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Lupo A, Valot B, Saras E, Drapeau A, Robert M, Bour M, Haenni M, Plésiat P, Madec JY, Potron A. Multiple host colonization and differential expansion of multidrug-resistant ST25-Acinetobacter baumannii clades. Sci Rep 2023; 13:21854. [PMID: 38071225 PMCID: PMC10710421 DOI: 10.1038/s41598-023-49268-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 12/06/2023] [Indexed: 12/18/2023] Open
Abstract
The Acinetobacter baumannii clonal lineage ST25 has been identified in humans and animals and found associated with outbreaks globally. To highlight possible similarities among ST25 A. baumannii of animal and human origins and to gather clues on the dissemination and evolution of the ST25 lineage, we conducted a phylogenetic analysis on n = 106 human and n = 35 animal A. baumannii ST25 genomes, including 44 sequenced for this study. Resistance genes and their genetic background were analyzed, as well. ST25 genomes are clustered into four clades: two are widespread in South America, while the other two are largely distributed in Europe, Asia and America. One particular clade was found to include the most recent strains and the highest number of acquired antibiotic resistance genes. OXA-23-type carbapenemase was the most common. Other resistance genes such as blaNDM-1, blaPER-7, and armA were found embedded in complex chromosomal regions present in human isolates. Genomic similarity among multidrug resistant ST25 isolates of either animal or human origin was revealed, suggesting cross-contaminations between the two sectors. Tracking the clonal complex ST25 between humans and animals should provide new insights into the mode of dissemination of these bacteria, and should help defining strategies for preserving global health.
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Affiliation(s)
- Agnese Lupo
- Unité Antibiorésistance et Virulence Bactériennes, ANSES - Université de Lyon 1, 31 Avenue Tony Garnier, 69007, Lyon, France.
| | - Benoît Valot
- UMR 6249 Chrono-Environnement, CNRS-Université de Bourgogne/Franche-Comté, Besançon, France
| | - Estelle Saras
- Unité Antibiorésistance et Virulence Bactériennes, ANSES - Université de Lyon 1, 31 Avenue Tony Garnier, 69007, Lyon, France
| | - Antoine Drapeau
- Unité Antibiorésistance et Virulence Bactériennes, ANSES - Université de Lyon 1, 31 Avenue Tony Garnier, 69007, Lyon, France
| | - Marine Robert
- Unité Antibiorésistance et Virulence Bactériennes, ANSES - Université de Lyon 1, 31 Avenue Tony Garnier, 69007, Lyon, France
| | - Maxime Bour
- CNR de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire de Besançon, Besançon, France
| | - Marisa Haenni
- Unité Antibiorésistance et Virulence Bactériennes, ANSES - Université de Lyon 1, 31 Avenue Tony Garnier, 69007, Lyon, France
| | - Patrick Plésiat
- UMR 6249 Chrono-Environnement, CNRS-Université de Bourgogne/Franche-Comté, Besançon, France
| | - Jean-Yves Madec
- Unité Antibiorésistance et Virulence Bactériennes, ANSES - Université de Lyon 1, 31 Avenue Tony Garnier, 69007, Lyon, France
| | - Anaïs Potron
- UMR 6249 Chrono-Environnement, CNRS-Université de Bourgogne/Franche-Comté, Besançon, France
- CNR de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire de Besançon, Besançon, France
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Itani R, Khojah HMJ, Karout S, Rahme D, Hammoud L, Awad R, Abu-Farha R, Mukattash TL, Raychouni H, El-Lakany A. Acinetobacter baumannii: assessing susceptibility patterns, management practices, and mortality predictors in a tertiary teaching hospital in Lebanon. Antimicrob Resist Infect Control 2023; 12:136. [PMID: 38031181 PMCID: PMC10685635 DOI: 10.1186/s13756-023-01343-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 11/22/2023] [Indexed: 12/01/2023] Open
Abstract
BACKGROUND Acinetobacter baumannii is a major nosocomial pathogen capable of causing life-threatening infections. This bacterium is highly resistant to antibiotics and associated with high mortality rates. Therefore, this study aimed to evaluate A. baumannii's susceptibility patterns to antimicrobials, assess the appropriateness of the initiated antimicrobial therapy, determine the mortality rate, and identify predictors associated with mortality. METHODS A retrospective observational study was conducted among patients infected with A. baumannii at a university hospital in Lebanon through the revision of medical records. Kaplan-Meier survival analysis and log-rank tests were used to analyze time-to-mortality. Binary logistic regression was performed to identify predictors of mortality. RESULTS The records of 188 patients were screened, and 111 patients with A. baumannii infection were enrolled. Almost all isolates were resistant to carbapenem, and 43% of the isolates were extensively-drug resistant. Almost half of the patients received initial inappropriate antimicrobial therapy (n = 50, 45.1%). The 30-day mortality rate associated with A. baumannii infection was 71.2% (79/111). The time to mortality in patients who received inappropriate antimicrobial therapy (5.70 ± 1.07 days) was significantly shorter than in those who received appropriate antimicrobial therapy (12.43 ± 1.01 days, P < 0.01). Binary logistic regression revealed that inappropriate antimicrobial therapy (adjusted odds ratio [AOR] = 16.22, 95% CI 2.68-9.97, P = 0.002), mechanical ventilation (AOR = 14.72, 95% CI 3.27-6.61, P < 0.001), and thrombocytopenia (AOR = 8.82, 95% CI 1.12-9.75, P = 0.003) were more likely associated with mortality. CONCLUSIONS A. baumannii exhibits an alarming mortality rate among infected patients. Thrombocytopenia, mechanical ventilation, and inappropriate antibiotic administration are associated with mortality in patients infected with A. baumannii. The prompt initiation of appropriate antimicrobial therapy, infection control measures, and effective stewardship program are crucial to reduce the incidence of A. baumannii and improve the treatment outcomes.
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Affiliation(s)
- Rania Itani
- Pharmacy Practice Department, Faculty of Pharmacy, Beirut Arab University, Riad El Solh, 1107 2809, P.O. Box: 11-5020, Beirut, Lebanon
| | - Hani M J Khojah
- Department of Pharmacy Practice, College of Pharmacy, Taibah University, P.O. Box: 30051, 41477, Madinah, Kingdom of Saudi Arabia
| | - Samar Karout
- Pharmacy Practice Department, Faculty of Pharmacy, Beirut Arab University, Riad El Solh, 1107 2809, P.O. Box: 11-5020, Beirut, Lebanon.
| | - Deema Rahme
- Pharmacy Practice Department, Faculty of Pharmacy, Beirut Arab University, Riad El Solh, 1107 2809, P.O. Box: 11-5020, Beirut, Lebanon
- INSPECT-LB (Institut National de Santé Publique, d'Épidémiologie Clinique et de Toxicologie-Liban), Beirut, Lebanon
| | - Lara Hammoud
- Pharmacy Department, Hammoud Hospital University Medical Center, Sidon, Lebanon
| | - Reem Awad
- Pharmacy Practice Department, Faculty of Pharmacy, Beirut Arab University, Riad El Solh, 1107 2809, P.O. Box: 11-5020, Beirut, Lebanon
| | - Rana Abu-Farha
- Department of Clinical Pharmacy and Therapeutics, Faculty of Pharmacy, Applied Science Private University, P.O. Box: 11931, Amman, Jordan
| | - Tareq L Mukattash
- Department of Clinical Pharmacy, Faculty of Pharmacy, Jordan University of Science and Technology, P.O. Box: 3030, Irbid, 22110, Jordan
| | - Hamza Raychouni
- Intensive Care Unit, Central Military Hospital, Military Healthcare, Lebanese Army, Beirut, Lebanon
- Intensive Care Unit, American University of Beirut Medical Center, Beirut, Lebanon
| | - Abdalla El-Lakany
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Beirut Arab University, Riad El Solh, 1107 2809, P.O. Box: 11-5020, Beirut, Lebanon
- Department of Pharmacognosy, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
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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: 0] [Impact Index Per Article: 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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Yin L, Wu N, Yan G, Lu L, Qian H, Yang W, Ma J, He L, Lu G, Zhai X, Wang C. Carbapenem-resistant gram-negative bacterial prevention practice in nosocomial infection and molecular epidemiological characteristics in a pediatric intensive care unit. Heliyon 2023; 9:e18969. [PMID: 37636465 PMCID: PMC10448463 DOI: 10.1016/j.heliyon.2023.e18969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 08/03/2023] [Accepted: 08/03/2023] [Indexed: 08/29/2023] Open
Abstract
Introduction The increasing prevalence of carbapenem-resistant gram-negative bacilli infection has emerged as a substantial threat to human health. Methodology In January 2017, a screening program for carbapenem-resistant gram-negative bacilli colonization was performed in a pediatric intensive care unit (PICU). Subsequently, different strategies for carbapenem-resistant gram-negative bacilli cohorting and patient placements were introduced in January 2018. Results The increase in the single room isolation (type A) and the resettlement of the same area placement (type B) resulted in a significant decrease in the nosocomial infection rate from 2.57% (50/1945) in 2017 to 0.87% (15/1720) in 2021 (P < 0.001). Notably, the incidence of nosocomial carbapenem-resistant gram-negative bacilli infections decreased in 2019 (P = 0.046) and 2020 (P = 0.041) compared with that in the respective previous year. During 2019 and 2020, a statistically significant increasing trend of type A and type B placements was observed (P < 0.05, each), which may have contributed to the decline of carbapenem-resistant gram-negative bacilli infection. The primary carbapenemase genes identified in carbapenem-resistant isolates of Klebsiella pneumoniae and Acinetobacter baumannii were blaKPC-2 from sequence type 11 and blaOXA-23 from sequence type 1712. Conclusion The integration of various placements for patients with carbapenem-resistant gram-negative bacilli infection with active screening has been demonstrated as an effective preventive strategy in the management of carbapenem-resistant gram-negative bacilli infection.
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Affiliation(s)
- Lijun Yin
- Department of Nosocomial Infection Control, Children's Hospital of Fudan University, Shanghai, China
| | - Nana Wu
- Department of Nosocomial Infection Control, Children's Hospital of Fudan University, Shanghai, China
| | - Gangfeng Yan
- Department of Pediatric Intensive Care Unit, Children's Hospital of Fudan University, Shanghai, China
| | - Lu Lu
- Department of Nosocomial Infection Control, Children's Hospital of Fudan University, Shanghai, China
| | - Huimin Qian
- Department of Nosocomial Infection Control, Children's Hospital of Fudan University, Shanghai, China
| | - Weijing Yang
- Department of Nosocomial Infection Control, Children's Hospital of Fudan University, Shanghai, China
| | - Jian Ma
- Department of Nosocomial Infection Control, Children's Hospital of Fudan University, Shanghai, China
| | - Leiyan He
- The Clinical Microbiology Laboratory, Children's Hospital of Fudan University, China
| | - Guoping Lu
- Department of Pediatric Intensive Care Unit, Children's Hospital of Fudan University, Shanghai, China
| | - Xiaowen Zhai
- Department of Hematology, Children's Hospital of Fudan University, Shanghai, China
| | - Chuanqing Wang
- Department of Nosocomial Infection Control and the Clinical Microbiology Laboratory, Children's Hospital of Fudan University, Shanghai, China
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Zhang S, Mi P, Wang J, Li P, Luo K, Liu S, Al-Shamiri MM, Lei J, Lai S, Han B, Chen Y, Han L, Han S. The optimized carbapenem inactivation method for objective and accurate detection of carbapenemase-producing Acinetobacter baumannii. Front Microbiol 2023; 14:1185450. [PMID: 37520356 PMCID: PMC10372451 DOI: 10.3389/fmicb.2023.1185450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 06/27/2023] [Indexed: 08/01/2023] Open
Abstract
The modified carbapenem inactivation method (mCIM) recommended by the Clinical and Laboratory Standards Institute is not applicable for detecting carbapenemases in Acinetobacter baumannii. Four currently reported phenotypic detection methods, namely, the modified Hodge test, the mCIM, the adjusted mCIM, and the simplified carbapenem inactivation method (sCIM), did not perform well in our 90 clinical A. baumannii isolates. Thus, the minimal inhibitory concentrations (MICs) of carbapenems and the existence and expression of carbapenemase-encoding genes were detected to explain the results. According to the E-test, which was more accurate than the VITEK 2 system, 80.0 and 41.1% were resistant to imipenem (IPM) and meropenem (MEM), respectively, and 14.4 and 53.3% exhibited intermediate resistance, respectively. Five β-lactamase genes were found, of which blaOXA-51-like, blaTEM, and blaOXA-23-like were detected more frequently in 85 non-susceptible strains. The expression of blaOXA-23-like was positively correlated with the MIC values of IPM and MEM. Therefore, an improved approach based on the mCIM, designated the optimized CIM (oCIM), was developed in this study to detect carbapenemases more accurately and reproducibly. The condition was improved by evaluating the factors of A. baumannii inoculum, incubation broth volume, and MEM disk incubation time. Obvious high sensitivity (92.94%) and specificity (100.00%) were obtained using the oCIM, which was cost-effective and reproducible in routine laboratory work.
