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Khan MAS, Chaity SC, Hosen A, Rahman SR. Genomic epidemiology of multidrug-resistant clinical Acinetobacter baumannii in Bangladesh. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024:105656. [PMID: 39116952 DOI: 10.1016/j.meegid.2024.105656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 07/04/2024] [Accepted: 08/05/2024] [Indexed: 08/10/2024]
Abstract
The rising frequency of multidrug-resistant (MDR) Acinetobacter baumannii infections represents a significant public health challenge in Bangladesh. Genomic analysis of bacterial pathogens enhances surveillance and control efforts by providing insights into genetic diversity, antimicrobial resistance (AMR) profiles, and transmission dynamics. In this study, we conducted a comprehensive bioinformatic analysis of 82 whole-genome sequences (WGS) of A. baumannii from Bangladesh to understand their genomic epidemiological characteristics. WGS of the MDR and biofilm-forming A. baumannii strain S1C revealed the presence of 28 AMR genes, predicting its pathogenicity and classification within sequence type ST2. Multi-locus sequence typing (MLST) genotyping suggested heterogeneity in the distribution of clinical A. baumannii strains in Bangladesh, with a predominance of ST575. The resistome diversity was evident from the detection of 82 different AMR genes, with antibiotic inactivation being the most prevalent resistance mechanism. All strains were predicted to be multidrug-resistant. The observed virulence genes were associated with immune evasion, biofilm formation, adherence, nutrient acquisition, effector delivery, and other mechanisms. Mobile genetic elements carrying AMR genes were predicted in 68.29% (N = 56) of the genomes. The "open" state of the pan-genome and a high proportion of accessory genes highlighted the genome plasticity and diversity of A. baumannii in Bangladesh. Additionally, phylogenomic analysis indicated clustering of A. baumannii strains into three separate clades according to sequence type. In summary, our findings offer detailed insights into the genomic landscape of A. baumannii in Bangladesh, contributing to our understanding of its epidemiology and pathogenicity and informing strategies to combat this pathogen.
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Affiliation(s)
| | | | - Arman Hosen
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
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Endo S, Tada T, Oshiro S, Hishinuma T, Tohya M, Watanabe S, Sekiguchi JI, Abe M, Nakada K, Kirikae T. Evaluation of antimicrobial susceptibility tests for Acinetobacter and Pseudomonas species using disks containing a high dose of meropenem. Sci Rep 2024; 14:2749. [PMID: 38302510 PMCID: PMC10834437 DOI: 10.1038/s41598-024-52538-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 01/19/2024] [Indexed: 02/03/2024] Open
Abstract
The emergence and dissemination of carbapenem-resistant species of Acinetobacter and Pseudomonas have become a serious health concern. Routine antimicrobial disk susceptibility tests in clinical laboratories cannot distinguish between isolates that are highly carbapenem-resistant and those that are moderately carbapenem-resistant. The present study describes antimicrobial susceptibility tests using disks containing high doses (1000 μg) of meropenem. The diameters of inhibition zones were significantly negatively correlated with the MICs of Pseudomonas and Acinetobacter species for meropenem (R2: 0.93 and 0.91, respectively) and imipenem (R2: 0.75 and 0.84, respectively). Double disk synergy tests using clavulanic acid or sodium mercaptoacetate can detect ESBL or MBL producers. Susceptibility tests using disks containing high doses of meropenem can easily detect highly carbapenem-resistant isolates in a quantitative manner. These disks may be useful in bacteriological laboratories because of their technical ease, stability, and relatively low cost.
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Affiliation(s)
- Shoichiro Endo
- Department of Microbiology, Juntendo University School of Medicine, Tokyo, Japan
- Department of Clinical Laboratory, The Jikei University Daisan Hospital, Tokyo, Japan
| | - Tatsuya Tada
- Department of Microbiology, Juntendo University School of Medicine, Tokyo, Japan
| | - Satoshi Oshiro
- Department of Microbiology, Juntendo University School of Medicine, Tokyo, Japan
| | - Tomomi Hishinuma
- Department of Microbiology, Juntendo University School of Medicine, Tokyo, Japan
| | - Mari Tohya
- Department of Microbiology, Juntendo University School of Medicine, Tokyo, Japan
| | - Shin Watanabe
- Department of Microbiome Research, Juntendo University School of Medicine, Tokyo, Japan
| | | | - Masaki Abe
- Department of Clinical Laboratory, The Jikei University Daisan Hospital, Tokyo, Japan
| | - Koji Nakada
- Department of Clinical Laboratory, The Jikei University Daisan Hospital, Tokyo, Japan
| | - Teruo Kirikae
- Department of Microbiology, Juntendo University School of Medicine, Tokyo, Japan.
- Department of Microbiome Research, Juntendo University School of Medicine, Tokyo, Japan.
- AMR Research Laboratory, Juntendo Advanced Research Institute for Health Science, Juntendo University, Tokyo, Japan.
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Miyoshi-Akiyama T, Thanh DV, Phuong TT, Huy NQ, Thuy PTP, Kirikae T, Nhung PH, Ohmagari N. Molecular Epidemiology of Escherichia coli Resistant to Carbapenems, Fluoroquinolones, and Aminoglycosides Isolated from One of the Largest Hospitals in Vietnam in 2014-2019. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2024; 2024:2711353. [PMID: 38328340 PMCID: PMC10849806 DOI: 10.1155/2024/2711353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 10/23/2023] [Accepted: 11/13/2023] [Indexed: 02/09/2024]
Abstract
Introduction Multidrug-resistant (MDR) Gram-negative bacilli including carbapenem-resistant Gram-negative Enterobacteriaceae (CRE) threaten global health. Little is known, however, about the distribution of antimicrobial resistance genes in MDR isolated from patients in Vietnamese hospitals. In this study, we collected MDR Escherichia coli, defined as E. coli resistance against all fluoroquinolones, aminoglycosides, and carbapenems. Aim This study was designed to clarify the molecular epidemiology of Escherichia coli isolates resistant to carbapenems, fluoroquinolones, and aminoglycosides isolated from patients admitted to one of the largest hospitals in Vietnam in 2014-2019 based on both whole-genome sequencing (WGS) and phenotypic data. Methodology. Sixty-seven Vietnamese isolates screened by drug resistance by the disk test were subjected to WGS, and their sequences were analyzed to determine their multilocus sequence type (MLST), O-types, H-types, distribution of drug resistance genes, plasmid types, pathogenicity islands (PIs), virulence factor distribution, and phylogenetic evolution using the WGS data. Results Among the STs detected, ST410 was relatively dominant. Dominant O-types and H-types were O102 and H9 and showed some links, such as those between O102 and H8. The most dominant plasmid type and carbapenemase type were 4 and NDM-5, respectively. MLST, O-types, H-types, plasmid types, and types of carbapenemases were very heterogeneous among the isolates, with no clear correlation between them. Dominant plasmid type carrying drug resistance gene was IncQ1_1. The percentage of isolates positive for drug resistance genes, such as anti-beta-lactams and aminoglycosides, was relatively high because the isolates screened were resistant to carbapenems, fluoroquinolones, and aminoglycosides. Conclusions MDR E. coli isolates isolated at a high-volume Vietnamese hospital were very heterogeneous, suggesting that they were acquired from different sources, including nosocomial infection, animals, and water. Eradication of MDR E. coli from hospitals and other clinical environments is very challenging because a single measure may be ineffective.
