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Wang R, Liu Y, Zhang Y, Yu S, Zhuo H, Huang Y, Lyu J, Lin Y, Zhang X, Mi Z, Liu Y. Identification and characterization of the capsule depolymerase Dpo27 from phage IME-Ap7 specific to Acinetobacter pittii. Front Cell Infect Microbiol 2024; 14:1373052. [PMID: 38808067 PMCID: PMC11130378 DOI: 10.3389/fcimb.2024.1373052] [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: 01/19/2024] [Accepted: 04/11/2024] [Indexed: 05/30/2024] Open
Abstract
Among the Acinetobacter genus, Acinetobacter pittii stands out as an important opportunistic infection causative agent commonly found in hospital settings, which poses a serious threat to human health. Recently, the high prevalence of carbapenem-resistant A. pittii isolates has created significant therapeutic challenges for clinicians. Bacteriophages and their derived enzymes are promising therapeutic alternatives or adjuncts to antibiotics effective against multidrug-resistant bacterial infections. However, studies investigating the depolymerases specific to A. pittii strains are scarce. In this study, we identified and characterized a capsule depolymerase, Dpo27, encoded by the bacteriophage IME-Ap7, which targets A. pittii. A total of 23 clinical isolates of Acinetobacter spp. were identified as A. pittii (21.91%, 23/105), and seven A. pittii strains with various K locus (KL) types (KL14, KL32, KL38, KL111, KL163, KL207, and KL220) were used as host bacteria for phage screening. The lytic phage IME-Ap7 was isolated using A. pittii 7 (KL220) as an indicator bacterium and was observed for depolymerase activity. A putative tail fiber gene encoding a polysaccharide-degrading enzyme (Dpo27) was identified and expressed. The results of the modified single-spot assay showed that both A. pittii 7 and 1492 were sensitive to Dpo27, which was assigned the KL220 type. After incubation with Dpo27, A. pittii strain was susceptible to killing by human serum; moreover, the protein displayed no hemolytic activity against erythrocytes. Furthermore, the protein exhibited sustained activity across a wide pH range (5.0-10.0) and at temperatures between 20 and 50°C. In summary, the identified capsule depolymerase Dpo27 holds promise as an alternative treatment for combating KL220-type A. pittii infections.
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Affiliation(s)
- Rentao Wang
- Senior Department of Respiratory and Critical Care Medicine, the Eighth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yannan Liu
- Emergency Medicine Clinical Research Center, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Yaqian Zhang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Shijun Yu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hailong Zhuo
- Department of Transfusion Medicine, The Fifth Medical Centre of Chinese PLA General Hospital, Beijing, China
| | - Yong Huang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jinhui Lyu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yu Lin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xianglilan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zhiqiang Mi
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Youning Liu
- Senior Department of Respiratory and Critical Care Medicine, the Eighth Medical Center of Chinese PLA General Hospital, Beijing, China
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Bouvier M, Kerbol A, Findlay J, Freire S, Poirel L, Nordmann P. Resist Acineto rapid immunological test for the detection of acquired carbapenemase producers among Acinetobacter spp. Diagn Microbiol Infect Dis 2023; 107:116043. [PMID: 37657230 DOI: 10.1016/j.diagmicrobio.2023.116043] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/13/2023] [Accepted: 07/24/2023] [Indexed: 09/03/2023]
Abstract
The Resist Acineto from Coris Bioconcept is a novel immunochromatographic test for detection of the major acquired carbapenemases (OXA-23, OXA-40, OXA-58, and NDM) identified in Acinetobacter spp. This rapid and easy-to-perform test showed an excellent specificity and sensitivity, with positive and negatives predictive values of 100% in both cases.