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Affiliation(s)
- Sirui Zhang
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University Health Science Center, Xi’an, China
| | - Peng Mi
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University Health Science Center, Xi’an, China
- Department of Laboratory Medicine, Shaanxi Provincial People’s Hospital, Xi’an, China
| | - Jingdan Wang
- School of Public Health, Xi’an Jiaotong University Health Science Center, Xi’an, China
| | - Pu Li
- School of Public Health, Xi’an Jiaotong University Health Science Center, Xi’an, China
| | - Kai Luo
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University Health Science Center, Xi’an, China
| | - Shuyan Liu
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University Health Science Center, Xi’an, China
| | - Mona Mohamed Al-Shamiri
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University Health Science Center, Xi’an, China
| | - Jin’e Lei
- Department of Laboratory Medicine, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Simin Lai
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University Health Science Center, Xi’an, China
| | - Bei Han
- School of Public Health, Xi’an Jiaotong University Health Science Center, Xi’an, China
| | - Yanjiong Chen
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University Health Science Center, Xi’an, China
| | - Lei Han
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University Health Science Center, Xi’an, China
| | - Shaoshan Han
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi'an, China
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Mateo-Estrada V, Tyrrell C, Evans BA, Aguilar-Vera A, Drissner D, Castillo-Ramirez S, Walsh F. Acinetobacter baumannii from grass: novel but non-resistant clones. Microb Genom 2023; 9:mgen001054. [PMID: 37439781 PMCID: PMC10438806 DOI: 10.1099/mgen.0.001054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 05/26/2023] [Indexed: 07/14/2023] Open
Abstract
Acinetobacter baumannii is one the most worrisome nosocomial pathogens, which has long been considered almost mainly as a hospital-associated bacterium. There have been some studies about animal and environmental isolates over the last decade. However, little effort has been made to determine if this pathogen dwells in the grass. Here, we aim to determine the evolutionary relationships and antibiotic resistance of clones of A. baumannii sampled from grass to the major human international clones and animal clones. Two hundred and forty genomes were considered in total from four different sources for this study. Our core and accessory genomic epidemiology analyses showed that grass isolates cluster in seven groups well differentiated from one another and from the major human and animal isolates. Furthermore, we found new sequence types under both multilocus sequence typing schemes: two under the Pasteur scheme and seven for the Oxford scheme. The grass isolates contained fewer antibiotic-resistance genes and were not resistant to the antibiotics tested. Our results demonstrate that these novel clones appear to have limited antibiotic resistance potential. Given our findings, we propose that genomic epidemiology and surveillance of A. baumannii should go beyond the hospital settings and consider the environment in an explicit One Health approach.
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Affiliation(s)
- Valeria Mateo-Estrada
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Ciara Tyrrell
- Department of Biology, The Kathleen Lonsdale Human Health Institute, Maynooth University, Maynooth, Co. Kildare, Ireland
| | | | - Alejandro Aguilar-Vera
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - David Drissner
- Department of Life Sciences, Albstadt-Sigmaringen University, 72488 Sigmaringen, Germany
| | - Santiago Castillo-Ramirez
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Fiona Walsh
- Department of Biology, The Kathleen Lonsdale Human Health Institute, Maynooth University, Maynooth, Co. Kildare, Ireland
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Adler A, Ghosh H, Gross A, Rechavi A, Lasnoy M, Assous MV, Geffen Y, Darawsha B, Wiener-Well Y, Alony A, Grundmann H, Reuter S. Clinical and molecular features of NDM-producing Acinetobacter baumannii in a multicenter study in Israel. Ann Clin Microbiol Antimicrob 2023; 22:52. [PMID: 37391819 DOI: 10.1186/s12941-023-00607-w] [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: 03/10/2023] [Accepted: 06/26/2023] [Indexed: 07/02/2023] Open
Abstract
BACKGROUND NDM-producing Acinetobacter baumannii (NDMAb) were reported sporadically worldwide but little is known about the transmission, epidemiology and clinical features of NDMAb-infected patients. The goals of this study were to characterize (1) the epidemiology and clinical features of NDMAb-infected patients; (2) the microbiological and molecular features of NDMAb isolates and (3) the transmission networks of NDMAb within healthcare facilities. METHODS The study was conducted at the Tel-Aviv Sourasky, Rambam and Sha'are-Zedek Medical centers (TASMC, RMC and SZMC, respectively) in Israel. All cases detected between January 2018 and July 2019 were included. Phylogenetic analysis was based on core genome SNP distances. Clonal transmission was defined according to molecular (≤ 5 SNP) and epidemiological criteria (overlapping hospital stay). NDMAb cases were compared at a ratio of 1:2 with non-NDM carbapenem-resistant A. baumannii (CRAb) cases. RESULTS The study included 54 NDMAb-positive out of 857 CRAb patients, including 6/179 (3.3%) in TASMC, 18/441 (4.0%) in SZMC and 30/237 (12.6%) in RMC. Patients infected by NDMAb had similar clinical features and risk factors as patients with non-NDM CRAb. The length-of-stay was higher in NDMAb cases (48.5 days vs. 36 days, respectively, p = 0.097) and the in-hospital mortality was similarly high in both groups. Most isolates (41/54, 76%) were first detected from surveillance culture. The majority of isolates harbored the blaNDM-2 gene allele (n = 33), followed by the blaNDM-1 (n = 20) allele and the blaNDM-4 allele (n = 1). The majority of isolates were related within the ST level to other isolates in SZMC and RMC: 17/18 and 27/30 isolates, respectfully. The common ST's were the blaNDM-1 harboring ST-2 (n = 3) and ST-107 (n = 8) in SZMC and the blaNDM-2 harboring ST-103 in SZMC (n = 6) and in RMC (n = 27). All blaNDM alleles were located within a conserved mobile genetic environment flanked by the ISAb125 and IS91 family transposon. Clonal transmission was identified in most hospital-acquired cases in RMC and SZMC. CONCLUSION NDMAb constitutes a minor part of CRAb cases and are clinically similar to non-NDM CRAb. Transmission of NDMAb occurs mostly by clonal spread.
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Affiliation(s)
- Amos Adler
- Clinical Microbiology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.
- Department of Epidemiology and Preventive Medicine, School of Public Health, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Hiren Ghosh
- Institute for Infection Prevention and Hospital Epidemiology, Medical Center - University of Freiburg, Freiburg, Germany
| | - Andrea Gross
- Institute for Infection Prevention and Hospital Epidemiology, Medical Center - University of Freiburg, Freiburg, Germany
| | | | - Michal Lasnoy
- Clinical Microbiology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Marc V Assous
- Laboratory of Clinical Microbiology, Faculty of Medicine, Shaare Zedek Medical Center, Hebrew University of Jerusalem, Jerusalem, Israel
| | | | | | - Yonit Wiener-Well
- Infectious disease unit, Sha'are Zedek Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Anat Alony
- Department of Epidemiology and Preventive Medicine, School of Public Health, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Hajo Grundmann
- Institute for Infection Prevention and Hospital Epidemiology, Medical Center - University of Freiburg, Freiburg, Germany
| | - Sandra Reuter
- Institute for Infection Prevention and Hospital Epidemiology, Medical Center - University of Freiburg, Freiburg, Germany
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Junaid M, Thirapanmethee K, Khuntayaporn P, Chomnawang MT. CRISPR-Based Gene Editing in Acinetobacter baumannii to Combat Antimicrobial Resistance. Pharmaceuticals (Basel) 2023; 16:920. [PMID: 37513832 PMCID: PMC10384873 DOI: 10.3390/ph16070920] [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: 05/25/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023] Open
Abstract
Antimicrobial resistance (AMR) poses a significant threat to the health, social, environment, and economic sectors on a global scale and requires serious attention to addressing this issue. Acinetobacter baumannii was given top priority among infectious bacteria because of its extensive resistance to nearly all antibiotic classes and treatment options. Carbapenem-resistant A. baumannii is classified as one of the critical-priority pathogens on the World Health Organization (WHO) priority list of antibiotic-resistant bacteria for effective drug development. Although available genetic manipulation approaches are successful in A. baumannii laboratory strains, they are limited when employed on newly acquired clinical strains since such strains have higher levels of AMR than those used to select them for genetic manipulation. Recently, the CRISPR-Cas (Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein) system has emerged as one of the most effective, efficient, and precise methods of genome editing and offers target-specific gene editing of AMR genes in a specific bacterial strain. CRISPR-based genome editing has been successfully applied in various bacterial strains to combat AMR; however, this strategy has not yet been extensively explored in A. baumannii. This review provides detailed insight into the progress, current scenario, and future potential of CRISPR-Cas usage for AMR-related gene manipulation in A. baumannii.
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Affiliation(s)
- Muhammad Junaid
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
| | - Krit Thirapanmethee
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
| | - Piyatip Khuntayaporn
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
| | - Mullika Traidej Chomnawang
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
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9
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Rafei R, Koong J, Osman M, Al Atrouni A, Hamze M, Hamidian M. Analysis of pCl107 a large plasmid carried by an ST25 Acinetobacter baumannii strain reveals a complex evolutionary history and links to multiple antibiotic resistance and metabolic pathways. FEMS MICROBES 2022; 3:xtac027. [PMID: 37332503 PMCID: PMC10117892 DOI: 10.1093/femsmc/xtac027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/13/2022] [Accepted: 11/14/2022] [Indexed: 09/14/2023] Open
Abstract
Acinetobacter baumannii has successfully spread during the last decades as one of the main critically important pathogens. However, many aspects including plasmids, are still under-investigated. Here, we report the complete sequence of an Acinetobacter baumannii strain, belonging to the ST25IP (Institut Pasteur) sequence type recovered in 2012 in Lebanon, using a combination of Illumina MiSeq and Oxford Nanopore sequencing and a hybrid assembly approach. This strain (Cl107) carries a 198 kb plasmid called pCl107 that encodes the MPFI conjugative transfer system. The plasmid carries the aacA1, aacC2, sul2, strAB, and tetA(B) antibiotic resistance genes. pCl107 region encompassing the sul2, strAB, tetA(B) is closely related to AbGRI1 chromosomal resistance islands, which are widespread in A. baumannii strains belonging to Global Clone 2. The resistance region found in pCl107 is one of the missing links in the evolutionary history of the AbGRI1 islands. pCl107 also contains a BREX Type 1 region and represents one of the two main evolution patterns observed in BREX clusters found in plasmids related to pCl107. pCl107 also harbours a ptx phosphonate metabolism module, which plays an ancestral structure compared to other large plasmids in ST25 strains. While the uric acid metabolic module found in pCl107 is incomplete, we identified possible ancestors from plasmids and chromosomes of Acinetobacter spp. Our analyses indicate a complex evolutionary history of plasmids related to pCl107 with many links to multiple antibiotic resistance and metabolic pathways.
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Affiliation(s)
- Rayane Rafei
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science & Technology, Faculty of Public Health, Lebanese University, Tripoli 1300, Lebanon
| | - Jonathan Koong
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo NSW 2007, Australia
| | - Marwan Osman
- Cornell Atkinson Center for Sustainability, Cornell University, Ithaca, NY 14853, United States
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, United States
| | - Ahmad Al Atrouni
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science & Technology, Faculty of Public Health, Lebanese University, Tripoli 1300, Lebanon
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science & Technology, Faculty of Public Health, Lebanese University, Tripoli 1300, Lebanon
| | - Mehrad Hamidian
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo NSW 2007, Australia
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10
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Al-Tamimi M, Albalawi H, Alkhawaldeh M, Alazzam A, Ramadan H, Altalalwah M, Alma’aitah A, Al Balawi D, Shalabi S, Abu-Raideh J, Khasawneh AI, Alhaj F, Hijawi K. Multidrug-Resistant Acinetobacter baumannii in Jordan. Microorganisms 2022; 10:microorganisms10050849. [PMID: 35630295 PMCID: PMC9144680 DOI: 10.3390/microorganisms10050849] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/11/2022] [Accepted: 04/11/2022] [Indexed: 02/05/2023] Open
Abstract
Background: Acinetobacter baumannii is a common cause of multi-drug (MDR)-resistant infections worldwide. The epidemiological and molecular characteristics of MDR-A. baumannii in Jordan is not known. Methods: A. baumannii isolates were collected from 2010 to 2020 from three tertiary hospitals in Jordan. Demographic and clinical data, isolates information, antibiotic susceptibility patterns, phenotypic, and molecular characterization of carbapenem resistance genes were performed. Results: A total of 622 A. baumannii isolates were collected during the study period. Most isolates were from males, aged 18−60 years, Jordanian, from infected wounds, and were patients in surgery or critical care units. Among patients from whom A. baumannii was isolated, associated risk factors for MDR were adults over 60, males, critically ill patients and infected wounds (OR 4.14, 2.45, 10, 7, respectively, p < 0.0001). Incidence rates from 2010 to 2015 showed a slight increase in MDR (3.75/1000 to 4.46/1000). Resistance patterns indicated high resistance for most cephalosporins, carbapenems, and fluoroquinolones, moderate resistance for trimethoprim/sulfamethoxazole and ampicillin/sulbactam, low resistance for aminoglycosides and tetracyclines, while colistin and tigecycline, have the lowest resistance rates. 76.8% of A. baumannii isolates were MDR and 99.2% were carbapenem-resistant. All isolates were positive for the OXA-51 gene (100%), 98.5% were positive for the OXA-23 gene, 26.6% for the VIM gene, while KPC and IMP genes were almost not detected (0% and 0.8% respectively). Conclusions: This is the first large, multicentric, prolonged study that provides insights into A. baumannii infections in Jordan. Attention to patients at higher risk is important for early identification. Colistin and tigecycline were the most effective antimicrobials.