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Affiliation(s)
- Tohru Miyoshi-Akiyama
- Pathogenic Microbe Laboratory, Research Institute, National Center for Global Health and Medicine, Toyama 1-21-1, Shinjuku-ku, Tokyo 162-8655, Japan
| | - Do Van Thanh
- Bach Mai Hospital, 78 Gia Phong Road, Phuong Mai, Dong Da District, Hanoi, Vietnam
| | - Truong Thai Phuong
- Bach Mai Hospital, 78 Gia Phong Road, Phuong Mai, Dong Da District, Hanoi, Vietnam
| | - Nguyen Quang Huy
- Bach Mai Hospital, 78 Gia Phong Road, Phuong Mai, Dong Da District, Hanoi, Vietnam
| | - Pham Thi Phuong Thuy
- NCGM-Bach Mai Hospital Medical Collaboration Center, 78 Gia Phong Road, Phuong Mai, Dong Da District, Hanoi, Vietnam
| | - Teruo Kirikae
- Department of Infectious Diseases, National Center for Global Health and Medicine, Toyama 1-21-1, Shinjuku-ku, Tokyo 162-8655, Japan
- Department of Microbiology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku 113-0033, Japan
| | - Pham Hong Nhung
- Bach Mai Hospital, 78 Gia Phong Road, Phuong Mai, Dong Da District, Hanoi, Vietnam
- Department of Microbiology, Hanoi Medical University, 1 Ton That Tung, Dong, Da District, Hanoi, Vietnam
| | - Norio Ohmagari
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Toyama 1-21-1, Shinjuku-ku, Tokyo 162-8655, Japan
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Findlay J, Nordmann P, Bouvier M, Kerbol A, Poirel L. Dissemination of ArmA- and OXA-23-co-producing Acinetobacter baumannii Global Clone 2 in Switzerland, 2020-2021. Eur J Clin Microbiol Infect Dis 2023:10.1007/s10096-023-04643-4. [PMID: 37470894 DOI: 10.1007/s10096-023-04643-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 07/11/2023] [Indexed: 07/21/2023]
Abstract
Following the observation of an increased number of isolation of OXA-23- and ArmA-producing Acinetobacter baumannii at the national level, our aim was to evaluate whether some given clone(s) might actually be spreading and/or emerging in Switzerland. To evaluate this possibility, our study investigated and characterized all A. baumannii isolates harboring both the blaOXA-23 and armA genes that had been collected at the Swiss National Reference Center for Emerging Antibiotic Resistance (NARA) from 2020 to 2021. Most isolates were obtained from infections rather than colonization with the majority being obtained from respiratory specimens. Pulsed-field gel electrophoresis (PFGE) analysis of 56 isolates identified nine profiles. Then, whole-genome sequencing that was performed on a subset of 11 isolates including at least one representative isolate of each PFGE profile identified three STs; one each of ST25 and ST1902, and nine ST2 (a member of Global Clone 2 (GC-2). The blaOXA-23 gene was always found embedded within Tn2006 structures, as commonly described with GC-2 (ST2) isolates. Susceptibility testing showed that most of those isolates, despite being highly resistant to all carbapenems and all aminoglycosides, remained susceptible to colistin (94.6%), sulbactam-durlobactam (87.5%), and cefiderocol (83.9% or 91.1% according to EUCAST or CLSI breakpoints, respectively). Overall, this study identified that the A. baumannii co-producing OXA-23 and ArmA are increasing in incidence in Switzerland, largely due to the dissemination of the high-risk GC-2. This highlights the importance of the monitoring of such MDR A. baumannii strains, in order to contribute to reduce their potential further spread.
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Affiliation(s)
- Jacqueline Findlay
- Medical and Molecular Microbiology, Department of Medicine, University of Fribourg, Chemin du Musée 18, CH-1700, Fribourg, Switzerland
| | - Patrice Nordmann
- Medical and Molecular Microbiology, Department of Medicine, University of Fribourg, Chemin du Musée 18, CH-1700, Fribourg, Switzerland
- Swiss National Reference Center for Emerging Antibiotic Resistance, University of Fribourg, Fribourg, Switzerland
| | - Maxime Bouvier
- Swiss National Reference Center for Emerging Antibiotic Resistance, University of Fribourg, Fribourg, Switzerland
| | - Auriane Kerbol
- Swiss National Reference Center for Emerging Antibiotic Resistance, University of Fribourg, Fribourg, Switzerland
| | - Laurent Poirel
- Medical and Molecular Microbiology, Department of Medicine, University of Fribourg, Chemin du Musée 18, CH-1700, Fribourg, Switzerland.
- Swiss National Reference Center for Emerging Antibiotic Resistance, University of Fribourg, Fribourg, Switzerland.
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Genomic characterisation of multidrug-resistant Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii in two intensive care units in Hanoi, Viet Nam: a prospective observational cohort study. THE LANCET. MICROBE 2022; 3:e857-e866. [PMID: 36206776 DOI: 10.1016/s2666-5247(22)00181-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 11/15/2022]
Abstract
BACKGROUND Viet Nam has high rates of antimicrobial resistance (AMR) but little capacity for genomic surveillance. This study used whole genome sequencing to examine the prevalence and transmission of three key AMR pathogens in two intensive care units (ICUs) in Hanoi, Viet Nam. METHODS A prospective surveillance study of all adults admitted to ICUs at the National Hospital for Tropical Diseases and Bach Mai Hospital was done between June 19, 2017, and Jan 16, 2018. Clinical and environmental samples were cultured on selective media, characterised with MALDI TOF mass spectrometry, and sequenced with Illumina. Phylogenies based on the de-novo assemblies (SPAdes) were constructed with MAFFT (PARsnp), Gubbins, and RAxML. Resistance genes were detected with Abricate against the US National Center for Biotechnology Information database. FINDINGS 3153 Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii isolates from 369 patients were analysed. Phylogenetic analysis revealed predominant lineages within A baumannii (global clone 2, sequence types ST2 and ST571) and K pneumoniae (ST15, ST16, ST656, ST11, and ST147) isolates. Isolation from stool was most common with E coli (87·0%) followed by K pneumoniae (62·5%). Of the E coli, 85·0% carried a blaCTX-M variant, while 81·8% of K pneumoniae isolates carried blaNDM (54·4%), or blaKPC (45·1%), or both. Transmission analysis with single nucleotide polymorphisms identified 167 clusters involving 251 (68%) of 369 patients, in some cases involving patients from both ICUs. There were no clear differences between the lineages or AMR genes recovered between the two ICUs. INTERPRETATION This study represents the largest prospective surveillance study of key AMR pathogens in Vietnamese ICUs. Clusters of closely related isolates in patients across both ICUs suggests recent transmission before ICU admission in other health-care settings or in the community. FUNDING UK Medical Research Council Newton Fund, Viet Nam Ministry of Science and Technology, Wellcome Trust, Academy of Medical Sciences, Health Foundation, and UK National Institute for Health and Care Research Cambridge Biomedical Research Centre.
