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Pearl S, Anbarasu A. Genomic landscape of nosocomial Acinetobacter baumannii: A comprehensive analysis of the resistome, virulome, and mobilome. Sci Rep 2025; 15:18203. [PMID: 40414962 DOI: 10.1038/s41598-025-03246-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2025] [Accepted: 05/19/2025] [Indexed: 05/27/2025] Open
Abstract
Acinetobacter baumannii (A. baumannii) is a major multidrug-resistant pathogen, posing serious threats in the healthcare settings. This study provides a comprehensive genomic analysis of nosocomial A. baumannii whole-genome sequences retrieved from NCBI Genome database. Multilocus sequence typing and capsule typing were performed to investigate the clonal diversity. The genomes were characterized to identify antimicrobial resistance genes (ARGs), virulence factors, and mobile genetic elements. Further, pangenome analysis was conducted to examine the core and accessory genomes of A. baumannii. Our dataset comprised of 609 genomes deposited from diverse geographic regions worldwide between 2004 and 2024. The genomes showed high clonal heterogeneity, with sequence type ST2 being the predominant sequence type. A total of 185 unique ARGs were identified, with majority of them associated with efflux pump and β-lactamase coding genes. Over 25,000 IS elements were detected, with IS4 family being the prevalent type. High abundance of integron-mediated resistance determinants, especially for aminoglycosides and β-lactams, were identified. The open pangenome window due to its larger accessory genome suggested substantial genome plasticity. Our findings highlight A. baumannii's rapid evolution and resistance potential, emphasizing need for alternative therapeutic strategies. Enhanced surveillance, infection control measures, and antimicrobial stewardship are crucial to combat this persistent threat.
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Affiliation(s)
- Sara Pearl
- Department of Biotechnology, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, 632014, India
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, 632014, India
| | - Anand Anbarasu
- Department of Biotechnology, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, 632014, India.
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, 632014, India.
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2
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Chen F, Lin J, Yang W, Chen J, Qian X, Yan T, Liu X, Lu Y, Chen Q. Secondary bacterial infections of Carbapenem-Resistant Acinetobacter baumannii in patients with COVID-19 admitted to Chinese ICUs. BMC Microbiol 2025; 25:319. [PMID: 40405103 PMCID: PMC12096753 DOI: 10.1186/s12866-025-04032-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 05/08/2025] [Indexed: 05/24/2025] Open
Abstract
BACKGROUND A significant proportion of patients who are hospitalized with coronavirus disease 2019 (COVID-19), particularly those being admitted to ICUs, exhibit the development of secondary bacterial infections (SBIs). However, there is a lack of detailed epidemiological investigations and genetic information of Carbapenem-Resistant Acinetobacter baumannii (CRAB) based on whole genome sequencing (WGS), which is one of the frequently detected bacteria among COVID-19 patients, to confirm alterations in the clonal structure and infection mechanism. RESULTS A total of 37 unique CRAB strains, sourced from patients, along with an additional 2 CRAB strains form the environment, were isolated. Among the cohort of 37 patients, 22 individuals succumbed to CRAB infection, resulting in a mortality rate of 54.46%. The median duration of illness for these patients was 7.95 days, highlighting the severity and rapid progression of CRAB infections in this patient population. A total of 22 CRAB strains, isolated from deceased individuals, in addition to two strains isolated from the environment, were subjected to further investigation. All 24 CRAB isolates exhibited a high ability to form biofilm and displayed a similar spectrum of resistance. Except for two isolates from patients with COVID-19, all the remaining CRAB isolates were categorized as ST195 and demonstrated highly close genetic background based on analysis of WGS. The ST195 strain of CRAB harbored three copies of the blaOXA-23 gene located on the chromosome, each of which was carried by Tn2006. Notably, one Tn2006 element was integrated within Tn6022, leading to the formation of AbaR4-like resistance islands Tn6166-I. CONCLUSIONS Our findings underscore the significance of SBIs in the COVID-19 pandemic, particularly those caused by CRAB and specifically those belonging to MLST types that were previously prevalent in ICUs.
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Affiliation(s)
- Fuhong Chen
- Department of Clinical Laboratory, Hangzhou Traditional Chinese Medicine Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, 310000, China
| | - Jia Lin
- Department of Clinical Laboratory, Hangzhou Traditional Chinese Medicine Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, 310000, China
| | - Wei Yang
- Department of Clinical Laboratory, Hangzhou Traditional Chinese Medicine Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, 310000, China
| | - Jie Chen
- Medical Intensive Care Unit, Hangzhou Traditional Chinese Medicine Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, 310000, China
| | - Xiang Qian
- Department of Clinical Laboratory, Hangzhou Traditional Chinese Medicine Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, 310000, China
| | - Tao Yan
- Department of Clinical Laboratory, Hangzhou Traditional Chinese Medicine Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, 310000, China
| | - Xiuping Liu
- Department of Clinical Laboratory, Hangzhou Traditional Chinese Medicine Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, 310000, China
| | - Yewei Lu
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, Zhejiang, 310020, China
| | - Qi Chen
- Department of Clinical Laboratory, Hangzhou Traditional Chinese Medicine Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, 310000, China.
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Sajerli B, Makai K, Lakatos L, Sarkadi-Nagy Á, Burián K, Orosz L. Aminoglycoside resistance dynamics and its predictive value for carbapenem resistance in multidrug-resistant Acinetobacter baumannii and Klebsiella pneumoniae. J Glob Antimicrob Resist 2025:S2213-7165(25)00118-3. [PMID: 40409495 DOI: 10.1016/j.jgar.2025.05.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2025] [Revised: 04/02/2025] [Accepted: 05/13/2025] [Indexed: 05/25/2025] Open
Abstract
OBJECTIVES The rise of multidrug-resistant (MDR) bacterial pathogens, including carbapenem-resistant Acinetobacter baumannii (CRAB) and Klebsiella pneumoniae (CRKP), poses a global healthcare challenge. Aminoglycosides remain among the few effective therapeutic options, but increasing resistance threatens their efficacy. This study investigates aminoglycoside consumption and resistance dynamics, focusing on the predictive value of aminoglycoside resistance for future carbapenem resistance. METHODS Data on aminoglycoside use (amikacin, gentamicin, tobramycin) and resistance were retrospectively collected (2010-2024). Resistance patterns were assessed using the Antibiotic Resistance Index and Resistance Instability Index. Correlation analyses examined associations between aminoglycoside consumption and resistance, including delayed effects, and between aminoglycoside and meropenem resistance. RESULTS We analyzed 4582 A. baumannii and 36,049 K. pneumoniae isolates. Among them, 2462 CRAB and 309 CRKP isolates were identified. Amikacin was the most used aminoglycoside, with stable resistance in CRAB and higher variability in CRKP. Gentamicin showed the most unstable resistance. In CRAB, aminoglycoside resistance - especially amikacin (r = 0.73) - was strongly correlated with meropenem resistance, suggesting predictive potential. In CRKP, predictive correlations were weaker; gentamicin showed the highest (r = 0.62). CONCLUSIONS Aminoglycoside resistance trends, particularly for amikacin in CRAB, may serve as early indicators of emerging carbapenem resistance. Integrating such data into surveillance and stewardship frameworks could improve early detection and response to MDR threats.
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Affiliation(s)
- Bence Sajerli
- Department of Medical Microbiology, University of Szeged, Szeged, Hungary.
| | - Klára Makai
- Central Pharmacy of Albert Szent-Györgyi Health Center, University of Szeged, Hungary.
| | | | - Ágnes Sarkadi-Nagy
- Department of Medical Microbiology, University of Szeged, Szeged, Hungary.
| | - Katalin Burián
- Department of Medical Microbiology, University of Szeged, Szeged, Hungary.
| | - László Orosz
- Department of Medical Microbiology, University of Szeged, Szeged, Hungary.
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Bhandari S, Upreti MK, Angbuhang KB, Shrestha B, Thapa Shrestha U. Biofilm formation capacity and Carbapenem-resistance in Acinetobacter-calcoaceticus-baumannii isolated from inpatients in a tertiary care hospital in Nepal. BMC Res Notes 2025; 18:225. [PMID: 40399960 PMCID: PMC12093812 DOI: 10.1186/s13104-025-07211-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2024] [Accepted: 03/27/2025] [Indexed: 05/23/2025] Open
Abstract
OBJECTIVE Acinetobacter calcoaceticus-baumannii complex (ACBC), as an emerging global burden to various clinical infections, has a huge problem in empirical therapy due to the increasing resistance to the majority of antibiotics. The ability of biofilm formation added to its antimicrobial resistance and helped its persistence and survival in the environment. To associate biofilm formation with carbapenem resistance, a hospital-based cross-sectional study was carried out from February 2020 to August 2020 at Kathmandu Model Hospital, Kathmandu, Nepal. ACBC was identified from the clinical samples following standard Microbiological procedures. A modified Kirby-Bauer disk diffusion method was performed to assay the antibiotic susceptibility testing of ACBC isolates to various antibiotic classes. A quantitative adherence assay was used to determine the biofilm assay. A conventional Polymerase Chain Reaction (PCR) method was used to find the targeted biofilm-related genes, Bap, csuE, and blaPER1 using specific primers. RESULTS Out of 665 different clinical samples, bacterial growth was observed in 281 (42.3%) clinical samples. Of these, 32 (11.4%) isolates were identified as ACBC. Out of 32 ACBC isolates, 29 (90.6%) of which were carbapenem-resistant. All carbapenem-resistant ACBC isolates were found to be sensitive to Polymixin B and Colistin. Out of 29 CR-ACBC, 17.2% of isolates were resistant to Tigecycline. The majority of ACBC isolates (93.8%) were multidrug-resistant (MDR) while 13 (40.6%) of isolates were extensively drug-resistant (XDR). A total of 31 ACBC isolates were biofilm producers, out of which 2 were strong biofilm producers followed by 8 moderate, and 21 were weak biofilm producers. The occurrence of biofilm-forming genes; Bap, csuE, and blaPER1 genes were found to be 65.6%, 65.6%, and 56.3% respectively among ACBC clinical isolates. A significant association was observed between carbapenem resistance, biofilm formation, and biofilm-related genes. CONCLUSION The higher rate of MDR and XDR ACBC isolates associated with biofilm formation in the study alarms the ACBC-related infection in clinical settings among inpatients. The hospital environment and clinical equipment are potential sources of biofilm-forming isolates. Hence, the effective sterilization of clinical equipment and hospital environment are utmost and a strong policy should be made to prescribe the proper antibiotic based on antibiogram profile to fight against an emerging threat of ACBC infections.
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Affiliation(s)
- Shova Bhandari
- GoldenGate International College, Battisputali, Kathmandu, Nepal
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Koong J, Hall RM, Hamidian M. Genomic characteristics of the multiresistant Acinetobacter baumannii global clone 1 reference strain A297/RUH875. J Antimicrob Chemother 2025:dkaf160. [PMID: 40387539 DOI: 10.1093/jac/dkaf160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2025] [Accepted: 05/09/2025] [Indexed: 05/20/2025] Open
Abstract
OBJECTIVES Acinetobacter baumannii ST1, also known as global clone 1 (GC1), is a globally distributed lineage associated with antimicrobial resistance (AMR). The multiresistant isolate A297/RUH8751, recovered from a urinary tract infection in the Netherlands in 1984, has served as a reference strain for ST1. We aimed to generate and analyse the complete genome sequence of A297/RUH8751 to provide insights into its genomic features, antibiotic resistance determinants and phylogenetic placement. METHODS WGS was performed using Oxford Nanopore GridION and Illumina HiSeq platforms. Assembly was conducted with Autocycler v0.2.1. Genomic features, including antibiotic resistance genes, insertion sequences and restriction-modification systems, were characterized using ResFinder, ISFinder and REBASE. Comparative analyses were conducted with the draft genome of NIPH 527, which also represents RUH875, to assess sequence variations. Phylogenetic analysis was performed to determine the evolutionary placement of A297/RUH875 within GC1. RESULTS The complete genome of RUH875 (A297) consists of a 3 965 450 bp chromosome and three plasmids: pA297-1 (pRAY*; 6078 bp), pA297-2 (8731 bp) and pA297-3 (a 200 kb conjugative plasmid). The chromosome harbours the AbaR21 genomic resistance island, carrying seven antibiotic resistance genes and six prophage regions. Notably, bap1 and bap2, biofilm-associated genes, were fully resolved, with bap1 identical to that of A. baumannii A1-the earliest GC1 isolate. Comparative analysis with A1 revealed 122 SNPs, with clustered variations suggesting potential recombination events. Phylogenetic analysis confirmed A297/RUH875 as a distinct lineage within GC1. The completed genome sequence provides a reference, in addition to strain A1, for studying AMR evolution in GC1 and enhances comparative genomic analyses.
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Affiliation(s)
- Jonathan Koong
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Ruth M Hall
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Mehrad Hamidian
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, NSW 2007, Australia
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6
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Morris TC, Reyneke B, Khan S, Khan W. Phage-antibiotic synergy to combat multidrug resistant strains of Gram-negative ESKAPE pathogens. Sci Rep 2025; 15:17235. [PMID: 40383795 PMCID: PMC12086229 DOI: 10.1038/s41598-025-01489-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2024] [Accepted: 05/06/2025] [Indexed: 05/20/2025] Open
Abstract
Bacteriophage-antibiotic-synergy (PAS) was investigated to target Pseudomonas aeruginosa, Klebsiella pneumoniae, Acinetobacter baumannii and Enterobacter cloacae. Whole genome sequencing indicated that bacteriophage KPW17 targeting K. pneumoniae, clustered with genus Webervirus, ECSR5 targeting E. cloacae clustered with Eclunavirus, PAW33 targeting P. aeruginosa clustered with Bruynoghevirus, while ABTW1 targeting A. baumannii clustered with Vieuvirus. PAS analysis showed that the combination of ciprofloxacin (CIP) and levofloxacin (LEV) with PAW33 resulted in the synergistic eradication of all tested P. aeruginosa strains. Similarly, the combined use of doripenem (DOR) and LEV with KPW17 resulted in the synergistic eradication of the environmental and clinical K. pneumoniae strains, while the combined use of DOR and gentamicin (CN) with ECSR5 was synergistic against the clinical E. cloacae NCTC 13406. Gentamicin with ECSR5, however, only exhibited an additive effect for E. cloacae 4L, while ABTW1 with piperacillin-tazobactam (TZP) and imipenem (IPM) resulted in an indifferent interaction between the bacteriophage and tested antibiotics against the clinical A. baumannii AB3, i.e., the activity of the combination is equal to the activity of most active agent. Thus, while the observed PAS may offer an opportunity for the re-introduction or more efficient application of certain antibiotics to combat antibiotic resistance, extensive research is required to determine the optimal phage-antibiotic combinations, dosages and treatment regiments.
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Affiliation(s)
- Tinta Carmen Morris
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
| | - Brandon Reyneke
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
| | - Sehaam Khan
- Faculty of Health Science, University of Johannesburg, PO Box 17011, Doornfontein, 2028, South Africa
| | - Wesaal Khan
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa.
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Brek TM, Muhajir AA, Alkuwaity KK, Haddad MA, Alattas EM, Eisa ZM, Al-Thaqafy MS, Albarraq AM, Al-Zahrani IA. Genomic insights of predominant international high-risk clone ST2 Acinetobacter baumannii isolates in Saudi Arabia. J Glob Antimicrob Resist 2025; 42:243-252. [PMID: 40158887 DOI: 10.1016/j.jgar.2025.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2024] [Revised: 03/24/2025] [Accepted: 03/25/2025] [Indexed: 04/02/2025] Open
Abstract
OBJECTIVES Carbapenem-resistant Acinetobacter baumannii (CRAB), particularly the globally prevalent ST2 clone, poses significant threats in the Gulf Cooperation Council region through extensive drug resistance, high virulence, and efficient gene transfer. This study investigates the epidemiological and genomic characteristics of CRAB in the Jazan region, using whole genome sequencing to understand its transmission and genetic determinants. METHODS Sixty-five clinical A. baumannii isolates exhibiting phenotypic resistance to carbapenems (meropenem, imipenem, and ertapenem) were collected from various tertiary hospitals in the Jazan region. The presence of prevalent carbapenemase genes among these isolates was examined using two sets of multiplex polymerase chain reaction (PCR). Forty-eight isolates confirmed as carbapenemase producers were selected for WGS analysis. RESULTS Among the 65 clinical CRAB isolates, the adult ICU exhibited the highest prevalence of CRAB (76.9%). Multiplex PCR identified 48 (73.8%) isolates as carbapenemase producers, all harboring blaOXA-51-like genes. Specifically, blaOXA-23 was detected in 39 isolates (60%), blaNDM in 8 (12.3%), and blaOXA-24 in one isolate. These 48 carbapenemase-producing isolates also carried virulence-associated genes related to adherence, biofilm formation, immune evasion, iron acquisition and regulation, and serum resistance. Whole-genome sequencing (WGS) revealed that 39 (81.2%) of the carbapenemase-positive isolates belonged to ST2, followed by ST85 and ST107, with the KL152 locus as the most common capsule type. CONCLUSIONS The study indicates a significant rise in the ST2 clone in the Arabian Gulf, particularly in Saudi Arabia, and underscores the need for ongoing surveillance of less common clones such as ST85 and ST107 to manage public health risks effectively.
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Affiliation(s)
- Thamer M Brek
- The regional laboratory, Jazan Health Cluster, Jazan, Saudi Arabia
| | | | - Khalil K Alkuwaity
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia; Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Moayad A Haddad
- Medical Laboratory Department, King Fahd hospital, Jazan Health Cluster, Jazan, Saudi Arabia
| | - Elaf M Alattas
- Medical Laboratory Department, King Fahd hospital, Jazan Health Cluster, Jazan, Saudi Arabia
| | - Zaki M Eisa
- Public Health Authority, Jazan, Saudi Arabia
| | - Majid S Al-Thaqafy
- Infection Prevention and Control Department, King Abdulaziz Medical City, Jeddah, Saudi Arabia; Epidemiology and Public Health, King Abdullah International Medical Research Center, Jeddah, Saudi Arabia; King Saud Bin Abdulaziz University for Health Sciences College of Medicine, Jeddah, Saudi Arabia
| | - Ahmed M Albarraq
- Public Health Laboratory, Public Health Authority, Riyadh, Saudi Arabia
| | - Ibrahim A Al-Zahrani
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia; Special Infectious Agents Unit-Biosafety Level-3, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia.
