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Raddaoui A, Mabrouk A, Chebbi Y, Frigui S, Salah Abbassi M, Achour W, Thabet L. Co-occurrence of blaNDM-1 and blaOXA-23 in carbapenemase-producing Acinetobacter baumannii belonging to high-risk lineages isolated from burn patients in Tunisia. J Appl Microbiol 2024; 135:lxae039. [PMID: 38346864 DOI: 10.1093/jambio/lxae039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 01/10/2024] [Accepted: 02/09/2024] [Indexed: 03/21/2024]
Abstract
AIMS Carbapenem-resistant Acinetobacter baumannii (CR-Ab) is an important cause of infections in burn patients. This study aimed to characterize the antimicrobial susceptibility pattern of CR-Ab isolated from burns in Burn Intensive Care Unit (BICU) of the Trauma and Burn Centre of Ben Arous, to determine the prevalence of β-lactamase-encoding genes and to search eventual genetic relatedness of CR-Ab strains. METHODS AND RESULTS From 15 December 2016 to 2 April 2017, all nonduplicated CR-Ab isolated in burn patients in the BICU were screened by simplex Polymerase Chain Reaction (PCR) for the class A, B, C, and D β-lactamase genes. Sequencing was performed for NDM gene only. Genetic relatedness was determined by using pulsed field gel electrophoresis (PFGE) and by multilocus sequence typing. During the study period, 34 strains of CR-Ab were isolated in burns, mainly in blood culture (n = 14) and central vascular catheter (n = 10). CR-Ab strains were susceptible to colistin but resistant to amikacin (91%), ciprofloxacin (100%), rifampicin (97%), and trimethoprim-sulfamethoxazole (100%). All strains harbored blaOXA-51-like and blaOXA-23 genes, only or associated to blaGES (n = 26; 76%), blaADC (n = 20; 59%), blaPER-1 (n = 6; 18%) or/and blaNDM-1 (n = 3; 9%). PFGE identified 16 different clusters and revealed that most strains belonged to one major cluster A (n = 15; 44.1%). Among NDM-1 isolates, two were clonally related in PFGE and belonged to two single locus variant sequence type ST-6 and ST-85. CONCLUSIONS This is the first description of clonally related NDM-1 and OXA-23-producing A. baumannii strains in the largest Tunisian BICU associated with two single locus variant sequence types ST6 and ST85.
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Affiliation(s)
- Anis Raddaoui
- Laboratory Ward, National Bone Marrow Transplant Center, 1006 Tunis, Tunisia
- Faculty of Medicine of Tunis, LR18ES39, University of Tunis El Manar, 1006 Tunis, Tunisia
| | - Aymen Mabrouk
- Laboratory Ward, National Bone Marrow Transplant Center, 1006 Tunis, Tunisia
- Faculty of Medicine of Tunis, LR18ES39, University of Tunis El Manar, 1006 Tunis, Tunisia
| | - Yosra Chebbi
- Laboratory Ward, National Bone Marrow Transplant Center, 1006 Tunis, Tunisia
- Faculty of Medicine of Tunis, LR18ES39, University of Tunis El Manar, 1006 Tunis, Tunisia
| | - Siwar Frigui
- Laboratory Ward, National Bone Marrow Transplant Center, 1006 Tunis, Tunisia
- Faculty of Medicine of Tunis, LR18ES39, University of Tunis El Manar, 1006 Tunis, Tunisia
| | - Mohamed Salah Abbassi
- Faculty of Medicine of Tunis, Laboratory of Antibiotic Resistance LR99ES09, University of Tunis El Manar, 1006 Tunis, Tunisia
- Institute of Veterinary Research of Tunisia, University of Tunis El Manar, 1006 Tunis, Tunisia
| | - Wafa Achour
- Laboratory Ward, National Bone Marrow Transplant Center, 1006 Tunis, Tunisia
- Faculty of Medicine of Tunis, LR18ES39, University of Tunis El Manar, 1006 Tunis, Tunisia
| | - Lamia Thabet
- Laboratory Ward, Traumatology and Great Burned Center, 2074 Ben Arous, Tunisia
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2
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Sánchez-Urtaza S, Ocampo-Sosa A, Rodríguez-Grande J, El-Kholy MA, Shawky SM, Alkorta I, Gallego L. Plasmid content of carbapenem resistant Acinetobacter baumannii isolates belonging to five International Clones collected from hospitals of Alexandria, Egypt. Front Cell Infect Microbiol 2024; 13:1332736. [PMID: 38264728 PMCID: PMC10803598 DOI: 10.3389/fcimb.2023.1332736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 12/20/2023] [Indexed: 01/25/2024] Open
Abstract
Multidrug resistant Acinetobacter baumannii is one of the most important nosocomial pathogens worldwide. During the last decades it has become a major threat for healthcare settings due to the high antibiotic resistance rates among these isolates. Many resistance determinants are coded by conjugative or mobilizable plasmids, facilitating their dissemination. The majority of plasmids harbored by Acinetobacter species are less than 20 Kb, however, high molecular weight elements are the most clinically relevant since they usually contain antibiotic resistance genes. The aim of this work was to describe, classify and determine the genetic content of plasmids harbored by carbapem resistant A. baumannii isolates belonging to predominant clonal lineages circulating in hospitals from Alexandria, Egypt. The isolates were subjected to S1-Pulsed Field Gel Electrophoresis experiments to identify high molecular weight plasmids. To further analyze the plasmid content and the genetic localization of the antibiotic resistance genes, isolates were sequenced by Illumina Miseq and MinION Mk1C and a hybrid assembly was performed using Unicycler v0.5.0. Plasmids were detected with MOBsuite 3.0.3 and Copla.py v.1.0 and mapped using the online software Proksee.ca. Replicase genes were further analyzed through a BLAST against the Acinetobacter Plasmid Typing database. Eleven plasmids ranging in size from 4.9 to 205.6 Kb were characterized and mapped. All isolates contained plasmids, and, in many cases, more than two elements were identified. Antimicrobial resistance genes such as bla OXA-23, bla GES-like, aph(3')-VI and qacEΔ1 were found in likely conjugative large plasmids; while virulence determinants such as septicolysin or TonB-dependent receptors were identified in plasmids of small size. Some of these resistance determinants were, in turn, located within transposons and class 1 integrons. Among the identified plasmids, the majority encoded proteins belonging to the Rep_3 family, but replicases of the RepPriCT_1 (Aci6) family were also identified. Plasmids are of high interest as antibiotic resistance control tools, since they may be used as genetic markers for antibiotic resistance and virulence, and also as targets for the development of compounds that can inhibit transfer processes.
