scholarly journals Population Biology and Epidemiological Studies of Acinetobacter baumannii in the Era of Whole Genome Sequencing: Is the Oxford Scheme Still Appropriate?

2020 ◽  
Vol 11 ◽  
Author(s):  
Xiaoting Hua ◽  
Linyue Zhang ◽  
Jintao He ◽  
Sebastian Leptihn ◽  
Yunsong Yu
Keyword(s):  
Whole Genome Sequencing ◽  
Acinetobacter Baumannii ◽  
Genome Sequencing ◽  
Population Biology ◽  
Epidemiological Studies ◽  
Whole Genome

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.

scholarly journals Genetic Characterization of Brucella spp.: Whole Genome Sequencing-Based Approach for the Determination of Multiple Locus Variable Number Tandem Repeat Profiles

2021 ◽  
Vol 12 ◽  
Author(s):  
Ana Pelerito ◽  
Alexandra Nunes ◽  
Teresa Grilo ◽  
Joana Isidro ◽  
Catarina Silva ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
In Silico ◽  
Variable Number Tandem Repeat ◽  
Epidemiological Studies ◽  
Variable Number ◽  
Epidemiological Surveillance ◽  
Future Application ◽  
Whole Genome

Brucellosis is an important zoonosis that is emerging in some regions of the world, gaining increased relevance with the inclusion of the causing agent Brucella spp. in the class B bioterrorism group. Until now, multi-locus VNTR Analysis (MLVA) based on 16 loci has been considered as the gold standard for Brucella typing. However, this methodology is laborious, and, with the rampant release of Brucella genomes, the transition from the traditional MLVA to whole genome sequencing (WGS)-based typing is on course. Nevertheless, in order to avoid a disruptive transition with the loss of massive genetic data obtained throughout the last decade and considering that the transition timings will vary considerably among different countries, it is important to determine WGS-based MLVA alleles of the nowadays sequenced genomes. On this regard, we aimed to evaluate the performance of a Python script that had been previously developed for the rapid in silico extraction of the MLVA alleles, by comparing it to the PCR-based MLVA procedure over 83 strains from different Brucella species. The WGS-based MLVA approach detected 95.3% of all possible 1,328 hits (83 strains×16 loci) and showed an agreement rate with the PCR-based MLVA procedure of 96.4% for MLVA-16. According to our dataset, we suggest the use of a minimal depth of coverage of ~50x and a maximum number of ~200 contigs as guiding “boundaries” for the future application of the script. In conclusion, the evaluated script seems to be a very useful and robust tool for the in silico determination of MLVA profiles of Brucella strains, allowing retrospective and prospective molecular epidemiological studies, which are important for maintaining an active epidemiological surveillance of brucellosis.

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 Whole-Genome Sequencing-Based Characterization of a Listeria monocytogenes Strain from an Aborted Water Buffalo in Southern Italy

2021 ◽  
Vol 9 (9) ◽  
pp. 1875
Author(s):  
Rubina Paradiso ◽  
Marita Georgia Riccardi ◽  
Bianca Cecere ◽  
Nunzia Riccone ◽  
Roberto Scialla ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Water Buffalo ◽  
Southern Italy ◽  
Antibiotic Resistance Genes ◽  
Epidemiological Studies ◽  
Whole Genome ◽  
Pathogenic Potential

Listeria monocytogenes is a Gram-positive pathogen causing life-threatening infections both in humans and animals. In livestock farms, it can persist for a long time and primarily causes uterine infections and encephalitis in farmed animals. Whole genome sequencing (WGS) is currently becoming the best method for molecular typing of this pathogen due to its high discriminatory power and efficiency of characterization. This study describes the WGS-based characterization of an L. monocytogenes strain from an aborted water buffalo fetus in southern Italy. The strain under study was classified as molecular serogroup IVb, phylogenetic lineage I, MLST sequence type 6, Clonal Complex 6, and cgMLST type CT3331, sublineage 6. Molecular analysis indicated the presence of 61 virulence genes and 4 antibiotic resistance genes. Phylogenetic analysis, including all the publicly available European L. monocytogenes serogroup IVb isolates, indicated that our strain clusterized with all the other CC6 strains and that different CCs were variably distributed within countries and isolation sources. This study contributes to the current understanding of the genetic diversity of L. monocytogenes from animal sources and highlights how the WGS strategy can provide insights into the pathogenic potential of this microorganism, acting as an important tool for epidemiological studies.

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