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Leelapsawas C, Yindee J, Nittayasut N, Chueahiran S, Boonkham P, Suanpairintr N, Chanchaithong P. Emergence and multi-lineages of carbapenemase-producing Acinetobacter baumannii-calcoaceticus complex from canine and feline origins. J Vet Med Sci 2022; 84:1377-1384. [PMID: 36031361 PMCID: PMC9586037 DOI: 10.1292/jvms.22-0276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The carbapenemase-producing Acinetobacter baumannii is an important
opportunistic bacterium and frequently causes hospital-acquired infections in humans. It
also has increasingly been reported in veterinary medicine. This study illustrates
multiple clones of carbapenemase-producing A. baumannii disseminating and
causing diseases in dogs and cats in Thailand. Between 2016 and 2020, 44 A.
baumannii and two A. pittii isolates exhibiting imipenem
resistance (MIC≥16 μg/mL) from diagnostic samples were characterized by Pasteur multilocus
sequence typing (MLST), sequence grouping (SG), repetitive extragenic palindromic element
(rep)-PCR fingerprint analysis and antimicrobial resistance (AMR)
profiling. All isolates contained blaOXA-23 in the
Tn2006 family, and A. baumannii showed the sequence
type (ST) 16 (14/44), ST149 (12/44), ST25 (6/44), ST2 (4/44), ST1581 (3/44), ST23 (2/44),
ST1575 (1/44) and ST1576 (1/44). DNA fingerprint analysis and SG illustrated clonal
relationships in the STs and its single locus variants, and AMR gene profiles, including
tetracycline and aminoglycoside resistance genes, showed minor variations in the clones.
The findings suggest that blaOXA-23 has been spread in
multiple clones of A. baumannii and A. pittii from
canine and feline hosts. With the collection of multiple AMR genes and intrinsic
resistance, antimicrobial options are limited for treatment, and pets can be a potential
reservoir of extensively drug-resistant, carbapenemase-producing A.
baumannii in the community. Epidemiological tracking by passive and active
surveillance in animals, veterinary personnel and hospital environment and preventive
measurements should be promoted to decrease the risk of infection and transmission to
humans.
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Affiliation(s)
- Chavin Leelapsawas
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University
| | - Jitrapa Yindee
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University
| | - Naiyaphat Nittayasut
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University
| | - Surawit Chueahiran
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University
| | - Pongthai Boonkham
- Veterinary Diagnostic Laboratory, Faculty of Veterinary Science, Chulalongkorn University
| | | | - Pattrarat Chanchaithong
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University.,Research Unit in Microbial Food Safety and Antimicrobial Resistance, Faculty of Veterinary Science, Chulalongkorn University
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Taylor E, Jauneikaite E, Sriskandan S, Woodford N, Hopkins KL. Novel 16S rRNA methyltransferase RmtE3 in Acinetobacter baumannii ST79. J Med Microbiol 2022; 71. [PMID: 35588089 DOI: 10.1099/jmm.0.001531] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Introduction. The 16S rRNA methyltransferase (16S RMTase) gene armA is the most common mechanism conferring high-level aminoglycoside resistance in Acinetobacter baumannii, although rmtA, rmtB, rmtC, rmtD and rmtE have also been reported.Hypothesis/Gap statement. The occurrence of 16S RMTase genes in A. baumannii in the UK and Republic of Ireland is currently unknown.Aim. To identify the occurrence of 16S RMTase genes in A. baumannii isolates from the UK and the Republic of Ireland between 2004 and 2015.Methodology. Five hundred and fifty pan-aminoglycoside-resistant A. baumannii isolates isolated from the UK and the Republic of Ireland between 2004 and 2015 were screened by PCR to detect known 16S RMTase genes, and then whole-genome sequencing was conducted to screen for novel 16S RMTase genes.Results. A total of 96.5 % (531/550) of isolates were positive for 16S RMTase genes, with all but 1 harbouring armA (99.8 %, 530/531). The remaining isolates harboured rmtE3, a new rmtE variant. Most (89.2 %, 473/530) armA-positive isolates belonged to international clone II (ST2), and the rmtE3-positive isolate belonged to ST79. rmtE3 shared a similar genetic environment to rmtE2 but lacked an ISCR20 element found upstream of rmtE2.Conclusion. This is the first report of rmtE in A. baumannii in Europe; the potential for transmission of rmtE3 to other bacterial species requires further research.