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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 (IDIVAL), Santander, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Jorge Rodríguez-Grande
- Microbiology Service, University Hospital Marqués de Valdecilla, Health Research Institute (IDIVAL), Santander, 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
| | - 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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3
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Müller C, Reuter S, Wille J, Xanthopoulou K, Stefanik D, Grundmann H, Higgins PG, Seifert H. A global view on carbapenem-resistant Acinetobacter baumannii. mBio 2023; 14:e0226023. [PMID: 37882512 PMCID: PMC10746149 DOI: 10.1128/mbio.02260-23] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 09/12/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE Carbapenem-resistant Acinetobacter baumannii are of increasing public health importance, as they are resistant to last-line antibiotics. International clones with well-characterized resistance genes dominate globally; however, locally, other lineages with different properties may be of importance to consider. This study investigated isolates from a broad geographic origin from 114 hospitals in 47 countries and from five world regions ensuring the greatest possible diversity in an organism known for its propensity for clonal epidemic spread and reflecting the current global epidemiology of carbapenem-resistant A. baumannii. In Latin America, a lineage different from other geographic regions circulates, with a different resistance gene profile. This knowledge is important to adjust local infection prevention measures. In a global world with migration and increasing use of antimicrobials, multidrug-resistant bacteria will continue to adapt and challenge our healthcare systems worldwide.
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Affiliation(s)
- Carina Müller
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Goldenfelsstr, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Sandra Reuter
- Institute for Infection Prevention and Hospital Epidemiology, Medical Centre–University of Freiburg, Freiburg, Germany
| | - Julia Wille
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Goldenfelsstr, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Kyriaki Xanthopoulou
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Goldenfelsstr, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Danuta Stefanik
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Goldenfelsstr, Cologne, Germany
| | - Hajo Grundmann
- Institute for Infection Prevention and Hospital Epidemiology, Medical Centre–University of Freiburg, Freiburg, Germany
| | - Paul G. Higgins
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Goldenfelsstr, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Harald Seifert
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Goldenfelsstr, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
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4
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Odih EE, Sunmonu GT, Okeke IN, Dalsgaard A. NDM-1- and OXA-23-producing Acinetobacter baumannii in wastewater of a Nigerian hospital. Microbiol Spectr 2023; 11:e0238123. [PMID: 37796014 PMCID: PMC10714947 DOI: 10.1128/spectrum.02381-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 08/22/2023] [Indexed: 10/06/2023] Open
Abstract
IMPORTANCE Acinetobacter baumannii is a leading cause of hospital-associated infections globally. A. baumannii reservoirs outside hospital settings are still unknown, and their occurrence in the environment is linked to clinical and anthropogenic activities. Although the risk of transmission of A. baumannii from environmental sources to humans is not fully understood, these sources pose significant risks for the continued dissemination of A. baumannii and their resistance traits. This study provides evidence that diverse and clinically relevant A. baumannii strains, many of which are resistant to carbapenems, are constantly being discharged into the environment through inadequately treated hospital wastewater. We further elucidate potential transmission routes between the environment and clinical infections and demonstrate the high prevalence of carbapenem resistance genes on highly mobile transposons among these strains. Our findings highlight the pressing need to address hospital wastewater as a crucial factor in curtailing the spread of carbapenem-resistant A. baumannii.
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Affiliation(s)
- Erkison Ewomazino Odih
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Gabriel Temitope Sunmonu
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Iruka N. Okeke
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Shelenkov A, Akimkin V, Mikhaylova Y. International Clones of High Risk of Acinetobacter Baumannii-Definitions, History, Properties and Perspectives. Microorganisms 2023; 11:2115. [PMID: 37630675 PMCID: PMC10459012 DOI: 10.3390/microorganisms11082115] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/24/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023] Open
Abstract
Acinetobacter baumannii is a Gram-negative coccobacillus with exceptional survival skills in an unfavorable environment and the ability to rapidly acquire antibiotic resistance, making it one of the most successful hospital pathogens worldwide, representing a serious threat to public health. The global dissemination of A. baumannii is driven by several lineages named 'international clones of high risk' (ICs), two of which were first revealed in the 1970s. Epidemiological surveillance is a crucial tool for controlling the spread of this pathogen, which currently increasingly involves whole genome sequencing. However, the assignment of a particular A. baumannii isolate to some IC based on its genomic sequence is not always straightforward and requires some computational skills from researchers, while the definitions found in the literature are sometimes controversial. In this review, we will focus on A. baumannii typing tools suitable for IC determination, provide data to easily determine IC assignment based on MLST sequence type (ST) and intrinsic blaOXA-51-like gene variants, discuss the history and current spread data of nine known ICs, IC1-IC9, and investigate the representation of ICs in public databases. MLST and cgMLST profiles, as well as OXA-51-like presence data are provided for all isolates available in GenBank. The possible emergence of a novel A. baumannii international clone, IC10, will be discussed.
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Affiliation(s)
- Andrey Shelenkov
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia
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6
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Sánchez-Urtaza S, Ocampo-Sosa A, Molins-Bengoetxea A, Rodríguez-Grande J, El-Kholy MA, Hernandez M, Abad D, Shawky SM, Alkorta I, Gallego L. Co-Existence of blaNDM-1, blaOXA-23, blaOXA-64, blaPER-7 and blaADC-57 in a Clinical Isolate of Acinetobacter baumannii from Alexandria, Egypt. Int J Mol Sci 2023; 24:12515. [PMID: 37569889 PMCID: PMC10419532 DOI: 10.3390/ijms241512515] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 07/30/2023] [Accepted: 08/05/2023] [Indexed: 08/13/2023] Open
Abstract
The increasing rates of antimicrobial resistance among carbapenem-resistant Acinetobacter baumannii in the Middle East and North Africa are one of the major concerns for healthcare settings. We characterised the first A. baumannii isolate harbouring five β-lactamases identified in Egypt. The isolate Ale25 was obtained from an ICU patient of a hospital from Alexandria. The isolate was phenotypically and genotypically screened for carbapenemase genes. The isolate was resistant to carbapenems, aminoglycosides, fluoroquinolones and cefiderocol. Whole-Genome Sequencing identified five β-lactamase genes, blaNDM-1, blaOXA-23, blaOXA-64, blaPER-7 and blaADC-57, together with other antibiotic resistance genes, conferring resistance to sulfonamides, macrolides, tetracyclines, rifamycin and chloramphenicol. Virulome analysis showed the presence of genes involved in adhesion and biofilm production, type II and VI secretion systems, exotoxins, etc. Multi-Locus Sequence Typing analysis identified the isolate as Sequence Types 113Pas and 2246Oxf, belonging to International Clone 7. Sequencing experiments revealed the presence of four plasmids of 2.7, 22.3, 70.4 and 240.8 Kb. All the β-lactamase genes were located in the chromosome, except the blaPER-7, gene which was found within the plasmid of 240.8 Kb. This study highlights the threat of the emergence and dissemination of these types of isolates.
