Characteristics of a Carbapenem-Resistant <i>Acinetobacter baumannii</i> Strain Causing Community-Acquired Pneumonia in a Young Healthy Women

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Abstract

Background

Multidrug-resistant Acinetobacter baumannii rarely causes community-acquired pneumonia. Here, we report the clinical and genomic characteristics of a multidrug-resistant A. baumannii strain responsible for community-acquired pneumonia in a 31-year-old healthy young women.

Methods

A. baumannii strain W2LL was recovered from the alveolar lavage fluid sample of a hospitalized patient with pulmonary infection. Growth rate studies were conducted under various conditions, and virulence assessments were performed using Galleria Mellonella larvae. Whole Genome Sequencing (WGS) was carried out using Oxford Nanopore MinIon and Illumina HiSeq. In silico multilocus sequence typing (MLST), plasmid replicons, antimicrobial resistance genes, and virulence genes were determined using the BacWGSTdb webserver. Phylogenetic analysis between strain W2LL and other closely related A. baumannii genomes retrieved from NCBI database was performed.

Results

WGS identified strain W2LL as a rare sporadic lineage sequence type (ST) 1431. In addition to the detection of the β-lactamase gene ( bla _OXA-98 ) on the chromosome, bla _OXA-58 was found on a 92,034 bp plasmid. Antimicrobial susceptibility testing revealed this strain was resistant to cephalosporins and carbapenems, with initial treatment using cefoxitin proving ineffective. Subsequent treatment with piperacillin-sulbactam combined with levofloxacin led to gradual improvement. Compared to A. baumannii ATCC 17978, W2LL exhibited similar growth rates at 37°C and 42°C, as well as in the presence of zinc. However, strain W2LL exhibited higher virulence phenotype compared to ATCC 17978 in G. mellonella model. The closest relative of A. baumannii W2LL was CAM180_1, another isolate recovered from Cambodia, which differed by 191 SNPs.

Conclusion

W2LL is a rare ST1431 carbapenem-resistant A. baumannii strain recovered from a patient with no prior hospitalization or typical risk factors. This underscores the growing menace posed by carbapenem-resistant A. baumannii, no longer limited to hospitalized patients, potentially impacting the broader, younger population.

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Most cited references 32

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BacWGSTdb 2.0: a one-stop repository for bacterial whole-genome sequence typing and source tracking

Ye Feng, Shengmei Zou, Hangfei Chen … (2020)

Abstract An increasing prevalence of hospital acquired infections and foodborne illnesses caused by pathogenic and multidrug-resistant bacteria has stimulated a pressing need for benchtop computational techniques to rapidly and accurately classify bacteria from genomic sequence data, and based on that, to trace the source of infection. BacWGSTdb (http://bacdb.org/BacWGSTdb) is a free publicly accessible database we have developed for bacterial whole-genome sequence typing and source tracking. This database incorporates extensive resources for bacterial genome sequencing data and the corresponding metadata, combined with specialized bioinformatics tools that enable the systematic characterization of the bacterial isolates recovered from infections. Here, we present BacWGSTdb 2.0, which encompasses several major updates, including (i) the integration of the core genome multi-locus sequence typing (cgMLST) approach, which is highly scalable and appropriate for typing isolates belonging to different lineages; (ii) the addition of a multiple genome analysis module that can process dozens of user uploaded sequences in a batch mode; (iii) a new source tracking module for comparing user uploaded plasmid sequences to those deposited in the public databases; (iv) the number of species encompassed in BacWGSTdb 2.0 has increased from 9 to 20, which represents bacterial pathogens of medical importance; (v) a newly designed, user-friendly interface and a set of visualization tools for providing a convenient platform for users are also included. Overall, the updated BacWGSTdb 2.0 bears great utility in continuing to provide users, including epidemiologists, clinicians and bench scientists, with a one-stop solution to bacterial genome sequence analysis.

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Carbapenem resistance in Acinetobacter baumannii , and their importance in hospital‐acquired infections: a scientific review

M. Nguyen, S.G. Joshi (2021)

Carbapenem is an important therapy for serious hospital-acquired infections and for the care of patients affected by multidrug-resistant organisms, specifically Acinetobacter baumannii; however, with the global increase of carbapenem-resistant A. baumannii, this pathogen has significantly threatened public health. Thus, there is a pressing need to better understand this pathogen in order to develop novel treatments and control strategies for dealing with A. baumannii. In this review, we discuss an overview of carbapenem, including its discovery, development, classification and biological characteristics, and its importance in hospital medicine especially in critical care units. We also describe the peculiarity of bacterial pathogen, A. baumannii, including its commonly reported virulence factors, environmental persistence and carbapenem resistance mechanisms. In closing, we discuss various control strategies for overcoming carbapenem resistance in hospitals and for limiting outbreaks. With the appearance of strains that resist carbapenem, the aim of this review is to highlight the importance of understanding this increasingly problematic healthcare-associated pathogen that creates significant concern in the field of nosocomial infections and overall public health.

