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Fang C, Liu KD, Tian FJ, Li JY, Li SJ, Zhang RM, Sun J, Fang LX, Ren H, Wang MG, Liao XP. Metagenomic analysis unveiled the response of microbial community and antimicrobial resistome in natural water body to duck farm sewage. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 361:124784. [PMID: 39182818 DOI: 10.1016/j.envpol.2024.124784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 07/06/2024] [Accepted: 08/19/2024] [Indexed: 08/27/2024]
Abstract
Sewages from duck farms are often recognized as a major source of antimicrobial resistance and pathogenic bacteria discharged to natural water bodies, but few studies depicted the dynamic changes in resistome and microbial communities in the rivers under immense exposure of sewage discharge. In this study, we investigated the ecological and environmental risks of duck sewages to the rivers that geographically near to the duck farms with short-distance (<1 km) using 16S rRNA amplicon and metagenomic sequencing. The results showed that a total of 20 ARG types were identified with abundances ranged from 0.61 to 1.33 cpc. Of note, the genes modulate resistances against aminoglycoside, bacitracin and beta-lactam were the most abundant ARGs. Limnohabitans, Fluviibacter and Cyanobium were the top 3 predominant genera in the microbial community. The alpha diversity of overall microbial community decrease while the abundance of pathogen increase during the input of sewage within 200 m. Sul1 and bacA were the dominant ARGs brought from duck farm sewage. The community variations of ARGs and microbiome were primarily driven by pH and temperature. Total phosphorus was significantly correlated to alpha diversity and top 30 ARGs subtype. Stochastic processes was the dominated microbial assembly pattern and did not be altered by sewage. We also highlighted the ecological risk caused by blaGES which possibly could be mitigated by Cyanobacteria, and the natural water body can purify partial ARGs as well as microbiome from duck farms sewage. These findings expanded our knowledge regarding the ecological risks by wastes from the livestock farm, and underscoring the necessity to monitor ARGs in farm-surrounding water bodies.
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Affiliation(s)
- Chang Fang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, PR China; Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, PR China; College of Marine Science, South China Agricultural University, Guangzhou, 510642, PR China
| | - Kai-di Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, PR China; Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, PR China
| | - Feng-Jie Tian
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, PR China; Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, PR China
| | - Jin-Ying Li
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, PR China; Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, PR China
| | - Si-Jie Li
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, PR China; Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, PR China
| | - Rong-Min Zhang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, PR China; Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, PR China
| | - Jian Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, PR China; Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, PR China
| | - Liang-Xing Fang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, PR China; Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, PR China
| | - Hao Ren
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, PR China; Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, PR China
| | - Min-Ge Wang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, PR China; Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, PR China; Phage Research Center, Liaocheng University, Liaocheng, 252000, PR China
| | - Xiao-Ping Liao
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, PR China; Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, PR China.
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Morales L, Cobo A, Frías MP, Gálvez A, Ortega E. The Prevalence of Antibiotic Resistance Phenotypes and Genotypes in Multidrug-Resistant Bacterial Isolates from the Academic Hospital of Jaén, Spain. Antibiotics (Basel) 2024; 13:429. [PMID: 38786157 PMCID: PMC11117780 DOI: 10.3390/antibiotics13050429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/07/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
The heterogenicity of antimicrobial resistance genes described in clinically significant bacterial isolates and their potential role in reducing the efficacy of classically effective antibiotics pose a major challenge for global healthcare, especially in infections caused by Gram-negative bacteria. We analyzed 112 multidrug-resistant (MDR) isolates from clinical samples in order to detect high resistance profiles, both phenotypically and genotypically, among four Gram-negative genera (Acinetobacter, Escherichia, Klebsiella, and Pseudomonas). We found that 9.8% of the total selected isolates were classified as extensively drug-resistant (XDR) (six isolates identified as A. baumannii and five among P. pneumoniae isolates). All other isolates were classified as MDR. Almost 100% of the isolates showed positive results for blaOXA-23 and blaNDM-1 genes among the A. baumannii samples, one resistance gene (blaCTX-M) among E. coli, and two genetic determinants (blaCTX-M and aac(6')-Ib) among Klebsiella. In contrast, P. aeruginosa showed just one high-frequency antibiotic resistance gene (dfrA), which was present in 68.42% of the isolates studied. We also describe positive associations between ampicillin and cefotaxime resistance in A. baumannii and the presence of blaVEB and blaGES genes, as well as between the aztreonam resistance phenotype and the presence of blaGES gene in E. coli. These data may be useful in achieving a better control of infection strategies and antibiotic management in clinical scenarios where these multidrug-resistant Gram-negative pathogens cause higher morbidity and mortality.
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Affiliation(s)
- Laura Morales
- Microbiolgy Unit, Department of Health Sciences, Faculty of Experimental Sciences, University of Jaén, 23071 Jaén, Spain; (L.M.); (A.C.); (A.G.)
| | - Antonio Cobo
- Microbiolgy Unit, Department of Health Sciences, Faculty of Experimental Sciences, University of Jaén, 23071 Jaén, Spain; (L.M.); (A.C.); (A.G.)
| | - María Pilar Frías
- Department of Statistics and Operation Research, Faculty of Experimental Sciences, University of Jaén, 23071 Jaén, Spain;
| | - Antonio Gálvez
- Microbiolgy Unit, Department of Health Sciences, Faculty of Experimental Sciences, University of Jaén, 23071 Jaén, Spain; (L.M.); (A.C.); (A.G.)
| | - Elena Ortega
- Microbiolgy Unit, Department of Health Sciences, Faculty of Experimental Sciences, University of Jaén, 23071 Jaén, Spain; (L.M.); (A.C.); (A.G.)
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3
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Barlow M, Tenover FC. Phylogenetic predictions of carbapenemase activity from the Guiana extended-spectrum (GES) family of β-lactamases. JAC Antimicrob Resist 2024; 6:dlad150. [PMID: 38213313 PMCID: PMC10783257 DOI: 10.1093/jacamr/dlad150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 11/27/2023] [Indexed: 01/13/2024] Open
Abstract
Objectives We investigated the amino acid substitutions in the GES family of ESBLs that were most likely to be involved in the evolution of carbapenemase activity. Methods To identify the substitutions that are functionally important, we analysed the evolutionary history of the GES β-lactamases using an alignment and phylogeny to identify sites in GES that show evidence of positive selection and the selected phenotypes. Results and Conclusions Data indicate that the substitutions G170S and G243A are associated with carbapenemase activity. The substitutions Q43E, E104K and T237A are most likely associated with ESBL activity.
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Affiliation(s)
- Miriam Barlow
- Department of Molecular and Cell Biology, University of California, Merced, CA 95343, USA
| | - Fred C Tenover
- College of Arts and Sciences: Biology, University of Dayton, Dayton, OH 45469, USA
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Sánchez-Urtaza S, Ocampo-Sosa A, Molins-Bengoetxea A, El-Kholy MA, Hernandez M, Abad D, Shawky SM, Alkorta I, Gallego L. Molecular characterization of multidrug resistant Acinetobacter baumannii clinical isolates from Alexandria, Egypt. Front Cell Infect Microbiol 2023; 13:1208046. [PMID: 37545857 PMCID: PMC10399577 DOI: 10.3389/fcimb.2023.1208046] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/03/2023] [Indexed: 08/08/2023] Open
Abstract
Carbapenem resistant Acinetobacter baumannii is a major global concern, especially in countries of the Middle East and North Africa, where the antibiotic resistance rates are on the rise. The aim of this study was to study the genomic characteristics and antimicrobial susceptibility profile of thirty-six multidrug resistant A. baumannii clinical isolates obtained in hospitals from Alexandria, Egypt. Antibiotic resistance rates were estimated by determination of Minimum Inhibitory Concentrations. Carbapenemase genes, other antibiotic resistance genes and virulence factors were then screened by the use of Whole Genome Sequencing. Isolates were also subjected to Multi Locus Sequence Typing (MLST) using the Pasteur Scheme and to core genome MLST to study their clonal relatedness. In addition, plasmid analysis was performed by the use of a commercial kit and S1- Pulsed Field Gel Electrophoresis, and Hybridization experiments with DIG-labeled DNA probes for bla NDM-1, blaPER-7 and bla GES-like were performed to locate these genes. The majority of isolates were resistant to β-lactams (including carbapenems), fluoroquinolones, aminoglycosides and trimethoprim; and some showed resistance to cefiderocol and minocycline. We identified 8 different bla OXA-51-like variants including bla OXA-51, bla OXA-64, bla OXA-65, bla OXA-66, bla OXA-68, bla OXA-91, bla OXA-94 and bla OXA-336; bla OXA-23, bla NDM-1, bla PER-7, bla GES-like and bla ADC-like and other antibiotic resistance genes, some of these genes were within transposons or class 1 integrons. Multiple virulence factors responsible for adherence, biofilm production, type II and type VI secretion systems, exotoxins, exoenzymes, immune modulation and iron uptake were observed and 34 out of 36 isolates showed motility. Thirty-five out of 36 isolates clustered with International Clones 2, 4, 5, 7, 8 and 9; and 9 STs were identified including ST570, ST2, ST600, ST15, ST113, ST613, ST85, ST158, ST164. Plasmids ranging in size from 1.7 to 70 kb were found; bla NDM-1 and blaPER-7 genes were located in the chromosome and bla GES-like genes were simultaneously located in the chromosome and in a plasmid of 70kb. In conclusion, this study revealed a wide spectrum of antibiotic resistance genes and a variety of lineages among A. baumannii isolated in hospitals from Alexandria, and highlights the importance of investigating the molecular epidemiology to control the spread of multi-drug resistant isolates.
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Affiliation(s)
- Sandra Sánchez-Urtaza
- Laboratory of Antibiotics and Molecular Bacteriology, Department of Immunology, Microbiology and Parasitology, Faculty of Medicine and Nursing, University of the Basque Country, Leioa, Spain
| | - Alain Ocampo-Sosa
- Microbiology Service, University Hospital Marqués de Valdecilla, Health Research Institute (Instituto de Investigación Valdecilla), Santander, Spain and CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain
| | - Ainhoa Molins-Bengoetxea
- Laboratory of Antibiotics and Molecular Bacteriology, Department of Immunology, Microbiology and Parasitology, Faculty of Medicine and Nursing, University of the Basque Country, Leioa, Spain
| | - Mohammed A. El-Kholy
- Department of Microbiology and Biotechnology, Division of Clinical and Biological Sciences, College of Pharmacy, Arab Academy for Science, Technology & Maritime Transport (AASTMT), Alexandria, Egypt
| | - Marta Hernandez
- Laboratory of Molecular Biology and Microbiology, One Health, Agricultural Technological, Institute of Castile and Leon (ITACyL), Valladolid, Spain
| | - David Abad
- Laboratory of Molecular Biology and Microbiology, One Health, Agricultural Technological, Institute of Castile and Leon (ITACyL), Valladolid, Spain
| | - Sherine M. Shawky
- Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Itziar Alkorta
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country, Leioa, Spain
| | - Lucia Gallego
- Laboratory of Antibiotics and Molecular Bacteriology, Department of Immunology, Microbiology and Parasitology, Faculty of Medicine and Nursing, University of the Basque Country, Leioa, Spain
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5
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Lynch JP, Clark NM, Zhanel GG. Infections Due to Acinetobacter baumannii-calcoaceticus Complex: Escalation of Antimicrobial Resistance and Evolving Treatment Options. Semin Respir Crit Care Med 2022; 43:97-124. [PMID: 35172361 DOI: 10.1055/s-0041-1741019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Bacteria within the genus Acinetobacter (principally A. baumannii-calcoaceticus complex [ABC]) are gram-negative coccobacilli that most often cause infections in nosocomial settings. Community-acquired infections are rare, but may occur in patients with comorbidities, advanced age, diabetes mellitus, chronic lung or renal disease, malignancy, or impaired immunity. Most common sites of infections include blood stream, skin/soft-tissue/surgical wounds, ventilator-associated pneumonia, orthopaedic or neurosurgical procedures, and urinary tract. Acinetobacter species are intrinsically resistant to multiple antimicrobials, and have a remarkable ability to acquire new resistance determinants via plasmids, transposons, integrons, and resistance islands. Since the 1990s, antimicrobial resistance (AMR) has escalated dramatically among ABC. Global spread of multidrug-resistant (MDR)-ABC strains reflects dissemination of a few clones between hospitals, geographic regions, and continents; excessive antibiotic use amplifies this spread. Many isolates are resistant to all antimicrobials except colistimethate sodium and tetracyclines (minocycline or tigecycline); some infections are untreatable with existing antimicrobial agents. AMR poses a serious threat to effectively treat or prevent ABC infections. Strategies to curtail environmental colonization with MDR-ABC require aggressive infection-control efforts and cohorting of infected patients. Thoughtful antibiotic strategies are essential to limit the spread of MDR-ABC. Optimal therapy will likely require combination antimicrobial therapy with existing antibiotics as well as development of novel antibiotic classes.