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Affiliation(s)
- Sandra Sánchez-Urtaza
- Department of Immunology, Microbiology and Parasitology, Faculty of Medicine and Nursing, University of the Basque Country, 48940 Leioa, Spain; (S.S.-U.); (A.M.-B.)
| | - Alain Ocampo-Sosa
- Microbiology Service, Health Research Institute (IDIVAL), University Hospital Marqués de Valdecilla, 39008 Santander, Spain;
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Ainhoa Molins-Bengoetxea
- Department of Immunology, Microbiology and Parasitology, Faculty of Medicine and Nursing, University of the Basque Country, 48940 Leioa, Spain; (S.S.-U.); (A.M.-B.)
| | - Jorge Rodríguez-Grande
- Microbiology Service, Health Research Institute (IDIVAL), University Hospital Marqués de Valdecilla, 39008 Santander, Spain;
| | - Mohammed A. El-Kholy
- Division of Clinical and Biological Sciences, Department of Microbiology and Biotechnology, College of Pharmacy, Arab Academy for Science, Technology & Maritime Transport (AASTMT), Alexandria P.O. Box 1029, Egypt;
| | - Marta Hernandez
- Laboratory of Molecular Biology and Microbiology, One Health, Agrarian Technological Institute of Castile and Leon (ITACyL), 47009 Valladolid, Spain; (M.H.); (D.A.)
| | - David Abad
- Laboratory of Molecular Biology and Microbiology, One Health, Agrarian Technological Institute of Castile and Leon (ITACyL), 47009 Valladolid, Spain; (M.H.); (D.A.)
| | - Sherine M. Shawky
- Medical Research Institute, Alexandria University, Alexandria 5422031, Egypt;
| | - Itziar Alkorta
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country, 48940 Leioa, Spain;
| | - Lucia Gallego
- Department of Immunology, Microbiology and Parasitology, Faculty of Medicine and Nursing, University of the Basque Country, 48940 Leioa, Spain; (S.S.-U.); (A.M.-B.)
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7
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Zafer MM, Hussein AFA, Al-Agamy MH, Radwan HH, Hamed SM. Retained colistin susceptibility in clinical Acinetobacter baumannii isolates with multiple mutations in pmrCAB and lpxACD operons. Front Cell Infect Microbiol 2023; 13:1229473. [PMID: 37600939 PMCID: PMC10436201 DOI: 10.3389/fcimb.2023.1229473] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 07/10/2023] [Indexed: 08/22/2023] Open
Abstract
The progressive increase in the resistance rates to first- and second-line antibiotics has forced the reuse of colistin as last-line treatment for Acinetobacter baumannii infections, but the emergence of colistin-resistant strains is not uncommon. This has been long linked to acquired chromosomal mutations in the operons pmrCAB and lpxACD. Hence, such mutations are routinely screened in colistin-resistant strains by most studies. The current study was designed to explore the possible existence of pmrCAB and lpxACD mutations in colistin-susceptible isolates. For this purpose, the whole genome sequences of eighteen multi-/extensively drug resistant A. baumannii were generated by Illumina sequencing and screened for missense mutations of the operons pmrCAB and lpxACD. Most of the isolates belonged to global clones (GCs) including GC1 (n=2), GC2 (n=7), GC7 (n=2), GC9 (n=3), and GC11 (n=1). The minimum inhibitory concentrations (MICs) of colistin were determined by the broth microdilution assay. Seventeen isolates were fully susceptible to colistin with MICs ranging from (≤0.125 to 0.5 µg/ml). Interestingly, all colistin-susceptible isolates carried missense mutations in pmrCAB and lpxACD operons with reference to A. baumannii ATCC 19606. Overall, 34 mutations were found. Most substitutions were detected in pmrC (n=20) while no mutations were found in pmrA or lpxA. Notably, the mutation pattern of the two operons was almost conserved among the isolates that belonged to the same sequence type (ST) or GC. This was also confirmed by expanding the analysis to include A. baumannii genomes deposited in public databases. Here, we demonstrated the possible existence of missense mutations in pmrCAB and lpxACD operons in colistin-susceptible isolates, shedding light on the importance of interpreting mutations with reference to colistin-susceptible isolates of the same ST/GC to avoid the misleading impact of the ST/GC-related polymorphism. In turn, this may lead to misinterpretation of mutations and, hence, overlooking the real players in colistin resistance that are yet to be identified.
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Affiliation(s)
- Mai M. Zafer
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ahram Canadian University, Cairo, Egypt
| | - Amira F. A. Hussein
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
- Faculty of Applied Health Science, Galala University, Cairo, Egypt
| | - Mohamed H. Al-Agamy
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
- Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhar University, Cairo, Egypt
| | - Hesham H. Radwan
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Samira M. Hamed
- Department of Microbiology and Immunology, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), 6th of October, Giza, Egypt
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Cain AK, Hamidian M. Portrait of a killer: Uncovering resistance mechanisms and global spread of Acinetobacter baumannii. PLoS Pathog 2023; 19:e1011520. [PMID: 37561719 PMCID: PMC10414682 DOI: 10.1371/journal.ppat.1011520] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023] Open
Abstract
Antibiotic resistance is a growing global concern in the field of medicine as it renders bacterial infections difficult to treat and often more severe. Acinetobacter baumannii is a gram-negative bacterial pathogen causing a wide range of infections, including pneumonia, sepsis, urinary tract infections, and wound infections. A. baumannii has emerged as a significant healthcare-associated pathogen due to its high level of antibiotic resistance. The global spread of antibiotic-resistant strains of A. baumannii has resulted in limited treatment options, leading to increased morbidity and mortality rates, especially in vulnerable populations such as the elderly and immunocompromised individuals, as well as longer hospital stays and higher healthcare costs. Further complicating the situation, multi- and pan-drug-resistant strains of A. baumannii are becoming increasingly common, and these deadly strains are resistant to all or almost all available antibiotics. A. baumannii employs various clever strategies to develop antibiotic resistance, including horizontal transfer of resistance genes, overexpression of inherent efflux pumps that remove drugs from the cell, intrinsic mutations, combined with natural selection under antibiotic selective pressure leading to emergence of successful resistance clones. The typical multidrug resistance phenotype of A. baumannii is, therefore, an orchestrated collimation of all these mechanisms combined with the worldwide spread of "global clones," rendering infections caused by this pathogen challenging to control and treat. To address the escalating problem of antibiotic resistance in A. baumannii, there is a need for increased surveillance, strict infection control measures, and the development of new treatment strategies, requiring a concerted effort by healthcare professionals, researchers, and policymakers.