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Affiliation(s)
- Maxime Bouvier
- National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, Fribourg and Institute for Microbiology, Fribourg, Switzerland; Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Auriane Kerbol
- National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, Fribourg and Institute for Microbiology, Fribourg, Switzerland
| | - Jacqueline Findlay
- Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Samanta Freire
- Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Laurent Poirel
- National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, Fribourg and Institute for Microbiology, Fribourg, Switzerland; Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland.
| | - Patrice Nordmann
- National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, Fribourg and Institute for Microbiology, Fribourg, Switzerland; Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland; University of Lausanne and University Hospital Centre, Lausanne, Switzerland
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Feng W, Jiang X, Zhang R, Guo Z, Gao D. Diagnosis of an Acinetobacter pittii from a patient in China with a multiplex PCR-based targeted gene sequencing platform of the cerebrospinal fluid: A case report with literature review. Medicine (Baltimore) 2022; 101:e31130. [PMID: 36281177 PMCID: PMC9592278 DOI: 10.1097/md.0000000000031130] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND The traditional diagnosis model has great challenges for the etiological diagnosis of the central nervous system (CNS) diseases with similar clinical manifestations, especially for the diagnosis of rare pathogens. It is very important to make rapid and accurate identification of pathogens for guiding clinical choices in administering countermeasures. CASE SUMMARY On August 22, 2020, a 49 years old Chinese male patient had a headache for two days, and then the computed tomography (CT) scan of the brain showed subarachnoid hemorrhage. Subsequently, he underwent twice craniotomy and about 3 weeks of hospitalization. Since September 20, the patient was in the local rehabilitation hospital for hyperbaric oxygen therapy for about three weeks. Then the patient developed acute purulent meningoencephalitis. In the absence of diagnosis of specific pathogenic bacteria, vancomycin (1 g every 12 hours), ceftazidime (2 g every 8 hours), mannitol dehydration (125 mL, every 8 hours), and sodium valproate (0.4 g tid) was used timely according to cerebrospinal fluid (CSF) examination and clinical manifestations. CSF smear and routine culture test were negative during hospitalization. We used the metagenomic next-generation sequencing (mNGS) analysis of CSF for quick and accurate diagnosis, which identified human herpesvirus type 4 (EBV), Corynebacterium corynebacterium, Achromobacter xylose oxidation, and Acinetobacter baumannii, But the mapping degree was not high. Then, we used the modified method-multiplex PCR-based targeted gene sequencing platform (ptNGS) to detect CSF samples and found that the sequences detected were Acinetobacter pittii (A. pittii) and Staphylococcus epidermidis. S. epidermidis might come from skin colonization during lumbar puncture, so it was excluded from the etiological diagnosis. Therefore, we highly suspected that A. pittii was the pathogen in this case. After about three weeks of hospitalization treatment, the patient's symptoms were relieved. CONCLUSION In conclusion, empirical medication before the identification of pathogens is very important. The ptNGS may be an effective method for the diagnosis of pathogens.
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Affiliation(s)
- Wenliang Feng
- Department of Critical Care Medicine, Fengtai Youanmen Hospital, Beijing, China
| | - Xuebin Jiang
- Intensive Care Unit, Renhe Hospital, Beijing, China
| | - Rujiang Zhang
- Department of Neurology, Yunnan St John’s Hospital, Yunnan, China
| | - Zhendong Guo
- Department of Science and Technology, Shanghai, China
| | - Daiquan Gao
- Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China
- *Correspondence: Daiquan Gao, Department of Neurology, Xuanwu Hospital of Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing 100053, China (e-mail: )
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Zhang L, Fu Y, Zhang L, Xu Q, Yang Y, He J, Leptihn S, Loh B, Moran RA, van Schaik W, Toleman MA, Chen Q, Liu L, Yu Y, Hua X. Co‐evolutionary adaptations of
Acinetobacter baumannii
and a clinical carbapenemase‐encoding plasmid during carbapenem exposure. Evol Appl 2022; 15:1045-1061. [PMID: 35899254 PMCID: PMC9309461 DOI: 10.1111/eva.13441] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 05/16/2022] [Accepted: 06/14/2022] [Indexed: 11/27/2022] Open
Abstract