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Affiliation(s)
- Joseph P Lynch
- Division of Pulmonary, Critical Care Medicine, Allergy, and Clinical Immunology; Department of Medicine; The David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Nina M Clark
- Division of Infectious Diseases, Department of Medicine, Loyola University Medical Center, Maywood, Illinois
| | - George G Zhanel
- Department of Medical Microbiology/Infectious Diseases, University of Manitoba, Max Rady College of Medicine, Winnipeg, Manitoba, Canada
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Abouelfetouh A, Mattock J, Turner D, Li E, Evans BA. Diversity of carbapenem-resistant Acinetobacter baumannii and bacteriophage-mediated spread of the Oxa23 carbapenemase. Microb Genom 2022; 8. [PMID: 35104206 PMCID: PMC8942029 DOI: 10.1099/mgen.0.000752] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Carbapenem-resistant Acinetobacter baumannii are prevalent in low- and middle-income countries such as Egypt, but little is known about the molecular epidemiology and mechanisms of resistance in these settings. Here, we characterize carbapenem-resistant A. baumannii from Alexandria, Egypt, and place it in a regional context. Fifty-four carbapenem-resistant isolates from Alexandria Main University Hospital (AMUH), Alexandria, Egypt, collected between 2010 and 2015 were genome sequenced using Illumina technology. Genomes were de novo assembled and annotated. Genomes for 36 isolates from the Middle East region were downloaded from GenBank. The core-gene compliment was determined using Roary, and analyses of recombination were performed in Gubbins. Multilocus sequence typing (MLST) sequence type (ST) and antibiotic-resistance genes were identified. The majority of Egyptian isolates belonged to one of three major clades, corresponding to Pasteur MLST clonal complex (CCPAS) 1, CCPAS2 and STPAS158. Strains belonging to STPAS158 have been reported almost exclusively from North Africa, the Middle East and Pakistan, and may represent a region-specific lineage. All isolates carried an oxa23 gene, six carried bla NDM-1 and one carried bla NDM-2. The oxa23 gene was located on a variety of different mobile elements, with Tn2006 predominant in CCPAS2 strains, and Tn2008 predominant in other lineages. Of particular concern, in 8 of the 13 CCPAS1 strains, the oxa23 gene was located in a temperate bacteriophage phiOXA, previously identified only once before in a CCPAS1 clone from the USA military. The carbapenem-resistant A. baumannii population in AMUH is very diverse, and indicates an endemic circulating population, including a region-specific lineage. A major mechanism for oxa23 dissemination in CCPAS1 isolates appears to be a bacteriophage, presenting new concerns about the ability of these carbapenemases to spread throughout the bacterial population.
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Affiliation(s)
- Alaa Abouelfetouh
- Department of Microbiology and Immunology, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
| | | | - Dann Turner
- Department of Applied Sciences, University of the West of England, Bristol, UK
| | - Erica Li
- Norwich Medical School, University of East Anglia, Norwich, UK
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Alali WQ, AlFouzan W, Dhar R. Prevalence of antimicrobial resistance in Gram-negative clinical isolates from a major secondary hospital in Kuwait: a retrospective descriptive study. Germs 2021; 11:498-511. [PMID: 35096667 PMCID: PMC8789362 DOI: 10.18683/germs.2021.1285] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 10/23/2021] [Accepted: 10/23/2021] [Indexed: 07/21/2023]
Abstract
INTRODUCTION Building an antimicrobial resistance (AMR) surveillance system in a country requires analysis of available data on AMR in clinical isolates. This study's objective was to determine the AMR prevalence of Gram-negative bacterial (GNB) isolates cultured from clinical specimens at a major general hospital in Kuwait. METHODS A retrospective descriptive study was conducted on AMR profiles of GNB clinical isolates (n=5290) between January and December 2018. Data were extracted from the laboratory information system in the hospital. The GNB organisms (i.e., Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii) were isolated from five main locations at the hospital (i.e., intensive care units [ICUs], surgical wards, medical wards, pediatric wards, and outpatient polyclinics). RESULTS Overall, high AMR prevalence (>50%) against ampicillin, cefuroxime, cefotaxime, ceftazidime, ciprofloxacin, and trimethoprim/sulfamethoxazole, were observed across the GNB organisms. However, low resistance prevalence (<10%) were observed against amikacin, ertapenem, meropenem, and piperacillin/tazobactam. In general, AMR prevalence in E. coli isolates from ICU, medical and surgical wards was significantly (p<0.05) higher compared to other locations, whereas, AMR prevalence in P. aeruginosa isolates from pediatric ward was higher (p<0.05) compared to other locations. The overall multidrug resistance (MDR) prevalence was 38.7% (95% CI: 37.4-40.0). The highest MDR prevalence was among E. coli isolates from respiratory specimens (48%); wounds, bones, or other tissues (47.7%); and body fluids (47.1%). Similarly, MDR prevalence in K. pneumoniae, P. aeruginosa, and A. baumannii isolated from respiratory specimens was significantly (p<0.05) higher compared to other specimen types. The most frequent MDR phenotypes in the four GNB organisms and across the different specimen types included three antimicrobial drug classes: penicillins, cephalosporins, and fluroquinolones. CONCLUSIONS Our findings demonstrate high AMR prevalence among common Gram-negative bacteria at this major hospital. Monitoring data on antimicrobial susceptibility of common bacterial organisms is critical for assessing trends in AMR at hospitals and for informing policy decisions.
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Affiliation(s)
- Walid Q. Alali
- DVM, PhD, Department of Epidemiology & Biostatistics, Faculty of Public Health, Kuwait University, Hawalli, postal code 13060, Kuwait
| | - Wadha AlFouzan
- MD, PhD, Microbiology Unit, Department of Laboratories, Farwaniya Hospital, Farwaniya, postal code 85000, Kuwait, Department of Microbiology, Faculty of Medicine, Kuwait University, Jabriya, postal code 85000, Kuwait
| | - Rita Dhar
- MD, PhD, Microbiology Unit, Department of Laboratories, Farwaniya Hospital, Farwaniya, postal code 85000, Kuwait
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Ragheb SM, Govinden U, Osei Sekyere J. Genetic support of carbapenemases: a One Health systematic review and meta-analysis of current trends in Africa. Ann N Y Acad Sci 2021; 1509:50-73. [PMID: 34753206 DOI: 10.1111/nyas.14703] [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: 05/21/2020] [Revised: 09/06/2021] [Accepted: 09/26/2021] [Indexed: 11/28/2022]
Abstract
Antimicrobial resistance (AMR) is a public health threat globally. Carbapenems are β-lactam antibiotics used as last-resort agents for treating antibiotic-resistant infections. Mobile genetic elements (MGEs) play an important role in the dissemination and expression of antimicrobial resistance genes (ARGs), including the mobilization of ARGs within and between species. The presence of MGEs around carbapenem-hydrolyzing enzymes, called carbapenemases, in bacterial isolates in Africa is concerning. The association between MGEs and carbapenemases is described herein. Specific plasmid replicons, integrons, transposons, and insertion sequences were found flanking specific and different carbapenemases across the same and different clones and species isolated from humans, animals, and the environment. Notably, similar genetic contexts have been reported in non-African countries, supporting the importance of MGEs in driving the intra- and interclonal and species transmission of carbapenemases in Africa and globally. Technical and budgetary limitations remain challenges for epidemiological analysis of carbapenemases in Africa, as studies undertaken with whole-genome sequencing remained relatively few. Characterization of MGEs in antibiotic-resistant infections can deepen our understanding of carbapenemase epidemiology and facilitate the control of AMR in Africa. Investment in genomic epidemiology will facilitate faster clinical interventions and containment of outbreaks.
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Affiliation(s)
- Suzan Mohammed Ragheb
- Department of Microbiology and Immunology, Faculty of Pharmacy, Modern University for Technology and Information (MTI), Cairo, Egypt
| | - Usha Govinden
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, KwaZulu-Natal, South Africa
| | - John Osei Sekyere
- Department of Microbiology & Immunology, Indiana University School of Medicine-Northwest, Gary, Indiana.,Department of Dermatology, School of Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
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Sleiman A, Fayad AGA, Banna H, Matar GM. Prevalence and molecular epidemiology of carbapenem-resistant Gram-negative bacilli and their resistance determinants in the Eastern Mediterranean Region over the last decade. J Glob Antimicrob Resist 2021; 25:209-221. [PMID: 33812049 DOI: 10.1016/j.jgar.2021.02.033] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 01/05/2021] [Accepted: 02/28/2021] [Indexed: 12/14/2022] Open
Abstract
Carbapenem resistance in Enterobacteriaceae, Acinetobacter baumannii and Pseudomonas aeruginosa is increasing worldwide, which has led the World Health Organization (WHO) to list these bacteria in the critical priority pathogens group. Infections by such pathogens pose a serious threat to hospitalised patients and are associated with clinical and economic consequences. What worsens the case is the weak pipeline of available antimicrobial agents to treat such infections and the absence of new drugs. The aim of this review was to shed light on all studies tackling carbapenem resistance in Enterobacteriaceae, A. baumannii and P. aeruginosa in the Eastern Mediterranean region, with indication for each country, description of studies timeline, prevalence of carbapenem resistance, and carbapenem resistance-encoding genes detected in these countries.
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Affiliation(s)
- Ahmad Sleiman
- Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon; Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon; World Health Organization (WHO) Collaborating Center for Reference and Research on Bacterial Pathogens, Beirut, Lebanon
| | - Antoine G Abou Fayad
- Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon; Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon; World Health Organization (WHO) Collaborating Center for Reference and Research on Bacterial Pathogens, Beirut, Lebanon.
| | - Hanin Banna
- Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon; Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon; World Health Organization (WHO) Collaborating Center for Reference and Research on Bacterial Pathogens, Beirut, Lebanon
| | - Ghassan M Matar
- Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon; Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon; World Health Organization (WHO) Collaborating Center for Reference and Research on Bacterial Pathogens, Beirut, Lebanon.