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Affiliation(s)
- Amy K. Cain
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
| | - Mehrad Hamidian
- Australian Institute of Microbiology and Infection, University of Technology Sydney, Ultimo, NSW, Australia
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9
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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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10
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Hamed SM, Elkhatib WF, Brangsch H, Gesraha AS, Moustafa S, Khater DF, Pletz MW, Sprague LD, Neubauer H, Wareth G. Acinetobacter baumannii Global Clone-Specific Resistomes Explored in Clinical Isolates Recovered from Egypt. Antibiotics (Basel) 2023; 12:1149. [PMID: 37508245 PMCID: PMC10376554 DOI: 10.3390/antibiotics12071149] [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: 06/08/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Acinetobacter baumannii (A. baumannii) is a highly problematic pathogen with an enormous capacity to acquire or upregulate antibiotic drug resistance determinants. The genomic epidemiology and resistome structure of 46 A. baumannii clinical isolates were studied using whole-genome sequencing. The isolates were chosen based on reduced susceptibility to at least three classes of antimicrobial compounds and were initially identified using MALDI-TOF/MS, followed by polymerase chain reaction amplification of blaOXA-51-like genes. The susceptibility profiles were determined using a broth microdilution assay. Multi-, extensive-, and pan-drug resistance was shown by 34.8%, 63.0%, and 2.2% of the isolates, respectively. These were most susceptible to colistin (95.7%), amikacin, and trimethoprim/sulfamethoxazole (32.6% each), while only 26.1% of isolates were susceptible to tigecycline. In silico multi-locus sequence typing revealed 8 Pasteur and 22 Oxford sequence types (STs) including four novel STs (STOxf 2805, 2806, 2807, and 2808). The majority of the isolates belonged to Global Clone (GC) 2 (76.4%), GC5 (19.6%), GC4 (6.5%), GC9 (4.3%), and GC7 (2.2%) lineages. An extensive resistome potentially conferring resistance to the majority of the tested antimicrobials was identified in silico. Of all known carbapenem resistance genes, blaOXA-23 was carried by most of the isolates (69.6%), followed by ISAba1-amplified blaADC (56.5%), blaNDM-1 and blaGES-11 (21.7% each), and blaGES-35 (2.2%) genes. A significant correlation was found between carbapenem resistance and carO mutations, which were evident in 35 (76.0%) isolates. A lower proportion of carbapenem resistance was noted for strains possessing both blaOXA-23- and blaGES-11. Amikacin resistance was most probably mediated by armA, aac(6')-Ib9, and aph(3')-VI, most commonly coexisting in GC2 isolates. No mutations were found in pmrABC or lpxACD operons in the colistin-resistant isolates. Tigecycline resistance was associated with adeS (N268Y) and baeS (A436T) mutations. While the lineage-specific distribution of some genes (e.g., blaADC and blaOXA-51-like alleles) was evident, some resistance genes, such as blaOXA-23 and sul1, were found in all GCs. The data generated here highlight the contribution of five GCs in A. baumannii infections in Egypt and enable the comprehensive analysis of GC-specific resistomes, thus revealing the dissemination of the carbapenem resistance gene blaOXA-23 in isolates encompassing all GCs.
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Affiliation(s)
- Samira M Hamed
- Department of Microbiology and Immunology, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza 12451, Egypt
| | - Walid F Elkhatib
- Microbiology and Immunology Department, Faculty of Pharmacy, Ain Shams University, African Union Organization Street, Cairo 11566, Egypt
- Department of Microbiology and Immunology, Faculty of Pharmacy, Galala University, Suez 43727, Egypt
| | - Hanka Brangsch
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler Institut, 07743 Jena, Germany
| | - Ahmed S Gesraha
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Tanta University, Tanta 31511, Egypt
| | - Shawky Moustafa
- Faculty of Veterinary Medicine, Benha University, Toukh 13736, Egypt
| | - Dalia F Khater
- Tanta Laboratory, Animal Health Research Institute, Agricultural Research Center, Tanta 31511, Egypt
| | - Mathias W Pletz
- Institute of Infectious Diseases and Infection Control, Jena University Hospital, 07747 Jena, Germany
| | - Lisa D Sprague
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler Institut, 07743 Jena, Germany
| | - Heinrich Neubauer
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler Institut, 07743 Jena, Germany
| | - Gamal Wareth
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler Institut, 07743 Jena, Germany
- Institute of Infectious Diseases and Infection Control, Jena University Hospital, 07747 Jena, Germany
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11
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Odih EE, Oaikhena AO, Underwood A, Hounmanou YMG, Oduyebo OO, Fadeyi A, Aboderin AO, Ogunleye VO, Argimón S, Akpunonu VN, Oshun PO, Egwuenu A, Okwor TJ, Ihekweazu C, Aanensen DM, Dalsgaard A, Okeke IN. High Genetic Diversity of Carbapenem-Resistant Acinetobacter baumannii Isolates Recovered in Nigerian Hospitals in 2016 to 2020. mSphere 2023; 8:e0009823. [PMID: 37067411 PMCID: PMC10286719 DOI: 10.1128/msphere.00098-23] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 03/22/2023] [Indexed: 04/18/2023] Open
Abstract
Acinetobacter baumannii causes difficult-to-treat infections mostly among immunocompromised patients. Clinically relevant A. baumannii lineages and their carbapenem resistance mechanisms are sparsely described in Nigeria. This study aimed to characterize the diversity and genetic mechanisms of carbapenem resistance among A. baumannii strains isolated from hospitals in southwestern Nigeria. We sequenced the genomes of all A. baumannii isolates submitted to Nigeria's antimicrobial resistance surveillance reference laboratory between 2016 and 2020 on an Illumina platform and performed in silico genomic characterization. Selected strains were sequenced using the Oxford Nanopore technology to characterize the genetic context of carbapenem resistance genes. The 86 A. baumannii isolates were phylogenetically diverse and belonged to 35 distinct Oxford sequence types (oxfSTs), 16 of which were novel, and 28 Institut Pasteur STs (pasSTs). Thirty-eight (44.2%) isolates belonged to none of the known international clones (ICs). Over 50% of the isolates were phenotypically resistant to 10 of 12 tested antimicrobials. The majority (n = 54) of the isolates were carbapenem resistant, particularly the IC7 (pasST25; 100%) and IC9 (pasST85; >91.7%) strains. blaOXA-23 (34.9%) and blaNDM-1 (27.9%) were the most common carbapenem resistance genes detected. All blaOXA-23 genes were carried on Tn2006 or Tn2006-like transposons. Our findings suggest that a 10-kb Tn125 composite transposon is the primary means of blaNDM-1 dissemination. Our findings highlight an increase in blaNDM-1 prevalence and the widespread transposon-facilitated dissemination of carbapenemase genes in diverse A. baumannii lineages in southwestern Nigeria. We make the case for improving surveillance of these pathogens in Nigeria and other understudied settings. IMPORTANCE Acinetobacter baumannii bacteria are increasingly clinically relevant due to their propensity to harbor genes conferring resistance to multiple antimicrobials, as well as their ability to persist and disseminate in hospital environments and cause difficult-to-treat nosocomial infections. Little is known about the molecular epidemiology and antimicrobial resistance profiles of these organisms in Nigeria, largely due to limited capacity for their isolation, identification, and antimicrobial susceptibility testing. Our study characterized the diversity and antimicrobial resistance profiles of clinical A. baumannii in southwestern Nigeria using whole-genome sequencing. We also identified the key genetic elements facilitating the dissemination of carbapenem resistance genes within this species. This study provides key insights into the clinical burden and population dynamics of A. baumannii in hospitals in Nigeria and highlights the importance of routine whole-genome sequencing-based surveillance of this and other previously understudied pathogens in Nigeria and other similar settings.