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8
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Luo Q, Chang M, Lu P, Guo Q, Jiang X, Xiao T, Zhang H, Ma Y, Zhang Y, Yu W, Zhang E, Chen Y, Shen P, Ji J, Ying C, Liu Z, Zhu H, Xiao Y. Genomic epidemiology and phylodynamics of Acinetobacter baumannii bloodstream isolates in China. Nat Commun 2025; 16:3536. [PMID: 40229304 PMCID: PMC11997098 DOI: 10.1038/s41467-025-58772-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2024] [Accepted: 04/01/2025] [Indexed: 04/16/2025] Open
Abstract
In recent decades, Acinetobacter baumannii has become a major global nosocomial pathogen, with bloodstream infections (BSIs) exhibiting mortality rates exceeding 60% and imposing substantial economic burdens. However, limited large-scale genomic epidemiology has hindered understanding of its population dynamics. Here, we analyzed 1506 non-repetitive BSI-causing A. baumannii isolates from 76 Chinese hospitals over a decade (2011-2021). We identified 149 sequence types (STs) and 101 K-locus types (KLs), revealing increased population diversity. International clone (IC) 2 accounted for 81.74% of isolates, with a notable shift in prevalent STs: ST208 increased while ST191 and ST195 declined, aligning with global trends. ST208 exhibited higher virulence, greater antibiotic resistance, enhanced desiccation tolerance, and more complex transmission patterns compared to ST191 and ST195. Its genomic plasticity drives its adaptation and spread. Using the high-resolution Oxford MLST scheme, this study uncovered greater diversity and genetic factors behind ST208's rise. A. baumannii is evolving from a low-virulence, multidrug-resistant pathogen to a more virulent one, highlighting the urgent need to address its growing threat. These findings have critical implications for infection control and public health policies.
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Affiliation(s)
- Qixia Luo
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medical School, College of medicine, Zhejiang University, Hangzhou, China
| | - Mengru Chang
- Department of Biomedical Engineering, College of Future Technology, Center for Quantitative Biology, and Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Ping Lu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medical School, College of medicine, Zhejiang University, Hangzhou, China
| | - Qian Guo
- Department of Biomedical Engineering, College of Future Technology, Center for Quantitative Biology, and Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Xiaoqing Jiang
- Department of Biomedical Engineering, College of Future Technology, Center for Quantitative Biology, and Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Tingting Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medical School, College of medicine, Zhejiang University, Hangzhou, China
| | - Haoyu Zhang
- Department of Biomedical Engineering, College of Future Technology, Center for Quantitative Biology, and Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Yingying Ma
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medical School, College of medicine, Zhejiang University, Hangzhou, China
| | - Yan Zhang
- Department of Biomedical Engineering, College of Future Technology, Center for Quantitative Biology, and Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Wei Yu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medical School, College of medicine, Zhejiang University, Hangzhou, China
| | - Erjia Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medical School, College of medicine, Zhejiang University, Hangzhou, China
| | - Yunbo Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medical School, College of medicine, Zhejiang University, Hangzhou, China
| | - Ping Shen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medical School, College of medicine, Zhejiang University, Hangzhou, China
| | - Jinru Ji
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medical School, College of medicine, Zhejiang University, Hangzhou, China
| | - Chaoqun Ying
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medical School, College of medicine, Zhejiang University, Hangzhou, China
| | - Zhiying Liu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medical School, College of medicine, Zhejiang University, Hangzhou, China
| | - Huaiqiu Zhu
- Department of Biomedical Engineering, College of Future Technology, Center for Quantitative Biology, and Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
| | - Yonghong Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medical School, College of medicine, Zhejiang University, Hangzhou, China.
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9
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Fuzi M. The fitness connection of antibiotic resistance. Front Microbiol 2025; 16:1556656. [PMID: 40276228 PMCID: PMC12020126 DOI: 10.3389/fmicb.2025.1556656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2025] [Accepted: 03/12/2025] [Indexed: 04/26/2025] Open
Abstract
More than three decades ago multidrug-resistant (MDR) clones of the pathogens: Staphylococcus aureus, Escherichia coli, Klebsiella pneumoniae, Clostridioides difficile, Enterococcus faecium, Pseudomonas aeruginosa and Acinetobacter baumannii have started to disseminate across wide geographical areas. A characteristic feature of all these MDR lineages is the carriage of some mutations in the quinolone resistance-determining regions (QRDRs) of DNA gyrase and topoisomerase IV which besides conferring resistance to fluoroquinolones are associated with a fitness benefit. Several lines of evidence strongly suggest that extra fitness conferred by these mutations facilitated the dissemination of the international MDR lineages. MDR pathogens require extra energy to cover the fitness cost conferred by the excess antibiotic resistance gene cargo. However, extra energy generated by upgraded metabolic activity was demonstrated to increase the uptake of antibiotics enhancing susceptibility. Accordingly, MDR bacteria need additional positive fitness schemes which, similarly to the QRDR advantage, will not compromise resistance. Some of these, not clone-specific effects are large genomes, the carriage of low-cost plasmids, the transfer of plasmid genes to the chromosome, the application of weak promoters in integrons and various techniques for the economic control of the activity of the integrase enzyme including a highly sophisticated system in A. baumannii. These impacts - among others - will confer a fitness advantage promoting the spread of MDR pathogens. However, even the potential of extra fitness generated by the combined effect of various schemes is not without limit and virulence-related genes or less relevant antibiotic resistance gene cargoes will often be sacrificed to permit the acquisition of high-priority resistance determinants. Accordingly major MDR clone strains are usually less virulent than susceptible isolates. In summary, a fitness approach to the research of antibiotic resistance is very useful since the fitness status of MDR bacteria seem to profoundly impact the capacity to disseminate in the healthcare setting.
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Affiliation(s)
- Miklos Fuzi
- Independent Researcher, Seattle, WA, United States
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10
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Ajoseh SO, Anjorin AAA, Salami WO, Brangsch H, Neubauer H, Wareth G, Akinyemi KO. Comprehensive molecular epidemiology of Acinetobacter baumannii from diverse sources in Nigeria. BMC Microbiol 2025; 25:178. [PMID: 40165088 PMCID: PMC11956268 DOI: 10.1186/s12866-025-03917-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2024] [Accepted: 03/20/2025] [Indexed: 04/02/2025] Open
Abstract
BACKGROUND Acinetobacter baumannii, a Gram-negative bacterium, is a public health threat due to its role in nosocomial infections and increasing antibiotic resistance. In Nigeria, data on the molecular epidemiology of A. baumannii is scarce. This study investigates the genetic diversity and the presence of antimicrobial resistance determinants and virulence-related genes in whole-genome sequencing data of 189 Nigerian A. baumannii isolates deposited in public repositories. Genotypes were determined in-silico by multilocus sequence typing (MLST) and core genome MLST (cgMLST). Further, antimicrobial resistance (AMR) and virulence-related genes were analyzed. RESULTS Most isolates (57.67%) originated from South-west Nigeria. Isolates of human origin accounted for 33.86%, while environmental sources comprised 6.87%, and 59.27% lacked information on the source of isolation. The cgMLST analysis revealed a multitude of genomic lineages circulating in Nigeria. The MLST Oxford scheme identified 44 sequence types (STs) in 62.96% of strains, with ST1089 being the most prevalent. The MLST Pasteur could assign 95.77% of strains to 49 STs, with ST2(IC2) and ST85(IC9) being the most dominant. Antimicrobial resistance analysis detected 168 genes encoding resistance to 12 antibiotic classes, with cephalosporin, carbapenem, and aminoglycoside resistance genes being the most prevalent. Notably, blaADC-79 (23.81%), blaOXA-23 (30.69%), and aph(3″)-Ib (30%) were frequent variants encountered. Seventeen multi-efflux system genes conferring resistance to multiple antibiotic classes were identified. Virulence gene analysis revealed 137 genes encoding six mechanisms, with genes for nutritional factors, effector delivery systems, and biofilm production being the most prevalent. CONCLUSION This study highlights the diversity in AMR and virulence genes of A. baumannii in Nigeria, emphasizing the need for ongoing genomic surveillance to inform infection control and develop antibiotic resistance management strategies.
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Affiliation(s)
- Samuel O Ajoseh
- Department of Microbiology, Faculty of Science, Lagos State University, P.M.B 0001, Ojo, Lagos, Nigeria
| | - Abdul-Azeez A Anjorin
- Department of Microbiology, Faculty of Science, Lagos State University, P.M.B 0001, Ojo, Lagos, Nigeria
| | - Wasiu O Salami
- Department of Microbiology, Faculty of Science, Lagos State University, P.M.B 0001, Ojo, Lagos, Nigeria
| | - Hanka Brangsch
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut (FLI), 07743, Jena, Germany
| | - Heinrich Neubauer
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut (FLI), 07743, Jena, Germany
| | - Gamal Wareth
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut (FLI), 07743, Jena, Germany.
| | - Kabiru O Akinyemi
- Department of Microbiology, Faculty of Science, Lagos State University, P.M.B 0001, Ojo, Lagos, Nigeria
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Li S, Jiang G, Wang S, Wang M, Wu Y, Zhang J, Liu X, Zhong L, Zhou M, Xie S, Ren Y, He P, Lou Y, Li H, Du J, Zhou Z. Emergence and global spread of a dominant multidrug-resistant clade within Acinetobacter baumannii. Nat Commun 2025; 16:2787. [PMID: 40118837 PMCID: PMC11928498 DOI: 10.1038/s41467-025-58106-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 03/12/2025] [Indexed: 03/24/2025] Open
Abstract
The proliferation of multi-drug resistant (MDR) bacteria is driven by the global spread of epidemic lineages that accumulate antimicrobial resistance genes (ARGs). Acinetobacter baumannii, a leading cause of nosocomial infections, displays resistance to most frontline antimicrobials and represents a significant challenge to public health. In this study, we conduct a comprehensive genomic analysis of over 15,000 A. baumannii genomes to identify a predominant epidemic super-lineage (ESL) accounting for approximately 70% of global isolates. Through hierarchical classification of the ESL into distinct lineages, clusters, and clades, we identified a stepwise evolutionary trajectory responsible for the worldwide expansion and transmission of A. baumannii over the last eight decades. We observed the rise and global spread of a previously unrecognized Clade 2.5.6, which emerged in East Asia in 2006. The epidemic of the clade is linked to the ongoing acquisition of ARGs and virulence factors facilitated by genetic recombination. Our results highlight the necessity for One Health-oriented research and interventions to address the spread of this MDR pathogen.
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Affiliation(s)
- Shengkai Li
- MOE Key Laboratory of Geriatric Diseases and Immunology, Cancer Institute, Suzhou Medical College, Soochow University, Suzhou, China
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Guilai Jiang
- MOE Key Laboratory of Geriatric Diseases and Immunology, Cancer Institute, Suzhou Medical College, Soochow University, Suzhou, China
- Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Soochow University, Suzhou, China
| | - Shengke Wang
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Min Wang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Yilei Wu
- MOE Key Laboratory of Geriatric Diseases and Immunology, Cancer Institute, Suzhou Medical College, Soochow University, Suzhou, China
- Department of Life Sciences, Imperial College London, London, UK
| | - Jinzhi Zhang
- Department of Critical Care Medicine, Zhejiang Provincial People's Hospital, Hangzhou, China
| | - Xiao Liu
- MOE Key Laboratory of Geriatric Diseases and Immunology, Cancer Institute, Suzhou Medical College, Soochow University, Suzhou, China
- Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Soochow University, Suzhou, China
| | - Ling Zhong
- MOE Key Laboratory of Geriatric Diseases and Immunology, Cancer Institute, Suzhou Medical College, Soochow University, Suzhou, China
| | - Min Zhou
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shichang Xie
- MOE Key Laboratory of Geriatric Diseases and Immunology, Cancer Institute, Suzhou Medical College, Soochow University, Suzhou, China
- Iotabiome Biotechnology Inc., Suzhou, China
| | - Yi Ren
- Iotabiome Biotechnology Inc., Suzhou, China
| | - Ping He
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yongliang Lou
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.
| | - Heng Li
- MOE Key Laboratory of Geriatric Diseases and Immunology, Cancer Institute, Suzhou Medical College, Soochow University, Suzhou, China.
- Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Soochow University, Suzhou, China.
| | - Jimei Du
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.
| | - Zhemin Zhou
- MOE Key Laboratory of Geriatric Diseases and Immunology, Cancer Institute, Suzhou Medical College, Soochow University, Suzhou, China.
- Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Soochow University, Suzhou, China.
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, China.
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
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12
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Ojo O, Njanje I, Abdissa D, Swart T, Higgitt RL, Dorrington RA. Newly isolated terpenoids (covering 2019-2024) from Aspergillus species and their potential for the discovery of novel antimicrobials. NATURAL PRODUCTS AND BIOPROSPECTING 2025; 15:19. [PMID: 40097883 PMCID: PMC11914449 DOI: 10.1007/s13659-025-00501-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2024] [Accepted: 02/23/2025] [Indexed: 03/19/2025]
Abstract
The rapid emergence of drug-resistant microbial pathogens has posed challenges to global health in the twenty-first century. This development has significantly made most antibiotics ineffective in the treatment of infections they cause, resulting in increasing treatment costs and annual death rates. To address the challenge posed by these pathogens, we explore the potential of secondary metabolites from Aspergillus species as a source of new and effective therapeutic agents to treat drug-resistant infections. Terpenoids, a distinct group of natural products, are extensively distributed in plants and fungi, and have been attributed with significant antibacterial, anticancer, and antiviral activities. In this review, we present an overview of Aspergillus species, and review the novel terpenoids isolated from them from 2019 to April 2024, highlighting anti-infective activity against members of the ESKAPE pathogens. We further focus on the strategies through which the structural framework of these new terpenoids could be modified and/or optimized to feed a pipeline of new lead compounds targeting microbial pathogens. Overall, this review provides insight into the therapeutic applications of terpenoids sourced from Aspergillus species and the potential for the discovery of new compounds from these fungi to combat antimicrobial resistance.
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Affiliation(s)
- Olusesan Ojo
- Department of Biochemistry, Microbiology and Bioinformatics, Rhodes University, Makhanda, South Africa.
- Department of Chemical Sciences, Lead City University, P.O. Box 30678, Ibadan, Oyo State, Nigeria.
| | - Idris Njanje
- Department of Biochemistry, Microbiology and Bioinformatics, Rhodes University, Makhanda, South Africa
| | - Dele Abdissa
- Department of Biochemistry, Microbiology and Bioinformatics, Rhodes University, Makhanda, South Africa
- Department of Chemistry, College of Natural Sciences, Jimma University, P.O Box 378, Jimma, Ethiopia
| | - Tarryn Swart
- Department of Biochemistry, Microbiology and Bioinformatics, Rhodes University, Makhanda, South Africa
| | - Roxanne L Higgitt
- Department of Biochemistry, Microbiology and Bioinformatics, Rhodes University, Makhanda, South Africa
| | - Rosemary A Dorrington
- Department of Biochemistry, Microbiology and Bioinformatics, Rhodes University, Makhanda, South Africa.
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Caddey B, Fisher S, Barkema HW, Nobrega DB. Companions in antimicrobial resistance: examining transmission of common antimicrobial-resistant organisms between people and their dogs, cats, and horses. Clin Microbiol Rev 2025; 38:e0014622. [PMID: 39853095 PMCID: PMC11905369 DOI: 10.1128/cmr.00146-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2025] Open
Abstract
SUMMARYNumerous questions persist regarding the role of companion animals as potential reservoirs of antimicrobial-resistant organisms that can infect humans. While relative antimicrobial usage in companion animals is lower than that in humans, certain antimicrobial-resistant pathogens have comparable colonization rates in companion animals and their human counterparts, which inevitably raises questions regarding potential antimicrobial resistance (AMR) transmission. Furthermore, the close contact between pets and their owners, as well as pets, veterinary professionals, and the veterinary clinic environment, provides ample opportunity for zoonotic transmission of antimicrobial-resistant pathogens. Here we summarize what is known about the transmission of AMR and select antimicrobial-resistant organisms between companion animals (primarily dogs, cats, and horses) and humans. We also describe the global distribution of selected antimicrobial-resistant organisms in companion animals. The impact of interspecies AMR transmission within households and veterinary care settings is critically reviewed and discussed in the context of methicillin-resistant staphylococci, extended-spectrum β-lactamase and carbapenemase-producing bacteria. Key research areas are emphasized within established global action plans on AMR, offering valuable insights for shaping future research and surveillance initiatives.
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Affiliation(s)
- Benjamin Caddey
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Sibina Fisher
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Herman W. Barkema
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Diego B. Nobrega
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
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Tobin LA, Abu Sabah E, Lebreton F, Myers GSA, McGann PT, Hamidian M. Genomic analysis of early ST32 Acinetobacter baumannii strains recovered in US military treatment facilities reveals distinct lineages and links to the origins of the Tn6168 ampC transposon. J Antimicrob Chemother 2025; 80:666-675. [PMID: 39680383 PMCID: PMC11879209 DOI: 10.1093/jac/dkae454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Accepted: 12/02/2024] [Indexed: 12/17/2024] Open
Abstract
OBJECTIVES To study the population structure and genomic characteristics, including antimicrobial resistance genes, plasmid types and surface polysaccharide type, of the globally distributed Acinetobacter baumannii belonging to ST32 (Institut Pasteur scheme). METHODS Antibiotic resistance phenotype for 19 antibiotics was determined using Vitek 2. Whole-genome sequencing was performed using the Illumina MiSeq platform. Genomes were assembled using Newbler. Phylogenetic analysis was done by determining the core-genome alignments using Panaroo v1.3, analysed in IQ-Tree2 v2.2.0.3 to construct Maximum Likelihood trees using the RaxML software. Resistance genes and IS were identified using the Abricate programme, and ISFinder databases. RESULTS One hundred and thirty-three (n = 133) ST32 A. baumannii isolates were analysed in this study. These genomes originated mainly from US military treatment facilities (n = 113), but also included additional publicly available genomes in GenBank (n = 20) recovered from a broad geographic distribution extending to Asia and South America. Phylogenetic analysis of all 133 genomes revealed at least four clades, with over 80 genomes forming a tightly clustered branch, suggesting they are likely to represent outbreak strains. Analysis of the ampC region showed that ST32 strains played a significant role in the formation of the widely distributed ampC transposon, Tn6168, and supplying DNA segments containing an ISAba1-ampC from ST32s via homologous recombination. CONCLUSIONS ST32 strains played a significant role in the evolution of antibiotic resistance in several widely distributed sequence types including ST1 (global clone 1) and ST3.