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Ayoub Moubareck C, Hammoudi Halat D, Nabi A, AlSharhan MA, AlDeesi ZO, Han A, Celiloglu H, Karam Sarkis D. Detection of OXA-23, GES-11 and NDM-1 among carbapenem-resistant Acinetobacter baumannii in Dubai: A preliminary study. J Glob Antimicrob Resist 2020; 24:27-28. [PMID: 33279684 DOI: 10.1016/j.jgar.2020.11.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 11/03/2020] [Accepted: 11/13/2020] [Indexed: 01/23/2023] Open
Affiliation(s)
- Carole Ayoub Moubareck
- Microbiology Laboratory, School of Pharmacy, Saint-Joseph University, Beirut, Lebanon; College of Natural and Health Sciences, Zayed University, Dubai, United Arab Emirates
| | - Dalal Hammoudi Halat
- Microbiology Laboratory, School of Pharmacy, Saint-Joseph University, Beirut, Lebanon; Department of Pharmaceutical Sciences, School of Pharmacy, Lebanese International University, Beirut and Bekaa Campuses, Lebanon.
| | - Anju Nabi
- Dubai Hospital, Dubai, United Arab Emirates
| | | | | | - Aaron Han
- American Hospital, Dubai, United Arab Emirates; Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | | | - Dolla Karam Sarkis
- Microbiology Laboratory, School of Pharmacy, Saint-Joseph University, Beirut, Lebanon
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Nasser M, Palwe S, Bhargava RN, Feuilloley MGJ, Kharat AS. Retrospective Analysis on Antimicrobial Resistance Trends and Prevalence of β-lactamases in Escherichia coli and ESKAPE Pathogens Isolated from Arabian Patients during 2000-2020. Microorganisms 2020; 8:microorganisms8101626. [PMID: 33096921 PMCID: PMC7589750 DOI: 10.3390/microorganisms8101626] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/18/2020] [Accepted: 10/19/2020] [Indexed: 12/11/2022] Open
Abstract
The production of diverse and extended spectrum β-lactamases among Escherichia coli and ESKAPE pathogens is a growing threat to clinicians and public health. We aim to provide a comprehensive analysis of evolving trends of antimicrobial resistance and β-lactamases among E. coli and ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acine to bacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) in the Arabian region. A systematic review was conducted in Medline PubMed on papers published between January 2000 and February 2020 on countries in the Arab region showing different antibiotic resistance among E. coli and ESKAPE pathogens. A total of n = 119,144 clinical isolates were evaluated for antimicrobial resistance in 19 Arab countries. Among these clinical isolates, 74,039 belonged to E. coli and ESKAPE pathogen. Distribution of antibiotic resistance among E. coli and ESKAPE pathogens indicated that E. coli (n = 32,038) was the predominant pathogen followed by K. pneumoniae (n = 17,128), P. aeruginosa (n = 11,074), methicillin-resistant S. aureus (MRSA, n = 4370), A. baumannii (n = 3485) and Enterobacter spp. (n = 1574). There were no reports demonstrating Enterococcus faecium producing β-lactamase. Analyses revealed 19 out of 22 countries reported occurrence of ESBL (Extended-Spectrum β-Lactamase) producing E. coli and ESKAPE pathogens. The present study showed significantly increased resistance rates to various antimicrobial agents over the last 20 years; for instance, cephalosporin resistance increased from 37 to 89.5%, fluoroquinolones from 46.8 to 70.3%, aminoglycosides from 40.2 to 64.4%, mono-bactams from 30.6 to 73.6% and carbapenems from 30.5 to 64.4%. An average of 36.9% of the total isolates were reported to have ESBL phenotype during 2000 to 2020. Molecular analyses showed that among ESBLs and Class A and Class D β-lactamases, blaCTX-M and blaOXA have higher prevalence rates of 57% and 52.7%, respectively. Among Class B β-lactamases, few incidences of blaVIM 27.7% and blaNDM 26.3% were encountered in the Arab region. Conclusion: This review highlights a significant increase in resistance to various classes of antibiotics, including cephalosporins, β-lactam and β-lactamase inhibitor combinations, carbapenems, aminoglycosides and quinolones among E. coli and ESKAPE pathogens in the Arab region.
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Affiliation(s)
- Mahfouz Nasser
- Department of Biotechnology, Dr. Babasaheb Ambedkar Marathwada University, Sub-Campus, Osmanabad 413 528, MS, India;
- National Center for Public Health Laboratories, Hodeidah, Yemen
| | - Snehal Palwe
- Department of Environmental Science, S. B. College of Science, Aurangabad 431001, India;
| | - Ram Naresh Bhargava
- Department of Microbiology, Babasaheb Bhimrao Ambedkar University, Lucknow 226025, India;
| | - Marc G. J. Feuilloley
- Laboratory of Microbiology Signals and Microenvironments, LMSM EA 4312, University of Rouen, Normandy, F-27000 Evreux, France
- Correspondence: (M.G.J.F.); (A.S.K.)
| | - Arun S. Kharat
- Laboratory of Applied Microbiology, School of Life Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi 110067, India
- Correspondence: (M.G.J.F.); (A.S.K.)
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Metallo-Beta-Lactamase-Producing Acinetobacter spp. from Clinical Isolates at a Tertiary Care Hospital in Ghana. BIOMED RESEARCH INTERNATIONAL 2020; 2020:3852419. [PMID: 33029505 PMCID: PMC7533015 DOI: 10.1155/2020/3852419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/24/2020] [Indexed: 11/18/2022]
Abstract
Metallo-beta-lactamase-producing Acinetobacter spp. is a major challenge for therapeutic treatment of nosocomial infections. This study is aimed at determining the prevalence of MBL-producing Acinetobacter spp. among 87 clinical isolates of Acinetobacter spp. from the Korle-Bu Teaching Hospital, Accra, between August 2014 and July 2015. Acinetobacter spp. was identified by standard bacteriological method, and resistance to different antibiotics was assessed with the Kirby–Bauer disc diffusion method. Meropenem-resistant Acinetobacter isolates were screened for enzyme activity using the modified Hodge test (MHT) and combined disc test (CDT). Additionally, multiplex PCR was used to determine MBL genes presence (blaVIM,blaIMP, and blaNDM). All Acinetobacter isolates showed high resistance to cefotaxime (90.8%), ceftazidime (75.9%), cotrimoxazole (70.1%), ciprofloxacin (64.4%), gentamicin (72.4%), levofloxacin (67.8%), and meropenem (59.8%). A total of 54 (62.1%) of Acinetobacter isolates were multidrug-resistant. Out of 52 (59.8%) meropenem-resistant Acinetobacter, 3 (5.8%) were carbapenemase producers by MHT, whilst, 23 (44.2%) were CDT positive. There was no significant difference between the resistance pattern of amikacin, ceftazidime, cotrimoxazole, ciprofloxacin, and meropenem amongst CDT-positive and CDT-negative isolates (p > 0.05). A total of 7/87 (8.1%) CDT-positive Acinetobacter isolates harboured blaNDM; of these, 4 (57.1%) were from wound swabs, urine (n = 2) (28.6%), and ear swab (n = 1) (14.3%). The study revealed that less than 9% of Acinetobacter spp. contained blaNDM encoding genes. Strict antibiotics usage plan and infection control measures are required to prevent the spread of these resistance genes.
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Singh M, De Silva PM, Al-Saadi Y, Switala J, Loewen PC, Hausner G, Chen W, Hernandez I, Castillo-Ramirez S, Kumar A. Characterization of Extremely Drug-Resistant and Hypervirulent Acinetobacter baumannii AB030. Antibiotics (Basel) 2020; 9:antibiotics9060328. [PMID: 32560407 PMCID: PMC7345994 DOI: 10.3390/antibiotics9060328] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 06/12/2020] [Accepted: 06/15/2020] [Indexed: 12/21/2022] Open
Abstract
Acinetobacter baumannii is an important nosocomial bacterial pathogen. Multidrug-resistant isolates of A. baumannii are reported worldwide. Some A. baumannii isolates display resistance to nearly all antibiotics, making treatment of infections very challenging. As the need for new and effective antibiotics against A. baumannii becomes increasingly urgent, there is a need to understand the mechanisms of antibiotic resistance and virulence in this organism. In this work, comparative genomics was used to understand the mechanisms of antibiotic resistance and virulence in AB030, an extremely drug-resistant and hypervirulent strain of A. baumannii that is a representative of a recently emerged lineage of A. baumannii International Clone V. In order to characterize AB030, we carried out a genomic and phenotypic comparison with LAC-4, a previously described hyper-resistant and hypervirulent isolate. AB030 contains a number of antibiotic resistance- and virulence-associated genes that are not present in LAC-4. A number of these genes are present on mobile elements. This work shows the importance of characterizing the members of new lineages of A. baumannii in order to determine the development of antibiotic resistance and virulence in this organism.
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Affiliation(s)
- Manu Singh
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; (M.S.); (P.M.D.S.); (Y.A.-S.); (J.S.); (P.C.L.); (G.H.)
| | - P. Malaka De Silva
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; (M.S.); (P.M.D.S.); (Y.A.-S.); (J.S.); (P.C.L.); (G.H.)
| | - Yasser Al-Saadi
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; (M.S.); (P.M.D.S.); (Y.A.-S.); (J.S.); (P.C.L.); (G.H.)
| | - Jacek Switala
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; (M.S.); (P.M.D.S.); (Y.A.-S.); (J.S.); (P.C.L.); (G.H.)
| | - Peter C. Loewen
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; (M.S.); (P.M.D.S.); (Y.A.-S.); (J.S.); (P.C.L.); (G.H.)
| | - Georg Hausner
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; (M.S.); (P.M.D.S.); (Y.A.-S.); (J.S.); (P.C.L.); (G.H.)
| | - Wangxue Chen
- Human Health Therapeutics, National Research Council Canada, 100 Sussex Drive, Ottawa, ON K1A 0R6, Canada;
| | - Ismael Hernandez
- Programa de Genómica Evolutiva, Centro de Ciencias Génomicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico; (I.H.); (S.C.-R.)
| | - Santiago Castillo-Ramirez
- Programa de Genómica Evolutiva, Centro de Ciencias Génomicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico; (I.H.); (S.C.-R.)
| | - Ayush Kumar
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; (M.S.); (P.M.D.S.); (Y.A.-S.); (J.S.); (P.C.L.); (G.H.)
- Correspondence:
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Leal NC, Campos TL, Rezende AM, Docena C, Mendes-Marques CL, de Sá Cavalcanti FL, Wallau GL, Rocha IV, Cavalcanti CLB, Veras DL, Alves LR, Andrade-Figueiredo M, de Barros MPS, de Almeida AMP, de Morais MMC, Leal-Balbino TC, Xavier DE, de-Melo-Neto OP. Comparative Genomics of Acinetobacter baumannii Clinical Strains From Brazil Reveals Polyclonal Dissemination and Selective Exchange of Mobile Genetic Elements Associated With Resistance Genes. Front Microbiol 2020; 11:1176. [PMID: 32655514 PMCID: PMC7326025 DOI: 10.3389/fmicb.2020.01176] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 05/08/2020] [Indexed: 12/13/2022] Open
Abstract
Acinetobacter baumannii is an opportunistic bacterial pathogen infecting immunocompromised patients and has gained attention worldwide due to its increased antimicrobial resistance. Here, we report a comparative whole-genome sequencing and analysis coupled with an assessment of antibiotic resistance of 46 Acinetobacter strains (45 A. baumannii plus one Acinetobacter nosocomialis) originated from five hospitals from the city of Recife, Brazil, between 2010 and 2014. An average of 3,809 genes were identified per genome, although only 2,006 genes were single copy orthologs or core genes conserved across all sequenced strains, with an average of 42 new genes found per strain. We evaluated genetic distance through a phylogenetic analysis and MLST as well as the presence of antibiotic resistance genes, virulence markers and mobile genetic elements (MGE). The phylogenetic analysis recovered distinct monophyletic A. baumannii groups corresponding to five known (ST1, ST15, ST25, ST79, and ST113) and one novel ST (ST881, related to ST1). A large number of ST specific genes were found, with the ST79 strains having the largest number of genes in common that were missing from the other STs. Multiple genes associated with resistance to β-lactams, aminoglycosides and other antibiotics were found. Some of those were clearly mapped to defined MGEs and an analysis of those revealed known elements as well as a novel Tn7-Tn3 transposon with a clear ST specific distribution. An association of selected resistance/virulence markers with specific STs was indeed observed, as well as the recent spread of the OXA-253 carbapenemase encoding gene. Virulence genes associated with the synthesis of the capsular antigens were noticeably more variable in the ST113 and ST79 strains. Indeed, several resistance and virulence genes were common to the ST79 and ST113 strains only, despite a greater genetic distance between them, suggesting common means of genetic exchange. Our comparative analysis reveals the spread of multiple STs and the genomic plasticity of A. baumannii from different hospitals in a single metropolitan area. It also highlights differences in the spread of resistance markers and other MGEs between the investigated STs, impacting on the monitoring and treatment of Acinetobacter in the ongoing and future outbreaks.