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Affiliation(s)
- Erkison Ewomazino Odih
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anderson O. Oaikhena
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Anthony Underwood
- Centre for Genomic pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Yaovi Mahuton Gildas Hounmanou
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Oyinlola O. Oduyebo
- Department of Medical Microbiology and Parasitology, Faculty of Basic Medical Sciences, College of Medicine, University of Lagos, Lagos, Nigeria
| | - Abayomi Fadeyi
- Department of Medical Microbiology and Parasitology, University of Ilorin, Ilorin, Kwara State, Nigeria
| | - Aaron O. Aboderin
- Department of Medical Microbiology and Parasitology, Obafemi Awolowo University Teaching Hospitals Complex, Ile-Ife, Nigeria
| | - Veronica O. Ogunleye
- Department of Medical Microbiology and Parasitology, University College Hospital, Ibadan, Oyo State, Nigeria
| | - Silvia Argimón
- Centre for Genomic pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
| | | | - Phillip O. Oshun
- Department of Medical Microbiology and Parasitology, Faculty of Basic Medical Sciences, College of Medicine, University of Lagos, Lagos, Nigeria
| | | | | | | | - David M. Aanensen
- Centre for Genomic pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Iruka N. Okeke
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
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12
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Hajikhani B, Sameni F, Ghazanfari K, Abdolali B, Yazdanparast A, Asarehzadegan Dezfuli A, Nasiri MJ, Goudarzi M, Dadashi M. Prevalence of blaNDM-producing Acinetobacter baumannii strains isolated from clinical samples around the world; a systematic review. GENE REPORTS 2023. [DOI: 10.1016/j.genrep.2022.101728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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13
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Gual-de-Torrella A, Delgado-Valverde M, Pérez-Palacios P, Oteo-Iglesias J, Rojo-Molinero E, Macià MD, Oliver A, Pascual Á, Fernández-Cuenca F. Prevalence of the fimbrial operon mrkABCD, mrkA expression, biofilm formation and effect of biocides on biofilm formation in carbapenemase-producing Klebsiella pneumoniae isolates belonging or not to high-risk clones. Int J Antimicrob Agents 2022; 60:106663. [PMID: 35995073 DOI: 10.1016/j.ijantimicag.2022.106663] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 11/03/2021] [Accepted: 08/11/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND The role of mrkA adhesin expression, biofilm production, biofilm viability and biocides in the biofilms of carbapenemase-producing K. pneumoniae isolates was investigated. METHODS Seventeen isolates representing different sequence types and carbapenemases were investigated. mrkA expression was determined by real-time RT-PCR. Biofilm production (25°C and 37°C, with and without humidity) was determined by the crystal violet assay. The effect of isopropanol, povidone-iodine, sodium hypochlorite, chlorhexidine digluconate, benzalkonium chloride, ethanol and triclosan on biofilms was determined. The effect of povidone-iodine on biofilm biomass and thickness was also determined by Confocal Laser Scanning Microscopy (CLSM). RESULTS mrkA expression ranged 28.2-1.3 (high or intermediate-level; 64% of HR clones) and 21.5-1.3 (50% of non-HR clones). At 25°C biofilm formation was observed in 41% of isolates (absence of humidity) and 35% of isolates (presence of humidity), whereas at 37°C it was observed in 76% of isolates, with and without humidity. At 25°C biofilm producers were more frequently observed in HR clones (45% with humidity and 55% without humidity) than non-HR clones (17% with and without humidity). Biofilm viability from day 21 was higher at 25°C than 37°C. The greatest decrease in biofilm formation was observed with povidone iodine (29% decrease), which also decrease biofilm thickness. CONCLUSIONS Biofilm formation in carbapenemase-producing K. pneumoniae is related to mrkA expression. Biofilm formation is affected by temperature (37°C>25°C) whereas humidity has little effect. Biofilm viability is affected by temperature (25°C>37°C). At 25°C, HR clones are more frequently biofilm producers than non-HR clones. Povidone-iodine can decrease biofilm production and biofilm thickness.
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Affiliation(s)
- Ana Gual-de-Torrella
- UGC Enfermedades Infecciosas, Microbiología Clínica y Medicina Preventiva. Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla; Instituto de Biomedicina de Sevilla IBIS, Hospital Universitario Virgen Macarena, CSIC, Universidad de Sevilla, Seville, Spain; Spanish Network for the Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Mercedes Delgado-Valverde
- UGC Enfermedades Infecciosas, Microbiología Clínica y Medicina Preventiva. Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla; Instituto de Biomedicina de Sevilla IBIS, Hospital Universitario Virgen Macarena, CSIC, Universidad de Sevilla, Seville, Spain; Spanish Network for the Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Patricia Pérez-Palacios
- UGC Enfermedades Infecciosas, Microbiología Clínica y Medicina Preventiva. Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla; Instituto de Biomedicina de Sevilla IBIS, Hospital Universitario Virgen Macarena, CSIC, Universidad de Sevilla, Seville, Spain; Spanish Network for the Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Jesús Oteo-Iglesias
- Spanish Network for the Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain; Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Estrella Rojo-Molinero
- Spanish Network for the Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain; Servicio de Microbiología, Hospital Son Espases, Instituto de Investigación Sanitaria de Palma (IdISPa), Palma de Mallorca, Spain
| | - María Dolores Macià
- Spanish Network for the Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain; Servicio de Microbiología, Hospital Son Espases, Instituto de Investigación Sanitaria de Palma (IdISPa), Palma de Mallorca, Spain
| | - Antonio Oliver
- Spanish Network for the Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain; Servicio de Microbiología, Hospital Son Espases, Instituto de Investigación Sanitaria de Palma (IdISPa), Palma de Mallorca, Spain
| | - Álvaro Pascual
- UGC Enfermedades Infecciosas, Microbiología Clínica y Medicina Preventiva. Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla; Instituto de Biomedicina de Sevilla IBIS, Hospital Universitario Virgen Macarena, CSIC, Universidad de Sevilla, Seville, Spain; Spanish Network for the Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain; Departamento de Microbiología, Universidad de Sevilla, Sevilla, Spain
| | - Felipe Fernández-Cuenca
- UGC Enfermedades Infecciosas, Microbiología Clínica y Medicina Preventiva. Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla; Spanish Network for the Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain.