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Affiliation(s)
- Liam A Tobin
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Eradah Abu Sabah
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Francois Lebreton
- Multidrug Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Garry S A Myers
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Patrick T McGann
- Multidrug Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Mehrad Hamidian
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, NSW 2007, Australia
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15
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Panda L, Gk K, Sawant AR, Singh SK, Gupta M, C SD, Shashikala P, Prashanth K. Genomic insights into drug resistance and virulence determinants in rare pyomelanin-producing clinical isolates of Acinetobacter baumannii. Eur J Clin Microbiol Infect Dis 2025; 44:533-547. [PMID: 39699780 DOI: 10.1007/s10096-024-05008-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2024] [Accepted: 11/29/2024] [Indexed: 12/20/2024]
Abstract
PURPOSE Clinical isolates of multi-drug resistant Acinetobacter baumannii are a major cause of nosocomial infections, often attributed to the highly adaptable genome that helps it to thrive under environmental selection pressure. Here, we aim to provide genotypic-based surveys and comparative whole genome sequencing (WGS) analysis to explore the genomics of the rare pyomelanin-forming clinical isolates of A. baumannii from India. METHODS A total of 54 clinical isolates of A. baumannii obtained from two tertiary care hospitals were genotyped using repetitive sequence-based PCR (REP-PCR) for elucidating their molecular epidemiology, followed by their resistance profiling through the determination of minimum inhibitory concentration using the micro broth dilution method. The isolates' virulence and antibiotic-resistant determinants were detected by PCR screening, followed by biofilm quantification. Pyomelanin pigment produced by A. baumannii isolates was isolated and chemically characterized. Finally, WGS of three pigment-producing and one non-producing A. baumannii strains was performed to explore the factors contributing to their variability. RESULTS REP-PCR genotyping identified around 8 clusters, with all isolates being multidrug-resistant (MDR). Pyomelanin-producing isolates were strong biofilm formers, characterized by the concurrent presence of 'pgaB, BfmR, BfmS, ompA, and cusE' biofilm-related genes. These pigmented strains belonged to ST2Pas and co-harbored blaOXA-23, blaADC-25, aph (3')-VIa, armA, aph (6)-Id, tet(B) and msr(E) genes. Thirteen common IS elements and biosynthetic gene clusters of arylpolyene, NI-siderophore, and NRP-metallophore were identified. Notably, genomic islands containing aminoglycoside 3'-phosphotransferase, oxidative stress, two-component response regulators, efflux pump-related, toxin-antitoxin protein, and virulence-related genes were also mapped by WGS. CONCLUSION The pyomelanin-forming isolates were MDR and virulent. The elucidation of WGS analysis provided critical insights for understanding the epidemiology, virulome, and mobilome of rare pigment-producing A. baumannii strains.
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Affiliation(s)
- Lipsa Panda
- Department of Biotechnology, School of Life Sciences, Pondicherry University, R. Venkataraman Nagar, Kalapet, Pondicherry, 605014, India
| | - Krishnapriya Gk
- Department of Biotechnology, School of Life Sciences, Pondicherry University, R. Venkataraman Nagar, Kalapet, Pondicherry, 605014, India
| | - Ajit Ramesh Sawant
- Department of Biotechnology, School of Life Sciences, Pondicherry University, R. Venkataraman Nagar, Kalapet, Pondicherry, 605014, India
| | | | - Minakshi Gupta
- Department of Microbiology, Manipal Tata Medical College, Jamshedpur, Jharkhand, India
| | - Sheela Devi C
- Department of Clinical Microbiology, Pondicherry Institute of Medical Sciences (PIMS), Pondicherry, 605014, India
| | - P Shashikala
- Department of Clinical Microbiology, Pondicherry Institute of Medical Sciences (PIMS), Pondicherry, 605014, India
| | - K Prashanth
- Department of Biotechnology, School of Life Sciences, Pondicherry University, R. Venkataraman Nagar, Kalapet, Pondicherry, 605014, India.
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16
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Chen J, Shao Y, Cheng Z, Li G, Wan F, Gao C, Wu D, Wei D, Liu Y, Li R. Exploring the clinical outcomes and molecular characteristics of Acinetobacter baumannii bloodstream infections: a study of sequence types, capsular types, and drug resistance in China. Front Cell Infect Microbiol 2025; 15:1549940. [PMID: 40034394 PMCID: PMC11872892 DOI: 10.3389/fcimb.2025.1549940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2024] [Accepted: 01/28/2025] [Indexed: 03/05/2025] Open
Abstract
Background Bloodstream infections (BSIs) caused by Acinetobacter baumannii have been associated with high mortality. To improve the outcomes of patients, this study explored the clinical characteristics and outcomes of patients with BSIs, as well as the phenotypic and genomic characteristics of these isolates. Methods A retrospective cohort study was conducted involving A. baumannii BSIs cases from 2020 to 2023 in a tertiary hospital. The clinical characteristics of all A. baumannii isolates were evaluated. Virulence phenotypes of all isolates were evaluated using the growth curve, biofilm-forming assay, antiserum complement killing, and G.mellonella killing assay. Furthermore, whole-genome sequencing (WGS) was utilized to analyze genomic characteristics. Results The 30-day mortality rate of 67 patients with BSIs was 55.22%. Patients in the death group had significantly lower platelet counts and higher CRP levels than those in the survival group. Additionally, higher rates of antibiotic use (≥2 classes) and greater carbapenem exposure were observed. Among the isolates, CRAb accounted for 80.6%, ST2 accounted for 76.12%, and KL2/3/7/77/160 accounted for 65.67%. The predominant KL type was KL3, found in 19.4% of the isolates. All ST2 and KL2/3/7/77/160 isolates were CRAb. Among the isolates, 90.7% of the CRAb isolates coharbored blaOXA-23 and blaOXA-66 , while one coharbored blaNDM-1 and blaOXA-23 . Compared with non-ST2 and non KL2/3/7/77/160 infections, ST2 and KL2/3/7/77/160 infections had higher mortality rates (66.0% vs. 23.5%, P=0.002; 65.90% vs. 34.78%, P=0.015). Patients with ST2 and KL2/3/7/77/160 infections underwent more invasive procedures, received two or more antibiotics and carbapenem therapy before isolation, and had lower serum albumin levels. These isolates exhibited significantly higher resistance to antimicrobial agents. No significant differences in virulence phenotypes were observed between the two groups, except for biofilm formation between the ST2 and non-ST2 groups (P=0.002). However, these isolates harbored more virulence genes related to iron uptake and biofilm formation. Conclusion The mortality rate associated with BSIs caused by A. baumannii is high. It is of great significance for clinicians to pay attention to the risk factors of the clinical characteristics of patients and to identify the ST and KL types of the strains causing the infection at an early stage.
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Affiliation(s)
- Jiao Chen
- School of Laboratory Medicine, Nanchang Medical College, Nanchang, China
| | - Yanting Shao
- School of Laboratory Medicine, Nanchang Medical College, Nanchang, China
| | - Zhibin Cheng
- School of Laboratory Medicine, Nanchang Medical College, Nanchang, China
| | - Guanghui Li
- School of Information Engineering, East China Jiaotong University, Nanchang, China
| | - Fen Wan
- School of Laboratory Medicine, Nanchang Medical College, Nanchang, China
| | - Chenyan Gao
- School of Laboratory Medicine, Nanchang Medical College, Nanchang, China
| | - Danqin Wu
- Neurology Intensive Care Unit (ICU), First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Dandan Wei
- Department of Clinical Microbiology, the First Affiliated Hospital of Nanchang University, Nanchang, China
- Clinical Laboratory, China-Japan Friendship Jiang Xi Hospital, Nanchang, China
| | - Yang Liu
- Department of Clinical Microbiology, the First Affiliated Hospital of Nanchang University, Nanchang, China
- Clinical Laboratory, China-Japan Friendship Jiang Xi Hospital, Nanchang, China
| | - Rong Li
- Department of Clinical Laboratory & Jiangxi Province Key Laboratory of Immunology and Inflammation, Jiangxi Provincial People's Hospital & The first Affiliated Hospital of Nanchang Medical College, Nanchang, China
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Din NS, Mohd. Rani F, Alattraqchi AG, Ismail S, A. Rahman NI, Cleary DW, Clarke SC, Yeo CC. Whole-genome sequencing of Acinetobacter baumannii clinical isolates from a tertiary hospital in Terengganu, Malaysia (2011-2020), revealed the predominance of the Global Clone 2 lineage. Microb Genom 2025; 11:001345. [PMID: 39908088 PMCID: PMC11798184 DOI: 10.1099/mgen.0.001345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2024] [Accepted: 12/13/2024] [Indexed: 02/06/2025] Open
Abstract
Carbapenem-resistant Acinetobacter baumannii is recognized by the World Health Organization (WHO) as one of the top priority pathogens. Despite its public health importance, genomic data of clinical isolates from Malaysia remain scarce. In this study, whole-genome sequencing was performed on 126 A. baumannii isolates collected from the main tertiary hospital in the state of Terengganu, Malaysia, over a 10-year period (2011-2020). Antimicrobial susceptibilities determined for 20 antibiotics belonging to 8 classes showed that 77.0% (n=97/126) of the isolates were categorized as multidrug resistant (MDR), with all MDR isolates being carbapenem resistant. Multilocus sequence typing analysis categorized the Terengganu A. baumannii clinical isolates into 34 Pasteur and 44 Oxford sequence types (STs), with ST2Pasteur of the Global Clone 2 lineage identified as the dominant ST (n=76/126; 60.3%). The ST2Pasteur isolates could be subdivided into six Oxford STs with the majority being ST195Oxford (n=35) and ST208Oxford (n=17). Various antimicrobial resistance genes were identified with the bla OXA-23-encoded carbapenemase being the predominant acquired carbapenemase gene (n=90/126; 71.4%). Plasmid-encoded rep genes were identified in nearly all (n=122/126; 96.8%) of the isolates with the majority being Rep_3 family (n=121). Various virulence factors were identified, highlighting the pathogenic nature of this bacterium. Only 14/126 (11.1%) of the isolates were positive for the carriage of CRISPR-Cas arrays with none of the prevalent ST2Pasteur isolates harbouring them. This study provided a genomic snapshot of the A. baumannii isolates obtained from a single tertiary healthcare centre in Malaysia over a 10-year period and showed the predominance of a single closely related ST2Pasteur lineage, indicating the entrenchment of this clone in the hospital.
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Affiliation(s)
- Nurul Saidah Din
- Centre for Research in Infectious Diseases and Biotechnology, Faculty of Medicine, Universiti Sultan Zainal Abidin, Kuala Terengganu, Malaysia
| | - Farahiyah Mohd. Rani
- Centre for Research in Infectious Diseases and Biotechnology, Faculty of Medicine, Universiti Sultan Zainal Abidin, Kuala Terengganu, Malaysia
| | - Ahmed Ghazi Alattraqchi
- Centre for Research in Infectious Diseases and Biotechnology, Faculty of Medicine, Universiti Sultan Zainal Abidin, Kuala Terengganu, Malaysia
| | - Salwani Ismail
- Centre for Research in Infectious Diseases and Biotechnology, Faculty of Medicine, Universiti Sultan Zainal Abidin, Kuala Terengganu, Malaysia
| | - Nor Iza A. Rahman
- Centre for Research in Infectious Diseases and Biotechnology, Faculty of Medicine, Universiti Sultan Zainal Abidin, Kuala Terengganu, Malaysia
| | - David W. Cleary
- Department of Microbes, Infections and Microbiomes, School of Infection, Inflammation and Immunology, College of Medicine and Health, University of Birmingham, Birmingham, UK
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Stuart C. Clarke
- Centre for Research in Infectious Diseases and Biotechnology, Faculty of Medicine, Universiti Sultan Zainal Abidin, Kuala Terengganu, Malaysia
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton Foundation NHS Trust, Southampton, UK
- Global Health Research Institute, University of Southampton, Southampton, UK
- Institute for Research, Development and Innovation, International Medical University, Kuala Lumpur, Malaysia
| | - Chew Chieng Yeo
- Centre for Research in Infectious Diseases and Biotechnology, Faculty of Medicine, Universiti Sultan Zainal Abidin, Kuala Terengganu, Malaysia
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Fatima K, Naqvi SZH, Ali H, Hassan N, Saqib A, Ansari F, Saleem S, Jahan S, Ahmad M. Analysis of the genome data of Acinetobacter baumannii UOL-KIMZ-24, exhibiting multiple drug resistance through efflux pumps. Data Brief 2025; 58:111188. [PMID: 39802840 PMCID: PMC11719380 DOI: 10.1016/j.dib.2024.111188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2024] [Revised: 11/25/2024] [Accepted: 11/25/2024] [Indexed: 01/16/2025] Open
Abstract
Acinetobacter baumannii is a well-known opportunistic pathogen, responsible for various nosocomial infections. A. baumannii UOL-KIMZ-24 was previously isolated from a clinical specimen, collected from Lahore General Hospital, Lahore (LGH), Pakistan, dated 3rd March, 2022. During the initial screening for antimicrobial susceptibility, the UOL-KIMZ-24 was found a multiple drug resistant (MDR) strain. However, the detailed genomic insights for genes e.g. responsible for exhibiting antibiotic resistance via efflux pumps, have not yet been reported from A. baumannii strains, recovered from LGH. The current research to fills this gap by isolating, whole genome sequencing and subsequent post-sequencing analysis for addressing and identifying the efflux pumps associated genes, responsible for multiple drug resistant in A. baumannii. In a hybrid approach, short reads were processed through Illumina platform, while long reads were sequenced by MinION MK1B sequencing technique. The assembled and annotated genome of the UOL-KIMZ-24 revealed that it has 4048631 bp genome size with 179 contigs, 38.9 % GC content, 3628 protein coding sequences, 80 tRNA and 7 rRNA. The analysis of antibiotic-resistance genes (AMR) depicted 27 genes. where the genes encoding efflux pumps such as adeABC, adeRS, adeJK, and adeMN were the more prominent. In addition, sequence typing (ST) study showed that UOL-KIMZ-24 strain lies in ST2, six prophage sequences and 73 virulence factors were also identified in the studied UOL-KIMZ-24. Such an all-inclusive study uncovered the genetic flexibility of UOL-KIMZ-24 genome for acquiring MDR against in-practice antibiotics.
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Affiliation(s)
- Kiran Fatima
- Department of Microbiology, Institute of Molecular Biology and Biotechnology, University of Lahore, Lahore 54000, Pakistan
- Departemnt of Pathology, Rawalpindi Medical University, Rawalpindi 46000, Pakistan
| | - Syed Zeeshan Haider Naqvi
- Department of Microbiology, Institute of Molecular Biology and Biotechnology, University of Lahore, Lahore 54000, Pakistan
| | - Hazrat Ali
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering-College, Pakistan Institute of Engineering and Applied Sciences, Islamabad 44000, Pakistan
| | - Noor Hassan
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering-College, Pakistan Institute of Engineering and Applied Sciences, Islamabad 44000, Pakistan
| | - Anam Saqib
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering-College, Pakistan Institute of Engineering and Applied Sciences, Islamabad 44000, Pakistan
| | - Farheen Ansari
- Department of Microbiology, University of Karachi, Karachi 75270, Pakistan
| | - Sidrah Saleem
- Department of Microbiology, University of Health Sciences, Lahore 54000, Pakistan
| | - Shah Jahan
- Department of Immunology, Allied Health Sciences, University of Health Sciences, Lahore 54000, Pakistan
| | - Mushtaq Ahmad
- Biomedical Optics, Rawalpindi Medical University, Rawalpindi 46000, Pakistan
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19
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Rajmichael R, Hemavathy N, Mathimaran A, Pandian CJ, Kingsley JD, Subramanian G, Jeyakanthan J. Whole genome sequencing characterization and comparative genome analysis of Acinetobacter baumannii JJAB01: A comprehensive insights on antimicrobial resistance and virulence genotype. Microb Pathog 2025; 199:107224. [PMID: 39675438 DOI: 10.1016/j.micpath.2024.107224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2024] [Revised: 10/30/2024] [Accepted: 12/11/2024] [Indexed: 12/17/2024]
Abstract
The emergence of antibiotic resistance has significantly elevated the threat posed by Acinetobacter baumannii as an opportunistic pathogen. A.baumannii, a notorious bacterium, poses a serious threat to health care, leading to severe nosocomial infections, particularly in immunocompromised individuals. Whole-Genome Sequencing studies are efficient in providing accurate genetic information, aiding in detecting outbreaks, surveillance of resistance, and controlling infection transmission. In this study, we investigated the whole genome of a clinical isolate A. baumannii JJAB01 which sourced from a urine sample of an Intensive Care Unit (ICU) patient. This strain showed resistance to 24 available antibiotics, signifying Extremely Drug Resistant (XDR) and high potential for pathogenicity. Whole Genome Sequencing was performed using Illumina, and the raw reads were evaluated using the FastQC tool. Genome assembly and annotation were performed with Unicycler and the RAST server. The JJAB01 genome is 4.07 Mb with a GC content of 38.9 %. A total of 51 and 31 virulence factors and antimicrobial-resistant (AMR) genes were predicted using the VFDB and CARD databases. Comparative genome studies were carried out on virulence factors, resistance genes, prophages, and Multi-Locus Sequence Typing (MLST) across twelve closely related A. baumannii genomes, including JJAB01, X4-584, X4-705, 2023CK-00423, 2023CK-00890, 2023CK-00127, 2022CK-00066, B20AB01, B20AB10, F20AB03, G20AB08, and X4-65. These computational investigations in this study emphasis the multidimensional nature of the ICU strain JJAB01 and its genetic similarity to other strains, thereby enhancing our understanding of drug resistance and the pathogenicity associated with A. baumannii infections.