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Affiliation(s)
- Emma Taylor
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, Reference Services Division, UK Health Security Agency, London NW9 5EQ, UK
- Present address: Department of Bacteriology, Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone, Surrey, KT15 3NB, UK
| | - Elita Jauneikaite
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
- School of Public Health, Imperial College London, London W2 1PG, UK
| | - Shiranee Sriskandan
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2DD, UK
| | - Neil Woodford
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, Reference Services Division, UK Health Security Agency, London NW9 5EQ, UK
| | - Katie L Hopkins
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, Reference Services Division, UK Health Security Agency, London NW9 5EQ, UK
- Healthcare Associated Infections, Fungal, Antimicrobial Resistance, Antimicrobial Usage and Sepsis Division, UK Health Security Agency, London NW9 5EQ, UK
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Molecular and genetic characterization of emerging carbapenemase-producing Acinetobacter baumannii strains from patients and hospital environments in Bangladesh. Infect Prev Pract 2022; 4:100215. [PMID: 35603008 PMCID: PMC9118665 DOI: 10.1016/j.infpip.2022.100215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 04/20/2022] [Indexed: 11/25/2022] Open
Abstract
Background Carbapenemase-producing multidrug-resistant (MDR) Acinetobacter baumannii is a global health care problem. MDR A. baumannii has emerged as an important nosocomial pathogen, costing many lives worldwide including Bangladesh. Aim To investigate the detailed molecular epidemiology of carbapenem-resistant A. baumannii (CRAB) both from patients and the hospital environment, to shed light on genetic characteristics and transmission dynamics. Methods A set of 49 clinical A. baumannii strains collected during early 2015 was received from the clinical microbiology laboratory of Dhaka Medical College Hospital (DMCH) in Bangladesh. Additionaly, 100 environmental samples were also collected from the hospital surfaces of Dhaka Medical College Hospital and analyzed for carbapenamase-producing A. baumannii. CRAB were identified by culture on selective plates, biochemical testing and MALDI-TOF. All isolates were characterized by susceptibility testing, realtime-PCRs, conventional PCR, MLST and sequencing. Findings Clinical A. baumannii were resistant to ciprofloxacin (100%), imipenem (91.8%), meropenem (91.8%), gentamicin (91.8%), amikacin (87.7%), and trimethoprim-sulfamethoxazole (61.2%). The majority (59%) of the isolates were MDR. All environmental A. baumannii (n=10) were resistant to imipenem, meropenem, gentamicin, amikacin, and ciprofloxacin. Strains carried the following antibiotic resistant genes; blaOXA-23,blaOXA-58,blaPER-7,qnrB1, qnrC1, aac(6′)1b-cr and armA. A total of 36 different clones were identified by rep-PCR and common clonal clusters were found both in patients and hospital environments. MLST analysis revealed different sequence types (ST2, ST10, ST149, ST575, ST1063 and ST1065). In clinical and environmental settings. A. baumannii ST2 dominated in both clinical and environmental settings. Both clinical and environmental A. baumannii strains with known STs carried several biofilm-related genes; bap, csuE, and pgaB. Conclusion Widespread dissemination of MDR A. baumannii in the DMC hospital of Bangladesh is a serious problem.
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Hirabayashi A, Yanagisawa H, Takahashi H, Yahara K, Boeing P, Wolfenden B, Nov V, Lorn V, Veng M, Ann V, Darapheak C, Shibayama K, Suzuki M. On-Site Genomic Epidemiological Analysis of Antimicrobial-Resistant Bacteria in Cambodia With Portable Laboratory Equipment. Front Microbiol 2021; 12:675463. [PMID: 34054783 PMCID: PMC8158813 DOI: 10.3389/fmicb.2021.675463] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/22/2021] [Indexed: 11/29/2022] Open
Abstract
The rapid emergence of carbapenemase-producing gram-negative bacteria (CPGNB) is a global threat due to the high mortality of infection and limited treatment options. Although there have been many reports of CPGNB isolated from Southeast Asian countries, to date there has been no genetic analysis of CPGNB isolated from Cambodia. Sequence-based molecular epidemiological analysis enables a better understanding of the genotypic characteristics and epidemiological significance of antimicrobial-resistant (AMR) bacteria in each country, and allows countries to enact measures related to AMR issues. In this study, we performed on-site genomic epidemiological analysis of CPGNB isolated in Cambodia using a portable laboratory equipment called Bento Lab, which combines a PCR thermal cycler, microcentrifuge, gel electrophoresis apparatus, and LED transilluminator, along with the MinION nanopore sequencer. PCR targeting of major carbapenemase genes using Bento Lab revealed that two Escherichia coli isolates and one Acinetobacter baumannii isolate harbored carbapenemase genes: blaNDM, blaOXA–48, and blaOXA–23, respectively. The results of phenotypic diagnostic tests for CPGNB, such as the carbapenem inactivation method and double-disk diffusion test using a specific inhibitor of metallo-β-lactamases, were consistent with their AMR genotypes. Whole-genome sequencing analysis using MinION revealed that blaNDM–5 gene was carried on a 93.9-kb plasmid with IncFIA/IncFIB/IncFII/IncQ1 replicons, and blaOXA–181 gene was carried on a 51.5-kb plasmid with the IncX3 replicon in E. coli isolates. blaOXA–23 was encoded in two locations on the chromosome of A. baumannii. Plasmids carrying blaNDM–5 or blaOXA–181 in E. coli were highly structurally identical to plasmids prevalent in Enterobacterales in China and other countries, suggesting that they disseminated from a common evolutionary origin. Our findings demonstrate the potential impact of portable laboratory equipment on AMR bacteria research in hospitals and research centers with limited research facilities, and provide the first glimpse into the genomic epidemiology of CPGNB in Cambodia.
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Affiliation(s)
- Aki Hirabayashi
- AMR Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Hiromizu Takahashi
- Department of General Medicine, Juntendo University School of Medicine, Tokyo, Japan
| | - Koji Yahara
- AMR Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | | | | | - Vandarith Nov
- National Institute of Public Health, Phnom Penh, Cambodia
| | - Vichet Lorn
- National Institute of Public Health, Phnom Penh, Cambodia
| | - Mom Veng
- National Institute of Public Health, Phnom Penh, Cambodia
| | - Vuth Ann
- National Institute of Public Health, Phnom Penh, Cambodia
| | - Chau Darapheak
- National Institute of Public Health, Phnom Penh, Cambodia
| | - Keigo Shibayama
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masato Suzuki
- AMR Research Center, National Institute of Infectious Diseases, Tokyo, Japan
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Taj Z, Rasool MH, Almatroudi A, Saqalein M, Khurshid M. Extensively Drug-resistant Acinetobacter baumannii Belonging to International Clone II from A Pet Cat with Urinary Tract Infection; The First Report from Pakistan. Pol J Microbiol 2020; 69:1-4. [PMID: 32343078 PMCID: PMC7324854 DOI: 10.33073/pjm-2020-017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 03/26/2020] [Accepted: 03/29/2020] [Indexed: 02/04/2023] Open
Abstract
The carbapenem-resistant Acinetobacter baumannii (CRAB) has got global attention as a notorious nosocomial pathogen. This study describes a case of urinary tract infection in a 2-years old pet female cat infected with A. baumannii. The susceptibility profiling, screening for the resistance determinants, and the multilocus sequence typing was performed. The A. baumannii isolate was found to harbor the blaOXA23-like gene and corresponded to International clone II that has been widely reported to be involved in human infections. The study proposes that the pets may contribute towards the spread of clinically relevant antimicrobial-resistant pathogens. The carbapenem-resistant Acinetobacter baumannii (CRAB) has got global attention as a notorious nosocomial pathogen. This study describes a case of urinary tract infection in a 2-years old pet female cat infected with A. baumannii. The susceptibility profiling, screening for the resistance determinants, and the multilocus sequence typing was performed. The A. baumannii isolate was found to harbor the blaOXA23-like gene and corresponded to International clone II that has been widely reported to be involved in human infections. The study proposes that the pets may contribute towards the spread of clinically relevant antimicrobial-resistant pathogens.