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Genomic Analysis of a Strain Collection Containing Multidrug-, Extensively Drug-, Pandrug-, and Carbapenem-Resistant Modern Clinical Isolates of Acinetobacter baumannii. Antimicrob Agents Chemother 2022; 66:e0089222. [PMID: 35969073 PMCID: PMC9487538 DOI: 10.1128/aac.00892-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this study, we characterize a new collection that comprises multidrug-resistant (MDR), extensively drug-resistant (XDR), pandrug-resistant (PDR), and carbapenem-resistant modern clinical isolates of Acinetobacter baumannii collected from hospitals through national microbiological surveillance in Belgium. Bacterial isolates (n = 43) were subjected to whole-genome sequencing (WGS), combining Illumina (MiSeq) and Nanopore (MinION) technologies, from which high-quality genomes (chromosome and plasmids) were de novo assembled. Antimicrobial susceptibility testing was performed along with genome analyses, which identified intrinsic and acquired resistance determinants along with their genetic environments and vehicles. Furthermore, the bacterial isolates were compared to the most prevalent A. baumannii sequence type 2 (ST2) (Pasteur scheme) genomes available from the BIGSdb database. Of the 43 strains, 40 carried determinants of resistance to carbapenems; blaOXA-23 (n = 29) was the most abundant acquired antimicrobial resistance gene, with 39 isolates encoding at least two different types of OXA enzymes. According to the Pasteur scheme, the majority of the isolates were globally disseminated clones of ST2 (n = 25), while less frequent sequence types included ST636 (n = 6), ST1 (n = 4), ST85 and ST78 (n = 2 each), and ST604, ST215, ST158, and ST10 (n = 1 each). Using the Oxford typing scheme, we identified 22 STs, including two novel types (ST2454 and ST2455). While the majority (26/29) of blaOXA-23 genes were chromosomally carried, all blaOXA-72 genes were plasmid borne. Our results show the presence of high-risk clones of A. baumannii within Belgian health care facilities with frequent occurrences of genes encoding carbapenemases, highlighting the crucial need for constant surveillance.
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15
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Gual-de-Torrella A, Delgado-Valverde M, Pérez-Palacios P, Oteo-Iglesias J, Pascual Á, Fernández-Cuenca F. In vitro activity of six biocides against carbapenemase-producing Klebsiella pneumoniae and presence of genes encoding efflux pumps. ENFERMEDADES INFECCIOSAS Y MICROBIOLOGIA CLINICA (ENGLISH ED.) 2022; 40:371-376. [PMID: 35906031 DOI: 10.1016/j.eimce.2021.05.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/07/2021] [Indexed: 06/15/2023]
Abstract
INTRODUCTION Acquisition of reduced susceptibility to biocides may contribute to the dissemination of high-risk (HR) clones of carbapenemase-producing Klebsiella pneumoniae (CP-Kp). The aim of this study was (a) to determinate the activity of biocides against CP-Kp, and (b) to analyse the relationship between biocide activity and the presence of efflux pumps. METHODS The minimal inhibitory concentrations (MICs) of 6 biocides (sodium hypochlorite, chlorhexidine digluconate, benzalkonium chloride, povidone-iodine, ethanol and triclosan) were determined in triplicate at 25°C and 37°C in Mueller-Hinton broth (MHB) and M9 minimum medium, against 17 CP-Kp isolates representing different clones (HR and no-HR), sequence-types (STs) and carbapenemases. Efflux pumps genes were detected by whole genome sequencing (MiSeq). RESULTS Median MICs were slightly higher at 37°C than at 25°C (p≤0.05), except for benzalkonium chloride, triclosan and ethanol. MIC medians were much higher in MHB than in M9, except for triclosan. No significant differences were observed in the median MICs, regarding the type of clone, ST or carbapenemase; cepA, acrAB, kpnEF and oqxAB genes were detected in all isolates, whereas qacE and qacA were not detected; smvAR, and qacΔE genes were detected in 94% and 47% of isolates, respectively. CONCLUSIONS Triclosan, chlorhexidine digluconate, benzalkonium chloride and ethanol were the most active biocides. The activity of some biocides is affected by temperature and growth media, suggesting that standardised procedures for biocide susceptibility testing based on MIC determination are required. This activity, in terms of MICs, are not related to the type of clone, ST, carbapenemase or the presence of the efflux pump genes.
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Affiliation(s)
- Ana Gual-de-Torrella
- UGC Enfermedades Infecciosas, Microbiología Clínica, Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, Sevilla, Spain; Spanish Network for the Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Mercedes Delgado-Valverde
- UGC Enfermedades Infecciosas, Microbiología Clínica, Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, Sevilla, Spain; Spanish Network for the Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Patricia Pérez-Palacios
- UGC Enfermedades Infecciosas, Microbiología Clínica, Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, Sevilla, Spain; Spanish Network for the Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Jesús Oteo-Iglesias
- Spanish Network for the Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain; Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Álvaro Pascual
- UGC Enfermedades Infecciosas, Microbiología Clínica, Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, Sevilla, Spain; Spanish Network for the Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain; Departamento de Microbiología, Universidad de Sevilla, Sevilla, Spain
| | - Felipe Fernández-Cuenca
- UGC Enfermedades Infecciosas, Microbiología Clínica, Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, Sevilla, Spain; Spanish Network for the Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain.
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16
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Odih EE, Irek EO, Obadare TO, Oaikhena AO, Afolayan AO, Underwood A, Adenekan AT, Ogunleye VO, Argimon S, Dalsgaard A, Aanensen DM, Okeke IN, Aboderin AO. Rectal Colonization and Nosocomial Transmission of Carbapenem-Resistant Acinetobacter baumannii in an Intensive Care Unit, Southwest Nigeria. Front Med (Lausanne) 2022; 9:846051. [PMID: 35321470 PMCID: PMC8936076 DOI: 10.3389/fmed.2022.846051] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 02/14/2022] [Indexed: 11/13/2022] Open
Abstract
Background Acinetobacter baumannii are of major human health importance because they cause life-threatening nosocomial infections and often are highly resistant to antimicrobials. Specific multidrug-resistant A. baumannii lineages are implicated in hospital outbreaks globally. We retrospectively investigated a suspected outbreak of carbapenem-resistant A. baumannii (CRAB) colonizing patients in an intensive care unit (ICU) of a tertiary hospital in Southwest Nigeria where genomic surveillance of Acinetobacter has hitherto not been conducted. Methods A prospective observational study was conducted among all patients admitted to the ICU between August 2017 and June 2018. Acinetobacter species were isolated from rectal swabs and verified phenotypically with the Biomerieux Vitek 2 system. Whole genome sequencing (WGS) was performed on the Illumina platform to characterize isolates from a suspected outbreak during the study period. Phylogenetic analysis, multilocus sequence typing, and antimicrobial resistance gene prediction were carried out in silico. Results Acinetobacter isolates belonging to the A. baumannii complex were recovered from 20 (18.5%) ICU patients. Single nucleotide polymorphism (SNP) analysis and epidemiological information revealed a putative outbreak clone comprising seven CRAB strains belonging to the globally disseminated international clone (IC) 2. These isolates had ≤2 SNP differences, identical antimicrobial resistance and virulence genes, and were all ST1114/1841. Conclusion We report a carbapenem-resistant IC2 A. baumannii clone causing an outbreak in an ICU in Nigeria. The study findings underscore the need to strengthen the capacity to detect A. baumannii in human clinical samples in Nigeria and assess which interventions can effectively mitigate CRAB transmission in Nigerian hospital settings.