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Affiliation(s)
- Raji Rajmichael
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, 630 004, Tamil Nadu, India
| | - Nagarajan Hemavathy
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, 630 004, Tamil Nadu, India
| | - Ahila Mathimaran
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, 630 004, Tamil Nadu, India
| | - Chitra Jeyaraj Pandian
- Department of Biotechnology, Dr. Umayal Ramanathan College for Women, Karaikudi, 630 003, Tamil Nadu, India
| | - Jemima D Kingsley
- Orbito Asia Diagnostics Private Limited, Coimbatore, 641 045, Tamil Nadu, India
| | | | - Jeyaraman Jeyakanthan
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, 630 004, Tamil Nadu, India.
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20
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Mat Ghani N, Hong KW, Liew YJM, Lau YY, Yong HS, Tee KK, Chan KG, Chua KO. Whole genome analysis revealed the role of blaOXA-23 and blaOXA-66 genes in carbapenem resistance of Acinetobacter baumannii strains. Pathog Glob Health 2025; 119:10-21. [PMID: 39699991 PMCID: PMC11905307 DOI: 10.1080/20477724.2024.2442194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2024] Open
Abstract
Acinetobacter baumannii is a multidrug-resistant bacterium that has emerged as a significant nosocomial pathogen globally and renowned for its ability to acquire antimicrobial resistance (AMR) genes. However, understanding of its resistance mechanisms to certain drug classes remains limited. This study focused on four bacterial strains (AB863, AB889, AB930, and AB960) exhibiting carbapenem resistance. They demonstrated high minimum inhibitory concentration (MIC) (128 mg/L) to meropenem and were categorized as extensively drug-resistant strains. Subsequently, they were identified as A. baumannii through 16S rRNA gene sequence analysis and species-specific PCR targeting the blaOXA51-like gene. Three strains were sequenced for their genomes to study the genetic determinants and functional relevance of carbapenem resistance. The draft genome length of the strains ranged from 3.8 to 4.0 Mbp. A total of 16 antibiotic resistance genes including the genes blaOXA-23 and blaOXA-66 which mediate carbapenem resistance were identified in the genomes. A comprehensive multilocus sequence typing analysis involving 95 A. baumannii strains from different Asian countries assigned the four strains to sequence type 2 (ST2), the most predominant ST circulating in Asia. Comparative genome analysis also revealed blaOXA-66 as the most dominant variant of blaOXA-51-like gene and also a widespread distribution of blaOXA-23 gene. In addition, various mobile genetic elements associated with AMR genes and three efflux pumps families were detected in the genomes of the strains. Transformation of blaOXA-23 and blaOXA-66 genes resulted in meropenem resistance in the transformant which exhibited a MIC of 2 mg/L, thus confirming direct involvement of both genes in carbapenem resistance.
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Affiliation(s)
- Nurizati Mat Ghani
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Kar-Wai Hong
- Novel Bacteria and Drug Discovery Research Group (NBDD), Microbiome and Bioresource Research Strength (MBRS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway, Malaysia
| | - Yvonne Jing Mei Liew
- Department of Pharmaceutical Life Sciences, Faculty of Pharmacy, Universiti Malaya, Kuala Lumpur, Malaysia
- Universiti Malaya, University of Malaya Centre for Proteomics Research, Kuala Lumpur, Malaysia
| | - Yin Yin Lau
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University Kuala Lumpur, Kuala Lumpur, Malaysia
| | - Hoi-Sen Yong
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Kok Keng Tee
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kok-Gan Chan
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia
- Institute of Marine Sciences, Shantou University, Shantou, China
- Research Center for Life Science and Healthcare, China Beacons of Excellence Research and Innovation Institute (CBI), University of Nottingham Ningbo China (UNNC), Zhejiang, China
| | - Kah-Ooi Chua
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia
- Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, Kuala Lumpur, Malaysia
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21
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Abouelhassan Y, Shen Y, Chen A, Ye X, Nicolau DP, Kuti JL. Ex vivo assessment of sulbactam-durlobactam clearance during continuous renal replacement therapy to guide dosing recommendations. Antimicrob Agents Chemother 2025; 69:e0167423. [PMID: 39655912 PMCID: PMC11784458 DOI: 10.1128/aac.01674-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 11/18/2024] [Indexed: 02/01/2025] Open
Abstract
Sulbactam-durlobactam is approved for the treatment of hospital-acquired and ventilator-associated bacterial pneumonia caused by susceptible isolates of Acinetobacter baumannii-calcoaceticus complex. Patients with serious Acinetobacter infections may require support with continuous renal replacement therapy (CRRT), which presents challenges for optimal dosing of antibiotics. Sulbactam-durlobactam dosing regimens were derived for this population using an ex vivo CRRT model and Monte Carlo simulation (MCS). Transmembrane clearance (CLTM) was determined in hemofiltration (CVVH) and hemodialysis (CVVHD) modes using the Prismaflex M100 and HF1400 hemofilter sets and with effluent rates of 1, 2, and 3 L/h. Pre-filter, post-filter blood, and effluent samples were collected over 60 min to calculate sieving (SC) and saturation (SA) coefficients for CVVH and CVVHD, respectively. An established population pharmacokinetic model was integrated with the CLTM; then, a 1,000 patient MCS was conducted to determine exposures of potential dosing regimens. Adsorption and degradation in the ex vivo CRRT model were negligible. The overall mean ± standard deviation SC/SA was 1.14 ± 0.12 and 0.93 ± 0.08 for sulbactam and durlobactam, respectively. In multivariable regression analyses, effluent rate was the primary driver of CLTM for both drugs. For effluent rates <3 L/h, sulbactam-durlobactam 1 g-1g q8h as 3 h infusion achieved a high probability of pharmacodynamic target attainment while retaining area under the curve exposures consistent with the standard dose in non-CRRT patients. For effluent rates ≥3 to 5 L/h, the optimal regimen was 1 g-1g q6h 3 h infusion. Sulbactam-durlobactam regimens that provide optimum drug exposures for efficacy and safety were identified for CRRT based on the prescribed effluent rate.
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Affiliation(s)
- Yasmeen Abouelhassan
- Center for Anti-Infective Research and Development, Hartford Hospital, Hartford, Connecticut, USA
| | - Yuwei Shen
- Center for Anti-Infective Research and Development, Hartford Hospital, Hartford, Connecticut, USA
| | - April Chen
- Innoviva Specialty Therapeutics Inc, Waltham, Massachusetts, USA
| | - Xiaoyi Ye
- Division of Nephrology, Hartford Hospital, Hartford, Connecticut, USA
| | - David P. Nicolau
- Center for Anti-Infective Research and Development, Hartford Hospital, Hartford, Connecticut, USA
- Division of Infectious Diseases, Hartford Hospital, Hartford, Connecticut, USA
| | - Joseph L. Kuti
- Center for Anti-Infective Research and Development, Hartford Hospital, Hartford, Connecticut, USA
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22
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He Z, Huang Y, Li W, Zhang H, Cao R, Ali MR, Dai Y, Lu H, Wang W, Niu Q, Sun B, Li Y. Characterization and genomic analysis of the highly virulent Acinetobacter baumannii ST1791 strain dominating in Anhui, China. Antimicrob Agents Chemother 2025; 69:e0126224. [PMID: 39641569 PMCID: PMC11784083 DOI: 10.1128/aac.01262-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Accepted: 11/11/2024] [Indexed: 12/07/2024] Open
Abstract
The multidrug-resistant Acinetobacter baumannii clonal complex 92 is spreading worldwide due to its high-frequency gene mutation and recombination, posing a significant threat to global medical and health safety. Between November 2021 and April 2022, a total of 132 clinical A. baumannii isolates were collected from a tertiary hospital in China. Their growth ability and virulence of these isolates were assessed using growth curve analyses and the Galleria mellonella infection model. The genetic characteristics of the isolates were further examined through whole-genome sequencing. ST1791O/ST2P isolates represented the largest proportion of isolates in our collection and exhibited the highest growth rate and strongest virulence among all sequence types (STs) analyzed. Whole-genome sequences from 14,159 clinical isolates were collected from the National Center for Biotechnology Information database, and only nine ST1791O/ST2P isolates were detected. Comparative genomic analysis revealed that ST1791O/ST2P carried 11 unique genes, 5 of which were located within the capsular polysaccharide synthesis (cps) gene cluster. Single nucleotide polymorphisms (SNPs) between ST1791O/ST2P and other isolates were primarily found in the cps gene cluster. Among the other isolates, ST195O/ST2P and ST208O/ST2P exhibited the smallest SNP differences from ST1791O/ST2P, while ST195O/ST2P and ST1486O/ST2P had high homology. The ST1791O/ST2P strain in Anhui, China, displayed significant homology with ST195O/ST2P, ST208O/ST2P, and ST1486O/ST2P isolates. Compared to other isolates in this study, ST1791O/ST2P exhibited strong growth ability and virulence. Therefore, preventing the further spread of ST1791O/ST2P should be a top public health priority.
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Affiliation(s)
- Zhien He
- Department of Oncology, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Yi Huang
- Department of Oncology, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Wei Li
- Department of Oncology, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Huanhuan Zhang
- Department of Cancer Epigenetics Program, The First Affiliated Hospital of University of Science and Technology of China, Hefei, Anhui, China
| | - Ruobing Cao
- Department of Oncology, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Md Roushan Ali
- Department of Oncology, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Yuanyuan Dai
- Department of Clinical Laboratory, the First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Huaiwei Lu
- Department of Clinical Laboratory, the First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Wanying Wang
- Department of Oncology, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Qiuhong Niu
- School of Life Science, Nanyang Normal University, Nanyang, Henan, China
| | - Baolin Sun
- Department of Oncology, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Yujie Li
- Department of Oncology, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
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23
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Zhang P, Hao J, Zhang Y, Su J, Sun G, Xie J, Hu J, Li G. Understanding the clinical and molecular epidemiological characteristics of carbapenem-resistant Acinetobacter baumannii infections within intensive care units of three teaching hospitals. Ann Clin Microbiol Antimicrob 2025; 24:2. [PMID: 39806310 PMCID: PMC11731405 DOI: 10.1186/s12941-024-00766-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 12/06/2024] [Indexed: 01/16/2025] Open
Abstract
BACKGROUND Carbapenem-resistant Acinetobacter baumannii (CRAB) is recognized as a common clinical conditional pathogen with blaOXA-23 gene-mediated multidrug-resistance that is a significant threat to public health safety. Timely and effective infection control measures are needed to prevent their spread. METHODS We conducted a retrospective study of CRAB patients at three teaching hospitals from 2019 to 2022. We identified bacterial isolates, collected clinical data, and performed antimicrobial susceptibility testing. Genome characteristics of isolates were investigated by whole genome sequencing. Multilocus sequence typing and phylogenetic trees were used to assess the genetic similarity of isolates. Acquired antimicrobial resistance genes and virulence factors carried in the isolated group genome were analyzed by ResFinder, PubMLST and VFDB. Sequence alignment was used to analyze genetic environment around blaOXA-23. Phylogenetic tree was constructed to analyze the genetic relationship of isolates. RESULTS A total of 92 non-repetitive CRAB isolates were collected, with sputum samples accounting for the majority (94.57%, n = 87) of samples. These were distributed into ST2, with ST2 identified to have the highest prevalence of infection, accounting for 99.99% (n = 91) of all isolates. The major resistance genes identified were blaOXA-23, blaOXA-66, blaOXA-51, and blaADC. Also, 92 CRAB strains showed high levels of resistance to common clinical antibiotics, but not minocycline. Meanwhile, most of the isolates carried virulence genes such as various ompA, csuA, csuB, csuC, csuD, abaI, abaR, lpxC, lpxA, and bmfRS. Single nucleotide polymorphism (SNP) analyses further indicated that the bacterial genome was progressively polymorphic with time. We analyzed the environment of the blaOXA-23 gene and found that CRAB accumulated in the context of prominent environmental antibiotic exposure and had longer survival times in the antibiotic environment, resulting in the tendency of bacteria to develop greater antibiotic resistance. CONCLUSIONS We find that CRAB is prevalent within the ICU and is progressively resistant to antibiotics over time. Enhanced clinical understanding and timely management of CRAB infections will be crucial to minimize or even eliminate the spread of CRAB within the ICU setting.
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Affiliation(s)
- Pengyu Zhang
- Department of Microbiology, Medical College, Yangzhou University, Yangzhou, 225001, China
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou, 225009, China
| | - Jingchen Hao
- Department of Microbiology, Medical College, Yangzhou University, Yangzhou, 225001, China
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou, 225009, China
| | - Yafen Zhang
- Department of Laboratory Medicine, Affiliated Hospital of Yangzhou University, Yangzhou, 225001, PR China
| | - Junfeng Su
- Department of Microbiology, Medical College, Yangzhou University, Yangzhou, 225001, China
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou, 225009, China
| | - Guozhuang Sun
- Department of Laboratory Medicine, Xuyi County People's Hospital / Clinical College, Yangzhou University, Yangzhou, 211799, China
| | - Jun Xie
- Department of Laboratory Medicine, Xuyi County People's Hospital / Clinical College, Yangzhou University, Yangzhou, 211799, China
| | - Jian Hu
- Department of Laboratory Medicine, Guangling College / Clinical College, Yixing Hospital of Traditional Chinese Medicine, Yangzhou University, Yangzhou, 214200, China.
| | - Guocai Li
- Department of Microbiology, Medical College, Yangzhou University, Yangzhou, 225001, China.
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou, 225009, China.
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24
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Zhang S, Xiao J, Li Y, Li W, Li Y, Pang M, Yan M, Han H, Cui Y, Zhang X, Wang H. An integrative review on the risk factors, prevention, and control strategies for carbapenem-resistant Acinetobacter baumannii colonization in critically ill patients. Front Microbiol 2025; 15:1519906. [PMID: 39867493 PMCID: PMC11757275 DOI: 10.3389/fmicb.2024.1519906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2024] [Accepted: 12/24/2024] [Indexed: 01/28/2025] Open
Abstract
The presence of carbapenem-resistant Acinetobacter baumannii (CRAb) has become one of the leading causes of life-threatening, hospital-acquired infections globally, especially with a notable prevalence in intensive care units (ICUs). The cross-transmission of microorganisms between patients and the hospital setting is crucial in the development of CRAb colonization and subsequent infections. Recent studies indicate that colonization typically precedes infection, suggesting the effectiveness and necessity of preventing CRAb colonization as a primary method to lower infection risks. As CRAb infections tend to draw more attention due to their severe symptoms and poor outcomes, understanding the link between colonization and infection is equally vital. To establish a foundation for prevention and control strategies against CRAb colonization in ICUs, we present a comprehensive review of research pertaining to CRAb in ICUs. This encompasses an analysis of the resistance mechanisms and epidemiological characteristics of CRAb, a discussion on associated risk factors, adverse outcomes, and an evaluation of detection methods and preventive strategies.
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Affiliation(s)
- Shihan Zhang
- Department of Critical Care Medicine, Qilu Hospital, Shandong University, Jinan, China
- Innovation Research Center for Sepsis and Multiple Organ Injury, Shandong University, Jinan, China
| | - Jie Xiao
- Department of Critical Care Medicine, Qilu Hospital, Shandong University, Jinan, China
- Innovation Research Center for Sepsis and Multiple Organ Injury, Shandong University, Jinan, China
| | - Yanan Li
- Department of Critical Care Medicine, Qilu Hospital, Shandong University, Jinan, China
- Innovation Research Center for Sepsis and Multiple Organ Injury, Shandong University, Jinan, China
| | - Wei Li
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China
| | - Yihui Li
- Department of Critical Care Medicine, Qilu Hospital, Shandong University, Jinan, China
- Innovation Research Center for Sepsis and Multiple Organ Injury, Shandong University, Jinan, China
| | - Mingmin Pang
- Department of Critical Care Medicine, Qilu Hospital, Shandong University, Jinan, China
- Innovation Research Center for Sepsis and Multiple Organ Injury, Shandong University, Jinan, China
| | - Meichen Yan
- Department of Critical Care Medicine, Qilu Hospital, Shandong University, Jinan, China
- Innovation Research Center for Sepsis and Multiple Organ Injury, Shandong University, Jinan, China
| | - Hui Han
- Department of Critical Care Medicine, Qilu Hospital, Shandong University, Jinan, China
- Innovation Research Center for Sepsis and Multiple Organ Injury, Shandong University, Jinan, China
| | - Yi Cui
- Department of Critical Care Medicine, Qilu Hospital, Shandong University, Jinan, China
- Innovation Research Center for Sepsis and Multiple Organ Injury, Shandong University, Jinan, China
| | - Xuehai Zhang
- Department of Critical Care Medicine, Qilu Hospital, Shandong University, Jinan, China
- Innovation Research Center for Sepsis and Multiple Organ Injury, Shandong University, Jinan, China
| | - Hao Wang
- Department of Critical Care Medicine, Qilu Hospital, Shandong University, Jinan, China
- Innovation Research Center for Sepsis and Multiple Organ Injury, Shandong University, Jinan, China
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25
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Iovleva A, Fowler VG, Doi Y. Treatment Approaches for Carbapenem-Resistant Acinetobacter baumannii Infections. Drugs 2025; 85:21-40. [PMID: 39607595 PMCID: PMC11950131 DOI: 10.1007/s40265-024-02104-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/22/2024] [Indexed: 11/29/2024]
Abstract
Carbapenem-resistant Acinetobacter baumannii has been associated with over three hundred thousand annual deaths globally. It is resistant to most available antibiotics and associated with high morbidity and mortality. No global consensus currently exists for treatment strategies that balance safety and efficacy because of heterogeneity of treatment regimens in current clinical practice and scarcity of large-scale controlled studies arising from difficulties in establishing robust clinical outcomes. This review outlines the epidemiology and resistance mechanisms of carbapenem-resistant A. baumannii, then summarizes available clinical data on each approved agent with activity against this pathogen. Emerging treatment options such as cefiderocol and sulbactam-durlobactam show promise, but their success hinges on comprehensive clinical validation and access in regions most impacted by this pathogen. New therapeutic modalities that are in various stages of clinical development are also discussed.