OXA‐23 is the predominant carbapenemase in carbapenem‐resistant Acinetobacter baumannii. The co‐evolutionary dynamics of A. baumannii and OXA‐23‐encoding plasmids are poorly understood. Here, we transformed A. baumannii ATCC 17978 with pAZJ221, a blaOXA−23‐containing plasmid from clinical A. baumannii isolate A221, and subjected the transformant to experimental evolution in the presence of a sub‐inhibitory concentration of imipenem for nearly 400 generations. We used population sequencing to track genetic changes at six time points and evaluated phenotypic changes. Increased fitness of evolving populations, temporary duplication of blaOXA−23 in pAZJ221, interfering allele dynamics, and chromosomal locus‐level parallelism were observed. To characterize genotype‐to‐phenotype associations, we focused on six mutations in parallel targets predicted to affect small RNAs and a cyclic dimeric (3′ → 5′) GMP‐metabolizing protein. Six isogenic mutants with or without pAZJ221 were engineered to test for the effects of these mutations on fitness costs and plasmid kinetics, and the evolved plasmid containing two copies of blaOXA−23 was transferred to ancestral ATCC 17978. Five of the six mutations contributed to improved fitness in the presence of pAZJ221 under imipenem pressure, and all but one of them impaired plasmid conjugation ability. The duplication of blaOXA−23 increased host fitness under carbapenem pressure but imposed a burden on the host in antibiotic‐free media relative to the ancestral pAZJ221. Overall, our study provides a framework for the co‐evolution of A. baumannii and a clinical blaOXA−23‐containing plasmid in the presence of imipenem, involving early blaOXA−23 duplication followed by chromosomal adaptations that improved the fitness of plasmid‐carrying cells.
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Affiliation(s)
- Linyue Zhang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, School of Medicine Zhejiang University Hangzhou China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province Hangzhou China
| | - Ying Fu
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province Hangzhou China
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, School of Medicine Zhejiang University Hangzhou China
| | - Linghong Zhang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, School of Medicine Zhejiang University Hangzhou China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province Hangzhou China
| | - Qingye Xu
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province Hangzhou China
- Department of Clinical laboratory, Affiliated Hangzhou First People's Hospital, School of Medicine Zhejiang University Hangzhou China
| | - Yunxing Yang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province Hangzhou China
- Department of Clinical laboratory, Affiliated Hangzhou First People's Hospital, School of Medicine Zhejiang University Hangzhou China
| | - Jintao He
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, School of Medicine Zhejiang University Hangzhou China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province Hangzhou China
| | - Sebastian Leptihn
- Zhejiang University ‐University of Edinburgh Institute, School of Medicine, Zhejiang University Hangzhou China
| | - Belinda Loh
- Zhejiang University ‐University of Edinburgh Institute, School of Medicine, Zhejiang University Hangzhou China
| | - Robert A. Moran
- Institute of Microbiology and Infection, College of Medical and Dental Sciences University of Birmingham Birmingham B15 2TT United Kingdom
| | - Willem van Schaik
- Institute of Microbiology and Infection, College of Medical and Dental Sciences University of Birmingham Birmingham B15 2TT United Kingdom
| | - Mark Alexander Toleman
- Department of Medical Microbiology, Division of Infection and Immunity Cardiff University Cardiff United Kingdom
| | - Qiong Chen
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province Hangzhou China
- Department of Clinical laboratory, Affiliated Hangzhou First People's Hospital, School of Medicine Zhejiang University Hangzhou China
| | - Lilin Liu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, School of Medicine Zhejiang University Hangzhou China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province Hangzhou China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, School of Medicine Zhejiang University Hangzhou China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province Hangzhou China
| | - Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, School of Medicine Zhejiang University Hangzhou China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province Hangzhou China