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Affiliation(s)
- Nilma C Leal
- Aggeu Magalhães Institute (IAM), Fundação Oswaldo Cruz (Fiocruz), Recife, Brazil
| | - Túlio L Campos
- Aggeu Magalhães Institute (IAM), Fundação Oswaldo Cruz (Fiocruz), Recife, Brazil
| | - Antonio M Rezende
- Aggeu Magalhães Institute (IAM), Fundação Oswaldo Cruz (Fiocruz), Recife, Brazil
| | - Cássia Docena
- Aggeu Magalhães Institute (IAM), Fundação Oswaldo Cruz (Fiocruz), Recife, Brazil
| | | | - Felipe L de Sá Cavalcanti
- Aggeu Magalhães Institute (IAM), Fundação Oswaldo Cruz (Fiocruz), Recife, Brazil.,Department of Pathology, Institute of Biological Sciences, University of Pernambuco, Recife, Brazil
| | - Gabriel L Wallau
- Aggeu Magalhães Institute (IAM), Fundação Oswaldo Cruz (Fiocruz), Recife, Brazil
| | - Igor V Rocha
- Aggeu Magalhães Institute (IAM), Fundação Oswaldo Cruz (Fiocruz), Recife, Brazil
| | | | - Dyana L Veras
- Aggeu Magalhães Institute (IAM), Fundação Oswaldo Cruz (Fiocruz), Recife, Brazil
| | - Lilian R Alves
- Department of Tropical Medicine, Federal University of Pernambuco, Recife, Brazil
| | | | | | | | | | | | - Danilo E Xavier
- Aggeu Magalhães Institute (IAM), Fundação Oswaldo Cruz (Fiocruz), Recife, Brazil
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Al-Hashem G, Rotimi VO, Albert MJ. Antimicrobial Resistance of Serial Isolates of Acinetobacter baumannii Colonizing the Rectum of Adult Intensive Care Unit Patients in a Teaching Hospital in Kuwait. Microb Drug Resist 2020; 27:64-72. [PMID: 32456599 DOI: 10.1089/mdr.2020.0106] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Objectives: Outbreak and endemic isolates of Acinetobacter baumannii are known to be polyclonal. In an ongoing study, we hypothesized that the patient gut was the source of the polyclonality where genetic exchanges take place. To test the hypothesis, we collected 270 serial rectal isolates from 32 adult intensive care unit patients over 16 months and investigated their drug resistance profiles. Methods: Antimicrobial susceptibility was determined according to recommended methods. The blaIMP, blaVIM, blaSIM, blaOXA-23, blaOXA-24/40, blaOXA-51, blaOXA-48, blaKPC, blaGES, blaNDM and blaOXA-58 were sought by PCR. A subset of 42 isolates were studied for plasmid-mediated resistance. Results: Most of the 270 isolates were multidrug resistant (MDR; with resistances to meropenem of 85.18% and imipenem of 87.04%), but susceptible to colistin and trimethoprim/sulfamethoxazole. There was no correlation between the pattern of resistance and antibiotics administered to treat infections. There was no consistent pattern of resistance or content of carbapenemase genes in serial rectal isolates suggesting polyclonality of the isolates. Genes mediating production of OXA-23, OXA-24/40, IMP, and GES enzymes were carried on plasmids and they mediated resistance to all carbapenems in conjugation studies. Conclusion: A. baumannii colonizing the rectum were polyclonal, MDR, and carbapenem resistance genes were found on plasmids and some plasmids were transferable.
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Affiliation(s)
- Ghayda Al-Hashem
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait, Kuwait
| | - Vincent O Rotimi
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait, Kuwait
| | - M John Albert
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait, Kuwait
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The Current Burden of Carbapenemases: Review of Significant Properties and Dissemination among Gram-Negative Bacteria. Antibiotics (Basel) 2020; 9:antibiotics9040186. [PMID: 32316342 PMCID: PMC7235769 DOI: 10.3390/antibiotics9040186] [Citation(s) in RCA: 114] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/29/2020] [Accepted: 04/01/2020] [Indexed: 11/16/2022] Open
Abstract
Carbapenemases are β-lactamases belonging to different Ambler classes (A, B, D) and can be encoded by both chromosomal and plasmid-mediated genes. These enzymes represent the most potent β-lactamases, which hydrolyze a broad variety of β-lactams, including carbapenems, cephalosporins, penicillin, and aztreonam. The major issues associated with carbapenemase production are clinical due to compromising the activity of the last resort antibiotics used for treating serious infections, and epidemiological due to their dissemination into various bacteria across almost all geographic regions. Carbapenemase-producing Enterobacteriaceae have received more attention upon their first report in the early 1990s. Currently, there is increased awareness of the impact of nonfermenting bacteria, such as Acinetobacter baumannii and Pseudomonas aeruginosa, as well as other Gram-negative bacteria that are carbapenemase-producers. Outside the scope of clinical importance, carbapenemases are also detected in bacteria from environmental and zoonotic niches, which raises greater concerns over their prevalence, and the need for public health measures to control consequences of their propagation. The aims of the current review are to define and categorize the different families of carbapenemases, and to overview the main lines of their spread across different bacterial groups.
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Abstract
PURPOSE OF REVIEW We reviewed recent data about epidemiology of Acinetobacter baumannii, resistance mechanisms, and therapeutic options for severe infections caused by multidrug-resistant strains. RECENT FINDINGS A. baumannii is a major cause of nosocomial infections affecting mainly to debilitating patients in the ICU, although the spread to regular wards and to long-term care facilities is increasing. It is characterized by its great persistence in the environment and to have an extraordinary capability to develop resistance to all antimicrobials.Carbapenems may not be considered the treatment of choice in areas with high rates of carbapenem-resistant A. baumannii. Nowadays, polymyxins are the antimicrobials with the greatest level of in-vitro activity against A. baumannii. Colistin is the most widely used in clinical practice although polymyxin B seems to be associated with less renal toxicity. Colistin is administered intravenously as its inactive prodrug colistimethate. A loading dose of 9 million IU and subsequently high, extended-interval maintenance doses (4.5 million IU/12 h) are recommended. Combination therapy instead of monotherapy increases the rates of microbiological eradication although no clinical study has demonstrated a reduction in clinical outcomes (mortality or length of stay). SUMMARY The optimal treatment for multidrug-resistant A. baumannii nosocomial infections has not been established. There are no compelling data to recommend combination therapy for severe A. baumannii infections.
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Karah N, Khalid F, Wai SN, Uhlin BE, Ahmad I. Molecular epidemiology and antimicrobial resistance features of Acinetobacter baumannii clinical isolates from Pakistan. Ann Clin Microbiol Antimicrob 2020; 19:2. [PMID: 31941492 PMCID: PMC6964048 DOI: 10.1186/s12941-019-0344-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 12/27/2019] [Indexed: 02/07/2023] Open
Abstract
Background Acinetobacter baumannii is a Gram-negative opportunistic pathogen with a notorious reputation of being resistant to antimicrobial agents. The capability of A. baumannii to persist and disseminate between healthcare settings has raised a major concern worldwide. Methods Our study investigated the antibiotic resistance features and molecular epidemiology of 52 clinical isolates of A. baumannii collected in Pakistan between 2013 and 2015. Antimicrobial susceptibility patterns were determined by the agar disc diffusion method. Comparative sequence analyses of the ampC and blaOXA-51-like alleles were used to assign the isolates into clusters. The whole genomes of 25 representative isolates were sequenced using the MiSeq Desktop Sequencer. Free online applications were used to determine the phylogeny of genomic sequences, retrieve the multilocus sequence types (ST), and detect acquired antimicrobial resistance genes. Results Overall, the isolates were grouped into 7 clusters and 3 sporadic isolates. The largest cluster, Ab-Pak-cluster-1 (blaOXA-66 and ISAba1-ampC-19) included 24 isolates, belonged to ST2 and International clone (IC) II, and was distributed between two geographical far-off cities, Lahore and Peshawar. Ab-Pak-clusters-2 (blaOXA-66, ISAba1-ampC-2), and -3 (blaOXA-66, ISAba1-ampC-20) and the individual isolate Ab-Pak-Lah-01 (ISAba1-blaOXA-66, ISAba1-ampC-2) were also assigned to ST2 and IC II. On the other hand, Ab-Pak-clusters-4 (blaOXA-69, ampC-1), -5 (blaOXA-69, ISAba1-ampC-78), and -6A (blaOXA-371, ISAba1-ampC-3) belonged to ST1, while Ab-Pak-cluster-6B (blaOXA-371, ISAba1-ampC-8) belonged to ST1106, with both ST1 and ST1106 being members of IC I. Five isolates belonged to Ab-Pak-cluster-7 (blaOXA-65, ampC-43). This cluster corresponded to ST158, showed a well-delineated position on the genomic phylogenetic tree, and was equipped with several antimicrobial resistance genes including blaOXA-23 and blaGES-11. Conclusions Our study detected the occurrence of 7 clusters of A. baumannii in Pakistan. Altogether, 6/7 of the clusters and 45/52 (86.5%) of the isolates belonged to IC I (n = 9) or II (n = 36), making Pakistan no exception to the global domination of these two clones. The onset of ST158 in Pakistan marked a geographical dispersal of this clone beyond the Middle East and brought up the need for a detailed characterization.
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Affiliation(s)
- Nabil Karah
- The Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, and Umea Centre for Microbial Research, Umea University, Umeå, Sweden.
| | - Fizza Khalid
- Department of Microbiology, University of Health Sciences, Lahore, Pakistan
| | - Sun Nyunt Wai
- The Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, and Umea Centre for Microbial Research, Umea University, Umeå, Sweden
| | - Bernt Eric Uhlin
- The Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, and Umea Centre for Microbial Research, Umea University, Umeå, Sweden
| | - Irfan Ahmad
- The Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, and Umea Centre for Microbial Research, Umea University, Umeå, Sweden. .,Institute of Biomedical and Allied Health Sciences, University of Health Sciences, Lahore, Pakistan.
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Lima WG, Silva Alves GC, Sanches C, Antunes Fernandes SO, de Paiva MC. Carbapenem-resistant Acinetobacter baumannii in patients with burn injury: A systematic review and meta-analysis. Burns 2019; 45:1495-1508. [DOI: 10.1016/j.burns.2019.07.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/09/2019] [Accepted: 07/03/2019] [Indexed: 12/25/2022]
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Al-Hamad A, Pal T, Leskafi H, Abbas H, Hejles H, Alsubikhy F, Darwish D, Ghazawi A, Sonnevend A. Molecular characterization of clinical and environmental carbapenem resistant Acinetobacter baumannii isolates in a hospital of the Eastern Region of Saudi Arabia. J Infect Public Health 2019; 13:632-636. [PMID: 31551188 DOI: 10.1016/j.jiph.2019.08.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 05/27/2019] [Accepted: 08/22/2019] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Environmental and clinical carbapenem-resistant Acinetobacter baumannii (CRAb) isolated in a hospital of the Eastern Region of Saudi Arabia were compared to assess the potential environmental contamination by this pathogen. METHODS Frequent-hand-touch surfaces of intensive care (ICU), medical (MW), and surgical (SW) units were randomly sampled for a month-long period, and the CRAb identified were compared to clinical isolates of the same period by PFGE and blaOXA-51-like gene sequencing. Carbapenemase and ribosomal methylase genes, ISAba1 link to blaOXA51-like or to blaOXA-23, respectively were detected by PCR. RESULTS CRAb was identified from 35.5% of surfaces. All environmental and clinical isolates were multi- or extremely drug resistant. PFGE of all clinical (n=21) and selected environmental (n=30) isolates identified a singleton and four clusters, all of which included both clinical and environmental isolates. In the two largest clusters isolates carried blaOXA-66, ISAba1-linked blaOXA-23, and were from the ICU, MW and the male SW. Isolates of the female SW carried blaOXA-69, ISAba1-linked blaOXA-23 and blaGES-11. A pair of clinical and environmental CRAb from the Male SW harboured blaNDM-1 in addition to ISAba1-linked blaOXA-94. CONCLUSION A worrying level of environmental contamination, often by CRAb belonging to international clones, was revealed, highlighting the importance of environmental hygiene.
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Affiliation(s)
- Arif Al-Hamad
- Division of Clinical Microbiology, Pathology and Laboratory Medicine, Qatif Central Hospital, Qatif, Saudi Arabia
| | - Tibor Pal
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Hussam Leskafi
- Division of Clinical Microbiology, Pathology and Laboratory Medicine, Qatif Central Hospital, Qatif, Saudi Arabia
| | - Hussein Abbas
- Division of Clinical Microbiology, Pathology and Laboratory Medicine, Qatif Central Hospital, Qatif, Saudi Arabia
| | - Heba Hejles
- Division of Clinical Microbiology, Pathology and Laboratory Medicine, Qatif Central Hospital, Qatif, Saudi Arabia
| | - Fatimah Alsubikhy
- Division of Clinical Microbiology, Pathology and Laboratory Medicine, Qatif Central Hospital, Qatif, Saudi Arabia
| | - Dania Darwish
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Akela Ghazawi
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Agnes Sonnevend
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates; Department of Medical Microbiology and Immunology, University of Pécs Medical School, Szigeti út 12, Pécs H-7624, Hungary.