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Affiliation(s)
- Mohammad Al-Tamimi
- Department of Basic Medical Sciences, Faculty of Medicine, The Hashemite University, Zarqa 13133, Jordan; (H.A.); (M.A.); (A.A.); (H.R.); (M.A.); (A.A.); (D.A.B.); (S.S.); (J.A.-R.); (A.I.K.); (F.A.)
- Correspondence: ; Tel.: +962-(5)-3903333; Fax: +962-(5)-3826613
| | - Hadeel Albalawi
- Department of Basic Medical Sciences, Faculty of Medicine, The Hashemite University, Zarqa 13133, Jordan; (H.A.); (M.A.); (A.A.); (H.R.); (M.A.); (A.A.); (D.A.B.); (S.S.); (J.A.-R.); (A.I.K.); (F.A.)
| | - Mohamd Alkhawaldeh
- Department of Basic Medical Sciences, Faculty of Medicine, The Hashemite University, Zarqa 13133, Jordan; (H.A.); (M.A.); (A.A.); (H.R.); (M.A.); (A.A.); (D.A.B.); (S.S.); (J.A.-R.); (A.I.K.); (F.A.)
| | - Abdullah Alazzam
- Department of Basic Medical Sciences, Faculty of Medicine, The Hashemite University, Zarqa 13133, Jordan; (H.A.); (M.A.); (A.A.); (H.R.); (M.A.); (A.A.); (D.A.B.); (S.S.); (J.A.-R.); (A.I.K.); (F.A.)
| | - Hassan Ramadan
- Department of Basic Medical Sciences, Faculty of Medicine, The Hashemite University, Zarqa 13133, Jordan; (H.A.); (M.A.); (A.A.); (H.R.); (M.A.); (A.A.); (D.A.B.); (S.S.); (J.A.-R.); (A.I.K.); (F.A.)
| | - Majd Altalalwah
- Department of Basic Medical Sciences, Faculty of Medicine, The Hashemite University, Zarqa 13133, Jordan; (H.A.); (M.A.); (A.A.); (H.R.); (M.A.); (A.A.); (D.A.B.); (S.S.); (J.A.-R.); (A.I.K.); (F.A.)
| | - Ahmad Alma’aitah
- Department of Basic Medical Sciences, Faculty of Medicine, The Hashemite University, Zarqa 13133, Jordan; (H.A.); (M.A.); (A.A.); (H.R.); (M.A.); (A.A.); (D.A.B.); (S.S.); (J.A.-R.); (A.I.K.); (F.A.)
| | - Dua’a Al Balawi
- Department of Basic Medical Sciences, Faculty of Medicine, The Hashemite University, Zarqa 13133, Jordan; (H.A.); (M.A.); (A.A.); (H.R.); (M.A.); (A.A.); (D.A.B.); (S.S.); (J.A.-R.); (A.I.K.); (F.A.)
| | - Sharif Shalabi
- Department of Basic Medical Sciences, Faculty of Medicine, The Hashemite University, Zarqa 13133, Jordan; (H.A.); (M.A.); (A.A.); (H.R.); (M.A.); (A.A.); (D.A.B.); (S.S.); (J.A.-R.); (A.I.K.); (F.A.)
| | - Jumana Abu-Raideh
- Department of Basic Medical Sciences, Faculty of Medicine, The Hashemite University, Zarqa 13133, Jordan; (H.A.); (M.A.); (A.A.); (H.R.); (M.A.); (A.A.); (D.A.B.); (S.S.); (J.A.-R.); (A.I.K.); (F.A.)
| | - Ashraf I. Khasawneh
- Department of Basic Medical Sciences, Faculty of Medicine, The Hashemite University, Zarqa 13133, Jordan; (H.A.); (M.A.); (A.A.); (H.R.); (M.A.); (A.A.); (D.A.B.); (S.S.); (J.A.-R.); (A.I.K.); (F.A.)
| | - Farah Alhaj
- Department of Basic Medical Sciences, Faculty of Medicine, The Hashemite University, Zarqa 13133, Jordan; (H.A.); (M.A.); (A.A.); (H.R.); (M.A.); (A.A.); (D.A.B.); (S.S.); (J.A.-R.); (A.I.K.); (F.A.)
| | - Kamal Hijawi
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, The Hashemite University, Zarqa 13133, Jordan;
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11
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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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12
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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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13
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Fleifel M, Machmouchi A, Alameddine O, Hoyek K, Melki D, Hallab E, Masri K, Sidaoui HR, Stockman D, Daoud Z. The Spread of Plasmidic AmpC in a General Lebanese Hospital Over Nine Consecutive Years and the Relationship With Restricted Isolation Protocols. Front Med (Lausanne) 2021; 8:633783. [PMID: 34765610 PMCID: PMC8576109 DOI: 10.3389/fmed.2021.633783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 10/04/2021] [Indexed: 11/13/2022] Open
Abstract
Background: The dreaded bacterial infection by extended-spectrum β-lactamases (ESBL)-producers has always troubled the medical field whether on the public, scientific, or clinical levels. One of the lesser known β-lactamases, which is capable of hydrolyzing broad and extended-spectrum cephalosporins—i.e., cephamycins plus oxyimino-β-lactams—are the AmpC β-lactamases. This group, which has also been termed occasionally—and incorrectly—as ESBL Class C, confers resistance to β-lactamase inhibitors. The prevalence of plasmidic AmpC (pAmpC) strains is possibly still a matter of debate considering the unevenly matched data between phenotypically-detected and molecularly-detected pAmpC. Aim: In the absence of any study in Lebanon addressing the AmpC, our intention was to determine the numbers and percentages of AmpC Enterobacteriaceae isolates, notably plasmid-mediated ones, across different wards at the Centre Hospitalier du Nord (CHN), Lebanon, and highlight the importance of infection control protocols. Materials and Methods: Carriage and infection with pAmpC Enterobacteriaceae were retrospectively investigated between 2011 and 2015 and prospectively between 2016 and 2019 at the Centre Hospitalier du Nord Hospital, North Lebanon. The rise or decline in the numbers of such strains, in concordance with the allegedly intensive isolation of the patients, were analyzed. Results: Intensive care unit (ICU) data shows an initial rise in infection isolates from 2012 to 2014 and in the carriage isolates from 2012 to 2013 with later notable overall decrease in the both isolates' numbers with the application of the isolation protocols at CHN from 2014 onwards. Floors 2, 3, and 4 seemed to house the bulk of the isolates as well. Conclusion: Preventive measures, such as on-going surveillance of the hospital wards by specialized healthcare personnel and strict implementation of infection control practices, should be a top priority in any medical center in order to isolate such strains and try to put a limit for the development and the dissemination of any possible multidrug resistant strains.
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Affiliation(s)
- Mohamad Fleifel
- Department of Internal Medicine, The Lebanese American University Gilbert and Rose-Marie Chagoury School of Medicine, Beirut, Lebanon
| | - Ahmad Machmouchi
- Faculty of Medicine and Medical Sciences, University of Balamand, Beirut, Lebanon
| | - Omar Alameddine
- Faculty of Medicine and Medical Sciences, University of Balamand, Beirut, Lebanon
| | - Kim Hoyek
- Faculty of Medicine and Medical Sciences, University of Balamand, Beirut, Lebanon
| | - Dimitri Melki
- Faculty of Medicine and Medical Sciences, University of Balamand, Beirut, Lebanon
| | - Elsa Hallab
- Faculty of Medicine and Medical Sciences, University of Balamand, Beirut, Lebanon
| | - Khalil Masri
- Centre Hospitalier du Nord Hospital, Department of Infectious Diseases, Zgharta, Lebanon
| | - Hiam R Sidaoui
- Centre Hospitalier du Nord Hospital, Department of Infectious Diseases, Zgharta, Lebanon
| | - David Stockman
- Clinical Microbiology and Infection Prevention, Michigan Health Clinics, Saginaw, MI, United States
| | - Ziad Daoud
- Clinical Microbiology and Infection Prevention, Michigan Health Clinics and College of Medicine-Central Michigan University, Saginaw, MI, United States
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14
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Adjei AY, Vasaikar SD, Apalata T, Okuthe EG, Songca SP. Phylogenetic analysis of carbapenem-resistant Acinetobacter baumannii isolated from different sources using Multilocus Sequence Typing Scheme. INFECTION GENETICS AND EVOLUTION 2021; 96:105132. [PMID: 34775079 DOI: 10.1016/j.meegid.2021.105132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 09/10/2021] [Accepted: 11/02/2021] [Indexed: 01/25/2023]
Abstract
The emergence and worldwide distribution of carbapenem-resistant Acinetobacter baumannii strains has become a major public health threat. The objective of this study was to investigate the clonal relatedness of A. baumannii isolates collected from clinical and extra-hospital environments in Mthatha, South Africa. Forty carbapenem-resistant isolates comprising of clinical (20) and extra-hospital (20) were identified and tested for antimicrobial susceptibility. Detection of carbapenemase encoding genes was performed by Real-time PCR. The clonal relationship of clinical isolates relative to extra-hospital isolates was determined via multilocus sequence typing (MLST). All isolates (clinical and extra-hospital) were resistant to most common antibiotics including carbapenems (imipenem; MIC ≥32 μg/mL and meropenem; MIC ≥32 μg/mL) with the only exception being amikacin (with 3 isolates susceptible), tigecycline (14 isolates susceptible) and colistin (all isolates susceptible). The bla OXA-23-like and the intrinsic bla OXA-51 -like genes were detected in all the isolates tested. The bla OXA-58-like and bla IMP-type genes were detected in 2 clinical isolates whilst the bla OXA-24-like, bla VIM-type, bla NDM-1, bla SIM, and bla AmpC were not detected. The bla OXA-24-like, bla OXA-58-like, bla IMP-type, bla VIM-type, bla NDM-1, bla SIM, and bla AmpC were negative in the extra-hospital isolates. Co-occurrence of bla OXA-23 -like, bla OXA-58-like and bla IMP-type was observed in 2 clinical isolates. The MLST performed on 33 isolates identified 5 existing sequence types (ST) (ST1, ST2, ST25, ST85 and ST215) in clinical isolates and 2 existing STs (ST1 and ST2) in extra-hospital isolates. The most dominant ST was ST2 accounting for 68.8% of the clinical isolates and 82.4% of the extra-hospital isolates. The study demonstrated high prevalence and potential clonal spread of globally-disseminated clonal complex 2 carrying bla OXA-23-like within our local settings. However, ST25 might be an emerging lineage carrying the bla OXA-23-like . Continuous monitoring is important in limiting the spread of these strains in other healthcare settings and the community.
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Affiliation(s)
- Anane Yaw Adjei
- Water Research Institute, Council for Scientific and Industrial Research-CSIR-Ghana, P. O. Box M 32. Accra Ghana 2nd CSIR Close, Accra, Ghana.
| | - Sandeep D Vasaikar
- Division of Medical Microbiology, Department of Laboratory Medicine & Pathology, Faculty of Health Sciences, Walter Sisulu University, Private Bag: X1, Mthatha - 5117 Eastern Cape Province, South Africa; Division of Medical Microbiology, National Health Laboratory Services (NHLS), Nelson Mandela Central Hospital, Mthatha 5100, South Africa..
| | - Teke Apalata
- Division of Medical Microbiology, Department of Laboratory Medicine & Pathology, Faculty of Health Sciences, Walter Sisulu University, Private Bag: X1, Mthatha - 5117 Eastern Cape Province, South Africa; Division of Medical Microbiology, National Health Laboratory Services (NHLS), Nelson Mandela Central Hospital, Mthatha 5100, South Africa..
| | - Emily Grace Okuthe
- Department of Biological and Environmental Sciences, Walter Sisulu University, Private Bag: X1, Mthatha - 5117 Eastern Cape Province, South Africa.
| | - Sandile Phinda Songca
- School of Chemistry and Physics, College of Agriculture Engineering and Science, University of KwaZulu-Natal, 2nd floor, Francis Stock Building, Howard College campus, UKZN, Durban 4041, South Africa.
