽  
Vol 5 (4) ◽  
Author(s):  
Ulrike Blaschke ◽  
Gottfried Wilharm
Keyword(s):  
Whole Genome Sequencing ◽  
Acinetobacter Baumannii ◽  
Genome Sequencing ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Insertion Sequences ◽  
Whole Genome ◽  
Nosocomial Pathogen ◽  
Content Type

ABSTRACT Whole-genome sequencing of Acinetobacter sp. strain NCu2D-2, isolated from the trachea of a mouse, revealed the presence of a plasmid of 309,964 bp with little overall similarity to known plasmids and enriched in insertion sequences (ISs) closely related to IS elements known from the nosocomial pathogen Acinetobacter baumannii.

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