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Zhao G, Luo Z, Wang Y, Liu J, Wu D, Zhang L, Yang X. Draft genome sequencing and annotation of a low-virulence Morganella morganii strain CQ-M7, a multidrug-resistant isolate from the giant salamander in China. J Glob Antimicrob Resist 2019; 20:248-252. [PMID: 31449965 DOI: 10.1016/j.jgar.2019.08.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 08/13/2019] [Accepted: 08/17/2019] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVES A multidrug-resistant Morganella morganii strain (CQ-M7), isolated from the kidney of a diseased Chinese giant salamander in China, was examined with whole genome sequencing to better understand drug tolerance and its pathogenicity. METHODS The draft genome of the investigated strain was assembled using HGA assembler and annotated using Rapid Annotations Subsystems Technology (RAST) server. The contigs were annotated by the appropriate bioinformatics tools available on the National Center for Biotechnology Information (NCBI) website. Antibiotic resistance genes were detected by PCR. Pathogenicity of the isolate was performed on 30 healthy Chinese giant salamanders with different infection dosages. RESULTS The CQ-M7 strain showed resistance to multiple antimicrobials, especially to aminoglycoside and β-lactam antibiotics. Seventeen drug-resistance genes were detected, which were related to β-lactams, aminoglycosides, fluoroquinolones, tetracyclines, peptide antibiotic, and fosfomycin resistance. Sequence analysis showed the assembled genome size to be 4 966 326bp with 51.16% of GC content, containing 4587 protein-coding genes, 71 pseudogenes, five rRNAs, 80 tRNAs, and five noncoding RNAs. The genome sequence was deposited in GenBank under accession number RQIJ00000000. Artificial infection results indicated that the CQ-M7 strain was a low-virulence strain for the Chinese giant salamander. CONCLUSION It is believed that this is the first draft genome of Chinese giant salamander original Morganella morganii strain harbouring multiple antibiotic resistance genes in China. The reported genome sequence could provide insights into antibiotic resistance mechanisms and control strategies of Morganella morganii.
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Affiliation(s)
- Guangwei Zhao
- College of Animal Science, Southwest University, No. 160, Xueyuan Road, Chongqing, 402460, PR China; Chongqing Sanjiezhongxin Bioengineering Co, Ltd, No.3 Southern Section of Yingbin Avenue, Chongqing, 402460, PR China
| | - Zeli Luo
- College of Animal Science, Southwest University, No. 160, Xueyuan Road, Chongqing, 402460, PR China
| | - Yan Wang
- Shanghai Customs, No.1208, Minsuring Road, Shanghai Pudong District, Shanghai, 200135, PR China
| | - Jia Liu
- College of Animal Science, Southwest University, No. 160, Xueyuan Road, Chongqing, 402460, PR China
| | - Di Wu
- College of Animal Science, Southwest University, No. 160, Xueyuan Road, Chongqing, 402460, PR China
| | - Liwu Zhang
- Chongqing Sanjiezhongxin Bioengineering Co, Ltd, No.3 Southern Section of Yingbin Avenue, Chongqing, 402460, PR China
| | - Xiaowei Yang
- College of Animal Science, Southwest University, No. 160, Xueyuan Road, Chongqing, 402460, PR China; Chongqing Sanjiezhongxin Bioengineering Co, Ltd, No.3 Southern Section of Yingbin Avenue, Chongqing, 402460, PR China.
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Mertins S, Higgins PG, Rodríguez MG, Borlon C, Gilleman Q, Mertens P, Seifert H, Krönke M, Klimka A. Generation and selection of antibodies for a novel immunochromatographic lateral flow test to rapidly identify OXA-23-like-mediated carbapenem resistance in Acinetobacter baumannii. J Med Microbiol 2019; 68:1021-1032. [PMID: 31188094 DOI: 10.1099/jmm.0.001015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
INTRODUCTION The spread of carbapenem-resistant Acinetobacter baumannii has led to a worldwide healthcare problem. Carbapenem resistance in A. baumannii is mainly mediated by the acquisition of the carbapenem-hydrolyzing oxacillinase OXA-23. The phenotypic detection of carbapenem-producing A. baumannii is challenging and time-consuming. Hence, there is an unmet medical need for reliable and rapid diagnostic tools to detect OXA-23-producing Acinetobacter isolates to enable successful patient management. AIM Development of an immunochromatographic lateral flow test (ICT) for the rapid and reliable detection of OXA-23-producing carbapenem-resistant Acinetobacter isolates. METHODOLOGY For the development of an antibody-based ICT, we generated anti-OXA-23 monoclonal antibodies (MoAbs) and screened them sequentially for their ability to bind native OXA-23. Selected OXA-23-specific MoAbs were tested in different combinations for their capacity to capture and detect OXA-23His6 by sandwich enzyme-linked immunosorbent assay (ELISA) and ICT. A well-characterized collection of carbapenem-resistant Acinetobacter isolates with defined carbapenem resistance mechanisms were used to evaluate the specificity of the final OXA-23 ICT prototype. RESULTS The antibody pairs best suited for the sandwich ELISA format did not match the best pairs in the ICT format selected during the development process of the final prototype OXA-23 ICT. This prototype was able to differentiate between OXA-23 subfamily-mediated carbapenem resistance and carbapenem-resistant Acinetobacter isolates overexpressing other OXAs with 100 % specificity and a turnaround time of 20 min from culture plate to result. CONCLUSION With this rapid detection assay one can save 12-48 h of diagnostic time, which could help avoid inappropriate use of carbapenems and enable earlier intervention to control the transmission of OXA-23-producing carbapenem-resistant Acinetobacter isolates to other patients and healthcare workers.
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Affiliation(s)
- Sonja Mertins
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute for Medical Microbiology, Immunology and Hygiene, Goldenfelsstr. 19-21, 50935 Cologne, Germany
- German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
| | - Paul G Higgins
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute for Medical Microbiology, Immunology and Hygiene, Goldenfelsstr. 19-21, 50935 Cologne, Germany
- German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
| | - María González Rodríguez
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute for Medical Microbiology, Immunology and Hygiene, Goldenfelsstr. 19-21, 50935 Cologne, Germany
| | - Céline Borlon
- Coris BioConcept, Science Park CREALYS, Rue Jean Sonet 4A, B-5032 Gembloux, Belgium
| | - Quentin Gilleman
- Coris BioConcept, Science Park CREALYS, Rue Jean Sonet 4A, B-5032 Gembloux, Belgium
| | - Pascal Mertens
- Coris BioConcept, Science Park CREALYS, Rue Jean Sonet 4A, B-5032 Gembloux, Belgium
| | - Harald Seifert
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute for Medical Microbiology, Immunology and Hygiene, Goldenfelsstr. 19-21, 50935 Cologne, Germany
- German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
| | - Martin Krönke
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute for Medical Microbiology, Immunology and Hygiene, Goldenfelsstr. 19-21, 50935 Cologne, Germany
- German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
| | - Alexander Klimka
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute for Medical Microbiology, Immunology and Hygiene, Goldenfelsstr. 19-21, 50935 Cologne, Germany
- German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
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Complete Genome Sequencing of Acinetobacter baumannii Strain K50 Discloses the Large Conjugative Plasmid pK50a Encoding Carbapenemase OXA-23 and Extended-Spectrum β-Lactamase GES-11. Antimicrob Agents Chemother 2018; 62:AAC.00212-18. [PMID: 29463529 DOI: 10.1128/aac.00212-18] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 02/03/2018] [Indexed: 12/21/2022] Open
Abstract
Multidrug-resistant (MDR) Acinetobacter baumannii strains appeared as serious emerging nosocomial pathogens in clinical environments and especially in intensive care units (ICUs). A. baumannii strain K50, recovered from a hospitalized patient in Kuwait, exhibited resistance to carbapenems and additionally to ciprofloxacin, chloramphenicol, sulfonamides, amikacin, and gentamicin. Genome sequencing revealed that the strain possesses two plasmids, pK50a (79.6 kb) and pK50b (9.5 kb), and a 3.75-Mb chromosome. A. baumannii K50 exhibits an average nucleotide identity (ANI) of 99.98% to the previously reported Iraqi clinical isolate AA-014, even though the latter strain lacked plasmid pK50a. Strain K50 belongs to sequence type 158 (ST158) (Pasteur scheme) and ST499 (Oxford scheme). Plasmid pK50a is a member of the Aci6 (replication group 6 [RG6]) group of Acinetobacter plasmids and carries a conjugative transfer module and two antibiotic resistance gene regions. The transposon Tn2008 carries the carbapenemase gene blaOXA-23, whereas a class 1 integron harbors the resistance genes blaGES-11, aacA4, dfrA7, qacEΔ1, and sul1, conferring resistance to all β-lactams and reduced susceptibility to carbapenems and resistance to aminoglycosides, trimethoprim, quaternary ammonium compounds, and sulfamethoxazole, respectively. The class 1 integron is flanked by MITEs (miniature inverted-repeat transposable elements) delimiting the element at its insertion site.
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Kayama S, Yano R, Yamasaki K, Fukuda C, Nishimura K, Miyamoto H, Ohge H, Sugai M. Rapid identification of carbapenemase-type bla GES and ESBL-type bla GES using multiplex PCR. J Microbiol Methods 2018; 148:117-119. [PMID: 29605523 DOI: 10.1016/j.mimet.2018.03.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 03/22/2018] [Accepted: 03/27/2018] [Indexed: 11/17/2022]
Abstract
Guiana extended-spectrum (GES) β-lactamases are emerging in Japan. The GES family can be classified into 2 groups, one with extended-spectrum β-lactamase (ESBL)-like activity, which hydrolyzes penicillins and cephalosporins, and the other with carbapenemase-like activity with an extended spectrum toward carbapenems. This difference is mediated by variations in a specific amino acid in the GES protein: G170 N or G170S substitutions. We developed an amplification refractory mutation system (ARMS) PCR assay that enabled rapid identification of these variant genes without sequencing.
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Affiliation(s)
- Shizuo Kayama
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima University Graduate School of Biomedical Sciences, 1-2-3 Kasumi Minami-ku, Hiroshima 734-8553, Japan; Department of Bacteriology, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima University Graduate School of Biomedical Sciences, 1-2-3 Kasumi Minami-ku, Hiroshima 734-8553, Japan
| | - Raita Yano
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima University Graduate School of Biomedical Sciences, 1-2-3 Kasumi Minami-ku, Hiroshima 734-8553, Japan; Department of Bacteriology, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima University Graduate School of Biomedical Sciences, 1-2-3 Kasumi Minami-ku, Hiroshima 734-8553, Japan; Department of Surgery I, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima University Graduate School of Biomedical Sciences, 1-2-3 Kasumi Minami-ku, Hiroshima 734-8553, Japan
| | - Katsutoshi Yamasaki
- Department of Medical Life Science, Kurashiki University of Science and the Arts, Okayama, Japan
| | - Chiemi Fukuda
- Kagawa Prefectural Research Institute for Environmental Sciences and Public Health, Kagawa, Japan
| | - Keiko Nishimura
- Department of Clinical Laboratory, Shikoku Medical Center for Children and Adults, Kagawa, Japan
| | - Hitoshi Miyamoto
- Department of Clinical Laboratory, Ehime University Hospital, Ehime, Japan
| | - Hiroki Ohge
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima University Graduate School of Biomedical Sciences, 1-2-3 Kasumi Minami-ku, Hiroshima 734-8553, Japan; Department of Infectious Diseases, Hiroshima University Hospital, Hiroshima, Japan
| | - Motoyuki Sugai
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima University Graduate School of Biomedical Sciences, 1-2-3 Kasumi Minami-ku, Hiroshima 734-8553, Japan; Department of Bacteriology, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima University Graduate School of Biomedical Sciences, 1-2-3 Kasumi Minami-ku, Hiroshima 734-8553, Japan.