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15
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Moghnieh RA, Moussa JA, Aziz MA, Matar GM. Phenotypic and genotypic characterisation of cephalosporin-, carbapenem- and colistin-resistant Gram-negative bacterial pathogens in Lebanon, Jordan and Iraq. J Glob Antimicrob Resist 2021; 27:175-199. [PMID: 34481122 DOI: 10.1016/j.jgar.2021.08.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 08/18/2021] [Accepted: 08/18/2021] [Indexed: 12/15/2022] Open
Abstract
Antimicrobial resistance (AMR) is a worldwide health concern that continues to escalate. A PubMed literature search identified articles from January 2015-August 2020 reviewing cephalosporin-, carbapenem- and colistin-resistant Gram-negative bacteria (GNB) in Lebanon, Jordan and Iraq, specifically focused on three main pathogens, namely Acinetobacter spp., Enterobacteriaceae (i.e. Escherichia coli and Klebsiella spp.) and Pseudomonas aeruginosa. Sixty-seven relevant articles published within the past 5 years highlighting trends in AMR in Lebanon, Jordan and Iraq were included. Increased resistance to carbapenems in Acinetobacter spp. isolates was observed in Lebanon, Jordan and Iraq; colistin resistance remained relatively low. Studies on Enterobacteriaceae isolates were more varied, with high rates of carbapenem and cephalosporin resistance and lower levels of colistin resistance in Lebanon. Studies from Iraq found high cephalosporin and colistin resistance along with increased susceptibility to carbapenems. In Jordan, most studies recorded high resistance to cephalosporins along with high susceptibility to carbapenems and colistin. Studies on P. aeruginosa isolates were limited: most isolates in Lebanon were carbapenem-resistant and colistin-susceptible; studies in Iraq showed varying levels of resistance to carbapenems and cephalosporins with high susceptibility to colistin; and studies in Jordan found varying levels of susceptibility to carbapenems, cephalosporins and colistin. The most commonly observed resistance mechanisms in GNB were genetic modifications causing increased expression of antimicrobial-inactivating enzymes and decreased permeability. Overall, this review highlights the concerning rise in AMR and the need for improved understanding of the resistance mechanisms to better inform healthcare providers when recommending treatment for patients in this region.
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Affiliation(s)
- Rima A Moghnieh
- Department of Internal Medicine, Division of Infectious Diseases, Makassed General Hospital, Beirut, Lebanon; Faculty of Medical Sciences, Lebanese University, Beirut, Lebanon; Faculty of Medicine, Beirut Arab University, Beirut, Lebanon.
| | | | | | - Ghassan M Matar
- Department of Experimental Pathology, Immunology & Microbiology, Center for Infectious Diseases Research, WHO Collaborating Center for Reference & Research on Bacterial Pathogens, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
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16
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Osman M, Rafei R, Ismail MB, Omari SA, Mallat H, Dabboussi F, Cazer C, Karah N, Abbara A, Hamze M. Antimicrobial resistance in the protracted Syrian conflict: halting a war in the war. Future Microbiol 2021; 16:825-845. [PMID: 34223789 DOI: 10.2217/fmb-2021-0040] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The Syrian conflict has damaged key infrastructure and indirectly affected almost all parts of the Middle East and Europe, with no end in sight. Exhausting conditions created by the Syrian crisis and related massive displacement promote the emergence of numerous public health problems that fuel antimicrobial resistance (AMR) development. Here, we explore the current situation of the Syrian displaced population, and AMR inside Syria and among refugees in host countries. We then suggest a roadmap of selected key interventions and strategies to address the threat of AMR in the context of the Syrian crisis. These recommendations are intended to urge health policy-makers in governments and international health organizations to optimize and push for implementing an effective policy taking into consideration the current obstacles.
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Affiliation(s)
- Marwan Osman
- Laboratoire Microbiologie, Santé et Environnement (LMSE), Doctoral School of Sciences & Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon.,Department of Population Medicine & Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14850, USA
| | - Rayane Rafei
- Laboratoire Microbiologie, Santé et Environnement (LMSE), Doctoral School of Sciences & Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Mohamad Bachar Ismail
- Laboratoire Microbiologie, Santé et Environnement (LMSE), Doctoral School of Sciences & Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon.,Faculty of Sciences, Lebanese University, Tripoli, Lebanon
| | - Sarah Al Omari
- Department of Epidemiology & Population Health, Faculty of Health Sciences, American University of Beirut, Beirut, Lebanon
| | - Hassan Mallat
- Laboratoire Microbiologie, Santé et Environnement (LMSE), Doctoral School of Sciences & Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Fouad Dabboussi
- Laboratoire Microbiologie, Santé et Environnement (LMSE), Doctoral School of Sciences & Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Casey Cazer
- Department of Population Medicine & Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14850, USA
| | - Nabil Karah
- Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Aula Abbara
- Department of Infection, Imperial College, London, UK
| | - Monzer Hamze
- Laboratoire Microbiologie, Santé et Environnement (LMSE), Doctoral School of Sciences & Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
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17
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Antibiotic-Resistant Acinetobacter baumannii in Low-Income Countries (2000-2020): Twenty-One Years and Still below the Radar, Is It Not There or Can They Not Afford to Look for It? Antibiotics (Basel) 2021; 10:antibiotics10070764. [PMID: 34201723 PMCID: PMC8300836 DOI: 10.3390/antibiotics10070764] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 12/30/2022] Open
Abstract
Acinetobacter baumannii is an emerging pathogen, and over the last three decades it has proven to be particularly difficult to treat by healthcare services. It is now regarded as a formidable infectious agent with a genetic setup for prompt development of resistance to most of the available antimicrobial agents. Yet, it is noticed that there is a gap in the literature covering this pathogen especially in countries with limited resources. In this review, we provide a comprehensive updated overview of the available data about A. baumannii, the multi-drug resistant (MDR) phenotype spread, carbapenem-resistance, and the associated genetic resistance determinants in low-income countries (LIICs) since the beginning of the 21st century. The coverage included three major databases; PubMed, Scopus, and Web of Science. Only 52 studies were found to be relevant covering only 18 out of the 29 countries included in the LIC group. Studies about two countries, Syria and Ethiopia, contributed ~40% of the studies. Overall, the survey revealed a wide spread of MDR and alarming carbapenem-resistance profiles. Yet, the total number of studies is still very low compared to those reported about countries with larger economies. Accordingly, a discussion about possible reasons and recommendations to address the issue is presented. In conclusion, our analyses indicated that the reported studies of A. baumannii in the LICs is far below the expected numbers based on the prevailing circumstances in these countries. Lack of proper surveillance systems due to inadequate financial resources could be a major contributor to these findings.
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18
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Ejaz H, Ahmad M, Younas S, Junaid K, Abosalif KOA, Abdalla AE, Alameen AAM, Elamir MYM, Bukhari SNA, Ahmad N, Qamar MU. Molecular Epidemiology of Extensively-Drug Resistant Acinetobacter baumannii Sequence Type 2 Co-Harboring bla NDM and bla OXA From Clinical Origin. Infect Drug Resist 2021; 14:1931-1939. [PMID: 34079303 PMCID: PMC8164867 DOI: 10.2147/idr.s310478] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 04/24/2021] [Indexed: 12/12/2022] Open
Abstract
Background The therapeutic management of carbapenem-resistant Acinetobacter baumannii (CR-AB) represents a serious challenge to the public health sector because these pathogens are resistant to a wide range of antibiotics, resulting in limited treatment options. The present study was planned to investigate the clonal spread of CR-AB in a clinical setting. Methodology A total of 174 A. baumannii clinical isolates were collected from a tertiary care hospitals in Lahore, Pakistan. The isolates were confirmed by VITEK 2 compact system and molecular identification of recA and blaOXA-51. Antimicrobial profile and the screening of carbapenem-resistant genes were carried out using VITEK 2 system and PCR, respectively. The molecular typing of the isolates was performed according to the Pasteur scheme. Results Of the 174 A. baumannii isolates collected, the majority were isolated from sputum samples (46.5%) and in the intensive care unit (ICU, 75%). Among these, 113/174 (64.9%) were identified as CR-AB, and 49.5% and 24.7% harbored blaOXA-23 and blaNDM-1, respectively. A total of 11 (9.7%) isolates co-harbored blaOXA-51, blaNDM-1, and blaOXA-23. Interestingly, 46.9% of the CR-AB belonged to sequence type 2 (ST2; CC1), whereas 15.9% belonged to ST1 (CC1). All of the CR-AB isolates showed extensive resistance to clinically relevant antibiotics, except colistin. Conclusion The study concluded CR-AB ST2 clone harboring blaOXA-23 and blaNDM-1 are widely distributed in Pakistan’s clinical settings, which could result in increased mortality. Strict compliance with the National Action Plan on Antimicrobial Resistance is necessary to reduce the impacts of these strains.
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Affiliation(s)
- Hasan Ejaz
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka, Al Jouf, 72388, Saudi Arabia
| | - Mahtab Ahmad
- Department of Microbiology, Faculty of Life Sciences, Government College University Faisalabad, Faisalabad, 38000, Pakistan
| | - Sonia Younas
- Department of Pathology, Tehsil Headquarter Hospital Kamoke, Kamoke, 50661, Pakistan
| | - Kashaf Junaid
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka, Al Jouf, 72388, Saudi Arabia
| | - Khalid Omer Abdalla Abosalif
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka, Al Jouf, 72388, Saudi Arabia
| | - Abualgasim Elgaili Abdalla
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka, Al Jouf, 72388, Saudi Arabia
| | - Ayman Ali Mohammed Alameen
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka, Al Jouf, 72388, Saudi Arabia
| | - Mohammed Yagoub Mohammed Elamir
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka, Al Jouf, 72388, Saudi Arabia
| | - Syed Nasir Abbas Bukhari
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Aljouf, 72388, Saudi Arabia
| | - Naveed Ahmad
- Department of Pharmaceutics, College of Pharmacy, Jouf University, Sakaka, Aljouf, 72388, Saudi Arabia
| | - Muhammad Usman Qamar
- Department of Microbiology, Faculty of Life Sciences, Government College University Faisalabad, Faisalabad, 38000, Pakistan
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19
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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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20
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Truppa C, Abo-Shehada MN. Antimicrobial resistance among GLASS pathogens in conflict and non-conflict affected settings in the Middle East: a systematic review. BMC Infect Dis 2020; 20:936. [PMID: 33297983 PMCID: PMC7724697 DOI: 10.1186/s12879-020-05503-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 10/12/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND In spite of the evident general negative effects of armed conflict on countries' health systems and populations' health outcomes, little is known about similar impacts of conflicts on the spread of antimicrobial resistances (AMR). This review was to address this evidence gap and describe: 1. Patterns of AMR in the Middle East (ME) and resistance profiles of pathogens included in the Global AMR Surveillance System (GLASS) supported by the World Health Organization; 2. Differences in proportions of AMR isolates between conflict and non-conflict countries. METHODS A systematic literature review was conducted following PRISMA guidelines and searching five electronic databases. Subject heading and free text were searched for "antimicrobial resistances" and "Middle East", to identify observational studies on AMR published from January 2011 to June 2018. Data were extracted from included articles on a predefined set of variables. Percentages of AMR were analysed as median and interquartile ranges. Risk of bias was assessed using the Newcastle-Ottawa Scale. RESULTS A total of 132 articles met the inclusion criteria. Included studies showed heterogeneity in study design, laboratory methods and standards for interpretation of results, and an overall high risk of bias. Main findings were the following: 1. High proportions of carbapenem resistance in Acinetobacter spp. (median 74.2%), and both carbapenem resistance (median 8.1 and 15.4% for E. coli and K. pneumoniae respectively) and ESBL-production (median 32.3 and 27.9% for E. coli and K. pneumoniae respectively) amongst Enterobacteriaceae. S. aureus isolates showed a median methicillin resistance percentage of 45.1%, while vancomycin resistance was almost absent. A median of 50% of the strains of S. pneumoniae showed non-susceptibility to penicillin. 2. Similar trends were observed in conflict and non-conflict affected countries. CONCLUSIONS There is a lack of standardization in the methodological approach to AMR research in the Middle East. The proportion of antibiotic resistances among specific GLASS pathogens is high, particularly among Acinetobacter spp.
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Affiliation(s)
- Claudia Truppa
- International Committee of the Red Cross, Geneva, Switzerland
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, University of London, London, UK
| | - Mahmoud N. Abo-Shehada
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, University of London, London, UK
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21
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Rodgers D, Pasteran F, Calderon M, Jaber S, Traglia GM, Albornoz E, Corso A, Vila AJ, Bonomo RA, Adams MD, Ramírez MS. Characterisation of ST25 NDM-1-producing Acinetobacter spp. strains leading the increase in NDM-1 emergence in Argentina. J Glob Antimicrob Resist 2020; 23:108-110. [PMID: 32890839 DOI: 10.1016/j.jgar.2020.08.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/23/2020] [Accepted: 08/18/2020] [Indexed: 11/19/2022] Open
Affiliation(s)
- Deja Rodgers
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, California, USA
| | - Fernando Pasteran
- National/Regional Reference Laboratory for Antimicrobial Resistance (NRL), Servicio Antimicrobianos, Instituto Nacional de Enfermedades Infecciosas, ANLIS 'Dr Carlos G. Malbrán', Buenos Aires, Argentina
| | - Manuel Calderon
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, California, USA
| | - Sara Jaber
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, California, USA
| | - German M Traglia
- Departamento de Desarrollo Biotecnología, Instituto de Higiene, Facultad de Medicina, Universidad de La República, Montevideo, Uruguay
| | - Ezequiel Albornoz
- National/Regional Reference Laboratory for Antimicrobial Resistance (NRL), Servicio Antimicrobianos, Instituto Nacional de Enfermedades Infecciosas, ANLIS 'Dr Carlos G. Malbrán', Buenos Aires, Argentina
| | - Alejandra Corso
- National/Regional Reference Laboratory for Antimicrobial Resistance (NRL), Servicio Antimicrobianos, Instituto Nacional de Enfermedades Infecciosas, ANLIS 'Dr Carlos G. Malbrán', Buenos Aires, Argentina
| | - Alejandro J Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Rosario, Argentina; Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Robert A Bonomo
- Research Service and GRECC, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Mark D Adams
- The Jackson Laboratory, Farmington, Connecticut, USA
| | - María Soledad Ramírez
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, California, USA.