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Affiliation(s)
- Zeeshan Taj
- Department of Microbiology , Government College University Faisalabad , Pakistan ; Pet Care Clinic , Faisalabad , Pakistan
| | | | - Ahmad Almatroudi
- Department of Medical Laboratories , College of Applied Medical Sciences , Qassim University , Qassim , Saudi Arabia
| | - Muhammad Saqalein
- Department of Microbiology , Government College University Faisalabad , Pakistan ; Pet Care Clinic , Faisalabad , Pakistan
| | - Mohsin Khurshid
- Department of Microbiology , Government College University Faisalabad , Pakistan
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11
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Ohno MK, Kirikae T, Yoshihara E, Kirikae F, Ishida I. Addition of L-cysteine to the N- or C-terminus of the all-D-enantiomer [ D(KLAKLAK) 2] increases antimicrobial activities against multidrug-resistant Pseudomonas aeruginosa, Acinetobacter baumannii and Escherichia coli. PeerJ 2020; 8:e10176. [PMID: 33335804 PMCID: PMC7713595 DOI: 10.7717/peerj.10176] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 09/22/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Antimicrobial peptides have a broad spectrum of antimicrobial activities and are attracting attention as promising next-generation antibiotics against multidrug-resistant (MDR) bacteria. The all-d-enantiomer [D(KLAKLAK)2] has been reported to have antimicrobial activity against Escherichia coli and Pseudomonas aeruginosa, and to be resistant to protein degradation in bacteria because it is composed of D-enantiomer compounds. In this study, we demonstrated that modification of [D(KLAKLAK)2] by the addition of an L-cysteine residue to its N- or C- terminus markedly enhanced its antimicrobial activities against Gram-negative bacteria such as MDR Acinetobacter baumannii, E. coli, and P. aeruginosa. METHODS The peptides [D(KLAKLAK)2] (DP), DP to which L-cysteine was added at the N-terminus C-DP, and DP to which L-cysteine was added at the C-terminus DP-C, were synthesized at >95% purity. The minimum inhibitory concentrations of peptides and antibiotics were determined by the broth microdilution method. The synergistic effects of the peptides and the antibiotics against MDR P. aeruginosa were evaluated using the checkerboard dilution method. In order to assess how these peptides affect the survival of human cells, cell viability was determined using a Cell Counting Kit-8. RESULTS C-DP and DP-C enhanced the antimicrobial activities of the peptide against MDR Gram-negative bacteria, including A. baumannii, E. coli, and P. aeruginosa. The antimicrobial activity of DP-C was greater than that of C-DP, with these peptides also having antimicrobial activity against drug-susceptible P. aeruginosa and drug-resistant P. aeruginosa overexpressing the efflux pump components. C-DP and DP-C also showed antimicrobial activity against colistin-resistant E. coli harboring mcr-1, which encodes a lipid A modifying enzyme. DP-C showed synergistic antimicrobial activity against MDR P. aeruginosa when combined with colistin. The LD50 of DP-C against a human cell line HepG2 was six times higher than the MIC of DP-C against MDR P. aeruginosa. The LD50 of DP-C was not altered by incubation with low-dose colistin. CONCLUSION Attachment of an L-cysteine residue to the N- or C-terminus of [D(KLAKLAK)2] enhanced its antimicrobial activity against A. baumannii, E. coli, and P. aeruginosa. The combination of C-DP or DP-C and colistin had synergistic effects against MDR P. aeruginosa. In addition, DP-C and C-DP showed much stronger antimicrobial activity against MDR A. baumannii and E. coli than against P. aeruginosa.
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Affiliation(s)
- Maki K. Ohno
- Faculty of Pharmaceutical Sciences, Teikyo Heisei University, Tokyo, Japan
| | - Teruo Kirikae
- Department of Microbiology, Juntendo University School of Medicine, Tokyo, Japan
| | | | - Fumiko Kirikae
- Department of Microbiology, Juntendo University School of Medicine, Tokyo, Japan
| | - Isao Ishida
- Faculty of Pharmaceutical Sciences, Teikyo Heisei University, Tokyo, Japan
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12
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Osman M, B Halimeh F, Rafei R, Mallat H, Tom JE, Raad EB, M Diene S, Jamal S, Atrouni AA, Dabboussi F, Moudani W, Madec JY, Saras E, Lupo A, Haenni M, Rolain JM, Hamze M. Investigation of an XDR-Acinetobacter baumannii ST2 outbreak in an intensive care unit of a Lebanese tertiary care hospital. Future Microbiol 2020; 15:1535-1542. [DOI: 10.2217/fmb-2020-0079] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Aim: We sought to investigate the genetic epidemiological relatedness of carbapenem-resistant Acinetobacter baumannii (CRAB) strains of a suspected outbreak in a Lebanese tertiary care hospital to implement necessary infection prevention and control measures. Methods: Twenty-eight nonduplicate CRAB isolates detected among hospitalized patients between January 2016 and July 2017 were studied by real-time polymerase chain reaction (PCR), pulsed-field gel electrophoresis and multilocus sequence typing analyses. Results: Twenty-seven isolates harbored blaOXA-23, of which one also carried blaNDM-1. The isolates distributed temporally in two presumably episodes were stratified by pulsed-field gel electrophoresis into many clusters. Although several clones have become endemic in the hospital, we have rapidly implemented appropriate infection prevention and control measures, achieving full eradication from August 2017 to November 2019. Conclusion: We have successfully investigated and controlled a polyclonal outbreak of OXA-23 producing ST2 CRAB.