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Alfouzan WA, Noel AR, Bowker KE, Attwood MLG, Tomaselli SG, MacGowan AP. Pharmacodynamics of minocycline against Acinetobacter baumannii studied in a pharmacokinetic model of infection. Int J Antimicrob Agents 2017; 50:715-717. [PMID: 28705678 DOI: 10.1016/j.ijantimicag.2017.06.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 06/16/2017] [Accepted: 06/24/2017] [Indexed: 11/30/2022]
Abstract
Minocycline (MNO) is an old antibiotic that may have an important role in the treatment of multidrug-resistant Gram-negative bacterial infections as the burden of such infections increases. In this study, a single-compartment dilutional pharmacokinetic model was used to determine the relationship between MNO exposure and antibacterial effect, including the risk of resistance emergence, against strains of Acinetobacter baumannii. The mean ± standard deviation area under the unbound drug concentration-time curve to minimum inhibitory concentration ratio (fAUC/MIC) associated with a 24-h bacteriostatic effect was 16.4 ± 2.6 and with a -1 log reduction in bacterial load at 24 h was 23.3 ± 3.7. None of the strains reached a -2 log reduction over 48 h. Changes in population profiles were noted for two of the three strains studied, especially at fAUC/MIC ratios of >5-15. A reasonable translational pharmacodynamic target for MNO against A. baumannii could be an fAUC/MIC of 20-25. However, if maximum standard 24-h doses of intravenous MNO are used (400 mg/day), many strains would be exposed to MNO concentrations likely to change population profiles and associated with the emergence of resistance. Either MNO combination therapy or an increased MNO dose (>400 mg/day) should be considered when treating A. baumannii infections.
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Affiliation(s)
- Wadha A Alfouzan
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait; Microbiology Unit, Department of Laboratories, Farwaniya Hospital, Farwaniya, Kuwait
| | - A R Noel
- Bristol Centre for Antimicrobial Research & Evaluation (BCARE), Department of Infection Sciences, Pathology Sciences, North Bristol NHS Trust, Southmead Hospital, Westbury-on-Trym, Bristol BS10 5NB, UK
| | - Karen E Bowker
- Bristol Centre for Antimicrobial Research & Evaluation (BCARE), Department of Infection Sciences, Pathology Sciences, North Bristol NHS Trust, Southmead Hospital, Westbury-on-Trym, Bristol BS10 5NB, UK
| | - M L G Attwood
- Bristol Centre for Antimicrobial Research & Evaluation (BCARE), Department of Infection Sciences, Pathology Sciences, North Bristol NHS Trust, Southmead Hospital, Westbury-on-Trym, Bristol BS10 5NB, UK
| | - S G Tomaselli
- Bristol Centre for Antimicrobial Research & Evaluation (BCARE), Department of Infection Sciences, Pathology Sciences, North Bristol NHS Trust, Southmead Hospital, Westbury-on-Trym, Bristol BS10 5NB, UK
| | - Alasdair P MacGowan
- Bristol Centre for Antimicrobial Research & Evaluation (BCARE), Department of Infection Sciences, Pathology Sciences, North Bristol NHS Trust, Southmead Hospital, Westbury-on-Trym, Bristol BS10 5NB, UK.
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GES-14-Producing Acinetobacter baumannii Isolates in a Neonatal Intensive Care Unit in Tunisia Are Associated with a Typical Middle East Clone and a Transferable Plasmid. Antimicrob Agents Chemother 2017; 61:AAC.00142-17. [PMID: 28348158 DOI: 10.1128/aac.00142-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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Clonal Spread of Acinetobacter baumannii Sequence Type 25 Carrying blaOXA-23 in Companion Animals in France. Antimicrob Agents Chemother 2016; 61:AAC.01881-16. [PMID: 27799214 DOI: 10.1128/aac.01881-16] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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28
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Al-Agamy MH, Jeannot K, El-Mahdy TS, Shibl AM, Kattan W, Plésiat P, Courvalin P. First Detection of GES-5 Carbapenemase-Producing Acinetobacter baumannii Isolate. Microb Drug Resist 2016; 23:556-562. [PMID: 27854148 DOI: 10.1089/mdr.2016.0152] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
This study was conducted to investigate the molecular epidemiology of resistance in Acinetobacter baumannii isolates collected at a hospital in Riyadh, Saudi Arabia, from January through December 2010. Twenty-seven A. baumannii were highly resistant (MIC90 > 256 μg/ml) to ceftazidime, cefepime, and aztreonam. Imipenem resistance was seen in 24 isolates, of which 18 had an minimum inhibitory concentration (MIC) >32 μg/mL. Ciprofloxacin, gentamicin, and amikacin resistance was found in 93%, 52%, and 37% of all the isolates, respectively. Moreover, 8 (30%) isolates showed colistin resistance, and 15 (56%) were found to have MICs ≥4 μg/mL for tigecycline. The frequency of ADC, GES-1, GES-11, and GES-5 were 96.3% (n = 26), 18.5% (n = 5), 11% (n = 3), and 3.7% (n = 1), respectively. OXA-23 was found in 63% (n = 17) of the isolates; ISAba1 was found upstream of OXA-23 in 16. OXA-24/40 was detected in only one strain. Multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) analysis revealed that the 27 strains were distributed in 8 sequence types (STs) and 16 clonal pulsotypes (A-P). Five singleton STs were identified, including ST15 and ST113-ST116. The emergence of multidrug-resistant A. baumannii is becoming a major concern in Saudi Arabia. Metallo-β-lactamases have no role in carbapenem resistance in this collection. The spread of OXA-23 in our strains occurred across different STs and pulsotypes, unlike what has been observed in many other countries. PFGE typing was more discriminatory than MLST. The high frequency of colistin and tigecycline resistance found in the isolates calls for continuous monitoring. This study describes the first identification of GES-5 conferring carbapenem resistance in A. baumannii.
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Affiliation(s)
- Mohamed H Al-Agamy
- 1 Department of Pharmaceutics, College of Pharmacy, King Saud University , Riyadh, Saudi Arabia .,2 Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhar University , Cairo, Egypt
| | - Katy Jeannot
- 3 Centre National de Référence "Résistance aux Antibiotiques," Institut Pasteur , Paris, France
| | - Taghrid S El-Mahdy
- 4 Department of Microbiology and Immunology, Faculty of Pharmacy, Helwan University , Cairo, Egypt
| | - Atef M Shibl
- 5 College of Medicine, Alfaisal University , Riyadh, Saudi Arabia
| | - Wael Kattan
- 5 College of Medicine, Alfaisal University , Riyadh, Saudi Arabia
| | - Patrick Plésiat
- 3 Centre National de Référence "Résistance aux Antibiotiques," Institut Pasteur , Paris, France
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Insights on the Horizontal Gene Transfer of Carbapenemase Determinants in the Opportunistic Pathogen Acinetobacter baumannii. Microorganisms 2016; 4:microorganisms4030029. [PMID: 27681923 PMCID: PMC5039589 DOI: 10.3390/microorganisms4030029] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 07/21/2016] [Accepted: 08/09/2016] [Indexed: 12/23/2022] Open
Abstract
Horizontal gene transfer (HGT) is a driving force to the evolution of bacteria. The fast emergence of antimicrobial resistance reflects the ability of genetic adaptation of pathogens. Acinetobacter baumannii has emerged in the last few decades as an important opportunistic nosocomial pathogen, in part due to its high capacity of acquiring resistance to diverse antibiotic families, including to the so-called last line drugs such as carbapenems. The rampant selective pressure and genetic exchange of resistance genes hinder the effective treatment of resistant infections. A. baumannii uses all the resistance mechanisms to survive against carbapenems but production of carbapenemases are the major mechanism, which may act in synergy with others. A. baumannii appears to use all the mechanisms of gene dissemination. Beyond conjugation, the mostly reported recent studies point to natural transformation, transduction and outer membrane vesicles-mediated transfer as mechanisms that may play a role in carbapenemase determinants spread. Understanding the genetic mobilization of carbapenemase genes is paramount in preventing their dissemination. Here we review the carbapenemases found in A. baumannii and present an overview of the current knowledge of contributions of the various HGT mechanisms to the molecular epidemiology of carbapenem resistance in this relevant opportunistic pathogen.
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The strategic plan for combating antimicrobial resistance in Gulf Cooperation Council States. J Infect Public Health 2016; 9:375-85. [DOI: 10.1016/j.jiph.2016.03.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Saral A, Leonard DA, Duzgun AO, Cicek AC, June CM, Sandalli C. Kinetic characterization of GES-22 β-lactamase harboring the M169L clinical mutation. J Antibiot (Tokyo) 2016; 69:858-862. [PMID: 27168312 DOI: 10.1038/ja.2016.48] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Revised: 03/16/2016] [Accepted: 03/30/2016] [Indexed: 12/18/2022]
Abstract
The class A β-lactamase GES-22 has been identified in Acinetobacter baumannii isolates in Turkey, and subsequently shown to differ from GES-11 by a single substitution (M169L). Because M169 is part of the omega loop, a structure that is known to have major effects on substrate selectivity in class A β-lactamases, we expressed, purified and kinetically characterized this novel variant. Our results show that compared with GES-116 × His, GES-226 × His displays more efficient hydrolysis of penicillins, and aztreonam, but a loss of efficiency against ceftazidime. In addition, the M169L substitution confers on GES-22 more efficient hydrolysis of the mechanistic inhibitors clavulanic acid and sulbactam. These effects are highly similar to other mutations at the homologous position in other class A β-lactamases, suggesting that this methionine has a key structural role in aligning active site residues and in substrate selectivity across the class.
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Affiliation(s)
- Aysegul Saral
- Department of Nutrition and Dietetics, Faculty of Health Sciences, Artvin Coruh University, Artvin, Turkey.,Microbiology and Molecular Biology Research Laboratory, Department of Biology, Faculty of Arts and Sciences, Recep Tayyip Erdogan University, Rize, Turkey
| | - David A Leonard
- Department of Chemistry, Grand Valley State University, Allendale, MI, USA
| | - Azer Ozad Duzgun
- Department of Genetics and Bioengineering, Faculty of Engineering and Natural Sciences, Gümüşhane University, Gumushane, Turkey
| | - Aysegul Copur Cicek
- Department of Medical Microbiology, Faculty of Medicine, Recep Tayyip Erdogan University, Rize, Turkey
| | - Cynthia M June
- Department of Chemistry, Grand Valley State University, Allendale, MI, USA
| | - Cemal Sandalli
- Microbiology and Molecular Biology Research Laboratory, Department of Biology, Faculty of Arts and Sciences, Recep Tayyip Erdogan University, Rize, Turkey
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Abstract
The OXA β-lactamases were among the earliest β-lactamases detected; however, these molecular class D β-lactamases were originally relatively rare and always plasmid mediated. They had a substrate profile limited to the penicillins, but some became able to confer resistance to cephalosporins. From the 1980s onwards, isolates of Acinetobacter baumannii that were resistant to the carbapenems emerged, manifested by plasmid-encoded β-lactamases (OXA-23, OXA-40, and OXA-58) categorized as OXA enzymes because of their sequence similarity to earlier OXA β-lactamases. It was soon found that every A. baumannii strain possessed a chromosomally encoded OXA β-lactamase (OXA-51-like), some of which could confer resistance to carbapenems when the genetic environment around the gene promoted its expression. Similarly, Acinetobacter species closely related to A. baumannii also possessed their own chromosomally encoded OXA β-lactamases; some could be transferred to A. baumannii, and they formed the basis of transferable carbapenem resistance in this species. In some cases, the carbapenem-resistant OXA β-lactamases (OXA-48) have migrated into the Enterobacteriaceae and are becoming a significant cause of carbapenem resistance. The emergence of OXA enzymes that can confer resistance to carbapenems, particularly in A. baumannii, has transformed these β-lactamases from a minor hindrance into a major problem set to demote the clinical efficacy of the carbapenems.