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BacWGSTdb, a database for genotyping and source tracking bacterial pathogens

Zhi Ruan, Ye Feng (2015)

Whole genome sequencing has become one of the routine methods in molecular epidemiological practice. In this study, we present BacWGSTdb (http://bacdb.org/BacWGSTdb), a bacterial whole genome sequence typing database which is designed for clinicians, clinical microbiologists and hospital epidemiologists. This database borrows the population structure from the current multi-locus sequence typing (MLST) scheme and adopts a hierarchical data structure: species, clonal complex and isolates. When users upload the pre-assembled genome sequences to BacWGSTdb, it offers the functionality of bacterial genotyping at both traditional MLST and whole-genome levels. More importantly, users are told which isolates in the public database are phylogenetically close to the query isolate, along with their clinical information such as host, isolation source, disease, collection time and geographical location. In this way, BacWGSTdb offers a rapid and convenient platform for worldwide users to address a variety of clinical microbiological issues such as source tracking bacterial pathogens.

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Author and article information

Journal

Journal ID (nlm-ta): Infect Drug Resist

Journal ID (iso-abbrev): Infect Drug Resist

Journal ID (publisher-id): idr

Title: Infection and Drug Resistance

Publisher: Dove

ISSN (Electronic): 1178-6973

Publication date (Electronic): 23 December 2023

Publication date Collection: 2023

Volume: 16

Pages: 7819-7826

Affiliations

[1 ]Department of General Practice, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine) , Hangzhou, Zhejiang Province, People’s Republic of China

[2 ]Department of Emergency Department, Affiliated Hospital of Hangzhou Normal University , Hangzhou, Zhejiang Province, People’s Republic of China

[3 ]Department of Respiratory Diseases, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine) , Hangzhou, Zhejiang Province, People’s Republic of China

[4 ]Institute of Respiratory Diseases of Traditional Chinese Medicine, Zhejiang Chinese Medical University , Hangzhou, Zhejiang Province, People’s Republic of China

Author notes

Correspondence: Jianfeng Wang, Department of Respiratory Diseases, The First Affiliated Hospital of Zhejiang Chinese Medical University , Hangzhou, Zhejiang Province, 310018, People’s Republic of China, Tel +86 571-87060305, Email 2001m@163.com

Author information

Yan Chen http://orcid.org/0009-0001-6328-7403

Jianfeng Wang http://orcid.org/0000-0002-6316-6361

Article

Publisher ID: 439614

DOI: 10.2147/IDR.S439614

PMC ID: 10752029

PubMed ID: 38152553

SO-VID: d648a5ab-80be-4d82-af11-158ac2dbcc76

License:

This work is published and licensed by Dove Medical Press Limited. The full terms of this license are available at https://www.dovepress.com/terms.php and incorporate the Creative Commons Attribution – Non Commercial (unported, v3.0) License ( http://creativecommons.org/licenses/by-nc/3.0/). By accessing the work you hereby accept the Terms. Non-commercial uses of the work are permitted without any further permission from Dove Medical Press Limited, provided the work is properly attributed. For permission for commercial use of this work, please see paragraphs 4.2 and 5 of our Terms ( https://www.dovepress.com/terms.php).

History

Date received : 02 October 2023

Date accepted : 01 December 2023

Page count

Figures: 4, Tables: 1, References: 32, Pages: 8

Funding

Funded by: Zhejiang Provincial Medical and Health Science and Technology Plan;

Funded by: the General Scientific Research Project of Zhejiang Provincial Department of Education;

Funded by: the Zhejiang Provincial Traditional Chinese Medicine Science and Technology Plan;

This research received support from the Zhejiang Provincial Medical and Health Science and Technology Plan (2020KY670, 2021KY827, 2023KY860), the General Scientific Research Project of Zhejiang Provincial Department of Education (Y202045219), and the Zhejiang Provincial Traditional Chinese Medicine Science and Technology Plan (Project Number: 2024ZL381).

Characteristics of a Carbapenem-Resistant Acinetobacter baumannii Strain Causing Community-Acquired Pneumonia in a Young Healthy Women

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Pneumonia, sex, and the environment

Most cited references 32

BacWGSTdb 2.0: a one-stop repository for bacterial whole-genome sequence typing and source tracking

Carbapenem resistance in Acinetobacter baumannii , and their importance in hospital‐acquired infections: a scientific review

BacWGSTdb, a database for genotyping and source tracking bacterial pathogens

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