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Affiliation(s)
- Alina Iovleva
- Center for Innovative Antimicrobial Therapy, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Vance G Fowler
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- Duke Clinical Research Institute, Durham, NC, USA
| | - Yohei Doi
- Center for Innovative Antimicrobial Therapy, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Departments of Microbiology and Infectious Diseases, Fujita Health University, Toyoake, Aichi, Japan.
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26
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Kamoshida G, Yamada N, Yamaguchi D, Yahiro K, Morita Y. Colistin Resistance in Acinetobacter baumannii: Basic and Clinical Insights. Biol Pharm Bull 2025; 48:213-221. [PMID: 40024691 DOI: 10.1248/bpb.b23-00642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2025]
Abstract
The emergence of drug-resistant bacteria has posed a significant problem in medical institutions worldwide. Colistin, which targets lipopolysaccharide (LPS), serves as a last-resort antimicrobial agent against multidrug-resistant Gram-negative bacteria. Nevertheless, Acinetobacter baumannii, a pathogen with a worldwide prevalence of antimicrobial resistance, has been reported to develop resistance to colistin frequently. In this review, we discuss how A. baumannii acquires resistance to colistin, focusing on modification as well as loss of LPS present in its outer membrane, which is the primary mechanism of A. baumannii's resistance to colistin. Basic and clinical insights regarding colistin resistance in A. baumannii have been discussed in isolation. Therefore, we discuss the relationship between these 2 colistin resistance mechanisms in terms of the frequency and fitness of genetic mutations based on the insights from basic studies and clinical settings. We concluded that understanding the detailed mechanisms of colistin drug resistance requires a comprehensive understanding of both the frequency of mutations and the effects of selection pressure. Finally, we highlight the importance of promoting research from both basic science and clinical perspectives.
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Affiliation(s)
- Go Kamoshida
- Department of Infection Control Science, Meiji Pharmaceutical University, 2-522-1 Noshio, Kiyose, Tokyo 204-8588, Japan
- Laboratory of Microbiology and Infection Control Sciences, Kyoto Pharmaceutical University, 5 Misasagi-nakauchi-cho, Yamashina-ku, Kyoto 607-8412, Japan
| | - Noriteru Yamada
- Laboratory of Microbiology and Infection Control Sciences, Kyoto Pharmaceutical University, 5 Misasagi-nakauchi-cho, Yamashina-ku, Kyoto 607-8412, Japan
| | - Daiki Yamaguchi
- Laboratory of Microbiology and Infection Control Sciences, Kyoto Pharmaceutical University, 5 Misasagi-nakauchi-cho, Yamashina-ku, Kyoto 607-8412, Japan
| | - Kinnosuke Yahiro
- Laboratory of Microbiology and Infection Control Sciences, Kyoto Pharmaceutical University, 5 Misasagi-nakauchi-cho, Yamashina-ku, Kyoto 607-8412, Japan
| | - Yuji Morita
- Department of Infection Control Science, Meiji Pharmaceutical University, 2-522-1 Noshio, Kiyose, Tokyo 204-8588, Japan
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Liu L, Huang Y, Wang Y, Jiang Y, Liu K, Pei Z, Li Z, Zhu Y, Liu D, Li X. Molecular Epidemiology and Genetic Characterization of Carbapenem-Resistant Acinetobacter baumannii Isolates from the ICU of a Tertiary Hospital in East China. Infect Drug Resist 2024; 17:5925-5945. [PMID: 39759767 PMCID: PMC11699857 DOI: 10.2147/idr.s491858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2024] [Accepted: 12/11/2024] [Indexed: 01/07/2025] Open
Abstract
Purpose To evaluate the clinical characteristics, antimicrobial resistance (AMR) phenotypes and genotypes, and homology features of carbapenem-resistant Acinetobacter baumannii (CRAB) in intensive care unit (ICU) and to provide basis for effectively prevention, control and treatment of nosocomial infections caused by CRAB. Methods A total of 39 CRAB strains isolated from hospitalized patients in the ICU and neurosurgical ICU (NICU) between 2020 and 2023 were subjected to antimicrobial susceptibility testing and whole-genome sequencing (WGS). Virulence factor genes (VFGs), antimicrobial resistance genes (ARGs), multilocus sequencing typing (MLST), complete genome multilocus sequencing typing (cgMLST), average nucleotide identity (ANI), and single nucleotide polymorphism (SNP) analyses were performed using WGS. Results All CRAB strains were 100% resistant to ciprofloxacin, ceftazidime, piperacillin/tazobactam, and ticarcillin/clavulanic acid. A total of 48 antimicrobial resistance genes (ARGs) were found in the 39 CRAB strains, including blaOXA-66, blaOXA-23, blaADC-30, blaADC-73, gyrA, ant(3″)-IIa, aph(3″)-Ib, aph(6)-Id, tetB, tetR, sul1, sul2, LpxC and LpxA which confered resistance to carbapenems, cephalosporins, fluoroquinolones, aminoglycosides, tetracycline and sulfonamides. There were 128 VFGs, including genes encoding the AdeFGH efflux pump, lipopolysaccharide (LpsBLC), outer membrane protein A (OmpA), penicillin-binding protein (PbpG), biofilm-associated proteins (bap, pgaBCD, CsuABCDE), type VI secretion system protein (Tss), quorum sensing protein (AbaI/AbaR). Six clonal lineages were identified by Oxford MLST method, whereas one sequence type (ST2) was identified using the Pasteur MLST method. ANI analysis, heat map of SNP analysis, and phylogenetic tree based on core SNP revealed six clusters, and the strain classification results were consistent with these different methods. Ten clonal lineages were identified by cgMLST. Conclusion The CRAB strains were ST2 clones accompanied by severe resistance to commonly used antibiotics and abundant ARGs and VFGs in genotype. Strict measures should be implemented to prevent and control transmissions and infections. CgMLST and SNPs analyses showed excellent discriminatory power in homology analysis.
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Affiliation(s)
- Lili Liu
- Department of Nosocomial Infection, Anqing First People’s Hospital of Anhui Medical University, Anqing City, Anhui Province, People’s Republic of China
| | - Yuan Huang
- Department of Science and Education, Anqing Municipal Hospital, Anqing City, Anhui Province, People’s Republic of China
| | - Yaping Wang
- Department of Clinical Laboratory, Anqing First People’s Hospital of Anhui Medical University, Anqing City, Anhui Province, People’s Republic of China
| | - Yunlan Jiang
- Department of Nosocomial Infection, Anqing First People’s Hospital of Anhui Medical University, Anqing City, Anhui Province, People’s Republic of China
| | - Kang Liu
- Department of Clinical Laboratory, Anqing First People’s Hospital of Anhui Medical University, Anqing City, Anhui Province, People’s Republic of China
| | - Zhongxia Pei
- Department of Nosocomial Infection, Anqing First People’s Hospital of Anhui Medical University, Anqing City, Anhui Province, People’s Republic of China
| | - Zhiping Li
- Department of Nosocomial Infection, Anqing First People’s Hospital of Anhui Medical University, Anqing City, Anhui Province, People’s Republic of China
| | - Yuqiong Zhu
- Department of Nosocomial Infection, Anqing First People’s Hospital of Anhui Medical University, Anqing City, Anhui Province, People’s Republic of China
| | - Dan Liu
- Department of Nosocomial Infection, Anqing First People’s Hospital of Anhui Medical University, Anqing City, Anhui Province, People’s Republic of China
| | - Xiaoyue Li
- Subdean Office, Anqing First People’s Hospital of Anhui Medical University, Anqing City, Anhui Province, People’s Republic of China
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Jia H, Li X, Zhuang Y, Wu Y, Shi S, Sun Q, He F, Liang S, Wang J, Draz MS, Xie X, Zhang J, Yang Q, Ruan Z. Neural network-based predictions of antimicrobial resistance phenotypes in multidrug-resistant Acinetobacter baumannii from whole genome sequencing and gene expression. Antimicrob Agents Chemother 2024; 68:e0144624. [PMID: 39540735 PMCID: PMC11619347 DOI: 10.1128/aac.01446-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2024] [Accepted: 10/22/2024] [Indexed: 11/16/2024] Open
Abstract
Whole genome sequencing (WGS) potentially represents a rapid approach for antimicrobial resistance genotype-to-phenotype prediction. However, the challenge still exists to predict fully minimum inhibitory concentrations (MICs) and antimicrobial susceptibility phenotypes based on WGS data. This study aimed to establish an artificial intelligence-based computational approach in predicting antimicrobial susceptibilities of multidrug-resistant Acinetobacter baumannii from WGS and gene expression data. Antimicrobial susceptibility testing (AST) was performed using the broth microdilution method for 10 antimicrobial agents. In silico multilocus sequence typing (MLST), antimicrobial resistance genes, and phylogeny based on cgSNP and cgMLST strategies were analyzed. High-throughput qPCR was performed to measure the expression level of antimicrobial resistance (AMR) genes. Most isolates exhibited a high level of resistance to most of the tested antimicrobial agents, with the majority belonging to the IC2/CC92 lineage. Phylogenetic analysis revealed undetected transmission events or local outbreaks. The percentage agreements between AMR phenotype and genotype ranged from 70.08% to 89.96%, with the coefficient of agreement (κ) extending from 0.025 and 0.881. The prediction of AST employed by deep neural network models achieved an accuracy of up to 98.64% on the testing data set. Additionally, several linear regression models demonstrated high prediction accuracy, reaching up to 86.15% within an error range of one gradient, indicating a linear relationship between certain gene expressions and the corresponding antimicrobial MICs. In conclusion, neural network-based predictions could be used as a tool for the surveillance of antimicrobial resistance in multidrug-resistant A. baumannii.
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Affiliation(s)
- Huiqiong Jia
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou, China
| | - Xinyang Li
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, China
| | - Yilu Zhuang
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, China
| | - Yuye Wu
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, China
| | - Shasha Shi
- Department of Laboratory Medicine, Wuyi First People’s Hospital, Jinhua, China
| | - Qingyang Sun
- Department of Clinical Laboratory, No. 903 Hospital of PLA Joint Logistic Support Force, Hangzhou, China
| | - Fang He
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital, Hangzhou Medical College), Hangzhou, China
| | - Shanyan Liang
- Department of Clinical Laboratory, Ningbo No.2 Hospital, Ningbo, China
| | - Jianfeng Wang
- Department of Respiratory and Critical Care Medicine, Zhejiang Provincial Hospital of Chinese Medicine, Hangzhou, China
| | - Mohamed S. Draz
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Biomedical Engineering, Cleveland Clinic, Cleveland, Ohio, USA
| | - Xinyou Xie
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, China
| | - Jun Zhang
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, China
| | - Qing Yang
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou, China
| | - Zhi Ruan
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, China
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Hummel D, Juhasz J, Kamotsay K, Kristof K, Xavier BB, Koster SD, Szabo D, Kocsis B. Genomic Investigation and Comparative Analysis of European High-Risk Clone of Acinetobacter baumannii ST2. Microorganisms 2024; 12:2474. [PMID: 39770677 PMCID: PMC11728346 DOI: 10.3390/microorganisms12122474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2024] [Revised: 11/22/2024] [Accepted: 11/27/2024] [Indexed: 01/16/2025] Open
Abstract
Multidrug-resistant Acinetobacter baumannii is a major concern in healthcare institutions worldwide. Several reports described the dissemination of A. baumannii high-risk clones that are responsible for a high number of difficult-to-treat infections. In our study, 19 multidrug-resistant A. baumannii strains from Budapest, Hungary, were investigated based on whole-genome sequencing (WGS). The obtained results were analysed together with data from 433 strains of A. baumannii from the Pathogenwatch database. WGS analysis of 19 A. baumannii strains detected that 12 belonged to ST2 and seven belonged to ST636. Among ST2 strains, 11 out of 12 carried either blaOXA-23 or blaOXA-58 genes; however, all strains of ST636 uniformly carried blaOXA-72 gene. All strains of ST2 and ST636 carried blaOXA-66 and blaADC-25 genes. Based on core genome multilocus sequence typing (cgMLST), 10 strains of ST2 belonged to cgMLST906, one strain to cgMLST458, and one strain to cgMLST1320; by contrast, all strains of ST636 belonged to cgMLST1178. Certain virulence determinants were present in all strains of both ST2 and ST636, namely, Ata, Bap, BfmRS, T2SS and PNAG. Interestingly, OmpA was present in all strains of ST2, but it was absent in all strains of ST636. Comparative analysis of 19 strains of this study and the collection of 433 isolates from Pathogenwatch database, proved a diverse clonal distribution of high-risk A. baumannii clones in Europe. The major clone in Europe is ST2, which is present all over the continent. However, ST636 has been mainly reported in Eastern Europe. Interestingly, cgMLSTs of ST2 correspond to the production of different beta-lactamases, namely, OXA-82 in cgMLST116, OXA-72 in cgMLST506, and cgMLST556, PER-1 in cgMLST456 and cgMLST1041. Our study demonstrates that the ST2 high-risk clone of A. baumannii is the most widespread in Europe; however, based on cgMLST analysis, a detailed detection of beta-lactamase production can be determined.
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Affiliation(s)
- David Hummel
- Institute of Medical Microbiology, Semmelweis University, 1089 Budapest, Hungary
| | - Janos Juhasz
- Institute of Medical Microbiology, Semmelweis University, 1089 Budapest, Hungary
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, 1083 Budapest, Hungary
| | - Katalin Kamotsay
- Central Microbiology Laboratory, National Institute of Hematology and Infectious Disease, Central Hospital of Southern-Pest, 1097 Budapest, Hungary
| | - Katalin Kristof
- Institute of Laboratory Medicine, Semmelweis University, 1083 Budapest, Hungary
| | - Basil Britto Xavier
- Laboratory of Medical Microbiology, University of Antwerp, 2610 Antwerpen, Belgium
- Department of Medical Microbiology and Infection Control, University of Groningen, University Medical Center Groningen, 9713 Groningen, The Netherlands
| | - Sien De Koster
- Microbiology Department, Antwerp University Hospital (UZA), 2650 Edegem, Belgium
| | - Dora Szabo
- Institute of Medical Microbiology, Semmelweis University, 1089 Budapest, Hungary
- HUN-REN-SU Human Microbiota Research Group, 1052 Budapest, Hungary
- Department of Neurosurgical and Neurointervention, Semmelweis University, 1085 Budapest, Hungary
| | - Bela Kocsis
- Institute of Medical Microbiology, Semmelweis University, 1089 Budapest, Hungary
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30
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Ghahramani A, Naghadian Moghaddam MM, Kianparsa J, Ahmadi MH. Overall status of carbapenem resistance among clinical isolates of Acinetobacter baumannii: a systematic review and meta-analysis. J Antimicrob Chemother 2024; 79:3264-3280. [PMID: 39392464 DOI: 10.1093/jac/dkae358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 09/19/2024] [Indexed: 10/12/2024] Open
Abstract
BACKGROUND Resistance to carbapenems, the first-line treatment for infections caused by Acinetobacter baumannii, is increasing throughout the world. The aim of the present study was to determine the global status of resistance to carbapenems in clinical isolates of this pathogen, worldwide. METHODS Electronic databases were searched using the appropriate keywords, including: 'Acinetobacter' 'baumannii', 'Acinetobacter baumannii' and 'A. baumannii', 'resistance', 'antibiotic resistance', 'antibiotic susceptibility', 'antimicrobial resistance', 'antimicrobial susceptibility', 'carbapenem', 'carbapenems', 'imipenem', 'meropenem' and 'doripenem'. Finally, following some exclusions, 177 studies from various countries were included in this study. The data were then subjected to a meta-analysis. RESULTS The average resistance rate of A. baumannii to imipenem, meropenem and doripenem was 44.7%, 59.4% and 72.7%, respectively. A high level of heterogeneity (I2 > 50%, P value < 0.05) was detected in the studies representing resistance to imipenem, meropenem and doripenem in A. baumannii isolates. Begg's and Egger's tests did not indicate publication bias (P value > 0.05). CONCLUSIONS The findings of the current study indicate that the overall resistance to carbapenems in clinical isolates of A. baumannii is relatively high and prevalent throughout the world. Moreover, time trend analysis showed that the resistance has increased from the year 2000 to 2023. This emphasizes the importance of conducting routine antimicrobial susceptibility testing before selecting a course of treatment, as well as monitoring and controlling antibiotic resistance patterns in A. baumannii strains, and seeking novel treatment options to lessen the emergence and spread of resistant strains and to reduce the treatment failure.
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Affiliation(s)
- Ali Ghahramani
- Student Research Committee, School of Medicine, Shahed University, Tehran, Iran
| | | | - Joben Kianparsa
- Student Research Committee, School of Medicine, Shahed University, Tehran, Iran
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31
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Luo Q, Lu P, Chen Y, Shen P, Zheng B, Ji J, Ying C, Liu Z, Xiao Y. ESKAPE in China: epidemiology and characteristics of antibiotic resistance. Emerg Microbes Infect 2024; 13:2317915. [PMID: 38356197 PMCID: PMC10896150 DOI: 10.1080/22221751.2024.2317915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 02/08/2024] [Indexed: 02/16/2024]
Abstract
The escalation of antibiotic resistance and the diminishing antimicrobial pipeline have emerged as significant threats to public health. The ESKAPE pathogens - Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. - were initially identified as critical multidrug-resistant bacteria, demanding urgently effective therapies. Despite the introduction of various new antibiotics and antibiotic adjuvants, such as innovative β-lactamase inhibitors, these organisms continue to pose substantial therapeutic challenges. People's Republic of China, as a country facing a severe bacterial resistance situation, has undergone a series of changes and findings in recent years in terms of the prevalence, transmission characteristics and resistance mechanisms of antibiotic resistant bacteria. The increasing levels of population mobility have not only shaped the unique characteristics of antibiotic resistance prevalence and transmission within People's Republic of China but have also indirectly reflected global patterns of antibiotic-resistant dissemination. What's more, as a vast nation, People's Republic of China exhibits significant variations in the levels of antibiotic resistance and the prevalence characteristics of antibiotic resistant bacteria across different provinces and regions. In this review, we examine the current epidemiology and characteristics of this important group of bacterial pathogens, delving into relevant mechanisms of resistance to recently introduced antibiotics that impact their clinical utility in China.