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Dang B, Mao D, Luo Y. Complete Nucleotide Sequence of IncP-1β Plasmid pDTC28 Reveals a Non-Functional Variant of the blaGES-Type Gene. PLoS One 2016; 11:e0154975. [PMID: 27152950 PMCID: PMC4859535 DOI: 10.1371/journal.pone.0154975] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 04/21/2016] [Indexed: 01/02/2023] Open
Abstract
Plasmid pDTC28 was isolated from the sediments of Haihe River using E. coli CV601 (gfp-tagged) as recipient and indigenous bacteria from the sediment as donors. This plasmid confers reduced susceptibility to tetracycline and sulfamethoxazole. The complete sequence of plasmid pDTC28 was 61,503 bp in length with an average G+C content of 64.09%. Plasmid pDTC28 belongs to the IncP-1β group by phylogenetic analysis. The backbones of plasmid pDTC28 and other IncP-1β plasmids are very classical and conserved, whereas the accessory regions of these plasmids are diverse. A blaGES-5-like gene was found on the accessory region, and this blaGES-5-like gene contained 18 silent mutations and 7 missense mutations compared with the blaGES-5 gene. The mutations resulted in 7 amino acid substitutions in GES-5 carbapenemase, causing the loss of function of the blaGES-5-like gene on plasmid pDTC28 against carbapenems and even β-lactams. The enzyme produced by the blaGES-5-like gene cassette may be a new variant of GES-type enzymes. Thus, the plasmid sequenced in this study will expand our understanding of GES-type β-lactamases and provide insights into the genetic platforms used for the dissemination of GES-type genes.
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Affiliation(s)
- Bingjun Dang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, China
| | - Daqing Mao
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
- * E-mail: (YL); (DM)
| | - Yi Luo
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, China
- * E-mail: (YL); (DM)
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GES-11-producing Acinetobacter baumannii clinical isolates from Tunisian hospitals: Long-term dissemination of GES-type carbapenemases in North Africa. J Glob Antimicrob Resist 2016; 5:47-50. [PMID: 27436466 DOI: 10.1016/j.jgar.2016.03.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 03/05/2016] [Accepted: 03/22/2016] [Indexed: 11/21/2022] Open
Abstract
Acinetobacter baumannii is an emerging threat in healthcare facilities owing to its ability to be multidrug-resistant (MDR) and to be involved in outbreaks. GES-type extended-spectrum β-lactamases (ESBLs) have been increasingly identified in A. baumannii. In this study, clinical A. baumannii isolates were characterised using standard biochemical methods and antibiotic susceptibility testing. Antibiotic resistance genes were sought by PCR and sequencing. Genetic support was characterised using S1 nuclease pulsed-field gel electrophoresis (PFGE) mapping, conjugation and electroporation assays. The genetic environment was investigated by PCR, and genetic relatedness was investigated by PFGE. Two MDR A. baumannii clinical isolates susceptible only to colistin and rifampicin were isolated from a tracheal aspirate of a 49-year-old woman hospitalised in 2006 at the Military Hospital of Tunis, Tunisia, and from a tracheal aspirate of a 53-year-old man hospitalised in 2010 at the Institut Orthopédique Mohamed El Kassab of Tunis, Tunisia. PCR revealed that the two isolates harboured the acquired carbapenemase blaOXA-23 and ESBL blaGES-11 genes along with chromosomally-encoded blaOXA-51 and blaADC-like genes. PFGE revealed that these A. baumannii isolates were unrelated; nevertheless, plasmid analysis revealed a similar sized plasmid following electrophoresis of the isolates. In addition, A. baumannii CIP70.10 transformants displayed similar resistance patterns. blaGES-11 was integron-borne and the ISAbaI element was identified upstream of blaOXA-23 and blaADC-like. Here we described two unrelated clinical A. baumannii isolates producing GES-11 ESBL and OXA-23 carbapenemase from two Tunisian hospitals. This work further illustrates the emergence of GES-type β-lactamases in A. baumannii in North Africa as early as 2006.
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Naas T, Dortet L, Iorga BI. Structural and Functional Aspects of Class A Carbapenemases. Curr Drug Targets 2016; 17:1006-28. [PMID: 26960341 PMCID: PMC5405625 DOI: 10.2174/1389450117666160310144501] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 07/02/2015] [Accepted: 03/05/2016] [Indexed: 01/28/2023]
Abstract
The fight against infectious diseases is probably one of the greatest public health challenges faced by our society, especially with the emergence of carbapenem-resistant gram-negatives that are in some cases pan-drug resistant. Currently,β-lactamase-mediated resistance does not spare even the newest and most powerful β-lactams (carbapenems), whose activity is challenged by carbapenemases. The worldwide dissemination of carbapenemases in gram-negative organisms threatens to take medicine back into the pre-antibiotic era since the mortality associated with infections caused by these "superbugs" is very high, due to limited treatment options. Clinically-relevant carbapenemases belong either to metallo-β- lactamases (MBLs) of Ambler class B or to serine-β-lactamases (SBLs) of Ambler class A and D enzymes. Class A carbapenemases may be chromosomally-encoded (SME, NmcA, SFC-1, BIC-1, PenA, FPH-1, SHV-38), plasmid-encoded (KPC, GES, FRI-1) or both (IMI). The plasmid-encoded enzymes are often associated with mobile elements responsible for their mobilization. These enzymes, even though weakly related in terms of sequence identities, share structural features and a common mechanism of action. They variably hydrolyse penicillins, cephalosporins, monobactams, carbapenems, and are inhibited by clavulanate and tazobactam. Three-dimensional structures of class A carbapenemases, in the apo form or in complex with substrates/inhibitors, together with site-directed mutagenesis studies, provide essential input for identifying the structural factors and subtle conformational changes that influence the hydrolytic profile and inhibition of these enzymes. Overall, these data represent the building blocks for understanding the structure-function relationships that define the phenotypes of class A carbapenemases and can guide the design of new molecules of therapeutic interest.
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Affiliation(s)
- Thierry Naas
- Service de Bactériologie- Hygiène, Hôpital de Bicêtre, APHP, EA7361, Faculté de Médecine Paris- Sud, LabEx LERMIT, Le Kremlin-Bicêtre, France.
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CHROMagar Acinetobacter medium for detection of carbapenemase-producing Acinetobacter spp. strains from spiked stools. Diagn Microbiol Infect Dis 2015; 83:234-6. [DOI: 10.1016/j.diagmicrobio.2015.06.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 06/12/2015] [Accepted: 06/24/2015] [Indexed: 11/19/2022]
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Zahedi bialvaei A, Samadi kafil H, Ebrahimzadeh Leylabadlo H, Asgharzadeh M, Aghazadeh M. Dissemination of carbapenemases producing Gram negative bacteria in the Middle East. IRANIAN JOURNAL OF MICROBIOLOGY 2015; 7:226-46. [PMID: 26719779 PMCID: PMC4695504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The emergence and spread of carbapenemase-producing bacteria, that hydolyze most β-lactams, including carbapenems, are a major concern of public health system worldwide, particularly in the Middle East area. Since the plasmids harboring resistance genes could be spread across other bacterial populations, detection of carbapenemase-producing organisms has become more problematic. These organisms produce different types of enzymes including the most prevalent types including KPC, VIM, IMP, NDM, and OXA-48. Carbapenemase producers are mostly identified among Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa and Acinetobacter baumannii. This study reviewed almost all papers, which conducted in the Middle East. In order to decrease the spread of resistance, the regional cooperation has been emphasized by the Middle East countries. The highest resistance, which is mediated by KPC has been observed in Afghanistan, Saudi Arabia and Jordan followed by NDM in Pakistan and OXA in Turkey and Pakistan. It is important to mention that the spread of these types have been reported sporadically in the other countries of this area. This review described the widespread carbapenemases in the Middle East area, which have been identified in an alarming rate.
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Affiliation(s)
- Abed Zahedi bialvaei
- Infectious Disease and Tropical Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Samadi kafil
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Corresponding author: Hossein Samadi Kafil PhD. Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran. E-mail:
| | | | - Mohammad Asgharzadeh
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Aghazadeh
- Infectious Disease and Tropical Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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Bakour S, Alsharapy SA, Touati A, Rolain JM. Characterization of Acinetobacter baumannii clinical isolates carrying bla(OXA-23) carbapenemase and 16S rRNA methylase armA genes in Yemen. Microb Drug Resist 2015; 20:604-9. [PMID: 24901296 DOI: 10.1089/mdr.2014.0018] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
PURPOSE The aim of this study was to investigate the molecular support of resistance to carbapenems, aminoglycosides, and fluoroquinolones in Acinetobacter baumannii clinical isolates collected from Yemen hospital. METHODS Three A. baumannii were isolated in February 2013 from three patients hospitalized at Al-Thawra University Hospital in Sana'a, Yemen. Antibiotic susceptibility testing was performed using the disk diffusion and E-test methods. Carbapenemase production was carried out by the modified Hodge test (MHT) and imipenem-ethylenediaminetetraacetic acid (EDTA) methods. Carbapenem, aminoglycoside, and fluoroquinolone resistance determinants were studied by polymerase chain reaction and sequencing. The epidemiological relatedness of the three strains was studied using multilocus sequence typing (MLST). RESULTS The isolates were resistant to almost all antibiotics tested with very high imipenem, amikacin, and ciprofloxacin minimum inhibitory concentrations (>32, >256, and >32 mg/L, respectively). The microbiological tests showed that the three A. baumannii were MHT positive, besides, the activity of β-lactamases was not inhibited by EDTA. All the three isolates contained the naturally occurring bla(OXA-51)-like gene and the bla(OXA-23)-like carbapenemase-encoding gene. The 16S rRNA methylase armA gene was detected in the three isolates. In addition, screening for genes encoding the aminoglycoside-modifying enzymes (AMEs) demonstrated that one isolate contained the acetyltransferase gene aac(6')-Ib. Fluoroquinolone resistance was associated with a single mutation Ser83Leu in the quinolone resistance determining region of the gyrA gene in all isolates. The MLST showed that the sequence type (ST) obtained corresponds to ST2 for the three strains. CONCLUSIONS Here we report the first identification of multidrug-resistant A. baumannii isolates harboring the bla(OXA-23)-like gene, AMEs [aac(6')-Ib], and the 16S rRNA methylase (armA) in the Yemen hospital.
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Affiliation(s)
- Sofiane Bakour
- 1 Laboratoire d'Ecologie Microbienne, FSNV, Université A/MIRA de Béjaia , Béjaia, Algérie
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Vali L, Dashti K, Opazo-Capurro AF, Dashti AA, Al Obaid K, Evans BA. Diversity of multi-drug resistant Acinetobacter baumannii population in a major hospital in Kuwait. Front Microbiol 2015; 6:743. [PMID: 26257720 PMCID: PMC4513246 DOI: 10.3389/fmicb.2015.00743] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 07/06/2015] [Indexed: 11/13/2022] Open
Abstract
Acinetobacter baumannii is one of the most important opportunistic pathogens that causes serious health care associated complications in critically ill patients. In the current study we report on the diversity of the clinical multi-drug resistant (MDR) A. baumannii in Kuwait by molecular characterization. One hundred A. baumannii were isolated from one of the largest governmental hospitals in Kuwait. Following the identification of the isolates by molecular methods, the amplified blaOXA-51-like gene product of one isolate (KO-12) recovered from blood showed the insertion of the ISAba19 at position 379 in blaOXA-78. Of the 33 MDR isolates, 28 (85%) contained blaOXA-23, 2 (6%) blaOXA-24 and 6 (18%) blaPER-1 gene. We did not detect blaOXA-58, blaVIM, blaIMP, blaGES,blaVEB, and blaNDM genes in any of the tested isolates. In three blaPER-1 positive isolates the genetic environment of blaPER-1 consisted of two copies of ISPa12 (tnpiA1) surrounding the blaPER-1 gene on a highly stable plasmid of ca. 140-kb. Multilocus-sequence typing (MLST) analysis of the 33 A. baumannii isolates identified 20 different STs, of which six (ST-607, ST-608, ST-609, ST-610, ST-611, and ST-612) were novel. Emerging STs such as ST15 (identified for the first time in the Middle East), ST78 and ST25 were also detected. The predominant clonal complex was CC2. Pulsed-field gel electrophoresis and MLST defined the MDR isolates as multi-clonal with diverse lineages. Our results lead us to believe that A. baumannii is diverse in clonal origins and/or is undergoing clonal expansion continuously while multiple lineages of MDR A. baumannii circulate in hospital ward simultaneously.