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Epidemiological Characteristics of OXA-232-Producing Carbapenem-Resistant Klebsiella pneumoniae Strains Isolated during Nosocomial Clonal Spread Associated with Environmental Colonization. Microbiol Spectr 2022; 10:e0257221. [PMID: 35730968 PMCID: PMC9430510 DOI: 10.1128/spectrum.02572-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Here, a program was designed to surveil the colonization and associated infection of OXA-232-producing carbapenem-resistant Klebsiella pneumoniae (CRKP) (OXA-232-CRKP) in an intensive care unit (ICU) and to describe the epidemiological characteristics during surveillance. Samples were sourced from patient and environment colonization sites in the ICU from August to December 2019. During the surveillance, 106 OXA-232-CRKP strains were isolated from 8,656 samples of colonization sites, with an average positive rate of 1.22%. The rate from patient colonization sites was 3.59% (60/1,672 samples), over 5 times higher than that of the environment (0.66% [46/6,984 samples]). Rectal swabs and ventilator-related sites had the highest positive rates among patient and environment colonization sites, respectively. Six of the 15 patients who had OXA-232-CRKP at colonization sites suffered from OXA-232-CRKP-related infections. Patients could obtain OXA-232-CRKP from the environment, while long-term patient colonization was mostly accompanied by environmental colonization with subsequent infection. Antimicrobial susceptibility testing presented similar resistance profiles, in which all isolates were resistant to ertapenem but showed different levels of resistance to meropenem and imipenem. Whole-genome sequencing and single-nucleotide polymorphism (SNP) analysis suggested that all OXA-232-CRKP isolates belonged to the sequence type 15 (ST15) clone and were divided into two clades with 0 to 45 SNPs, sharing similar resistance genes, virulence genes, and plasmid types, indicating that the wide dissemination of OXA-232-CRKP between the environment and patients was due to clonal spread. The strains all contained β-lactam resistance genes, including blaOXA-232, blaCTX-M-15, and blaSHV-106, and 75.21% additionally carried blaTEM-1. In brief, wide ST15 clonal spread and long-term colonization of OXA-232-CRKP between patients and the environment were observed, with microevolution and subsequent infection. IMPORTANCE OXA-232 is a variant of OXA-48 carbapenemase, which has been increasingly reported in nosocomial outbreaks in ICUs. However, the OXA-232-CRKP transmission relationship between the environment and patients in ICUs was still not clear. Our study demonstrated the long-term colonization of OXA-232-CRKP in the ICU environment, declared that the colonization was a potential risk to ICU patients, and revealed the possible threat that this OXA-232-CRKP clone would bring to public health. The wide dissemination of OXA-232-CRKP between the environment and patients was due to ST15 clonal spread, which presented a multidrug-resistant profile and carried disinfectant resistance genes and virulence clusters, posing a challenge to infection control. The study provided a basis for environmental disinfection, including revealing common environmental colonization sites of OXA-232-CRKP and suggesting appropriate usage of disinfectants to prevent the development of disinfectant resistance.
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Sanz-García F, Gil-Gil T, Laborda P, Ochoa-Sánchez LE, Martínez JL, Hernando-Amado S. Coming from the Wild: Multidrug Resistant Opportunistic Pathogens Presenting a Primary, Not Human-Linked, Environmental Habitat. Int J Mol Sci 2021; 22:8080. [PMID: 34360847 PMCID: PMC8347278 DOI: 10.3390/ijms22158080] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/22/2021] [Accepted: 07/24/2021] [Indexed: 12/24/2022] Open
Abstract
The use and misuse of antibiotics have made antibiotic-resistant bacteria widespread nowadays, constituting one of the most relevant challenges for human health at present. Among these bacteria, opportunistic pathogens with an environmental, non-clinical, primary habitat stand as an increasing matter of concern at hospitals. These organisms usually present low susceptibility to antibiotics currently used for therapy. They are also proficient in acquiring increased resistance levels, a situation that limits the therapeutic options for treating the infections they cause. In this article, we analyse the most predominant opportunistic pathogens with an environmental origin, focusing on the mechanisms of antibiotic resistance they present. Further, we discuss the functions, beyond antibiotic resistance, that these determinants may have in the natural ecosystems that these bacteria usually colonize. Given the capacity of these organisms for colonizing different habitats, from clinical settings to natural environments, and for infecting different hosts, from plants to humans, deciphering their population structure, their mechanisms of resistance and the role that these mechanisms may play in natural ecosystems is of relevance for understanding the dissemination of antibiotic resistance under a One-Health point of view.
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Affiliation(s)
| | | | | | | | - José L. Martínez
- Centro Nacional de Biotecnología, CSIC, 28049 Madrid, Spain; (F.S.-G.); (T.G.-G.); (P.L.); (L.E.O.-S.); (S.H.-A.)
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