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Affiliation(s)
- Qixia Luo
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medical School, College of medicine, Zhejiang University, Hangzhou, People’s Republic of China
| | - Ping Lu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medical School, College of medicine, Zhejiang University, Hangzhou, People’s Republic of China
| | - Yunbo Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medical School, College of medicine, Zhejiang University, Hangzhou, People’s Republic of China
| | - Ping Shen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medical School, College of medicine, Zhejiang University, Hangzhou, People’s Republic of China
| | - Beiwen Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medical School, College of medicine, Zhejiang University, Hangzhou, People’s Republic of China
| | - Jinru Ji
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medical School, College of medicine, Zhejiang University, Hangzhou, People’s Republic of China
| | - Chaoqun Ying
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medical School, College of medicine, Zhejiang University, Hangzhou, People’s Republic of China
| | - Zhiying Liu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medical School, College of medicine, Zhejiang University, Hangzhou, People’s Republic of China
| | - Yonghong Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medical School, College of medicine, Zhejiang University, Hangzhou, People’s Republic of China
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Lucidi M, Visaggio D, Migliaccio A, Capecchi G, Visca P, Imperi F, Zarrilli R. Pathogenicity and virulence of Acinetobacter baumannii: Factors contributing to the fitness in healthcare settings and the infected host. Virulence 2024; 15:2289769. [PMID: 38054753 PMCID: PMC10732645 DOI: 10.1080/21505594.2023.2289769] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 11/27/2023] [Indexed: 12/07/2023] Open
Abstract
Acinetobacter baumannii is a common cause of healthcare-associated infections and hospital outbreaks, particularly in intensive care units. Much of the success of A. baumannii relies on its genomic plasticity, which allows rapid adaptation to adversity and stress. The capacity to acquire novel antibiotic resistance determinants and the tolerance to stresses encountered in the hospital environment promote A. baumannii spread among patients and long-term contamination of the healthcare setting. This review explores virulence factors and physiological traits contributing to A. baumannii infection and adaptation to the hospital environment. Several cell-associated and secreted virulence factors involved in A. baumannii biofilm formation, cell adhesion, invasion, and persistence in the host, as well as resistance to xeric stress imposed by the healthcare settings, are illustrated to give reasons for the success of A. baumannii as a hospital pathogen.
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Affiliation(s)
- Massimiliano Lucidi
- Department of Science, Roma Tre University, Rome, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Daniela Visaggio
- Department of Science, Roma Tre University, Rome, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
- Santa Lucia Foundation IRCCS, Rome, Italy
| | | | | | - Paolo Visca
- Department of Science, Roma Tre University, Rome, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
- Santa Lucia Foundation IRCCS, Rome, Italy
| | - Francesco Imperi
- Department of Science, Roma Tre University, Rome, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
- Santa Lucia Foundation IRCCS, Rome, Italy
| | - Raffaele Zarrilli
- Department of Public Health, University of Naples Federico II, Naples, Italy
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Grenier F, Baby V, Allard S, Lévesque S, Papale F, Sullivan R, Landecker HL, Higgins PG, Rodrigue S, Haraoui LP. Isolation of a blaNDM-1-positive strain in Israel predating the earliest observations from India. Microbiol Spectr 2024; 12:e0100224. [PMID: 39320107 PMCID: PMC11537007 DOI: 10.1128/spectrum.01002-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 08/28/2024] [Indexed: 09/26/2024] Open
Abstract
blaNDM, the most prevalent carbapenemase among carbapenem-resistant Enterobacteriaceae, is thought to have emerged in India, as its initial detection in 2008 was linked to this country, and subsequent retrospective surveys had so far established the earliest blaNDM-positive strains to be isolated in India in 2005. Molecular dating and analyses suggest blaNDM emerged within Acinetobacter species decades prior to 2005 on a Tn125 transposon. Despite early reports of elevated rates of carbapenem-resistant Acinetobacter species in Israel starting in the 1990s, limited molecular data are available from this location. We searched for blaNDM among Acinetobacter species isolated in Israel between 2001 and 2006. One A. junii strain, Ajun-H1-3, isolated in January 2004, carried blaNDM-1 within a Tn125-like transposon on a 49-kb plasmid, pNDM-Ajun-H1-3, making Ajun-H1-3 the earliest NDM-positive isolate observed to date. The pNDM-Ajun-H1-3 plasmid matched numerous BJ01-like NDM-positive plasmids identified from 2005 onward in Acinetobacter species as well as Enterobacterales. These results indicate the need for further retrospective work on global strain archives to shed light on the conditions favoring the emergence as well as subsequent evolution and spread of blaNDM. IMPORTANCE This study presents the earliest observation of blaNDM-1, isolated in a geographical region distant from where it is believed to have originated. In doing so, this study provides novel insights into the emergence and spread of blaNDM, the most prevalent carbapenemase among carbapenem-resistant Enterobacteriaceae, and its associated mobile genetic elements. It also sheds light on the conditions that foster the evolution of antimicrobial resistance, one of the greatest public health challenges we face.
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Affiliation(s)
- Frédéric Grenier
- Department of Biology, Faculty of Science, Université de Sherbrooke, Sherbrooke, Sherbrooke, Québec, Canada
| | - Vincent Baby
- Department of Biology, Faculty of Science, Université de Sherbrooke, Sherbrooke, Sherbrooke, Québec, Canada
| | - Sarah Allard
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Simon Lévesque
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Canada
- CIUSSS de l’Estrie - CHUS, Sherbrooke, Québec, Canada
| | - François Papale
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Richard Sullivan
- Conflict and Health Research Group, King’s College London, London, United Kingdom
| | | | - Paul G. Higgins
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- German Centre for Infection Research (DZIF), partner site Cologne-Bonn, Cologne, Germany
| | - Sébastien Rodrigue
- Department of Biology, Faculty of Science, Université de Sherbrooke, Sherbrooke, Sherbrooke, Québec, Canada
| | - Louis-Patrick Haraoui
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Canada
- Centre de recherche Charles-Le Moyne, CISSS Montérégie-Centre, Longueuil, Québec, Canada
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Liu H, Moran RA, Doughty EL, Hua X, Snaith AE, Zhang L, Chen X, Guo F, van Schaik W, McNally A, Yu Y. Longitudinal genomics reveals carbapenem-resistant Acinetobacter baumannii population changes with emergence of highly resistant ST164 clone. Nat Commun 2024; 15:9483. [PMID: 39488505 PMCID: PMC11531505 DOI: 10.1038/s41467-024-53817-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Accepted: 10/23/2024] [Indexed: 11/04/2024] Open
Abstract
Carbapenem-resistant Acinetobacter baumannii (CRAB) is a persistent nosocomial pathogen that poses a significant threat to global public health, particularly in intensive care units (ICUs). Here we report a three-month longitudinal genomic surveillance study conducted in a Hangzhou ICU in 2021. This followed a three-month study conducted in the same ICU in 2019, and infection prevention and control (IPC) interventions targeting patients, staff and the ICU environment. Most A. baumannii isolated in this ICU in 2021 were CRAB (80.9%; 419/518) with higher-level resistance to carbapenems. This was accompanied by the proportion of global clone 2 (GC2) isolates falling from 99.5% in 2019 to 50.8% (213/419) in 2021. The phylogenetic diversity of GC2 increased, apparently driven by regular introductions of distinct clusters in association with patients. The remaining CRAB (40.2%; 206/419) were a highly clonal population of ST164. Isolates of ST164 carried blaNDM-1 and blaOXA-23 carbapenemase genes, and exhibited higher carbapenem MIC50/MIC90 values than GC2. Comparative analysis of publicly available genomes from 26 countries (five continents) revealed that ST164 has evolved towards carbapenem resistance on multiple independent occasions. Its success in this ICU and global capacity for acquiring resistance determinants indicate that ST164 CRAB is an emerging high-risk lineage of global concern.
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Affiliation(s)
- Haiyang Liu
- Centre of Laboratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, 158 Shangtang Road, 310014, Hangzhou, Zhejiang, China
- Zhejiang University School of Medicine, Hangzhou, 310016, Hangzhou, Zhejiang, China
| | - Robert A Moran
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Emma L Doughty
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 310016, Hangzhou, Zhejiang, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, 310016, Hangzhou, Zhejiang, China
| | - Ann E Snaith
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Linghong Zhang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 310016, Hangzhou, Zhejiang, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, 310016, Hangzhou, Zhejiang, China
| | - Xiangping Chen
- Intensive Care Unit, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 310016, Hangzhou, Zhejiang, China
| | - Feng Guo
- Intensive Care Unit, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 310016, Hangzhou, Zhejiang, China
| | - Willem van Schaik
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
| | - Yunsong Yu
- Centre of Laboratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, 158 Shangtang Road, 310014, Hangzhou, Zhejiang, China.
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 310016, Hangzhou, Zhejiang, China.
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Li H, Talanaite D, Pan Z, Wang Z, Wang S, Wang H. Characteristics of Oral Acinetobacter spp. and Evolution of Plasmid-Mediated Carbapenem Resistance in Bacteremia Patients with Hematological Malignancies. Infect Drug Resist 2024; 17:4753-4761. [PMID: 39494231 PMCID: PMC11531724 DOI: 10.2147/idr.s478362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Accepted: 10/18/2024] [Indexed: 11/05/2024] Open
Abstract
Background Patients with hematological malignancies are more susceptible to infections, leading to a poor prognosis. Acinetobacter colonization is a risk factor for secondary bacteremia. Methods Antibiotic susceptibility phenotypes and genomic characteristics of 48 oral Acinetobacter spp. and one bloodstream Acinetobacter baumannii from patients with hematological malignancies were analyzed by antimicrobial susceptibility tests and whole-genome sequencing. We conducted comparative genomic analysis of oral and blood isolates from the same patient. Results A. baumannii was the most common (72.92%, 35/48) Acinetobacter species in oral Acinetobacter spp. isolates. Seventeen different A. baumannii sequence types were identified using the Pasteur MLST scheme; however, the dominant global clones GC1 and GC2 were not present. Among the isolates, 46 (95.8%) were carbapenem-susceptible Acinetobacter spp. One patient treated with meropenem for 15 days developed A. baumannii bacteremia 46 days after the isolation of oral A. baumannii AOR07. Oral and bloodstream isolates from the same patient were closely related to only four non-synonymous mutations on the chromosome. The bla OXA-58 gene was transferred between plasmids through XerCD-mediated recombination, leading to an elevated copy number, causing carbapenem resistance in bloodstream isolates. Conclusion Oral Acinetobacter spp. may cause secondary bacteremia. The amplification and transfer of bla OXA-58 in the plasmids explained the increased carbapenem resistance in the bloodstream isolate.
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Affiliation(s)
- Henan Li
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, People’s Republic of China
| | - Didaer Talanaite
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, People’s Republic of China
| | - Zitong Pan
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, People’s Republic of China
| | - Zhiren Wang
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, People’s Republic of China
| | - Shuyi Wang
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, People’s Republic of China
| | - Hui Wang
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, People’s Republic of China
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Shashkov AS, Arbatsky NP, Senchenkova SN, Kasimova AA, Dmitrenok AS, Shneider MM, Knirel YA, Hall RM, Kenyon JJ. Characterization of the carbapenem-resistant Acinetobacter baumannii clinical reference isolate BAL062 (CC2:KL58:OCL1): resistance properties and capsular polysaccharide structure. mSystems 2024; 9:e0094124. [PMID: 39254035 PMCID: PMC11494974 DOI: 10.1128/msystems.00941-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2024] [Accepted: 08/19/2024] [Indexed: 09/11/2024] Open
Abstract
The carbapenem-resistant Acinetobacter baumannii isolate BAL062 is a clinical reference isolate used in several recent experimental studies. It is from a ventilator-associated pneumonia (VAP) patient in an intensive care unit at the Hospital for Tropical Diseases (HTD), Ho Chi Minh City, Vietnam in 2009. Here, BAL062 was found to belong to the B sub-lineage of global clone 2 (GC2) isolates in the previously reported outbreak (2008 and 2012) of carbapenem-resistant VAP A. baumannii at the HTD. While related sub-lineage B outbreak isolates were extensively antibiotic-resistant and carry GC2-associated genomic resistance islands, AbGRI1, AbGRI2, and AbGRI3, BAL062 has lost AbGRI3 and three aminoglycoside resistance genes, armA, aacA4, and aphA1, leading to amikacin, tobramycin and kanamycin susceptibility. The location of Tn2008VAR found in the chromosome of this sub-lineage was also corrected. Like many of the outbreak isolates, BAL062 carries the KL58 gene cluster at the capsular polysaccharide (CPS) synthesis locus and an annotation key is provided. As information about K type is important for the development of novel CPS-targeting therapies, the BAL062 K58-type CPS structure was established using NMR spectroscopy. It is most closely related to K2 and K93, sharing similar configurations and linkages between K units, and contains the rare higher monosaccharide, 5,7-diacetamido-3,5,7,9-tetradeoxy-d-glycero-l-manno-non-2-ulosonic acid (5,7-di-N-acetyl-8-epipseudaminic acid; 8ePse5Ac7Ac), the 8-epimer of Pse5Ac7Ac (5,7-di-N-acetylpseudaminic acid). Inspection of publicly available A. baumannii genomes revealed a wide distribution of the KL58 locus in geographically diverse isolates belonging to several sequence types that were recovered over two decades from clinical, animal, and environmental sources.IMPORTANCEMany published experimental studies aimed at developing a clearer understanding of the pathogenicity of carbapenem-resistant Acinetobacter baumannii strains currently causing treatment failure due to extensive antibiotic resistance are undertaken using historic, laboratory-adapted isolates. However, it is ideal if not imperative that recent clinical isolates are used in such studies. The clinical reference isolate characterized here belongs to the dominant A. baumannii GC2 clone causing extensively resistant infections and has been used in various recent studies. The correlation of resistance profiles and resistance gene data is key to identifying genes available for gene knockout and complementation analyses, and we have mapped the antibiotic resistance genes to find candidates. Novel therapies, such as bacteriophage or monoclonal antibody therapies, currently under investigation as alternatives or adjuncts to antibiotic treatment to combat difficult-to-treat CRAb infections often exhibit specificity for specific structural epitopes of the capsular polysaccharide (CPS), the outer-most polysaccharide layer. Here, we have solved the structure of the CPS type found in BAL062 and other extensively resistant isolates. As consistent gene naming and annotation are important for locus identification and interpretation of experimental studies, we also have correlated automatic annotations to the standard gene names.
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Affiliation(s)
- Alexander S. Shashkov
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Nikolay P. Arbatsky
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Sof’ya N. Senchenkova
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Anastasiya A. Kasimova
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Andrei S. Dmitrenok
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Mikhail M. Shneider
- M. M. Shemyakin & Y. A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Yuriy A. Knirel
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Ruth M. Hall
- School of Life and Environmental Science, The University of Sydney, Sydney, Australia
| | - Johanna J. Kenyon
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Australia
- School of Pharmacy and Medical Sciences, Health Group, Griffith University, Gold Coast, Australia
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Hamrock F, Ryan D, Shaibah A, Ershova A, Mogre A, Sulimani M, Ben Taarit S, Reichardt S, Hokamp K, Westermann A, Kröger C. Global analysis of the RNA-RNA interactome in Acinetobacter baumannii AB5075 uncovers a small regulatory RNA repressing the virulence-related outer membrane protein CarO. Nucleic Acids Res 2024; 52:11283-11300. [PMID: 39149883 PMCID: PMC11472050 DOI: 10.1093/nar/gkae668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 07/11/2024] [Accepted: 07/19/2024] [Indexed: 08/17/2024] Open
Abstract
Acinetobacter baumannii is an opportunistic Gram-negative pathogen that infects critically ill patients. The emergence of antimicrobial resistant A. baumannii has exacerbated the need to characterize environmental adaptation, antibiotic resistance and pathogenicity and their genetic regulators to inform intervention strategies. Critical to adaptation to changing environments in bacteria are small regulatory RNAs (sRNAs), however, the role that sRNAs play in the biology of A. baumannii is poorly understood. To assess the regulatory function of sRNAs and to uncover their RNA interaction partners, we employed an RNA proximity ligation and sequencing method (Hi-GRIL-seq) in three different environmental conditions. Forty sRNAs were ligated to sRNA-RNA chimeric sequencing reads, suggesting that sRNA-mediated gene regulation is pervasive in A. baumannii. In-depth characterization uncovered the sRNA Aar to be a post-transcriptional regulator of four mRNA targets including the transcript encoding outer membrane protein CarO. Aar initiates base-pairing with these mRNAs using a conserved seed region of nine nucleotides, sequestering the ribosome binding sites and inhibiting translation. Aar is differentially expressed in multiple stress conditions suggesting a role in fine-tuning translation of the Aar-target molecules. Our study provides mechanistic insights into sRNA-mediated gene regulation in A. baumannii and represents a valuable resource for future RNA-centric research endeavours.