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Affiliation(s)
- Marwan Osman
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science & Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Fatima B Halimeh
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science & Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
- Aix-Marseille University, IRD, APHM, MEPHI, IHU Méditerranée infection, Faculté de Médecine et de Pharmacie, 19-21 boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
| | - Rayane Rafei
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science & Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Hassan Mallat
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science & Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
- El Youssef Hospital Center, Halba, Lebanon
| | - Jad El Tom
- El Youssef Hospital Center, Halba, Lebanon
| | | | - Seydina M Diene
- Aix-Marseille University, IRD, APHM, MEPHI, IHU Méditerranée infection, Faculté de Médecine et de Pharmacie, 19-21 boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
| | - Sabah Jamal
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science & Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Ahmad Al Atrouni
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science & Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Fouad Dabboussi
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science & Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Walid Moudani
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science & Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Jean-Yves Madec
- Université de Lyon – ANSES laboratoire de Lyon, Unité Antibiorésistance et Virulence Bactériennes, France
| | - Estelle Saras
- Université de Lyon – ANSES laboratoire de Lyon, Unité Antibiorésistance et Virulence Bactériennes, France
| | - Agnese Lupo
- Université de Lyon – ANSES laboratoire de Lyon, Unité Antibiorésistance et Virulence Bactériennes, France
| | - Marisa Haenni
- Université de Lyon – ANSES laboratoire de Lyon, Unité Antibiorésistance et Virulence Bactériennes, France
| | - Jean-Marc Rolain
- Aix-Marseille University, IRD, APHM, MEPHI, IHU Méditerranée infection, Faculté de Médecine et de Pharmacie, 19-21 boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science & Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
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13
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Ogbolu DO, Alli OAT, Oluremi AS, Ogunjimi YT, Ojebode DI, Dada V, Alaka OO, Foster-Nyarko E, Webber MA. Contribution of NDM and OXA-type carbapenemases to carbapenem resistance in clinical Acinetobacter baumannii from Nigeria. Infect Dis (Lond) 2020; 52:644-650. [PMID: 32516021 DOI: 10.1080/23744235.2020.1775881] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Objective: Acinetobacter baumannii infections are rarely diagnosed in many hospitals in Nigeria due to a lack of capacity for the identification of the organism in spite of the clinical significance of this opportunistic nosocomial organism. We assembled a panel of presumptive isolates of A. baumannii from tertiary hospitals in Nigeria and analysed mechanisms of resistance phenotypically and by whole genome sequencing.Materials and methods: Twenty-one clinical isolates of A. baumannii identified using standard microbiological tests were tested for susceptibility to a panel of antibiotics by the agar dilution method, and production of ESBLs using phenotypic tests. Whole genome sequencing and comparative genomic analysis were used to determine the antimicrobial resistance genes, strain types, phylogenetic relationships and genetic context of resistance genes.Results: The MIC50 and MIC90 of most antibiotics were very high with no difference between MIC50 and MIC90 values apart for amikacin, meropenem and colistin where MIC50 and MIC90 ranged between 1-4 µg/ml and 64->64 µg/ml, respectively. Multiple resistance genes were detected in most of the isolates including blaNDM-1, various blaOXA-51 family alleles and blaOXA-23. Interestingly, blaNDM-1 carriage did not always result in phenotypic carbapenem resistance. Whole genome alignments typing showed strains belonged to three major clades. Strains within these clades had different resistance genes and resistance patterns.Conclusions: This report shows a high level of resistance to important antibiotics and carbapenem resistance in A. baumannii in Nigeria. We hope this work will serve as a reference for future study in the sub-Saharan region of Africa.
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Affiliation(s)
- David O Ogbolu
- Department of Biomedical Sciences, Ladoke Akintola University of Technology, Osogbo Campus, Ogbomoso, Nigeria.,Antimicrobials Research Group, Institute for Microbiology and Infection, School of Immunity and Infection, University of Birmingham, Birmingham, UK.,The Quadram Institute, Norwich Research Park, Colney, Norwich, UK
| | - Oyebode A Terry Alli
- Department of Biomedical Sciences, Ladoke Akintola University of Technology, Osogbo Campus, Ogbomoso, Nigeria
| | - Adeolu S Oluremi
- Department of Biomedical Sciences, Ladoke Akintola University of Technology, Osogbo Campus, Ogbomoso, Nigeria
| | - Y Temilola Ogunjimi
- Department of Biomedical Sciences, Ladoke Akintola University of Technology, Osogbo Campus, Ogbomoso, Nigeria
| | - D Iyanu Ojebode
- Department of Biomedical Sciences, Ladoke Akintola University of Technology, Osogbo Campus, Ogbomoso, Nigeria
| | - Veronica Dada
- Department of Medical Microbiology, University College Hospital, Ibadan, Nigeria
| | - Olubunmi O Alaka
- Department of Medical Microbiology, Obafemi Awolowo University Teaching Hospitals Complex, Ile-Ife, Nigeria
| | - Ebenezer Foster-Nyarko
- The Quadram Institute, Norwich Research Park, Colney, Norwich, UK.,Norwich Medical School, Norwich Research Park, Colney, Norwich, UK
| | - Mark A Webber
- The Quadram Institute, Norwich Research Park, Colney, Norwich, UK.,Norwich Medical School, Norwich Research Park, Colney, Norwich, UK
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14
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Intercellular Transfer of Chromosomal Antimicrobial Resistance Genes between Acinetobacter baumannii Strains Mediated by Prophages. Antimicrob Agents Chemother 2019; 63:AAC.00334-19. [PMID: 31138576 DOI: 10.1128/aac.00334-19] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 05/22/2019] [Indexed: 01/01/2023] Open
Abstract
The spread of antimicrobial resistance genes (ARGs) among Gram-negative pathogens, including Acinetobacter baumannii, is primarily mediated by transferable plasmids; however, ARGs are frequently integrated into its chromosome. How ARG gets horizontally incorporated into the chromosome of A. baumannii, and whether it functions as a cause for further spread of ARG, remains unknown. Here, we demonstrated intercellular prophage-mediated transfer of chromosomal ARGs without direct cell-cell interaction in A. baumannii We prepared ARG-harboring extracellular DNA (eDNA) components from the culture supernatant of a multidrug-resistant (MDR) A. baumannii NU-60 strain and exposed an antimicrobial-susceptible (AS) A. baumannii ATCC 17978 strain to the eDNA components. The antimicrobial-resistant (AR) A. baumannii ATCC 17978 derivatives appeared to acquire various ARGs, originating from dispersed loci of the MDR A. baumannii chromosome, along with their surrounding regions, by homologous recombination, with the ARGs including armA (aminoglycoside resistance), bla TEM-1 (β-lactam resistance), tet(B) (tetracycline resistance), and gyrA-81L (nalidixic acid resistance) genes. Notably, the eDNAs conferring antimicrobial resistance were enveloped in specific capsid proteins consisting of phage particles, thereby protecting the eDNAs from detergent and DNase treatments. The phages containing ARGs were likely released into the extracellular space from MDR A. baumannii, thereby transducing ARGs into AS A. baumannii, resulting in the acquisition of AR properties by the recipient. We concluded that the generalized transduction, in which phages were capable of carrying random pieces of A. baumannii genomic DNAs, enabled efficacious intercellular transfer of chromosomal ARGs between A. baumannii strains without direct cell-cell interaction.