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Affiliation(s)
- Erkison Ewomazino Odih
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, University of Ibadan, Oyo, Nigeria
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- *Correspondence: Erkison Ewomazino Odih,
| | - Emmanuel Oladayo Irek
- Department of Medical Microbiology and Parasitology, Obafemi Awolowo University Teaching Hospitals Complex, Ife, Nigeria
| | - Temitope O. Obadare
- Department of Medical Microbiology and Parasitology, Obafemi Awolowo University Teaching Hospitals Complex, Ife, Nigeria
| | - Anderson O. Oaikhena
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, University of Ibadan, Oyo, Nigeria
| | - Ayorinde O. Afolayan
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, University of Ibadan, Oyo, Nigeria
| | - Anthony Underwood
- Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, Cambridge, United Kingdom
- Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Anthony T. Adenekan
- Department of Anaesthesia and Intensive Care, Obafemi Awolowo University, Ife, Nigeria
| | | | - Silvia Argimon
- Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, Cambridge, United Kingdom
- Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - David M. Aanensen
- Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, Cambridge, United Kingdom
- Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Iruka N. Okeke
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, University of Ibadan, Oyo, Nigeria
| | - A. Oladipo Aboderin
- Department of Medical Microbiology and Parasitology, Obafemi Awolowo University, Ife, Nigeria
- A. Oladipo Aboderin,
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Liu N, Zheng X, Zhu Q, He Z, Hu S. The Dissemination of NDM-1 in Acinetobacter baumannii Strains. Curr Microbiol 2022; 79:117. [PMID: 35218435 DOI: 10.1007/s00284-022-02812-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 02/14/2022] [Indexed: 11/03/2022]
Abstract
Acinetobacter baumannii is a common pathogen in hospitals and usually causes bacteremia, pneumonia, meningitis, peritonitis and other diseases. Isolates carried NDM-1 gene can make several antibiotics such as carbapenems and other beta-lactams ineffective. Nowadays, the number of A. baumannii strains carrying NDM-1 has been climbing year by year in recent years. To characterise the transmission of NDM-1 in A. baumannii, we collected 2576 human-derived genomes of A. baumannii strains from NCBI database and found that 186 strains contained NDM-1 gene. The multi-locus sequence typing, phylogenetic tree, NDM-1 gene organization and the single nucleotide polymorphisms of NDM-1 were investigated. We hope that our work will provide a theoretical basis for the prevention of dissemination of NDM-1 in A. baumannii.
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Affiliation(s)
- Na Liu
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Interdisciplinary Innovation Institute of Medicine and Engineering, Beihang University, Beijing, 100191, People's Republic of China.,School of Engineering Medicine, Beihang University, 37 Xueyuan Road, Haidian District, Beijing, 100191, People's Republic of China
| | - Xin Zheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qianhui Zhu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zilong He
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Interdisciplinary Innovation Institute of Medicine and Engineering, Beihang University, Beijing, 100191, People's Republic of China. .,School of Engineering Medicine, Beihang University, 37 Xueyuan Road, Haidian District, Beijing, 100191, People's Republic of China.
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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Variants of Tn 6924, a Novel Tn 7 Family Transposon Carrying the blaNDM Metallo-β-Lactamase and 14 Copies of the aphA6 Amikacin Resistance Genes Found in Acinetobacter baumannii. Microbiol Spectr 2022; 10:e0174521. [PMID: 35019774 PMCID: PMC8754128 DOI: 10.1128/spectrum.01745-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Carbapenem resistance in Acinetobacter baumannii is primarily due to the global spread of two main clones that carry oxa23, oxa24, and oxa58. However, new carbapenem-resistant clones are emerging that are also resistant to a wide range of antibiotics. Strains belonging to ST85IP (Institut Pasteur) carry the blaNDM metallo-β-lactamase carbapenem resistance gene. Here, we completed the genome sequence of an ST85IP strain, Cl300, recovered in 2015 in Lebanon, using a combination of Illumina MiSeq and Oxford Nanopore sequencing and a hybrid assembly approach. Cl300 is highly resistant to meropenem and amikacin, and consistent with this, a copy of the blaNDM carbapenem and 14 copies of the aphA6 amikacin resistance genes were found in the genome. Cl300 also contains the sul2 sulfonamide and the msr(E) macrolide resistance genes. All aphA6 copies and blaNDM are in a novel 76-kb Tn7 family transposon designated Tn6924. Like Tn7, Tn6924 is bounded by 29-bp inverted repeats with additional TnsB binding sites at each end. Several variants of Tn6924 were found in a set of diverse strains, including ST85IP strains as well as members of global clones 1 and 2. sul2 and msr(E) are in a 13.0-kb pseudocompound transposon (PCT) bounded by IS1008. ST85s represent a diverse group of strains, particularly in their antibiotic resistance gene content and the K and OC surface polysaccharide loci. Acquisition of Tn6924 by members of global clones indicates the significance of this transposon in spreading two clinically significant resistance genes, blaNDM and aphA6. IMPORTANCE To date, efforts to study the resistance mechanisms of carbapenem-resistant Acinetobacter baumannii have been largely focused on the two major globally distributed clones (GC1 and GC2). ST85 is an emerging sequence type, and unlike other clones, it is associated with the carriage of the blaNDM gene. Here, we completed the genome sequence of an ST85 strain and showed that blaNDM and 14 copies of the aphA6 amikacin resistance genes are in Tn6924, a novel Tn7 family transposon. Analysis of all publicly available ST85s predicted that all strains in the main lineage carry a variant of Tn6924. Variants of Tn6924 were also found in other clones, including GC1 and GC2. Tn6924 is an important mobile element given that it carries two clinically important resistance genes (blaNDM and aphA6) and has spread to other clones. Therefore, outbreaks caused by ST85s should be studied and tracked.