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Affiliation(s)
- Fergal J Hamrock
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Daniel Ryan
- Department of Microbiology, Biocentre, University of Würzburg, Würzburg, Germany
| | - Ali Shaibah
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Anna S Ershova
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Aalap Mogre
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Maha M Sulimani
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Safa Ben Taarit
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Sarah Reichardt
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Karsten Hokamp
- Department of Genetics, School of Genetics & Microbiology, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Alexander J Westermann
- Department of Microbiology, Biocentre, University of Würzburg, Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Carsten Kröger
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
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Wei L, Feng Y, Lin J, Kang X, Zhuang H, Wen H, Ran S, Zheng L, Zhang Y, Xiang Q, Liu Y, Wu X, Duan X, Zhang W, Li Q, Guo H, Tao C, Qiao F. Handwashing sinks as reservoirs of carbapenem-resistant Acinetobacter baumannii in the intensive care unit: a prospective multicenter study. Front Public Health 2024; 12:1468521. [PMID: 39444981 PMCID: PMC11496070 DOI: 10.3389/fpubh.2024.1468521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Accepted: 09/16/2024] [Indexed: 10/25/2024] Open
Abstract
Introduction The extent to which sinks are contaminated by carbapenem-resistant Acinetobacter baumannii (CRAB) in intensive care units (ICUs) and the association between these contaminated sinks and hospital-acquired CRAB infections during the non-cluster period remains largely unknown. Here, we performed a prospective multicenter study in 16 ICUs at 11 tertiary hospitals in Chengdu, China. Methods We sampled sinks, collected CRAB clinical isolates, and conducted whole-genome sequencing and analysis. Results A total of 789 swabs were collected from 158 sinks, and 16 CRAB isolates were recovered from 16 sinks, resulting in a contamination rate of 10.16%. Twenty-seven clinical isolates were collected during the study period. The majority (97.67%, 42/43) of the CRAB isolates belonged to ST2, and 36 (83.72%) of them had both bla OXA-23 and bla OXA-66. The 43 strains belonged to 12 clones. One certain clone caused multiple contaminations of seven sinks in one GICU. Two clones of ST2 bla OXA-23 and bla OXA-66-carrying sink strains were likely the sources of the two clusters in the two GICUs, respectively. Five ST2 bla OXA-23-carrying isolates were found to be common clones but were recovered from two hospitals. Conclusion The contamination rate of CRAB in handwashing sinks is high in some local ICUs, and the contaminated sinks can serve as environmental reservoirs for CRAB clusters.
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Affiliation(s)
- Li Wei
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
- Department of Infection Control, West China Hospital, Sichuan University, Chengdu, China
| | - Yu Feng
- Center for Pathogen Research, West China Hospital, Sichuan University, Chengdu, China
| | - Ji Lin
- Department of Infection Control, West China Hospital, Sichuan University, Chengdu, China
| | - Xia Kang
- Department of Infection Control, West China Hospital, Sichuan University, Chengdu, China
| | - Hongdi Zhuang
- Department of Infection Control, West China Hospital, Sichuan University, Chengdu, China
| | - Hongxia Wen
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
- Center for Pathogen Research, West China Hospital, Sichuan University, Chengdu, China
| | - Shasha Ran
- Department of Infection Control, Chengdu Women and Children Hospital, Chengdu, China
| | - Lan Zheng
- Department of Infection Control, Chengdu Second People’s Hospital, Chengdu, China
| | - Yujing Zhang
- Department of Infection Control, Chengdu First People’s Hospital, Chengdu, China
| | - Qian Xiang
- Department of Infection Control, Sichuan Provincial People’s Hospital, Chengdu, China
| | - Yan Liu
- Department of Infection Control, Affiliated Hospital of Chengdu University, Chengdu, China
| | - Xueqin Wu
- Department of Infection Control, The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Xiaofei Duan
- Department of Infection Control, Chengdu Public Health Center, Chengdu, China
| | - Wensheng Zhang
- Department of Infection Control, Traditional Chinese Medicine Hospital of Sichuan Province, Chengdu, China
| | - Qu Li
- Department of Infection Control, Sichuan Provincial Maternity and Child Health Care Hospital, Chengdu, China
| | - Hua Guo
- Department of Infection Control, Chengdu Third People’s Hospital, Chengdu, China
| | - Chuanmin Tao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Fu Qiao
- Department of Infection Control, West China Hospital, Sichuan University, Chengdu, China
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He X, Tang J, He S, Huang X. Analysis of risk factors and different treatments for infections caused by carbapenem-resistant Acinetobacter baumannii in Shaanxi, China. BMC Infect Dis 2024; 24:1130. [PMID: 39385067 PMCID: PMC11465493 DOI: 10.1186/s12879-024-10036-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 10/01/2024] [Indexed: 10/11/2024] Open
Abstract
BACKGROUND The global threat of Carbapenem-resistant Acinetobacter baumannii (CRAB) has intensified as resistance to carbapenems continues to rise in recent decades. We aimed to explore risk factors, molecular epidemiology, and antimicrobial therapy of CRAB infection. METHODS The clinical data of 110 patients infected with A. baumannii from December 2021 to December 2022 were retrospectively analyzed. Patients were divided into a carbapenem-resistance group (55 patients) and carbapenem-sensitive group (CSAB; 55 patients) based on resistance to carbapenem, and the risk factors of patients infected with CRAB were analyzed. Fifty-five patients with CRAB infection who received antimicrobial therapy were divided into a combination therapy group (45 patients) and a monotherapy group (10 patients), and differences between the two groups were compared. Whole-genome sequencing analysis was performed to assess resistance genes. Phylogenetic analysis was performed to explore the characteristics of CRAB isolates. RESULTS Among the total 110 patients, the rate of poor prognosis in the CRAB group was 43.6% (24/55). Mechanical ventilation (odds ratio [OR] = 5.364, 95% confidence interval [CI] 1.462-19.679, P = 0.011) and puncture (OR = 19.935, 95% CI 1.261-315.031, P = 0.012) were independent risk factors for CRAB infection. Of 55 patients in the antimicrobial regimen study, 45 received combination therapy (including dual, triple, or quadruple antibiotic therapy) and 10 received monotherapy. Univariate analysis revealed significant differences between the combination group and monotherapy group for admission to the intensive care unit and wound infection (P < 0.05). The CRAB strains of 26 patients taking carbapenem-based combination therapy were mainly ST208, ST1968, and ST195, among which patients with ST1968 strains had higher 28-day mortality. Furthermore, the blaOXA-23 gene was harbored in ST1968, ST195, and ST208. CONCLUSIONS Mortality was significantly higher in patients infected with CRAB than with CSAB. Mechanical ventilation and puncture were independent risk factors in predicting CRAB infections. The distribution of CRAB was dominated by ST208, ST1968, and ST195, among which patients with ST1968 had higher 28-day mortality. The blaOXA-23 gene appears to be widely disseminated.
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Affiliation(s)
- Xiaoliang He
- Department of Clinical Laboratory, Hanzhong Central Hospital, 22 Kangfu Road, Hanzhong, Shaanxi, People's Republic of China
| | - Jin Tang
- Department of Clinical Laboratory, Hanzhong Central Hospital, 22 Kangfu Road, Hanzhong, Shaanxi, People's Republic of China
| | - Sanjun He
- Department of Clinical Laboratory, Hanzhong Central Hospital, 22 Kangfu Road, Hanzhong, Shaanxi, People's Republic of China
| | - Xiaoxia Huang
- Department of Clinical Laboratory, Hanzhong Central Hospital, 22 Kangfu Road, Hanzhong, Shaanxi, People's Republic of China.
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Wajid Odhafa M, Al-Kadmy I, Pourmand MR, Naderi G, Asadian M, Ghourchian S, Douraghi M. The context of bla OXA-23 gene in Iraqi carbapenem-resistant Acinetobacter baumannii isolates belonging to global clone 1 and global clone 2. BMC Res Notes 2024; 17:300. [PMID: 39380025 PMCID: PMC11463083 DOI: 10.1186/s13104-024-06890-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 08/05/2024] [Indexed: 10/10/2024] Open
Abstract
BACKGROUND AND OBJECTIVES Of the genes conferring resistance to carbapenems in Acinetobacter baumannii, the blaOXA-23 gene is the most widely found across the world. The gene carrying blaOXA-23 transposons in A. baumannii isolates of global clones GC1 and GC2 is found worldwide. Here, we examined whether transposons play a role in the dissemination of the blaOXA-23 in globally distributed clones, GC1 and GC2 A. baumannii isolates from Iraq. MATERIALS AND METHODS The 119 non-repetitive A. baumannii isolates including 94 recovered from clinical specimens and 25 isolates from hospital environment between September 2021 and April 2022 from different medical centers located at various regions in Baghdad, Iraq. The global clones (GC) and the genes encoding carbapenem resistance, including blaOXA-23, blaOXA-24, and blaOXA-58 were identified using multiplex PCR assays. Antibiotic susceptibility testing was performed by the Kirby-Bauer disk diffusion susceptibility method. The transposons carrying blaOXA-23 were examined using PCR mapping. In cases when carbapenem susceptible A. baumannii isolates were found, they were subjected to E test, full length sequencing of blaOXA-Ab (blaOXA-51-like) and Institut Pasteur multi-locus sequence typing scheme. RESULTS All but two isolates (92 clinical and 25 environmental) were identified carbapenem-resistant A. baumannii (CRAB). Of 117 CRAB isolates, 20 belong to GC1, 19 contained blaOXA-23; of them, 17 isolates harbored the blaOXA-23 located on Tn2006. Among the 46 CRAB belonging to GC2, 39 contained blaOXA-23; of them, 34 carried the blaOXA-23 located on Tn2006. The remaining GC1 and GC2 isolates, one GC1 as well as one GC2 isolate, were susceptible to imipenem, doripenem, and meropenem and considered carbapenem-susceptible A. baumannii (CSAB). Full-length sequencing of the blaOXA-Ab and MLST for the two CSAB isolates belonging to GC1 and GC2 confirmed that the GC1 isolate belongs to ST 623 and contained an allele that encodes an blaOXA-69 variant of the blaOXA-Ab while the GC2 belong to ST2 and carried an blaOXA-66 variant. CONCLUSION This study provides evidence for the dissemination of blaOXA-23 on the Tn2006 in CRAB isolates in Baghdad, Iraq. It appears that this transposon is widespread in GC1 and 2 isolates as in the other parts of the world. Interestingly, one GC1 and one GC2 isolate from Iraq were found to be susceptible to carbapenem while the isolates belonging to GC1 and GC2 have so far rarely been found to be susceptible to carbapenem globally.
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Affiliation(s)
- Melak Wajid Odhafa
- Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Israa Al-Kadmy
- Department of Biology, College of Science, Mustansiriyah University, Baghdad, Iraq
| | - Mohammad Reza Pourmand
- Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Ghazal Naderi
- Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahla Asadian
- Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Sedighe Ghourchian
- Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Masoumeh Douraghi
- Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
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Carascal MB, Destura RV, Rivera WL. Colorimetric Loop-Mediated Isothermal Amplification Assays Accurately Detect blaOXA-23-like and ISAba1 Genes from Acinetobacter baumannii in Pure Cultures and Spiked Human Sera. Microb Drug Resist 2024; 30:432-441. [PMID: 39193641 DOI: 10.1089/mdr.2024.0075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024] Open
Abstract
Carbapenem resistance in Acinetobacter baumannii is a critical global health threat attributed to transferrable carbapenemase genes. Carbapenemase genotyping using polymerase chain reaction (PCR) presents a challenge in resource-limited settings because of its technical requirements. This study designed new loop-mediated isothermal amplification (LAMP) primers using multiple sequence alignment-based workflows, validated the primer performance against multiple target variants in silico, and developed novel LAMP assays (LAntRN-OXA23 and LAntRN-ISAba1) to detect the transferable blaOXA-23-like carbapenemase genes and ISAba1 elements in pure cultures and A. baumannii-spiked serum samples. The designed LAMP primers bind to the conserved regions of their highly polymorphic targets, with their in silico performance comparable with other published primers. The in vitro LAMP assays (using 30 PCR-profiled A. baumannii and 10 standard multidrug-resistant gram-negative isolates) have 100% concordance with the PCR-positive clinical samples, limits of detection as low as 1 pg/µL (200 copies/µL), and specificities of 57.89-100%. Both assays produced positive results when testing DNA samples (extracted using a commercial kit) from blaOXA-23-like and ISAba1-blaOXA-51-like PCR-positive A. baumannii-spiked normal human sera (five set-ups per target). In summary, the LAMP assays accurately detected the target genes and have applications in infection management, control, and point-of-care testing in resource-limited healthcare settings.
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Affiliation(s)
- Mark B Carascal
- Pathogen-Host-Environment Interactions Research Laboratory, Institute of Biology, College of Science, University of the Philippines, Diliman, Quezon City, Philippines
- Clinical and Translational Research Institute, The Medical City, Pasig City, Philippines
| | - Raul V Destura
- Clinical and Translational Research Institute, The Medical City, Pasig City, Philippines
- National Training Center for Biosafety and Biosecurity, National Institutes of Health, University of the Philippines, Manila, Philippines
| | - Windell L Rivera
- Pathogen-Host-Environment Interactions Research Laboratory, Institute of Biology, College of Science, University of the Philippines, Diliman, Quezon City, Philippines
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Miller WR, Arias CA. ESKAPE pathogens: antimicrobial resistance, epidemiology, clinical impact and therapeutics. Nat Rev Microbiol 2024; 22:598-616. [PMID: 38831030 DOI: 10.1038/s41579-024-01054-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2024] [Indexed: 06/05/2024]
Abstract
The rise of antibiotic resistance and a dwindling antimicrobial pipeline have been recognized as emerging threats to public health. The ESKAPE pathogens - Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp. - were initially identified as critical multidrug-resistant bacteria for which effective therapies were rapidly needed. Now, entering the third decade of the twenty-first century, and despite the introduction of several new antibiotics and antibiotic adjuvants, such as novel β-lactamase inhibitors, these organisms continue to represent major therapeutic challenges. These bacteria share several key biological features, including adaptations for survival in the modern health-care setting, diverse methods for acquiring resistance determinants and the dissemination of successful high-risk clones around the world. With the advent of next-generation sequencing, novel tools to track and combat the spread of these organisms have rapidly evolved, as well as renewed interest in non-traditional antibiotic approaches. In this Review, we explore the current epidemiology and clinical impact of this important group of bacterial pathogens and discuss relevant mechanisms of resistance to recently introduced antibiotics that affect their use in clinical settings. Furthermore, we discuss emerging therapeutic strategies needed for effective patient care in the era of widespread antimicrobial resistance.
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Affiliation(s)
- William R Miller
- Department of Internal Medicine, Division of Infectious Diseases, Houston Methodist Hospital, Houston, TX, USA
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, TX, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Cesar A Arias
- Department of Internal Medicine, Division of Infectious Diseases, Houston Methodist Hospital, Houston, TX, USA.
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, TX, USA.
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
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Wu J, Thompson TP, O'Connell NH, McCracken K, Powell J, Gilmore BF, Dunne CP, Kelly SA. More than just the gene: investigating expression using a non-native plasmid and host and its impact on resistance conferred by β-lactamase OXA-58 isolated from a hospital wastewater microbiome. Lett Appl Microbiol 2024; 77:ovae097. [PMID: 39375834 DOI: 10.1093/lambio/ovae097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Revised: 10/01/2024] [Accepted: 10/04/2024] [Indexed: 10/09/2024]
Abstract
With the escalation of hospital-acquired infections by multidrug resistant bacteria, understanding antibiotic resistance is of paramount importance. This study focuses on the β-lactamase gene, blaOXA-58, an important resistance determinant identified in a patient-facing hospital wastewater system. This study aimed to characterize the behaviour of the OXA-58 enzyme when expressed using a non-native plasmid and expression host. blaOXA-58 was cloned using a pET28a(+)/Escherichia coli BL21(DE3) expression system. Nitrocefin hydrolysis and antimicrobial susceptibility of OXA-58-producing cells were assessed against penicillin G, ampicillin, meropenem, and amoxicillin. blaOXA-58 conferred resistance to amoxicillin, penicillin G, and ampicillin, but not to meropenem. This was unexpected given OXA-58's annotation as a carbapenemase. The presence of meropenem also reduced nitrocefin hydrolysis, suggesting it acts as a competitive inhibitor of the OXA-58 enzyme. This study elucidates the phenotypic resistance conferred by an antimicrobial resistance gene (ARG) obtained from a clinically relevant setting and reveals that successful functional expression of ARGs is multifaceted. This study challenges the reliability of predicting antimicrobial resistance based solely on gene sequence alone, and serves as a reminder of the intricate interplay between genetics and structural factors in understanding resistance profiles across different host environments.
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Affiliation(s)
- J Wu
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, United Kingdom
| | - T P Thompson
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, United Kingdom
| | - N H O'Connell
- Microbiology Department, University Hospital Limerick, Limerick, V94 F858, Ireland
- School of Medicine and Centre for Interventions in Infection, Inflammation, and Immunity (4i), University of Limerick, Limerick, V94 T9PX, Ireland
| | - K McCracken
- Keith McCracken Consulting Limited, The Manor House, Greencastle, Co. Donegal, F93 R9Y0, Ireland
| | - J Powell
- Microbiology Department, University Hospital Limerick, Limerick, V94 F858, Ireland
- School of Medicine and Centre for Interventions in Infection, Inflammation, and Immunity (4i), University of Limerick, Limerick, V94 T9PX, Ireland
| | - B F Gilmore
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, United Kingdom
- School of Medicine and Centre for Interventions in Infection, Inflammation, and Immunity (4i), University of Limerick, Limerick, V94 T9PX, Ireland
| | - C P Dunne
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, United Kingdom
- School of Medicine and Centre for Interventions in Infection, Inflammation, and Immunity (4i), University of Limerick, Limerick, V94 T9PX, Ireland
| | - S A Kelly
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, United Kingdom
- School of Medicine and Centre for Interventions in Infection, Inflammation, and Immunity (4i), University of Limerick, Limerick, V94 T9PX, Ireland
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Sharma S, Tiwari V. Polyvinylpyrrolidone capped silver nanoparticles enhance the autophagic clearance of Acinetobacter baumannii from human pulmonary cells. DISCOVER NANO 2024; 19:154. [PMID: 39313578 PMCID: PMC11420407 DOI: 10.1186/s11671-024-04107-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 09/09/2024] [Indexed: 09/25/2024]
Abstract
Acinetobacter baumannii, an opportunistic pathogen has shown an upsurge in its multi-drug resistant isolates. OmpA of A. baumannii induces incomplete autophagy and apoptosis in host cells. Various therapeutic alternatives are under investigation against A. baumannii. Here, the major emphasis has been laid on comparing the efficacy of AgNP with different capping agents. OmpA targeted lead, Ivermectin capped AgNP (IVM-AgNP) has been compared with the antibacterial polyvinylpyrrolidone capped AgNP (PVP-AgNP) for their role in the modulations of host autophagy. Upregulation of p62 and LC3B confirmed by real-time PCR analysis indicated an increased autophagic flux upon the treatment with AgNPs. The elongation and closure of autophagic vacuoles was also supported by upregulated Atg genes (Atg4, Atg3, Atg5) in A. baumannii infected cells after treatment with AgNP. Autophagic flux increased on treatment with PVP-AgNP as suggested by the rise in mcherryLC3B fluorescence in A549 cells treated with PVP-AgNP as compared to the GFP-LC3B of IVM-AgNP. This suggests that PVP-AgNP treatment more effectively promotes the elongation and maturation stages of autophagy by increasing autophagic flux. These results indicate that capped AgNPs have the efficiency to revert the incomplete autophagy induced by A. baumannii back to normal autophagic levels.