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15
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Munier AL, Biard L, Rousseau C, Legrand M, Lafaurie M, Lomont A, Donay JL, de Beaugrenier E, Flicoteaux R, Mebazaa A, Mimoun M, Molina JM. Incidence, risk factors, and outcome of multidrug-resistant Acinetobacter baumannii acquisition during an outbreak in a burns unit. J Hosp Infect 2017; 97:226-233. [PMID: 28751010 DOI: 10.1016/j.jhin.2017.07.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 07/19/2017] [Indexed: 12/31/2022]
Abstract
BACKGROUND Multidrug-resistant Acinetobacter baumannii (MR-AB) can cause outbreaks in a burns unit. AIM To study the incidence, risk factors and outcome of MR-AB colonization during an outbreak. METHODS A prospective study was conducted from April to November 2014 in a burns unit in Paris. Weekly surveillance cultures of patients and their environment were performed. MR-AB acquisition, discharge, or death without MR-AB colonization were considered as competing events. To identify risk factors for colonization, baseline characteristics and time-dependent variables were investigated in univariate and multivariate analyses using Cox models. MR-AB strains were genotypically compared using multi-locus sequence typing. FINDINGS Eighty-six patients were admitted in the burns unit during the study period. Among 77 patients without MR-AB colonization at admission, 25 (32%) acquired MR-AB with a cumulative incidence of 30% at 28 days (95% CI: 20-40). Median time to MR-AB acquisition was 13 days (range: 5-34). In multivariate analysis, risk factors for MR-AB acquisition were ≥2 skin graft procedures performed [hazard ratio (HR): 2.97; 95% confidence interval (CI): 1.10-8.00; P = 0.032] and antibiotic therapy during hospitalization (HR: 4.42; 95% CI: 1.19-16.4; P = 0.026). A major sequence type of MR-AB (ST2) was found in 94% and 92% of patients and environmental strains, respectively, with all strains harbouring the blaOXA-23 gene. MR-AB colonization increased length of hospitalization (HR: 0.32; 95% CI: 0.17-0.58; P = 0.0002) by a median of 12 days. CONCLUSION A high incidence of MR-AB acquisition was seen during this outbreak with most strains from patients and their environment belonging to single sequence type. MR-AB colonization was associated with more skin graft procedures, antibiotic use, and prolonged hospitalization.
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Affiliation(s)
- A-L Munier
- Infectious Disease Department, St Louis Hospital, APHP and University Paris Diderot, Paris, France.
| | - L Biard
- Department of Biostatistics, St Louis Hospital, APHP and University Paris Diderot, Paris, France
| | - C Rousseau
- Microbiology Department, St Louis Hospital, APHP and EA4065, University Paris Descartes, Paris, France
| | - M Legrand
- Department of Anesthesiology, Critical Care and Burn Unit, St Louis Hospital, APHP and University Paris Diderot, Paris, France; INSERM U942, France
| | - M Lafaurie
- Infectious Disease Department, St Louis Hospital, APHP and University Paris Diderot, Paris, France
| | - A Lomont
- Microbiology Department, St Louis Hospital, APHP and EA4065, University Paris Descartes, Paris, France
| | - J-L Donay
- Microbiology Department, St Louis Hospital, APHP and EA4065, University Paris Descartes, Paris, France
| | - E de Beaugrenier
- Pharmacy Department, St Louis Hospital, APHP and University Paris Diderot, Paris, France
| | - R Flicoteaux
- Department of Biostatistics, St Louis Hospital, APHP and University Paris Diderot, Paris, France
| | - A Mebazaa
- Department of Anesthesiology, Critical Care and Burn Unit, St Louis Hospital, APHP and University Paris Diderot, Paris, France
| | - M Mimoun
- Plastic Surgery Department, St Louis Hospital, APHP and University Paris Diderot, Paris, France
| | - J-M Molina
- Infectious Disease Department, St Louis Hospital, APHP and University Paris Diderot, Paris, France
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16
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Hsu LY, Apisarnthanarak A, Khan E, Suwantarat N, Ghafur A, Tambyah PA. Carbapenem-Resistant Acinetobacter baumannii and Enterobacteriaceae in South and Southeast Asia. Clin Microbiol Rev 2017; 30:1-22. [PMID: 27795305 PMCID: PMC5217790 DOI: 10.1128/cmr.masthead.30-1] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Carbapenem-resistant Gram-negative bacteria, in particular the Acinetobacter baumannii-calcoaceticus complex and Enterobacteriaceae, are escalating global public health threats. We review the epidemiology and prevalence of these carbapenem-resistant Gram-negative bacteria among countries in South and Southeast Asia, where the rates of resistance are some of the highest in the world. These countries house more than a third of the world's population, and several are also major medical tourism destinations. There are significant data gaps, and the almost universal lack of comprehensive surveillance programs that include molecular epidemiologic testing has made it difficult to understand the origins and extent of the problem in depth. A complex combination of factors such as inappropriate prescription of antibiotics, overstretched health systems, and international travel (including the phenomenon of medical tourism) probably led to the rapid rise and spread of these bacteria in hospitals in South and Southeast Asia. In India, Pakistan, and Vietnam, carbapenem-resistant Enterobacteriaceae have also been found in the environment and community, likely as a consequence of poor environmental hygiene and sanitation. Considerable political will and effort, including from countries outside these regions, are vital in order to reduce the prevalence of such bacteria in South and Southeast Asia and prevent their global spread.
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Affiliation(s)
- Li-Yang Hsu
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Tan Tock Seng Hospital, Singapore
| | | | - Erum Khan
- Aga Khan University, Karachi, Pakistan
| | - Nuntra Suwantarat
- Chulabhorn International College of Medicine, Thammasat University, Pathum Thani, Thailand
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17
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Carbapenem-Resistant Acinetobacter baumannii and Enterobacteriaceae in South and Southeast Asia. Clin Microbiol Rev 2016. [PMID: 27795305 DOI: 10.1128/cmr.00042-16] [Citation(s) in RCA: 183] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Carbapenem-resistant Gram-negative bacteria, in particular the Acinetobacter baumannii-calcoaceticus complex and Enterobacteriaceae, are escalating global public health threats. We review the epidemiology and prevalence of these carbapenem-resistant Gram-negative bacteria among countries in South and Southeast Asia, where the rates of resistance are some of the highest in the world. These countries house more than a third of the world's population, and several are also major medical tourism destinations. There are significant data gaps, and the almost universal lack of comprehensive surveillance programs that include molecular epidemiologic testing has made it difficult to understand the origins and extent of the problem in depth. A complex combination of factors such as inappropriate prescription of antibiotics, overstretched health systems, and international travel (including the phenomenon of medical tourism) probably led to the rapid rise and spread of these bacteria in hospitals in South and Southeast Asia. In India, Pakistan, and Vietnam, carbapenem-resistant Enterobacteriaceae have also been found in the environment and community, likely as a consequence of poor environmental hygiene and sanitation. Considerable political will and effort, including from countries outside these regions, are vital in order to reduce the prevalence of such bacteria in South and Southeast Asia and prevent their global spread.