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22
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Antibiotic Resistance Profiles, Molecular Mechanisms and Innovative Treatment Strategies of Acinetobacter baumannii. Microorganisms 2020; 8:microorganisms8060935. [PMID: 32575913 PMCID: PMC7355832 DOI: 10.3390/microorganisms8060935] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/19/2020] [Accepted: 06/19/2020] [Indexed: 12/18/2022] Open
Abstract
Antibiotic resistance is one of the biggest challenges for the clinical sector and industry, environment and societal development. One of the most important pathogens responsible for severe nosocomial infections is Acinetobacter baumannii, a Gram-negative bacterium from the Moraxellaceae family, due to its various resistance mechanisms, such as the β-lactamases production, efflux pumps, decreased membrane permeability and altered target site of the antibiotic. The enormous adaptive capacity of A. baumannii and the acquisition and transfer of antibiotic resistance determinants contribute to the ineffectiveness of most current therapeutic strategies, including last-line or combined antibiotic therapy. In this review, we will present an update of the antibiotic resistance profiles and underlying mechanisms in A. baumannii and the current progress in developing innovative strategies for combating multidrug-resistant A. baumannii (MDRAB) infections.
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23
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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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24
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Dandachi I, Chaddad A, Hanna J, Matta J, Daoud Z. Understanding the Epidemiology of Multi-Drug Resistant Gram-Negative Bacilli in the Middle East Using a One Health Approach. Front Microbiol 2019; 10:1941. [PMID: 31507558 PMCID: PMC6716069 DOI: 10.3389/fmicb.2019.01941] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Accepted: 08/07/2019] [Indexed: 12/16/2022] Open
Abstract
In the last decade, extended-spectrum cephalosporin and carbapenem resistant Gram-negative bacilli (GNB) have been extensively reported in the literature as being disseminated in humans but also in animals and the environment. These resistant organisms often cause treatment challenges due to their wide spectrum of antibiotic resistance. With the emergence of colistin resistance in animals and its subsequent detection in humans, the situation has worsened. Several studies reported the transmission of resistant organisms from animals to humans. Studies from the middle east highlight the spread of resistant organisms in hospitals and to a lesser extent in livestock and the environment. In view of the recent socio-economical conflicts that these countries are facing in addition to the constant population mobilization; we attempt in this review to highlight the gaps of the prevalence of resistance, antibiotic consumption reports, infection control measures and other risk factors contributing in particular to the spread of resistance in these countries. In hospitals, carbapenemases producers appear to be dominant. In contrast, extended spectrum beta lactamases (ESBL) and colistin resistance are becoming a serious problem in animals. This is mainly due to the continuous use of colistin in veterinary medicine even though it is now abandoned in the human sphere. In the environment, despite the small number of reports, ESBL and carbapenemases producers were both detected. This highlights the importance of the latter as a bridge between humans and animals in the transmission chain. In this review, we note that in the majority of the Middle Eastern area, little is known about the level of antibiotic consumption especially in the community and animal farms. Furthermore, some countries are currently facing issues with immigrants, poverty and poor living conditions which has been imposed by the civil war crisis. This all greatly facilitates the dissemination of resistance in all environments. In the one health concept, this work re-emphasizes the need to have global intervention measures to avoid dissemination of antibiotic resistance in humans, animals and the environment in Middle Eastern countries.
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Affiliation(s)
- Iman Dandachi
- Faculty of Medicine and Medical Sciences, Clinical Microbiology Laboratory, University of Balamand, Beirut, Lebanon
| | - Amer Chaddad
- Faculty of Medicine and Medical Sciences, Clinical Microbiology Laboratory, University of Balamand, Beirut, Lebanon
| | - Jason Hanna
- Faculty of Medicine and Medical Sciences, Clinical Microbiology Laboratory, University of Balamand, Beirut, Lebanon
| | - Jessika Matta
- Faculty of Medicine and Medical Sciences, Clinical Microbiology Laboratory, University of Balamand, Beirut, Lebanon
| | - Ziad Daoud
- Faculty of Medicine and Medical Sciences, Clinical Microbiology Laboratory, University of Balamand, Beirut, Lebanon
- Division of Clinical Microbiology, Saint George Hospital University Medical Center, Beirut, Lebanon
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25
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Rafei R, Osman M, Dabboussi F, Hamze M. Update on the epidemiological typing methods for Acinetobacter baumannii. Future Microbiol 2019; 14:1065-1080. [DOI: 10.2217/fmb-2019-0134] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The outstanding ability of Acinetobacter baumannii to cause outbreaks and acquire multidrug resistance motivated the development of a plethora of typing techniques, which can help infection preventionists and hospital epidemiologists to more efficiently implement intervention controls. Nowadays, the world is witnessing a gradual transition from traditional typing methodology to whole genome sequencing-based approaches. Such approaches are opening new prospects and applications never achieved by existing typing methods. Herein, we provide the reader with an updated review on A. baumannii typing methods recapping the added value of well-established techniques previously applied for A. baumannii and detailing new ones (as clustered regularly interspaced short palindromic repeats-based typing) with a special focus on whole genome sequencing.
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Affiliation(s)
- Rayane Rafei
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Marwan Osman
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Fouad Dabboussi
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
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26
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Kumar S, Patil PP, Singhal L, Ray P, Patil PB, Gautam V. Molecular epidemiology of carbapenem-resistant Acinetobacter baumannii isolates reveals the emergence of bla OXA-23 and bla NDM-1 encoding international clones in India. INFECTION GENETICS AND EVOLUTION 2019; 75:103986. [PMID: 31362071 DOI: 10.1016/j.meegid.2019.103986] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 07/18/2019] [Accepted: 07/26/2019] [Indexed: 01/09/2023]
Abstract
Acinetobacter baumannii is a nosocomial pathogen increasingly affecting the critically ill patients and represents a major public health challenge. Carbapenem-resistant A. baumannii (CRAB) is found to be associated with International Clones (ICs) and different classes of carbapenemases. The objective of the present study was to investigate the prevalence of carbapenem resistance genes, clonal relationship and genetic structure of clinical isolates of A. baumannii. In the present study, multi-locus sequence typing (MLSTOX) and analysis were carried out using Oxford scheme for 86 clinical isolates of CRAB along with 11 carbapenem sensitive A. baumannii (CSAB) collected over a period of two years (2014-2016) from two tertiary care hospitals of North India. We observed a high prevalence of the blaOXA-23-like (97.7%) among the CRAB followed by blaNDM-1 (29.1%) and blaOXA58-like (3.5%). Forty-seven Sequence Types (STs) were represented by all 97 isolates, out of which, 28 (59.6%) were novel STs that were assigned to 41 isolates. STs 451 (13%), 447 (7%), 195 (6%) and 848 (5%) were the most common STs. The majority of CRAB isolates (44.3%) belonged to the CC92, followed by the CC447 (15.1%), CC109 (9.3%) and CC110 (3.4%), which corresponds to the IC2, 8, 1 and 7 respectively. Phylogenetic and recombination analysis suggested two major and one minor lineage in the population. Further linkage disequilibrium analysis suggested clonal nature of the population as recombination was noticed at a low frequency, which was not enough to split the clonal relationship. The knowledge of genetic structure of CRAB from this study will be invaluable to illustrate epidemiology, surveillance and understanding its global diversity.
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Affiliation(s)
- Sunil Kumar
- Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh 160012, India; Department of Biotechnology, Maharishi Markandeshwar (Deemed to be) University, Mullana, Ambala, Haryana 133207, India
| | - Prashant P Patil
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Sector - 39A, Chandigarh 160036, India
| | - Lipika Singhal
- Government Medical College and Hospital, Sector -32B, Chandigarh 160030, India
| | - Pallab Ray
- Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh 160012, India
| | - Prabhu B Patil
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Sector - 39A, Chandigarh 160036, India.
| | - Vikas Gautam
- Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh 160012, India.
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27
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D'Souza R, Pinto NA, Phuong NL, Higgins PG, Vu TN, Byun JH, Cho YL, Choi JR, Yong D. Phenotypic and Genotypic Characterization of Acinetobacter spp. Panel Strains: A Cornerstone to Facilitate Antimicrobial Development. Front Microbiol 2019; 10:559. [PMID: 30972044 PMCID: PMC6446969 DOI: 10.3389/fmicb.2019.00559] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 03/05/2019] [Indexed: 12/27/2022] Open
Abstract
Acinetobacter spp. have emerged as significant pathogens causing nosocomial infections. Treatment of these pathogens has become a major challenge to clinicians worldwide, due to their increasing tendency to antibiotic resistance. To address this, much revenue and technology are currently being dedicated toward developing novel drugs and antibiotic combinations to combat antimicrobial resistance. To address this issue, we have constructed a panel of Acinetobacter spp. strains expressing different antimicrobial resistance determinants such as narrow spectrum β-lactamases, extended-spectrum β-lactamases, OXA-type-carbapenemase, metallo-beta-lactamase, and over-expressed AmpC β-lactamase. Bacterial strains exhibiting different resistance phenotypes were collected between 2008 and 2013 from Severance Hospital, Seoul. Antimicrobial susceptibility was determined according to the CLSI guidelines using agar dilution method. Selected strains were sequenced using Ion Torrent PGM system, annotated using RAST server and analyzed using Geneious pro 8.0. Genotypic determinants, such as acquired resistance genes, changes in the expression of efflux pumps, mutations, and porin alternations, contributing to the relevant expressed phenotype were characterized. Isolates expressing ESBL phenotype consisted of bla PER-1 gene, the overproduction of intrinsic AmpC beta-lactamase associated with ISAba1 insertion, and carbapenem resistance associated with production of carbapenem-hydrolyzing Ambler class D β-lactamases, such as OXA-23, OXA-66, OXA-120, OXA-500, and metallo-β-lactamase, SIM-1. We have analyzed the relative expression of Ade efflux systems, and determined the sequences of their regulators to correlate with phenotypic resistance. Quinolone resistance-determining regions were analyzed to understand fluoroquinolone-resistance. Virulence factors responsible for pathogenesis were also identified. Due to several mutations, acquisition of multiple resistance genes and transposon insertion, phenotypic resistance decision scheme for for evaluating the resistance proved inaccurate, which highlights the urgent need for modification to this scheme. This complete illustration of mechanism contributing to specific resistance phenotypes can be used as a target for novel drug development. It can also be used as a reference strain in the clinical laboratory and for the evaluation of antibiotic efficacy for specific resistance mechanisms.
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Affiliation(s)
- Roshan D'Souza
- Department of Laboratory Medicine, Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea.,J. Craig Venter Institute, Rockville, MD, United States
| | - Naina A Pinto
- Department of Laboratory Medicine, Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University, Seoul, South Korea
| | - Nguyen Le Phuong
- Department of Laboratory Medicine, Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University, Seoul, South Korea
| | - Paul G Higgins
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany.,German Centre for Infection Research, Partner site Bonn-Cologne, Germany
| | - Thao Nguyen Vu
- Department of Laboratory Medicine, Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University, Seoul, South Korea
| | - Jung-Hyun Byun
- Department of Laboratory Medicine, Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea.,Department of Laboratory Medicine, Gyeongsang National University College of Medicine, Jinju, South Korea
| | - Young Lag Cho
- German Centre for Infection Research, Partner site Bonn-Cologne, Germany
| | - Jong Rak Choi
- Department of Laboratory Medicine, Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
| | - Dongeun Yong
- Department of Laboratory Medicine, Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
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Nawfal Dagher T, Al-Bayssari C, Chabou S, Antar N, Diene SM, Azar E, Rolain JM. Investigation of multidrug-resistant ST2 Acinetobacter baumannii isolated from Saint George hospital in Lebanon. BMC Microbiol 2019; 19:29. [PMID: 30710998 PMCID: PMC6359860 DOI: 10.1186/s12866-019-1401-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 01/24/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Acinetobacter baumannii is an opportunistic pathogen causing various nosocomial infections. The spread of multidrug-resistant A. baumannii is a major public health problem. The aim of this study was to investigate the molecular epidemiology and the genetic support of multidrug-resistant A. baumannii isolates collected from Saint-Georges Hospital in Lebanon. METHODS Between January and August 2016, 31 A. baumannii isolates were collected from sputum samples of patients infected with ventilator-associated pneumonia (VAP) and treated with colistin-carbapenem combination therapy. Antibiotic susceptibility testing was performed using the disk diffusion method. Carbapenemases, extended spectrum β-lactamases encoding genes and mcr-1/2 genes were investigated by RT-PCR and standard PCR. The epidemiological relatedness of the strains was studied using MLST analysis. RESULTS Most of the isolates exhibited multidrug-resistant phenotypes. All the isolates were carbapenem-resistant and among them, 30 carried the class D carbapenemase blaoxa-23 gene while one isolate carried blaoxa-72 gene. MLST results revealed three sequence types, namely ST2, ST699, and ST627. Isolates having ST2 were the most prevalent clone (29/31, 93.5%). CONCLUSIONS This study shows a nosocomial spread of multidrug-resistant A. baumannii ST2 having blaOXA-23 gene in Saint-George in Lebanon. Monitoring and control measures need to be adopted to avoid the spread of A. baumannii to patients.