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Affiliation(s)
- Saroj Sharma
- Department of Biochemistry, Central University of Rajasthan, Ajmer, 305817, India
| | - Vishvanath Tiwari
- Department of Biochemistry, Central University of Rajasthan, Ajmer, 305817, India.
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Mohamed RAE, Moustafa NM, Mahmoud FM, Elsaadawy YS, Aziz HSA, Gaber SAB, Hussin AM, Seadawy MG. Whole-genome sequencing of two multidrug-resistant acinetobacter baumannii strains isolated from a neonatal intensive care unit in Egypt: a prospective cross-sectional study. BMC Microbiol 2024; 24:362. [PMID: 39306657 PMCID: PMC11415996 DOI: 10.1186/s12866-024-03482-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 08/28/2024] [Indexed: 09/25/2024] Open
Abstract
BACKGROUND Acinetobacter baumannii (A. baumannii) is a life-threatening and challenging pathogen. In addition, it accounts for numerous serious infections, particularly among immunocompromised patients. Resistance to nearly all clinically used antibiotics and their ability to spread this resistance is one of the most important concerns related to this bacterium. OBJECTIVES This study describes different molecular mechanisms of two multidrug-resistant A. baumannii isolates obtained from endotracheal aspirates collected from the neonatal intensive care unit (NICU), Ain Shams University Hospital, Egypt. METHODS Following the identification of two isolates, they were examined for susceptibility to antimicrobial agents. This was followed by multilocus sequence typing as well as whole-genome sequence (WGS). Additionally, a Pathosystems Resources Integration Center (PATRIC) analysis was performed. RESULTS Two isolates, Ab119 and Ab123, exhibited resistance to all tested antibiotics except for tigecycline and colistin. The WGS analysis of antimicrobial resistance genes (AMR) indicated that both isolates shared beta-lactam, aminoglycoside, macrolides, and sulfonamide resistance genes. Furthermore, each strain revealed different resistance genes such as blaNDM-1, blaNDM-10, OXA-64, aph (3')-VI, Tet-B in Ab119 strain and blaOXA-68, blaPER-1, blaPER-7, Tet-39 in Ab123 strain. Multiple efflux pump genes were detected. Multilocus sequence typing indicated that both isolates belong to the same sequence type (ST931), which belongs to international clone (IC3). Both isolates exhibited the presence of multiple mobile genetic elements (MGEs), but no plasmid was detected in either of them. CONCLUSIONS A low prevalence of the IC3 sequence type was identified among two A. baumannii isolates obtained from the NICU in Egypt, exhibiting a high resistance level. Healthcare workers must have knowledge regarding the prevalence of A. baumannii among different populations in order to administer suitable treatment, improve patient outcomes, and apply effective infection control practices.
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Affiliation(s)
- Rania Alam Eldin Mohamed
- Medical Microbiology and Immunology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Nouran Magdy Moustafa
- Medical Microbiology and Immunology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
- Basic Medical Science Department, College of Medicine, Dar Al Uloom University, Riyadh, Saudi Arabia
| | - Fatma Mostafa Mahmoud
- Medical Microbiology and Immunology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Yara Said Elsaadawy
- Medical Microbiology and Immunology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Heba Sherif Abdel Aziz
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Cairo, Egypt.
| | | | | | - Mohamed G Seadawy
- Biodefense Center for Infectious and Emerging Diseases, Ministry of Defense, Cairo, Egypt
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Boonyalai N, Peerapongpaisarn D, Thamnurak C, Oransathid W, Wongpatcharamongkol N, Oransathid W, Lurchachaiwong W, Griesenbeck JS, Waters NC, Demons ST, Ruamsap N, Vesely BA. Screening of the Pandemic Response Box library identified promising compound candidate drug combinations against extensively drug-resistant Acinetobacter baumannii. Sci Rep 2024; 14:21709. [PMID: 39289446 PMCID: PMC11408719 DOI: 10.1038/s41598-024-72603-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 09/09/2024] [Indexed: 09/19/2024] Open
Abstract
Infections caused by antimicrobial-resistant Acinetobacter baumannii pose a significant threat to human health, particularly in the context of hospital-acquired infections. As existing antibiotics lose efficacy against Acinetobacter isolates, there is an urgent need for the development of novel antimicrobial agents. In this study, we assessed 400 structurally diverse compounds from the Medicines for Malaria Pandemic Response Box for their activity against two clinical isolates of A. baumannii: A. baumannii 5075, known for its extensive drug resistance, and A. baumannii QS17-1084, obtained from an infected wound in a Thai patient. Among the compounds tested, seven from the Pathogen box exhibited inhibitory effects on the in vitro growth of A. baumannii isolates, with IC50s ≤ 48 µM for A. baumannii QS17-1084 and IC50s ≤ 17 µM for A. baumannii 5075. Notably, two of these compounds, MUT056399 and MMV1580854, shared chemical scaffolds resembling triclosan. Further investigations involving drug combinations identified five synergistic drug combinations, suggesting potential avenues for therapeutic development. The combination of MUT056399 and brilacidin against A. baumannii QS17-1084 and that of MUT056399 and eravacycline against A. baumannii 5075 showed bactericidal activity. These combinations significantly inhibited biofilm formation produced by both A. baumannii strains. Our findings highlight the drug combinations as promising candidates for further evaluation in murine wound infection models against multidrug-resistant A. baumannii. These compounds hold potential for addressing the critical need for effective antibiotics in the face of rising antimicrobial resistance.
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Affiliation(s)
- Nonlawat Boonyalai
- Department of Bacterial and Parasitic Diseases, Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
- Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK
| | - Dutsadee Peerapongpaisarn
- Department of Bacterial and Parasitic Diseases, Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Chatchadaporn Thamnurak
- Department of Bacterial and Parasitic Diseases, Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Wilawan Oransathid
- Department of Bacterial and Parasitic Diseases, Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Nantanat Wongpatcharamongkol
- Department of Bacterial and Parasitic Diseases, Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Wirote Oransathid
- Department of Bacterial and Parasitic Diseases, Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Woradee Lurchachaiwong
- Department of Bacterial and Parasitic Diseases, Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
- Division of Global Health Protection, Thailand MoPH-US CDC Collaboration, Nonthaburi, Thailand
| | - John S Griesenbeck
- Department of Bacterial and Parasitic Diseases, Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Norman C Waters
- Department of Bacterial and Parasitic Diseases, Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Samandra T Demons
- Department of Bacterial and Parasitic Diseases, Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Nattaya Ruamsap
- Department of Bacterial and Parasitic Diseases, Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Brian A Vesely
- Department of Bacterial and Parasitic Diseases, Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand.
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Vital M, Woltemate S, Schlüter D, Krezdorn N, Dieck T, Dastagir K, Bange FC, Ebadi E, Vogt PM, Knegendorf L, Baier C. Molecular epidemiology, microbiological features and infection control strategies for carbapenem-resistant Acinetobacter baumannii in a German burn and plastic surgery center (2020-2022). Antimicrob Resist Infect Control 2024; 13:99. [PMID: 39242542 PMCID: PMC11378564 DOI: 10.1186/s13756-024-01459-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Accepted: 08/29/2024] [Indexed: 09/09/2024] Open
Abstract
BACKGROUND Carbapenem-resistant Acinetobacter baumannii (CRAB) frequently causes both healthcare-associated infections and nosocomial outbreaks in burn medicine/plastic surgery and beyond. Owing to the high antibiotic resistance, infections are difficult to treat, and patient outcomes are often compromised. The environmental persistence capability of CRAB favors its transmission in hospitals. A comprehensive analysis and understanding of CRAB epidemiology and microbiology are essential for guiding management. METHODS A three-year retrospective cohort study (2020-2022) was conducted in a German tertiary burn and plastic surgery center. In addition to epidemiological analyses, microbiological and molecular techniques, including whole-genome sequencing, were applied for the comprehensive examination of isolates from CRAB-positive patients. RESULTS During the study period, eight CRAB cases were found, corresponding to an overall incidence of 0.2 CRAB cases per 100 cases and an incidence density of 0.35 CRAB cases per 1000 patient-days. Six cases (75%) were treated in the burn intensive care unit, and four cases (50%) acquired CRAB in the hospital. Molecular analyses comprising 74 isolates supported the epidemiologic assumption that hospital acquisitions occurred within two separate clusters. In one of these clusters, environmental CRAB contamination of anesthesia equipment may have enabled transmission. Furthermore, molecular diversity of CRAB isolates within patients was observed. CONCLUSIONS CRAB can pose a challenge in terms of infection prevention and control, especially if cases are clustered in time and space on a ward. Our study demonstrates that high-resolution phylogenetic analysis of several bacterial isolates from single patients can greatly aid in understanding transmission chains and helps to take precision control measures.
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Affiliation(s)
- Marius Vital
- Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany.
| | - Sabrina Woltemate
- Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
| | - Dirk Schlüter
- Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
| | - Nicco Krezdorn
- Department of Plastic, Aesthetic, Hand and Reconstructive Surgery, Burn Center, Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
- Department of Plastic and Breast Surgery, Roskilde University Hospital, 4000, Roskilde, Denmark
- Zealand University Hospital, Køge, Denmark
| | - Thorben Dieck
- Department of Plastic, Aesthetic, Hand and Reconstructive Surgery, Burn Center, Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
| | - Khaled Dastagir
- Department of Plastic, Aesthetic, Hand and Reconstructive Surgery, Burn Center, Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
| | - Franz-Christoph Bange
- Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
| | - Ella Ebadi
- Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
| | - Peter M Vogt
- Department of Plastic, Aesthetic, Hand and Reconstructive Surgery, Burn Center, Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
| | - Leonard Knegendorf
- Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany.
| | - Claas Baier
- Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany.
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Wang W, Weng J, Wei J, Zhang Q, Zhou Y, He Y, Zhang L, Li W, Zhang Y, Zhang Z, Li X. Whole genome sequencing insight into carbapenem-resistant and multidrug-resistant Acinetobacter baumannii harboring chromosome-borne blaOXA-23. Microbiol Spectr 2024; 12:e0050124. [PMID: 39101706 PMCID: PMC11370241 DOI: 10.1128/spectrum.00501-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 06/26/2024] [Indexed: 08/06/2024] Open
Abstract
Carbapenem-resistant Acinetobacter baumannii (CRAB) poses a significant threat to hospitalized patients as effective therapeutic options are scarce. Based on the genomic characteristics of the CRAB strain AB2877 harboring chromosome-borne blaOXA-23, which was isolated from the bronchoalveolar lavage fluid (BALF) of a patient in a respiratory intensive care unit (RICU), we systematically analyzed antibiotic resistance genes (ARGs) and the genetic context associated with ARGs carried by CRAB strains harboring chromosome-borne blaOXA-23 worldwide. Besides blaOXA-23, other ARGs were detected on the chromosome of the CRAB strain AB2877 belonging to ST208/1806 (Oxford MLST scheme). Several key genetic contexts associated with the ARGs were identified on the chromosome of the CRAB strain AB2877, including (1) the MDR region associated with blaOXA-23, tet(B)-tetR(B), aph(3'')-Ib, and aph(6)-Id (2); the resistance island AbGRI3 harboring armA and mph(E)-msr(E) (3); the Tn3-like composite transposon containing blaTEM-1D and aph(3')-Ia; and (4) the structure "ISAba1-blaADC-25." The first two genetic contexts were most common in ST195/1816, followed by ST208/1806. The last two genetic contexts were found most frequently in ST208/1806, followed by ST195/1816.IMPORTANCEThe blaOXA-23 gene can be carried by plasmid or chromosome, facilitating horizontal genetic transfer and increasing carbapenem resistance in healthcare settings. In this study, we focused on the genomic characteristics of CRAB strains harboring the chromosome-borne blaOXA-23 gene, and the important genetic contexts associated with blaOXA-23 and other ARGs were identified, and their prevalent clones worldwide were determined. Notably, although the predominant clonal CRAB lineages worldwide containing the MDR region associated with blaOXA-23, tet(B)-tetR(B), aph(3'')-Ib, and aph (6)-Id was ST195/1816, followed by ST208/1806, the CRAB strain AB2877 in our study belonged to ST208/1806. Our findings contribute to the knowledge regarding the dissemination of CRAB strains and the control of nosocomial infection.
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Affiliation(s)
- Wei Wang
- Department of Pulmonary and Critical Care Medicine, Zhuhai People’s Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, China
- Department of Critical Care Medicine, Zhuhai People’s Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, China
| | - Jiahui Weng
- School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jie Wei
- Department of Clinical Laboratory, Zhuhai People’s Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, China
| | - Qinghuan Zhang
- Department of Clinical Laboratory, Zhuhai People’s Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, China
| | - Yu Zhou
- Department of Anesthesiology, Zhuhai People’s Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, China
| | - Yanju He
- Department of Pulmonary and Critical Care Medicine, Zhuhai People’s Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, China
| | - Limei Zhang
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People’s Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, China
| | - Wenting Li
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People’s Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, China
| | - Yi Zhang
- Department of Pulmonary and Critical Care Medicine, Zhuhai People’s Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, China
| | - Zhiren Zhang
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People’s Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, China
| | - Xiaobin Li
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People’s Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, China
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Aggarwal R, Mahajan P, Pandiya S, Bajaj A, Verma SK, Yadav P, Kharat AS, Khan AU, Dua M, Johri AK. Antibiotic resistance: a global crisis, problems and solutions. Crit Rev Microbiol 2024; 50:896-921. [PMID: 38381581 DOI: 10.1080/1040841x.2024.2313024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 01/09/2024] [Accepted: 01/28/2024] [Indexed: 02/23/2024]
Abstract
Healthy state is priority in today's world which can be achieved using effective medicines. But due to overuse and misuse of antibiotics, a menace of resistance has increased in pathogenic microbes. World Health Organization (WHO) has announced ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) as the top priority pathogens as these have developed resistance against certain antibiotics. To combat such a global issue, it is utmost important to identify novel therapeutic strategies/agents as an alternate to such antibiotics. To name certain antibiotic adjuvants including: inhibitors of beta-lactamase, efflux pumps and permeabilizers for outer membrane can potentially solve the antibiotic resistance problems. In this regard, inhibitors of lytic domain of lytic transglycosylases provide a novel way to not only act as an alternate to antibiotics but also capable of restoring the efficiency of previously resistant antibiotics. Further, use of bacteriophages is another promising strategy to deal with antibiotic resistant pathogens. Taking in consideration the alternatives of antibiotics, a green synthesis nanoparticle-based therapy exemplifies a good option to combat microbial resistance. As horizontal gene transfer (HGT) in bacteria facilitates the evolution of new resistance strains, therefore identifying the mechanism of resistance and development of inhibitors against it can be a novel approach to combat such problems. In our perspective, host-directed therapy (HDT) represents another promising strategy in combating antimicrobial resistance (AMR). This approach involves targeting specific factors within host cells that pathogens rely on for their survival, either through replication or persistence. As many new drugs are under clinical trials it is advisable that more clinical data and antimicrobial stewardship programs should be conducted to fully assess the clinical efficacy and safety of new therapeutic agents.
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Affiliation(s)
- Rupesh Aggarwal
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Pooja Mahajan
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sameeksha Pandiya
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Aayushi Bajaj
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Shailendra Kumar Verma
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Puja Yadav
- Department of Microbiology, Central University of Haryana, Mahendergarh, India
| | - Arun S Kharat
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Asad Ullah Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Meenakshi Dua
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Atul Kumar Johri
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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50
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Wu C, Yuan Y, Tang S, Liu C, He C. Clinical and microbiological features of a cohort of patients with Acinetobacter baumannii bloodstream infections. Eur J Clin Microbiol Infect Dis 2024; 43:1721-1730. [PMID: 39023632 PMCID: PMC11349859 DOI: 10.1007/s10096-024-04881-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 06/15/2024] [Indexed: 07/20/2024]
Abstract
PURPOSE Acinetobacter baumannii is emerging as a pathogen that is a focus of global concern due to the frequent occurrence of the strains those are extensively resistant to antibiotics. This study was aimed to analyze the clinical and microbiological characteristics of a cohort of patients with A. baumannii bloodstream infections (BSIs) in western China. METHODS A retrospective study of the patients at West China Hospital of Sichuan University with A. baumannii BSIs between Jan, 2018 and May, 2023 was conducted. Antimicrobial susceptibility of A. baumannii isolates was tested by microdilution broth method. Whole-genome sequencing and genetic analysis were also performed for these isolates. RESULTS Among the 117 patients included, longer intensive care unit stay, higher mortality, and more frequent invasive procedures and use of more than 3 classes of antibiotics were observed among the carbapenem-resistant A. baumannii (CRAB)-infected group (n = 76), compared to the carbapenem-susceptible A. baumannii (CSAB)-infected group (n = 41, all P ≤ 0.001). Twenty-four sequence types (STs) were determined for the 117 isolates, and 98.7% (75/76) of CRAB were identified as ST2. Compared to non-ST2 isolates, ST2 isolates exhibited higher antibiotic resistance, and carried more resistance and virulence genes (P < 0.05). In addition, 80 (68.4%) isolates were CRISPR-positive, showed higher antibiotic susceptibility, and harbored less resistance and virulence genes, in comparison to CRISPR-negative ones (P < 0.05). Phylogenetic clustering based on coregenome SNPs indicated a sporadic occurrence of clonal transmission. CONCLUSION Our findings demonstrate a high frequency of ST2 among A. baumannii causing BSIs, and high antibiotic susceptibility of non-ST2 and CRISPR-positive isolates. It is necessary to strengthen the surveillance of this pathogen.
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Affiliation(s)
- Chongyang Wu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yu Yuan
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Sishi Tang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Chen Liu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Chao He
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
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