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López-Hernández I, Delgado-Valverde M, Fernández-Cuenca F, López-Cerero L, Machuca J, Pascual Á. Carbapenemase-Producing Gram-Negative Bacteria in Andalusia, Spain, 2014-2018. Emerg Infect Dis 2021; 26:2218-2222. [PMID: 32818413 PMCID: PMC7454067 DOI: 10.3201/eid2609.191772] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The emergence and spread of carbapenemase-producing gram-negative bacteria is a major public health concern. We used data collected from microbiology laboratories as part of the PIRASOA program during 2014-2018 to study the epidemiology of carbapenemase-producing bacteria in Andalusia, Spain. Our findings highlight the importance of ongoing surveillance and epidemiologic studies for these bacteria.
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Gual-de-Torrella A, Delgado-Valverde M, Pérez-Palacios P, Oteo-Iglesias J, Pascual Á, Fernández-Cuenca F. In vitro activity of six biocides against carbapenemase-producing Klebsiella pneumoniae and presence of genes encoding efflux pumps. Enferm Infecc Microbiol Clin 2021; 40:S0213-005X(21)00187-7. [PMID: 34130887 DOI: 10.1016/j.eimc.2021.05.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/04/2021] [Accepted: 05/07/2021] [Indexed: 11/24/2022]
Abstract
INTRODUCTION Acquisition of reduced susceptibility to biocides may contribute to the dissemination of high-risk (HR) clones of carbapenemase-producing Klebsiella pneumoniae (CP-Kp). The aim of this study was (a) to determinate the activity of biocides against CP-Kp, and (b) to analyse the relationship between biocide activity and the presence of efflux pumps. METHODS The minimal inhibitory concentrations (MICs) of 6 biocides (sodium hypochlorite, chlorhexidine digluconate, benzalkonium chloride, povidone-iodine, ethanol and triclosan) were determined in triplicate at 25°C and 37°C in Mueller-Hinton broth (MHB) and M9 minimum medium, against 17 CP-Kp isolates representing different clones (HR and no-HR), sequence-types (STs) and carbapenemases. Efflux pumps genes were detected by whole genome sequencing (MiSeq). RESULTS Median MICs were slightly higher at 37°C than at 25°C (p≤0.05), except for benzalkonium chloride, triclosan and ethanol. MIC medians were much higher in MHB than in M9, except for triclosan. No significant differences were observed in the median MICs, regarding the type of clone, ST or carbapenemase; cepA, acrAB, kpnEF and oqxAB genes were detected in all isolates, whereas qacE and qacA were not detected; smvAR, and qacΔE genes were detected in 94%and 47% of isolates, respectively. CONCLUSIONS Triclosan, chlorhexidine digluconate, benzalkonium chloride and ethanol were the most active biocides. The activity of some biocides is affected by temperature and growth media, suggesting that standardised procedures for biocide susceptibility testing based on MIC determination are required. This activity, in terms of MICs, are not related to the type of clone, ST, carbapenemase or the presence of the efflux pump genes.
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Affiliation(s)
- Ana Gual-de-Torrella
- UGC Enfermedades Infecciosas, Microbiología Clínica, Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, Sevilla, Spain; Spanish Network for the Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Mercedes Delgado-Valverde
- UGC Enfermedades Infecciosas, Microbiología Clínica, Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, Sevilla, Spain; Spanish Network for the Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Patricia Pérez-Palacios
- UGC Enfermedades Infecciosas, Microbiología Clínica, Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, Sevilla, Spain; Spanish Network for the Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Jesús Oteo-Iglesias
- Spanish Network for the Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain; Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Álvaro Pascual
- UGC Enfermedades Infecciosas, Microbiología Clínica, Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, Sevilla, Spain; Spanish Network for the Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain; Departamento de Microbiología, Universidad de Sevilla, Sevilla, Spain
| | - Felipe Fernández-Cuenca
- UGC Enfermedades Infecciosas, Microbiología Clínica, Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, Sevilla, Spain; Spanish Network for the Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain.
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21
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Xanthopoulou K, Urrutikoetxea-Gutiérrez M, Vidal-Garcia M, Diaz de Tuesta Del Arco JL, Sánchez-Urtaza S, Wille J, Seifert H, Higgins PG, Gallego L. First Report of New Delhi Metallo- β-Lactamase-6 (NDM-6) in a Clinical Acinetobacter baumannii Isolate From Northern Spain. Front Microbiol 2020; 11:589253. [PMID: 33240245 PMCID: PMC7683408 DOI: 10.3389/fmicb.2020.589253] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/15/2020] [Indexed: 12/29/2022] Open
Abstract
The objective of this study was the phenotypic and genotypic characterization of a carbapenem resistant Acinetobacter baumannii (CRAB) isolate. The isolate, recovered in Northern Spain in 2019, was identified by MALDI-TOF to the species level. Antimicrobial susceptibility testing was performed using the Phoenix BD NMIC-502 Panel, E-test, and broth microdilution methods. The presence of a metallo-β-lactamase (MBL) was verified by PCR and immunochromatographic assays. The genetic location of the MBL was confirmed using S1-pulsed-field gel electrophoresis (S1-PFGE) followed by Southern blot hybridization. Whole genome sequencing (WGS) was completed using the Miseq and MinION platforms, followed by core-genome MLST (cgMLST) and seven-locus MLST analysis. The CRAB was assigned ST85 (Pasteur scheme) and ST957 (Oxford scheme) representing international clone (IC) 9 and harbored the intrinsic β-lactamase OXA-94 with ISAba1 upstream of it, and the MBL bla NDM-6. Hybridization experiments revealed that the bla NDM-6 was encoded on the chromosome. Using WGS the bla NDM-6 environment could be identified arranged in the following order: ISAba14, aphA6, ISAba125, bla NDM-6, ble MBL, trpF, dsbC, cutA, and ISAba14. Downstream, a 10,462 bp duplication was identified, including a second copy of bla NDM-6 in the following genetic composition: ISAba125, bla NDM-6, ble MBL, trpF, dsbC, cutA, and ISAba14. To our knowledge, this is the first description of bla NDM-6 in A. baumannii. The MBL was present in two copies in the chromosome in a new genetic environment associated with IS elements highlighting the contribution of mobile genetic elements in the dissemination of this gene.
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Affiliation(s)
- Kyriaki Xanthopoulou
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany.,German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Mikel Urrutikoetxea-Gutiérrez
- Servicio de Microbiología y Control de Infección, Hospital Universitario Basurto, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Matxalen Vidal-Garcia
- Servicio de Microbiología y Control de Infección, Hospital Universitario Basurto, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - José-Luis Diaz de Tuesta Del Arco
- Servicio de Microbiología y Control de Infección, Hospital Universitario Basurto, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Sandra Sánchez-Urtaza
- Department of Immunology, Microbiology, and Parasitology, Faculty of Medicine and Nursing, University of the Basque Country UPV/EHU, Bilbao, Spain
| | - Julia Wille
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany.,German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Harald Seifert
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany.,German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Paul G Higgins
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany.,German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Lucía Gallego
- Department of Immunology, Microbiology, and Parasitology, Faculty of Medicine and Nursing, University of the Basque Country UPV/EHU, Bilbao, Spain
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