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Affiliation(s)
- Tania Nawfal Dagher
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Faculté de Médecine et de Pharmacie, 19-21 boulevard Jean Moulin, 13385, Marseille, Cedex 05, France.,Saint George Hospital University Medical Center, Faculty of Medicine and Medical Sciences, University of Balamand, Beirut, Lebanon
| | | | - Selma Chabou
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Faculté de Médecine et de Pharmacie, 19-21 boulevard Jean Moulin, 13385, Marseille, Cedex 05, France
| | - Nadine Antar
- Saint George Hospital University Medical Center, Faculty of Medicine and Medical Sciences, University of Balamand, Beirut, Lebanon
| | - Seydina M Diene
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Faculté de Médecine et de Pharmacie, 19-21 boulevard Jean Moulin, 13385, Marseille, Cedex 05, France
| | - Eid Azar
- Saint George Hospital University Medical Center, Faculty of Medicine and Medical Sciences, University of Balamand, Beirut, Lebanon
| | - Jean-Marc Rolain
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Faculté de Médecine et de Pharmacie, 19-21 boulevard Jean Moulin, 13385, Marseille, Cedex 05, France.
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Jamal S, Al Atrouni A, Rafei R, Dabboussi F, Hamze M, Osman M. Molecular mechanisms of antimicrobial resistance in Acinetobacter baumannii, with a special focus on its epidemiology in Lebanon. J Glob Antimicrob Resist 2018; 15:154-163. [PMID: 29859266 DOI: 10.1016/j.jgar.2018.05.022] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 02/24/2018] [Accepted: 05/22/2018] [Indexed: 10/16/2022] Open
Abstract
Acinetobacter baumannii is an opportunistic bacterium involved in several types of infection with high mortality and morbidity, especially in intensive care units. Treatment of these infections remains a challenge due to the worldwide emergence of broad-spectrum resistance to many antibiotics. Following the implementation of molecular techniques to study A. baumannii outbreaks, it has been shown that they are mainly caused by specific clones such as international clones I, II and III. The present work aims to review the available data on the mechanisms underlying antimicrobial resistance in A. baumannii, with a special focus on the molecular epidemiology of this species in Lebanon.
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Affiliation(s)
- Sabah Jamal
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie, Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon
| | - Ahmad Al Atrouni
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie, Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon
| | - Rayane Rafei
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie, Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon
| | - Fouad Dabboussi
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie, Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie, Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon.
| | - Marwan Osman
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie, Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon
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Genomic mapping of ST85 bla NDM-1 and bla OXA-94 producing Acinetobacter baumannii isolates from Syrian Civil War Victims. Int J Infect Dis 2018; 74:100-108. [PMID: 30053579 DOI: 10.1016/j.ijid.2018.07.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 07/17/2018] [Accepted: 07/18/2018] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVES The rapid emergence of carbapenem-resistant Acinetobacter baumannii is a global health concern. A comparative genomic analysis was performed on two ST85 A. baumannii strains harboring blaNDM-1 and blaOXA-94 collected in Lebanon from Syrian Civil War victims. METHODS Genome sequencing data of ACMH-6200 and ACMH-6201 were used for in silico extraction of multilocus sequence types (MLST), resistance genes, and virulence factors. Plasmids were genetically mapped in silico and using PCR-based replicon typing (PBRT). The genetic environment of blaNDM-1 and blaOXA-94 was determined, and whole-genome single nucleotide polymorphism (wgSNP) analysis in comparison with 41 publicly available A. baumannii genomes was performed. RESULTS Tn125 carrying blaNDM-1 was truncated by the insertion of ISAba14 downstream of dct, generating ΔTn125. blaOXA-94 was upstream of ISAba13 and ISAba17. Resistance to ceftazidime could be attributed to AmpC cephalosporinase encoded by blaADC-25, and to blaNDM-1 on plasmids. GyrA (S83L) and ParC (S80L) substitutions conferred resistance to fluoroquinolones. wgSNP analysis separated the isolates based on their sequence types. CONCLUSIONS The role of refugees in the transmission of antimicrobial resistance in developing countries is understudied. As such, this study sheds light on the correlation between population mobility and the importation of drug-resistant pathogens. It also highlights the manifold mechanisms underlying antibiotic resistance in A. baumannii.
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Abbara A, Rawson TM, Karah N, El-Amin W, Hatcher J, Tajaldin B, Dar O, Dewachi O, Abu Sitta G, Uhlin BE, Sparrow A. A summary and appraisal of existing evidence of antimicrobial resistance in the Syrian conflict. Int J Infect Dis 2018; 75:26-33. [PMID: 29936319 DOI: 10.1016/j.ijid.2018.06.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 06/13/2018] [Accepted: 06/14/2018] [Indexed: 11/30/2022] Open
Abstract
Antimicrobial resistance (AMR) in populations experiencing war has yet to be addressed, despite the abundance of contemporary conflicts and the protracted nature of twenty-first century wars, in combination with growing global concern over conflict-associated bacterial pathogens. The example of the Syrian conflict is used to explore the feasibility of using existing global policies on AMR in conditions of extreme conflict. The available literature on AMR and prescribing behaviour in Syria before and since the onset of the conflict in March 2011 was identified. Overall, there is a paucity of rigorous data before and since the onset of conflict in Syria to contextualize the burden of AMR. However, post onset of the conflict, an increasing number of studies conducted in neighbouring countries and Europe have reported AMR in Syrian refugees. High rates of multidrug resistance, particularly Gram-negative organisms, have been noted amongst Syrian refugees when compared with local populations. Conflict impedes many of the safeguards against AMR, creates new drivers, and exacerbates existing ones. Given the apparently high rates of AMR in Syria, in neighbouring countries hosting refugees, and in European countries providing asylum, this requires the World Health Organization and other global health institutions to address the causes, costs, and future considerations of conflict-related AMR as an issue of global governance.
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Affiliation(s)
- Aula Abbara
- Department of Infection, Imperial College Healthcare NHS Trust, London, UK.
| | - Timothy M Rawson
- National Institute for Health Research, Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, UK.
| | - Nabil Karah
- Department of Molecular Biology, Laboratory for Molecular Infection Medicine Sweden, and Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden.
| | - Wael El-Amin
- Department of Microbiology, Broomfield Hospital, Chelmsford, Essex, UK.
| | - James Hatcher
- Department of Infection, Imperial College Healthcare NHS Trust, London, UK
| | | | - Osman Dar
- Public Health England, London, UK; Chatham House Centre on Global Health Security, London, UK.
| | - Omar Dewachi
- Conflict and Health Program, American University of Beirut, Lebanon.
| | | | - Bernt Eric Uhlin
- Department of Molecular Biology, Laboratory for Molecular Infection Medicine Sweden, and Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Annie Sparrow
- Department of Population Health Sciences and Policy, Icahn School of Medicine at Mount Sinai, New York, USA.
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Hajjar Soudeiha M, Dahdouh E, Daoud Z, Sarkis DK. Phenotypic and genotypic detection of β-lactamases in Acinetobacter spp. isolates recovered from Lebanese patients over a 1-year period. J Glob Antimicrob Resist 2018; 12:107-112. [DOI: 10.1016/j.jgar.2017.09.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 05/19/2017] [Accepted: 09/21/2017] [Indexed: 10/18/2022] Open
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Joshi PR, Acharya M, Kakshapati T, Leungtongkam U, Thummeepak R, Sitthisak S. Co-existence of blaOXA-23 and blaNDM-1 genes of Acinetobacter baumannii isolated from Nepal: antimicrobial resistance and clinical significance. Antimicrob Resist Infect Control 2017; 6:21. [PMID: 28191309 PMCID: PMC5297125 DOI: 10.1186/s13756-017-0180-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 02/03/2017] [Indexed: 01/22/2023] Open
Abstract
Background Molecular analysis of carbapenem-resistant genes in Acinetobacter baumannii, an emerging pathogen, is less commonly reported from Nepal. In this study we determined the antibiotic susceptibility profile and genetic mechanism of carbapenem resistance in clinical isolates of A. baumannii. Methods A. baumannii were isolated from various clinical specimens and identified based on Gram staining, biochemical tests, and PCR amplification of organism specific 16S rRNA and blaOXA-51 genes. The antibiotic susceptibility testing was performed using disc diffusion and E-test method. Multiplex PCR assays were used to detect the following β-lactamase genes: four class D carbapenem hydrolyzing oxacillinases (blaOXA-51, blaOXA-23, blaOXA-24 and blaOXA-58). Uniplex PCRs were used to detect three class B metallo-β-lactamases genes (blaIMP, blaVIM and blaNDM-1), class C cephalosporin resistance genes (blaADC), aminoglycoside resistance gene (aphA6), and ISAba1 of all isolates. Insertion sequence ISAba125 among NDM-1 positive strains was detected. Clonal relatedness of all isolates were analyzed using repetitive sequence-based PCR (rep-PCR). Results Of total 44 analyzed isolates, 97.7% (n = 43) were carbapenem-resistant A. baumannii (CR-AB) and 97.7% (n = 43) were multidrug resistant A. baumannii (MDR-AB). One isolate was detected to be extremely drug resistant A. baumannii (XDR-AB). All the isolates were fully susceptible to colistin (MICs < 2 μg/ml). The blaOXA-23 gene was detected in all isolates, while blaNDM-1 was detected in 6 isolates (13.6%). Insertion sequence, ISAba1 was detected in all of blaOXA-23 positive isolates. ISAba125 was detected in all blaNDM-1 positive strains. The blaADC and aphA6 genes were detected in 90.1 and 40.1%, respectively. The rep-PCR of all isolates represented 7 different genotypes. Conclusion We found high prevalence of CR-AB and MDR-AB with blaOXA-23 gene in a tertiary care hospital in Nepal. Systemic network surveillance should be established for monitoring and controlling the spread of these resistant strains. Electronic supplementary material The online version of this article (doi:10.1186/s13756-017-0180-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Prabhu Raj Joshi
- Central Department of Microbiology, Tribhuvan University, Kirtipur, Kathmandu Nepal
| | - Mahesh Acharya
- Central Department of Microbiology, Tribhuvan University, Kirtipur, Kathmandu Nepal
| | - Trishna Kakshapati
- Annapurna Neurological Institute and Allied Sciences, Maitighar, Kathmandu Nepal
| | - Udomluk Leungtongkam
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Rapee Thummeepak
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Sutthirat Sitthisak
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand.,Centre of Excellence in Medical Biotechnology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
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Mohajeri P, Farahani A, Mehrabzadeh RS. Molecular Characterization of Multidrug Resistant Strains of Acinetobacter baumannii Isolated from Intensive Care Units in West of Iran. J Clin Diagn Res 2017; 11:DC20-DC22. [PMID: 28384861 DOI: 10.7860/jcdr/2017/21156.9397] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 07/08/2016] [Indexed: 11/24/2022]
Abstract
INTRODUCTION According to the results of various studies using phenotypic methods, the prevalence of Multidrug Resistant (MDR) Acinetobacter baumannii (A. baumannii) isolates has been increasing worldwide. Pulsed-Field Gel Electrophoresis (PFGE) technique is known as the gold standard method to determine clonal characterization of bacterial species, especially A. baumannii. AIM To determine the clonal relatedness and investigate the prevalence of integron classes 1 and 2 and genes encoding OXA-23 and 24 in A.baumanii isolates. MATERIALS AND METHODS A cross-sectional study was conducted from November 2011 to January 2013. A total of 140 A.baumannii isolates collected from three hospitals of Kermanshah were considered out of which 75 ICU isolates were included in this study. Antibiotics susceptibility test was done by disk diffusion method. Polymerase Chain Reaction (PCR) was performed in order to detect class 1 and 2 integrons and blaOXA-23-like, blaOXA-24-like genes. Isolates identified as MDR from a total of 75 Intensive Care Units (ICU) strains were subjected to genotyping for clonal relatedness. RESULTS A total of 37 isolates among 75 ICU isolates were identified as MDR. The maximum drug resistance was observed against ceftriaxone, mezlocycline, cefotaxime, piperacilin, ciprofloxacin and imipenem. Frequency of Class 1 and Class 2 Integrons, blaOXA-23-like and blaOXA-24-like genes were 33(44%), 27(36%), 60(80%) and 14(18.6%) respectively. Four clusters with high level of similarity were obtained showing homogeneity among MDR isolates. CONCLUSION Significant correlation between presence of integrons and resistance to different classes of antibiotic was observed in this study. Monitoring of drug resistance using gene integrase PCR and blaOXA gene by cluster analysis is very important to plan specific infection control measures due to MDR A. baumannii.