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Affiliation(s)
- Leila Vali
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, Kuwait University Sulaibekhat, Kuwait
| | - Khadija Dashti
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, Kuwait University Sulaibekhat, Kuwait
| | - Andrés F Opazo-Capurro
- Laboratorio de Investigación en Agentes Antibacterianos, Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción Concepción, Chile
| | - Ali A Dashti
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, Kuwait University Sulaibekhat, Kuwait
| | | | - Benjamin A Evans
- Department of Biomedical and Forensic Sciences, Faculty of Science and Technology, Anglia Ruskin University Cambridge, UK
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Hammoudi D, Moubareck CA, Hakime N, Houmani M, Barakat A, Najjar Z, Suleiman M, Fayad N, Sarraf R, Sarkis DK. Spread of imipenem-resistant Acinetobacter baumannii co-expressing OXA-23 and GES-11 carbapenemases in Lebanon. Int J Infect Dis 2015; 36:56-61. [DOI: 10.1016/j.ijid.2015.05.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 05/15/2015] [Accepted: 05/18/2015] [Indexed: 10/23/2022] Open
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Bedenić B, Beader N, Godič-Torkar K, Vranić-Ladavac M, Luxner J, Veir Z, Grisold AJ, Zarfel G. Nursing Home as a Reservoir of Carbapenem-ResistantAcinetobacter baumannii. Microb Drug Resist 2015; 21:270-8. [DOI: 10.1089/mdr.2014.0157] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Branka Bedenić
- Department of Microbiology, School of Medicine, University of Zagreb, Zagreb, Croatia
- Department of Clinical and Molecular Microbiology, Clinical Hospital Center Zagreb, Zagreb, Croatia
| | - Nataša Beader
- Department of Microbiology, School of Medicine, University of Zagreb, Zagreb, Croatia
- Department of Clinical and Molecular Microbiology, Clinical Hospital Center Zagreb, Zagreb, Croatia
| | - Karmen Godič-Torkar
- Department for Sanitary Engineering, Faculty of Health Sciences, University of Ljubljana, Ljubljana, Slovenia
| | - Mirna Vranić-Ladavac
- Department of Microbiology, Public Health Institute of Istria County, Pula, Croatia
| | - Josefa Luxner
- Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Zoran Veir
- Department of Surgery, Clinical Hospital Center Zagreb, Zagreb, Croatia
| | - Andrea J. Grisold
- Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Gernot Zarfel
- Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
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O'Brien TF, Stelling J. The world's microbiology laboratories can be a global microbial sensor network. BIOMEDICA : REVISTA DEL INSTITUTO NACIONAL DE SALUD 2015; 34 Suppl 1:9-15. [PMID: 24968031 DOI: 10.1590/s0120-41572014000500002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 11/22/2013] [Indexed: 02/02/2023]
Abstract
The microbes that infect us spread in global and local epidemics, and the resistance genes that block their treatment spread within and between them. All we can know about where they are to track and contain them comes from the only places that can see them, the world's microbiology laboratories, but most report each patient's microbe only to that patient's caregiver. Sensors, ranging from instruments to birdwatchers, are now being linked in electronic networks to monitor and interpret algorithmically in real-time ocean currents, atmospheric carbon, supply-chain inventory, bird migration, etc. To so link the world's microbiology laboratories as exquisite sensors in a truly lifesaving real-time network their data must be accessed and fully subtyped. Microbiology laboratories put individual reports into inaccessible paper or mutually incompatible electronic reporting systems, but those from more than 2,200 laboratories in more than 108 countries worldwide are now accessed and translated into compatible WHONET files. These increasingly web-based files could initiate a global microbial sensor network. Unused microbiology laboratory byproduct data, now from drug susceptibility and biochemical testing but increasingly from new technologies (genotyping, MALDI-TOF, etc.), can be reused to subtype microbes of each genus/species into sub-groupings that are discriminated and traced with greater sensitivity. Ongoing statistical delineation of subtypes from global sensor network data will improve detection of movement into any patient of a microbe or resistance gene from another patient, medical center or country. Growing data on clinical manifestations and global distributions of subtypes can automate comments for patient's reports, select microbes to genotype and alert responders.
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Affiliation(s)
- Thomas F O'Brien
- Department of Medicine, Brigham and Women´s Hospital and Harvard Medical School, Boston, MA, USA
| | - John Stelling
- Department of Medicine, Brigham and Women´s Hospital and Harvard Medical School, Boston, MA, USA
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Potron A, Poirel L, Nordmann P. Emerging broad-spectrum resistance in Pseudomonas aeruginosa and Acinetobacter baumannii: Mechanisms and epidemiology. Int J Antimicrob Agents 2015; 45:568-85. [PMID: 25857949 DOI: 10.1016/j.ijantimicag.2015.03.001] [Citation(s) in RCA: 457] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 03/05/2015] [Indexed: 02/07/2023]
Abstract
Multidrug resistance is quite common among non-fermenting Gram-negative rods, in particular among clinically relevant species including Pseudomonas aeruginosa and Acinetobacter baumannii. These bacterial species, which are mainly nosocomial pathogens, possess a diversity of resistance mechanisms that may lead to multidrug or even pandrug resistance. Extended-spectrum β-lactamases (ESBLs) conferring resistance to broad-spectrum cephalosporins, carbapenemases conferring resistance to carbapenems, and 16S rRNA methylases conferring resistance to all clinically relevant aminoglycosides are the most important causes of concern. Concomitant resistance to fluoroquinolones, polymyxins (colistin) and tigecycline may lead to pandrug resistance. The most important mechanisms of resistance in P. aeruginosa and A. baumannii and their most recent dissemination worldwide are detailed here.
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Affiliation(s)
- Anaïs Potron
- Laboratoire de Bactériologie, Faculté de Médecine-Pharmacie, Centre Hospitalier Régional Universitaire, Université de Franche-Comté, Besançon, France
| | - Laurent Poirel
- Emerging Antibiotic Resistance Medical and Molecular Microbiology Unit, Department of Medicine, Faculty of Science, University of Fribourg, Fribourg, Switzerland.
| | - Patrice Nordmann
- Emerging Antibiotic Resistance Medical and Molecular Microbiology Unit, Department of Medicine, Faculty of Science, University of Fribourg, Fribourg, Switzerland; HFR - Hôpital Cantonal de Fribourg, Fribourg, Switzerland
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Molecular epidemiology of carbapenem-resistant Acinetobacter baumannii isolates in the Gulf Cooperation Council States: dominance of OXA-23-type producers. J Clin Microbiol 2015; 53:896-903. [PMID: 25568439 DOI: 10.1128/jcm.02784-14] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The molecular epidemiology and mechanisms of resistance of carbapenem-resistant Acinetobacter baumannii (CRAB) were determined in hospitals in the states of the Cooperation Council for the Arab States of the Gulf (Gulf Cooperation Council [GCC]), namely, Saudi Arabia, United Arab Emirates, Oman, Qatar, Bahrain, and Kuwait. Isolates were subjected to PCR-based detection of antibiotic resistance genes and repetitive sequence-based PCR (rep-PCR) assessments of clonality. Selected isolates were subjected to multilocus sequence typing (MLST). We investigated 117 isolates resistant to carbapenem antibiotics (either imipenem or meropenem). All isolates were positive for OXA-51. The most common carbapenemases were the OXA-23-type, found in 107 isolates, followed by OXA-40-type (OXA-24-type), found in 5 isolates; 3 isolates carried the ISAba1 element upstream of blaOXA-51-type. No OXA-58-type, NDM-type, VIM-type, or IMP-type producers were detected. Multiple clones were detected with 16 clusters of clonally related CRAB. Some clusters involved hospitals in different states. MLST analysis of 15 representative isolates from different clusters identified seven different sequence types (ST195, ST208, ST229, ST436, ST450, ST452, and ST499), as well as three novel STs. The vast majority (84%) of the isolates in this study were associated with health care exposure. Awareness of multidrug-resistant organisms in GCC states has important implications for optimizing infection control practices; establishing antimicrobial stewardship programs within hospital, community, and agricultural settings; and emphasizing the need for establishing regional active surveillance systems. This will help to control the spread of CRAB in the Middle East and in hospitals accommodating transferred patients from this region.
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Stewart NK, Smith CA, Frase H, Black DJ, Vakulenko SB. Kinetic and structural requirements for carbapenemase activity in GES-type β-lactamases. Biochemistry 2014; 54:588-97. [PMID: 25485972 PMCID: PMC4303295 DOI: 10.1021/bi501052t] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
Carbapenems are the last resort antibiotics
for treatment of life-threatening
infections. The GES β-lactamases are important contributors
to carbapenem resistance in clinical bacterial pathogens. A single
amino acid difference at position 170 of the GES-1, GES-2, and GES-5
enzymes is responsible for the expansion of their substrate profile
to include carbapenem antibiotics. This highlights the increasing
need to understand the mechanisms by which the GES β-lactamases
function to aid in development of novel therapeutics. We demonstrate
that the catalytic efficiency of the enzymes with carbapenems meropenem,
ertapenem, and doripenem progressively increases (100-fold) from GES-1
to -5, mainly due to an increase in the rate of acylation. The data
reveal that while acylation is rate limiting for GES-1 and GES-2 for
all three carbapenems, acylation and deacylation are indistinguishable
for GES-5. The ertapenem–GES-2 crystal structure shows that
only the core structure of the antibiotic interacts with the active
site of the GES-2 β-lactamase. The identical core structures
of ertapenem, doripenem, and meropenem are likely responsible for
the observed similarities in the kinetics with these carbapenems.
The lack of a methyl group in the core structure of imipenem may provide
a structural rationale for the increase in turnover of this carbapenem
by the GES β-lactamases. Our data also show that in GES-2 an
extensive hydrogen-bonding network between the acyl-enzyme complex
and the active site water attenuates activation of this water molecule,
which results in poor deacylation by this enzyme.
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Affiliation(s)
- Nichole K Stewart
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
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Multidrug-resistant Acinetobacter baumannii strains carrying the blaOxA-23 and the blaGES-11 genes in a neonatology center in Tunisia. Microb Pathog 2014; 74:20-4. [DOI: 10.1016/j.micpath.2014.07.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 07/09/2014] [Accepted: 07/10/2014] [Indexed: 11/19/2022]
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Al-Agamy MH, Khalaf NG, Tawfick MM, Shibl AM, Kholy AE. Molecular characterization of carbapenem-insensitive Acinetobacter baumannii in Egypt. Int J Infect Dis 2014; 22:49-54. [DOI: 10.1016/j.ijid.2013.12.004] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 12/01/2013] [Accepted: 12/02/2013] [Indexed: 10/25/2022] Open
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Cicek A, Saral A, Iraz M, Ceylan A, Duzgun A, Peleg A, Sandalli C. OXA- and GES-type β-lactamases predominate in extensively drug-resistant Acinetobacter baumannii isolates from a Turkish University Hospital. Clin Microbiol Infect 2014; 20:410-5. [DOI: 10.1111/1469-0691.12338] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Revised: 07/01/2013] [Accepted: 07/14/2013] [Indexed: 12/01/2022]
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49
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Computational gene network study on antibiotic resistance genes of Acinetobacter baumannii. Comput Biol Med 2014; 48:17-27. [DOI: 10.1016/j.compbiomed.2014.02.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 02/12/2014] [Accepted: 02/14/2014] [Indexed: 12/27/2022]
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CarbAcineto NP test for rapid detection of carbapenemase-producing Acinetobacter spp. J Clin Microbiol 2014; 52:2359-64. [PMID: 24759709 DOI: 10.1128/jcm.00594-14] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Multidrug-resistant Acinetobacter baumannii isolates, particularly those that produce carbapenemases, are increasingly reported worldwide. The biochemically based Carba NP test, extensively validated for the detection of carbapenemase producers among Enterobacteriaceae and Pseudomonas spp., has been modified to detect carbapenemase production in Acinetobacter spp. A collection of 151 carbapenemase-producing and 69 non-carbapenemase-producing Acinetobacter spp. were tested using the Carba NP test and a modified Carba NP protocol (the CarbAcineto NP test) in this study. The CarbAcineto NP test requires modified lysis conditions and an increased bacterial inoculum compared to those of the original Carba NP test. The Carba NP test detects metallo-β-lactamase producers but failed to detect the production of other carbapenemase types among Acinetobacter spp. In contrast, the newly designed CarbAcineto NP test, which is rapid and reproducible, detects all types of carbapenemases with a sensitivity of 94.7% and a specificity of 100%. This cost-effective technique offers a reliable and affordable technique for identifying carbapenemase production in Acinetobacter spp., which is a marker of multidrug resistance in those species. Its use will facilitate the recognition of these carbapenemases and prevent their spread.
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