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Affiliation(s)
- Parviz Mohajeri
- Associate Professor, Department of Microbiology, Kermanshah University of Medical Sciences , Kermanshah, Iran
| | - Abbas Farahani
- Student Research Committee, Ahvaz Jundishapur University of Medical Sciences , Ahvaz, Iran; PhD Candidate, Research Assistant, Department of Microbiology, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Rasa Sheini Mehrabzadeh
- PhD Student, Research Assistant, Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz , Ahvaz, Iran
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Dahdouh E, Hajjar M, Suarez M, Daoud Z. Acinetobacter baumannii Isolated from Lebanese Patients: Phenotypes and Genotypes of Resistance, Clonality, and Determinants of Pathogenicity. Front Cell Infect Microbiol 2016; 6:163. [PMID: 27933276 PMCID: PMC5122575 DOI: 10.3389/fcimb.2016.00163] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 11/09/2016] [Indexed: 12/20/2022] Open
Abstract
Introduction:Acinetobacter baumannii is a nosocomial pathogen that usually affects critically ill patients. High mortality rates have been associated with MDR A. baumannii infections. Carbapenem resistance among these isolates is increasing worldwide and is associated with certain International Clones (ICs) and oxacillinases (OXAs). Moreover, this organism possesses a wide range of virulence factors, whose expression is not yet fully understood. In this study, clinical A. baumannii isolates are characterized in terms of antibiotic resistance, mechanisms of carbapenem resistance, clonality, and virulence. Materials and Methods:A. baumannii clinical isolates (n = 90) where obtained from a tertiary care center in Beirut, Lebanon. API 20NE strips in addition to the amplification of blaOXA−51−like were used for identification. Antibiotic susceptibility testing by disk diffusion was then performed in addition to PCRs for the detection of the most commonly disseminated carbapenemases. Clonality was determined by tri-locus PCR typing and doubling times were determined for isolates with varying susceptibility profiles. Biofilm formation, hemolysis, siderophore production, proteolytic activity, and surface motility was then determined for all the isolates. Statistical analysis was then performed for the determination of associations. Results and Discussion: 81 (90%) of the isolates were resistant to carbapenems. These high rates are similar to other multi-center studies in the country suggesting the need of intervention on a national level. 74 (91.3%) of the carbapenem resistant isolates harbored blaOXA−23−like including two that also harbored blaOXA−24−like. 88.9% of the A. baumannii isolates pertained to ICII and three other international clones were detected, showing the wide dissemination of clones into geographically distinct locations. Virulence profiles were highly diverse and no specific pattern was observed. Nevertheless, an association between motility, siderophore production, and biofilm formation was detected (p < 0.05). Conclusions: A very high rate of carbapenem resistance was detected, showing the need for immediate intervention. IC II and OXA-23-like were the most disseminated, reflecting their international dissemination. No specific associations were made between virulence and resistance, but instead associations among certain virulence factors were found. Investigating a more clonally diverse pool of isolates could help in the determination of associations between virulence and resistance.
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Affiliation(s)
- Elias Dahdouh
- Department of Animal Health, Faculty of Veterinary, Universidad Complutense de Madrid Madrid, Spain
| | - Micheline Hajjar
- Department of Clinical Microbiology, Faculty of Medicine, University of Balamand Balamand, Lebanon
| | - Monica Suarez
- Department of Animal Health, Faculty of Veterinary, Universidad Complutense de Madrid Madrid, Spain
| | - Ziad Daoud
- Department of Clinical Microbiology, Faculty of Medicine, University of Balamand Balamand, Lebanon
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Biglari S, Hanafiah A, Mohd Puzi S, Ramli R, Rahman M, Lopes BS. Antimicrobial Resistance Mechanisms and Genetic Diversity of Multidrug-Resistant Acinetobacter baumannii Isolated from a Teaching Hospital in Malaysia. Microb Drug Resist 2016; 23:545-555. [PMID: 27854165 DOI: 10.1089/mdr.2016.0130] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Multidrug-resistant (MDR) Acinetobacter baumannii has increasingly emerged as an important nosocomial pathogen. The aim of this study was to determine the resistance profiles and genetic diversity in A. baumannii clinical isolates in a tertiary medical center in Malaysia. The minimum inhibitory concentrations of carbapenems (imipenem and meropenem), cephalosporins (ceftazidime and cefepime), and ciprofloxacin were determined by E-test. PCR and sequencing were carried out for the detection of antibiotic resistance genes and mutations. Clonal relatedness among A. baumannii isolates was determined by REP-PCR. Sequence-based typing of OXA-51 and multilocus sequence typing were performed. One hundred twenty-five of 162 (77.2%) A. baumannii isolates had MDR phenotype. From the 162 A. baumannii isolates, 20 strain types were identified and majority of A. baumannii isolates (66%, n = 107) were classified as strain type 1 and were positive for ISAba1-blaOXA-23 and ISAba1-blaADC and had mutations in both gyrA and parC genes at positions, 83 and 80, resulting in serine-to-leucine conversion. REP-PCR analysis showed 129 REP types that generated 31 clones with a 90% similarity cutoff value. OXA-66 variant of the blaOXA-51-like genes was predominantly detected among our A. baumannii clinical isolates belonging to ST195 (found in six clones: 1, 8, 9, 19, 27, and 30) and ST208 (found in clone 21). The study helps us in understanding the genetic diversity of A. baumannii isolates in our setting and confirms that international clone II is the most widely distributed clone in Universiti Kebangsaan Malaysia Medical Centre, Malaysia.
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Affiliation(s)
- Shirin Biglari
- 1 Department of Medical Microbiology and Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre , Kuala Lumpur, Malaysia
| | - Alfizah Hanafiah
- 1 Department of Medical Microbiology and Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre , Kuala Lumpur, Malaysia
| | - Shaliawani Mohd Puzi
- 1 Department of Medical Microbiology and Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre , Kuala Lumpur, Malaysia
| | - Ramliza Ramli
- 1 Department of Medical Microbiology and Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre , Kuala Lumpur, Malaysia
| | - Mostafizur Rahman
- 1 Department of Medical Microbiology and Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre , Kuala Lumpur, Malaysia
| | - Bruno Silvester Lopes
- 2 Department of Medical Microbiology, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen , Aberdeen, United Kingdom
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Jasemi S, Douraghi M, Adibhesami H, Zeraati H, Rahbar M, Boroumand MA, Aliramezani A, Ghourchian S, Mohammadzadeh M. Trend of extensively drug-resistant Acinetobacter baumannii and the remaining therapeutic options: a multicenter study in Tehran, Iran over a 3-year period. Lett Appl Microbiol 2016; 63:466-472. [PMID: 27626896 DOI: 10.1111/lam.12669] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 08/19/2016] [Accepted: 09/08/2016] [Indexed: 12/22/2022]
Abstract
Comprehensive data on drug-resistant patterns of Acinetobacter baumannii isolates in developing countries is limited. We conducted a multihospital study to assess the rate and trend of drug-resistant phenotypes in Ac. baumannii using standardized definitions and to determine the remaining therapeutic options against resistant phenotypes. The 401 nonduplicate isolates were collected from six hospitals which are geographically distributed across Tehran, Iran over a 3-year period. Following PCR of blaOXA-51-like gene, susceptibility testing was performed against nine antimicrobial agent categories. Three hundred and ninety (97%) isolates were resistant to least two carbapenems; carbapenem-resistant Ac. baumannii. The majority of isolates (366, 91·3%) were extensively drug resistant (XDR) and the rest of the isolates were classified as multidrug resistant (26, 6·8%) and susceptible (9, 2·2%). The rate of XDR-AB slightly decreased from 93·8% in 2011 to 89·8% in 2013. A considerable decrease in resistance to doxycycline, minocycline and tigecycline was demonstrated. The XDR-AB isolates showed susceptibility to gentamicin (10·4%), tobramycin (23%), ampicilin-sulbactam (30·1%), minocycline (32·8%), tigecycline (10·7%), doxycycline (21·6%), colistin (100%) and polymixin B (100%). We demonstrated the rising trend of resistance to all antibiotic categories except tetracyclines and folate pathway inhibitors. We found that the treatment options against XDR-AB are extremely limited and each treatment alternative including even old, but safe, antibiotics might be considered. SIGNIFICANCE AND IMPACT OF THE STUDY The high frequency of drug-resistant phenotypes including carbapenem-resistant Acinetobacter baumannii, multidrug-resistant, and extensively resistant has been demonstrated in Ac. baumannii isolates tested here. As the antibiotic resistance pattern of isolates varies in different geographical regions, this study can provide comprehensive information about the antibiotic resistance profile of Ac. baumannii isolates in Tehran. In addition, the resistance profiles could be effectively considered by clinicians to manage antibiotic therapy. This work also emphasizes on the prudent use of antibiotics and the monitoring of antibiotic susceptibility trend and rate.
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Affiliation(s)
- S Jasemi
- Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - M Douraghi
- Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.,Food Microbiology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - H Adibhesami
- Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - H Zeraati
- Department of Epidemiology and Biostatistics, Tehran University of Medical Sciences, Tehran, Iran
| | - M Rahbar
- Department of Microbiology, Reference Health Laboratories, Ministry of Health, Tehran, Iran
| | - M A Boroumand
- Department of Pathology, Tehran Heart Center, Tehran University of Medical Sciences, Tehran, Iran
| | - A Aliramezani
- Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - S Ghourchian
- Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - M Mohammadzadeh
- Department of Infectious Diseases, Pediatrics Infectious Diseases Research Center, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
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Jiang M, Liu L, Ma Y, Zhang Z, Li N, Zhang F, Zhao S. Molecular Epidemiology of Multi-Drug Resistant Acinetobacter baumannii Isolated in Shandong, China. Front Microbiol 2016; 7:1687. [PMID: 27818659 PMCID: PMC5073130 DOI: 10.3389/fmicb.2016.01687] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 10/07/2016] [Indexed: 12/20/2022] Open
Abstract
Acinetobacter baumannii is an emerging nosocomial pathogen prevalent in hospitals worldwide. In order to understand the molecular epidemiology of multi-drug resistant (MDR) A. baumannii, we investigated the genotypes of A. baumannii isolated from 10 hospitals in Shandong, China, from August 2013 to December 2013, by pulsed field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Antimicrobial resistance genes were analyzed by PCR and DNA sequencing. By PFGE analysis, we discovered 11 PFGE types in these 10 hospitals. By MLST, we assigned these isolates to 12 sequence types (STs), 10 of which belong to the cloning complex CC92, including the prevalent ST369, ST208, ST195, and ST368. Two new STs, namely ST794 and ST809, were detected only in one hospital. All isolates of the MDR A. baumannii were resistant to carbapenem, except 2 isolates, which did not express the blaOXA-23 carbapenemase gene, indicating blaOXA-23 is the major player for carbapenem resistance. We also discovered armA is likely to be responsible for amikacin resistance, and may play a role in gentamicin and tobramycin resistance. aac(3)-I is another gene responsible for gentamicin and tobramycin resistance. In summary, we discovered that the majority of the isolates in Shandong, China, were the STs belonging to the CC92. Besides, two new STs were detected in one hospital. These new STs should be further investigated for prevention of outbreaks caused by A. baumannii.
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Affiliation(s)
- Meijie Jiang
- The Department of Clinical Laboratory, Tai'an City Central Hospital Tai'an, China
| | - Lijuan Liu
- The Department of Hematology, Laiwu City People's Hospital Laiwu, China
| | - Yunhua Ma
- The Department of Clinical Laboratory, Zoucheng City People's Hospital Zoucheng, China
| | - Zhijun Zhang
- The Department of Clinical Laboratory, Tai'an City Central Hospital Tai'an, China
| | - Ning Li
- The Department of Preventive Veterinary, College of Veterinary Medicine, Shandong Agricultural University Tai'an, China
| | - Fusen Zhang
- Intensive Medicine, Tai'an City Central Hospital Tai'an, China
| | - Shuping Zhao
- The Department of Clinical Laboratory, Tai'an City Central Hospital Tai'an, China
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Voulgari E, Politi L, Pitiriga V, Dendrinos J, Poulou A, Georgiadis G, Tsakris A. First report of an NDM-1 metallo-β-lactamase-producing Acinetobacter baumannii clinical isolate in Greece. Int J Antimicrob Agents 2016; 48:761-762. [PMID: 27773496 DOI: 10.1016/j.ijantimicag.2016.09.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 09/12/2016] [Indexed: 11/16/2022]
Affiliation(s)
- Evangelia Voulgari
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Lida Politi
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Vassiliki Pitiriga
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | | | - Aggeliki Poulou
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | | | - Athanassios Tsakris
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece.
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Al Atrouni A, Hamze M, Jisr T, Lemarié C, Eveillard M, Joly-Guillou ML, Kempf M. Wide spread of OXA-23-producing carbapenem-resistant Acinetobacter baumannii belonging to clonal complex II in different hospitals in Lebanon. Int J Infect Dis 2016; 52:29-36. [PMID: 27663910 DOI: 10.1016/j.ijid.2016.09.017] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 09/14/2016] [Accepted: 09/15/2016] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVES To investigate the molecular epidemiology of Acinetobacter baumannii strains isolated from different hospitals in Lebanon. METHODS A total of 119 non-duplicate Acinetobacter strains were identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and partial rpoB gene sequencing. Antibiotic susceptibility testing was performed by disc diffusion method and all identified carbapenem-resistant isolates were investigated by PCR assays for the presence of the carbapenemase-encoding genes. Multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) were used for molecular typing. RESULTS Of the 119 A. baumannii isolates, 76.5% were resistant to carbapenems. The most common carbapenemase was the OXA-23-type, found in 82 isolates. The study of population structure using MLST revealed the presence of 30 sequence types (STs) including 18 new ones, with ST2 being the most commonly detected, accounting for 61% of the isolates typed. PFGE performed on all strains of ST2 identified a major cluster of 53 isolates, in addition to three other minor clusters and ten unique profiles. CONCLUSIONS This study highlights the wide dissemination of highly related OXA-23-producing carbapenem-resistant A. baumannii belonging to the international clone II in Lebanon. Thus, appropriate infection control measures are recommended in order to control the geographical spread of this clone in this country.
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Affiliation(s)
- Ahmad Al Atrouni
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie et Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon; ATOMycA, InsermAtip-Avenir Team, CRCNA, Inserm U892, 6299 CNRS, University of Angers, Angers, France
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie et Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon
| | - Tamima Jisr
- Department of Clinical Laboratory, Makassed General Hospital, Beirut, Lebanon
| | - Carole Lemarié
- Laboratoire de Bactériologie, Institut de Biologie en Santé - Centre Hospitalier Universitaire Angers, 4 rue Larrey, 49933 Angers cedex, France
| | - Matthieu Eveillard
- ATOMycA, InsermAtip-Avenir Team, CRCNA, Inserm U892, 6299 CNRS, University of Angers, Angers, France; Laboratoire de Bactériologie, Institut de Biologie en Santé - Centre Hospitalier Universitaire Angers, 4 rue Larrey, 49933 Angers cedex, France
| | - Marie-Laure Joly-Guillou
- ATOMycA, InsermAtip-Avenir Team, CRCNA, Inserm U892, 6299 CNRS, University of Angers, Angers, France; Laboratoire de Bactériologie, Institut de Biologie en Santé - Centre Hospitalier Universitaire Angers, 4 rue Larrey, 49933 Angers cedex, France
| | - Marie Kempf
- ATOMycA, InsermAtip-Avenir Team, CRCNA, Inserm U892, 6299 CNRS, University of Angers, Angers, France; Laboratoire de Bactériologie, Institut de Biologie en Santé - Centre Hospitalier Universitaire Angers, 4 rue Larrey, 49933 Angers cedex, France.
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Al Atrouni A, Hamze M, Rafei R, Eveillard M, Joly-Guillou ML, Kempf M. Diversity of Acinetobacter species isolated from different environments in Lebanon: a nationwide study. Future Microbiol 2016; 11:1147-56. [DOI: 10.2217/fmb-2016-0082] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Aim: To investigate the extrahospital reservoirs of Acinetobacter spp. in Lebanon. Materials & methods: Two thousand three hundred and sixty-one samples from different ecological niches were analyzed by culture methods. Species identification was confirmed by rpoB-gene sequencing. Multilocus sequence typing was used to characterize the Acinetobacter baumannii clones. Results & conclusion: Acinetobacter spp. were detected in 14% of environmental samples and 8% of food samples. Furthermore, 9% of animals and 3.4% of humans were colonized. Non-baumannii Acinetobacter were the most common species isolated and newly susceptible A. baumannii clones were detected. Interestingly, 21 isolates were not identified at the species level and were considered as putative novel species. To our knowledge, this is the largest epidemiological study investigating the epidemiology of Acinetobacter spp. outside hospitals.
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Affiliation(s)
- Ahmad Al Atrouni
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie et Faculté de Santé Publique, Université Libanaise, Tripoli, Liban
- ATOMycA, Inserm Atip-Avenir Team, CRCNA, Inserm U892, 6299 CNRS, University of Angers, France
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie et Faculté de Santé Publique, Université Libanaise, Tripoli, Liban
| | - Rayane Rafei
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie et Faculté de Santé Publique, Université Libanaise, Tripoli, Liban
| | - Matthieu Eveillard
- ATOMycA, Inserm Atip-Avenir Team, CRCNA, Inserm U892, 6299 CNRS, University of Angers, France
- Laboratoire de Bactériologie, Institut de Biologie en Santé – Centre Hospitalier Universitaire, Angers, France
| | - Marie-Laure Joly-Guillou
- ATOMycA, Inserm Atip-Avenir Team, CRCNA, Inserm U892, 6299 CNRS, University of Angers, France
- Laboratoire de Bactériologie, Institut de Biologie en Santé – Centre Hospitalier Universitaire, Angers, France
| | - Marie Kempf
- ATOMycA, Inserm Atip-Avenir Team, CRCNA, Inserm U892, 6299 CNRS, University of Angers, France
- Laboratoire de Bactériologie, Institut de Biologie en Santé – Centre Hospitalier Universitaire, Angers, France
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Yang Q, Rui Y. Two Multiplex Real-Time PCR Assays to Detect and Differentiate Acinetobacter baumannii and Non- baumannii Acinetobacter spp. Carrying blaNDM, blaOXA-23-Like, blaOXA-40-Like, blaOXA-51-Like, and blaOXA-58-Like Genes. PLoS One 2016; 11:e0158958. [PMID: 27391234 PMCID: PMC4938629 DOI: 10.1371/journal.pone.0158958] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Accepted: 06/26/2016] [Indexed: 01/01/2023] Open
Abstract
Nosocomial infections caused by Acinetobacter spp. resistant to carbapenems are increasingly reported worldwide. Carbapenem-resistant Acinetobacter (CRA) is becoming a serious concern with increasing patient morbidity, mortality, and lengths of hospital stay. Therefore, the rapid detection of CRA is essential for epidemiological surveillance. Polymerase chain reaction (PCR) has been extensively used for the rapid identification of most pathogens. In this study, we have developed two multiplex real-time PCR assays to detect and differentiate A. baumannii and non-A. baumannii Acinetobacter spp, and common carbapenemase genes, including blaNDM, blaOXA-23-like, blaOXA-40-like, blaOXA-51-like, and blaOXA-58-like. We demonstrate the potential utility of these assays for the direct detection of blaNDM-, blaOXA-23-like-, blaOXA-40-like-, blaOXA-51-like-, and blaOXA-58-like-positive CRA in clinical specimens. Primers were specifically designed, and two multiplex real-time PCR assays were developed: multiplex real-time PCR assay1 for the detection of Acinetobacter baumannii 16S–23S rRNA internal transcribed spacer sequence, the Acinetobacter recA gene, and class-B-metalloenzyme-encoding gene blaNDM; and multiplex real-time PCR assay2 to detect class-D-oxacillinase-encoding genes (blaOXA-23-like, blaOXA-40-like, blaOXA-51-like,and blaOXA-58-like). The assays were performed on an ABI Prism 7500 FAST Real-Time PCR System. CRA isolates were used to compare the assays with conventional PCR and sequencing. Known amounts of CRA cells were added to sputum and fecal specimens and used to test the multiplex real-time PCR assays. The results for target and nontarget amplification showed that the multiplex real-time PCR assays were specific, the limit of detection for each target was 10 copies per 20 μL reaction volume, the assays were linear over six log dilutions of the target genes (r2 > 0.99), and the Ct values of the coefficients of variation for intra- and interassay reproducibility were less than 5%. The multiplex real-time PCR assays showed 100% concordance with conventional PCR when tested against 400 CRA isolates and their sensitivity for the target DNA in sputum and fecal specimens was 102 CFU/mL. Therefore, these novel multiplex real-time PCR assays allow the sensitive and specific characterization and differentiation of blaNDM-, blaOXA-23-like-, blaOXA-40-like-, blaOXA-51-like-, and blaOXA-58-like-positive CRA, making them potential tools for the direct detection of CRA in clinical specimens and the surveillance of nosocomial infections.
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Affiliation(s)
- Qiu Yang
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yongyu Rui
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
- * E-mail:
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Mathlouthi N, Al-Bayssari C, Bakour S, Rolain JM, Chouchani C. RETRACTED ARTICLE: Prevalence and emergence of carbapenemases-producing Gram-negative bacteria in Mediterranean basin. Crit Rev Microbiol 2016; 43:43-61. [DOI: 10.3109/1040841x.2016.1160867] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Najla Mathlouthi
- Université Tunis El-Manar, Faculté des Sciences de Tunis, Laboratoire des Microorganismes et Biomolécules Actives, Campus Universitaire, El-Manar II, Tunisia
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM 63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
- Université de Carthage, Institut Supérieur des Sciences et Technologies de l’Environnement de Borj-Cedria, Technopôle de Borj-Cedria, BP-1003, Hammam-Lif, Tunisia
| | - Charbel Al-Bayssari
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM 63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
| | - Sofiane Bakour
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM 63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
| | - Jean Marc Rolain
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM 63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
| | - Chedly Chouchani
- Université Tunis El-Manar, Faculté des Sciences de Tunis, Laboratoire des Microorganismes et Biomolécules Actives, Campus Universitaire, El-Manar II, Tunisia
- Université de Carthage, Institut Supérieur des Sciences et Technologies de l’Environnement de Borj-Cedria, Technopôle de Borj-Cedria, BP-1003, Hammam-Lif, Tunisia
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Ozaras R, Leblebicioglu H, Sunbul M, Tabak F, Balkan II, Yemisen M, Sencan I, Ozturk R. The Syrian conflict and infectious diseases. Expert Rev Anti Infect Ther 2016; 14:547-55. [PMID: 27063349 DOI: 10.1080/14787210.2016.1177457] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The conflict in Syria is a big humanitarian emergency. More than 200,000 Syrians have been killed, with more than half of the population either having been displaced or having immigrated. Healthcare has been interrupted due to the destruction of facilities, a lack of medical staff, and a critical shortage of life-saving medications. It produced suitable conditions leading to the re-emergence of tuberculosis, cutaneous leishmaniasis, polio, and measles. Lebanon and Jordan reported increased rates of tuberculosis among Syrian refugees. Cutaneous leishmaniasis outbreaks were noted not only in Syria but also in Turkey, Jordan, and Lebanon. After a polio-free 15 years, Syria reported a polio outbreak. Ongoing measles outbreaks in the region was accelerated by the conflict. Iraq declared a cholera outbreak among the Syrian refugees. The healthcare facilities of the countries hosting immigrants, mainly Turkey, Lebanon, Jordan, Iraq, and Egypt, are overburdened. The majority of the immigrants live in crowded and unsanitary conditions. Infectious diseases are big challenges for Syria and for the countries hosting immigrants. More structured support from international organizations is needed for the prevention, control, diagnosis, and treatment of infectious diseases.
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Affiliation(s)
- Resat Ozaras
- a Department of Infectious Diseases and Clinical Microbiology , Istanbul University, Cerrahpasa Medical School , Istanbul , Turkey
| | - Hakan Leblebicioglu
- b Department of Infectious Diseases and Clinical Microbiology , Ondokuz Mayis University, Medical School , Samsun , Turkey
| | - Mustafa Sunbul
- b Department of Infectious Diseases and Clinical Microbiology , Ondokuz Mayis University, Medical School , Samsun , Turkey
| | - Fehmi Tabak
- a Department of Infectious Diseases and Clinical Microbiology , Istanbul University, Cerrahpasa Medical School , Istanbul , Turkey
| | - Ilker Inanc Balkan
- a Department of Infectious Diseases and Clinical Microbiology , Istanbul University, Cerrahpasa Medical School , Istanbul , Turkey
| | - Mucahit Yemisen
- a Department of Infectious Diseases and Clinical Microbiology , Istanbul University, Cerrahpasa Medical School , Istanbul , Turkey
| | - Irfan Sencan
- c Department. of Infectious Diseases and Clinical Microbiology , Sakarya University, Medical School , Sakarya , Turkey.,d Ministry of Health , Head of Turkish Public Health Institution , Ankara , Turkey
| | - Recep Ozturk
- a Department of Infectious Diseases and Clinical Microbiology , Istanbul University, Cerrahpasa Medical School , Istanbul , Turkey
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Microbiology and risk factors associated with war-related wound infections in the Middle East. Epidemiol Infect 2016; 144:2848-57. [PMID: 26931769 DOI: 10.1017/s0950268816000431] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The Middle East region is plagued with repeated armed conflicts that affect both civilians and soldiers. Injuries sustained during war are common and frequently associated with multiple life-threatening complications. Wound infections are major consequences of these war injuries. The microbiology of war-related wound infections is variable with predominance of Gram-negative bacteria in later stages. The emergence of antimicrobial resistance among isolates affecting war-related wound injuries is a serious problem with major regional and global implications. Factors responsible for the increase in multidrug-resistant pathogens include timing and type of surgical management, wide use of antimicrobial drugs, and the presence of metallic or organic fragments in the wound. Nosocomial transmission is the most important factor in the spread of multidrug-resistant pathogens. Wound management of war-related injuries merits a multidisciplinary approach. This review aims to describe the microbiology of war-related wound infections and factors affecting their incidence from conflict areas in Iraq, Syria, Israel, and Lebanon.
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