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18
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Tran DN, Tran HH, Matsui M, Suzuki M, Suzuki S, Shibayama K, Pham TD, Van Phuong TT, Dang DA, Trinh HS, Loan CT, Nga LTV, van Doorn HR, Wertheim HFL. Emergence of New Delhi metallo-beta-lactamase 1 and other carbapenemase-producing Acinetobacter calcoaceticus-baumannii complex among patients in hospitals in Ha Noi, Viet Nam. Eur J Clin Microbiol Infect Dis 2016; 36:219-225. [PMID: 27714593 PMCID: PMC5253155 DOI: 10.1007/s10096-016-2784-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 09/05/2016] [Indexed: 11/29/2022]
Abstract
Acinetobacter baumannii is an important cause of multidrug-resistant hospital acquired infections in the world. Here, we investigate the presence of NDM-1 and other carbapenemases among carbapenem-resistant A. baumannii isolated between August 2010 and December 2014 from three large hospitals in Hanoi, Vietnam. We identified 23/582 isolates (4 %) (11 from hospital A, five from hospital B, and seven from hospital C) that were NDM-1 positive, and among them 18 carried additional carbapenemase genes, including seven isolates carrying NDM-1, IMP-1, and OXA-58 with high MICs for carbapenems. Genotyping indicated that NDM-1 carrying A. baumannii have expanded clonally in these hospitals. Five new STs (ST1135, ST1136, ST1137, ST1138, and ST1139) were identified. One isolate carried NDM-1 on a plasmid belonging to the N-repA replicon type; no NDM-1-positive plasmids were identified in the other isolates. We have shown the extent of the carbapenem resistance and the local clonal spread of A. baumannii carrying NDM-1 in these hospitals; coexistence of NDM-1 and IMP-1 is reported for the first time from Vietnam here, and this will further seriously limit future therapeutic options.
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Affiliation(s)
- D N Tran
- National Institute of Hygiene and Epidemiology, Yersin 1, Hanoi, Vietnam
| | - H H Tran
- National Institute of Hygiene and Epidemiology, Yersin 1, Hanoi, Vietnam.
| | - M Matsui
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - M Suzuki
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - S Suzuki
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - K Shibayama
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - T D Pham
- National Institute of Hygiene and Epidemiology, Yersin 1, Hanoi, Vietnam
| | - T T Van Phuong
- National Institute of Hygiene and Epidemiology, Yersin 1, Hanoi, Vietnam
| | - D A Dang
- National Institute of Hygiene and Epidemiology, Yersin 1, Hanoi, Vietnam
| | | | - C T Loan
- Saint Paul Hospital, Hanoi, Vietnam
| | | | - H R van Doorn
- Oxford University Clinical Research Unit, Hanoi, Vietnam; Nuffield Department of Clinical Medicine, Centre for Tropical Medicine, University of Oxford, Oxford, UK
| | - H F L Wertheim
- Oxford University Clinical Research Unit, Hanoi, Vietnam; Nuffield Department of Clinical Medicine, Centre for Tropical Medicine, University of Oxford, Oxford, UK.,Department of Clinical Microbiology, Radboud UMC, Nijmegen, Netherlands
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19
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Hassan A, Naz A, Obaid A, Paracha RZ, Naz K, Awan FM, Muhmmad SA, Janjua HA, Ahmad J, Ali A. Pangenome and immuno-proteomics analysis of Acinetobacter baumannii strains revealed the core peptide vaccine targets. BMC Genomics 2016; 17:732. [PMID: 27634541 PMCID: PMC5025611 DOI: 10.1186/s12864-016-2951-4] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 07/19/2016] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Acinetobacter baumannii has emerged as a significant nosocomial pathogen during the last few years, exhibiting resistance to almost all major classes of antibiotics. Alternative treatment options such as vaccines tend to be most promising and cost effective approaches against this resistant pathogen. In the current study, we have explored the pan-genome of A. baumannii followed by immune-proteomics and reverse vaccinology approaches to identify potential core vaccine targets. RESULTS The pan-genome of all available A. baumannii strains (30 complete genomes) is estimated to contain 7,606 gene families and the core genome consists of 2,445 gene families (~32 % of the pan-genome). Phylogenetic tree, comparative genomic and proteomic analysis revealed both intra- and inter genomic similarities and evolutionary relationships. Among the conserved core genome, thirteen proteins, including P pilus assembly protein, pili assembly chaperone, AdeK, PonA, OmpA, general secretion pathway protein D, FhuE receptor, Type VI secretion system OmpA/MotB, TonB dependent siderophore receptor, general secretion pathway protein D, outer membrane protein, peptidoglycan associated lipoprotein and peptidyl-prolyl cis-trans isomerase are identified as highly antigenic. Epitope mapping of the target proteins revealed the presence of antigenic surface exposed 9-mer T-cell epitopes. Protein-protein interaction and functional annotation have shown their involvement in significant biological and molecular processes. The pipeline is validated by predicting already known immunogenic targets against Gram negative pathogen Helicobacter pylori as a positive control. CONCLUSION The study, based upon combinatorial approach of pan-genomics, core genomics, proteomics and reverse vaccinology led us to find out potential vaccine candidates against A. baumannii. The comprehensive analysis of all the completely sequenced genomes revealed thirteen putative antigens which could elicit substantial immune response. The integration of computational vaccinology strategies would facilitate in tackling the rapid dissemination of resistant A.baumannii strains. The scarcity of effective antibiotics and the global expansion of sequencing data making this approach desirable in the development of effective vaccines against A. baumannii and other bacterial pathogens.
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Affiliation(s)
- Afreenish Hassan
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, Pakistan
| | - Anam Naz
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, Pakistan
| | - Ayesha Obaid
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, Pakistan
| | - Rehan Zafar Paracha
- Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), H-12, Islamabad, Pakistan
| | - Kanwal Naz
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, Pakistan
| | - Faryal Mehwish Awan
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, Pakistan
| | - Syed Aun Muhmmad
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | - Hussnain Ahmed Janjua
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, Pakistan
| | - Jamil Ahmad
- Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), H-12, Islamabad, Pakistan
- Department of Computer Science and Information Technology, Stratford University, Falls Church, VA 22043 USA
| | - Amjad Ali
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, Pakistan
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Ramoul A, Loucif L, Bakour S, Amiri S, Dekhil M, Rolain JM. Co-occurrence of blaNDM-1 with blaOXA-23 or blaOXA-58 in clinical multidrug-resistant Acinetobacter baumannii isolates in Algeria. J Glob Antimicrob Resist 2016; 6:136-141. [PMID: 27530856 DOI: 10.1016/j.jgar.2016.05.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 05/04/2016] [Accepted: 05/06/2016] [Indexed: 11/19/2022] Open
Abstract
The aim of this study was to characterise the mechanisms of carbapenem resistance in Acinetobacter baumannii strains isolated in an Algerian hospital. A total of 43 imipenem-resistant A. baumannii clinical isolates collected between 2010 and 2013 were identified using API 20NE and were confirmed by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF/MS). Antibiotic susceptibility testing was performed by the disk diffusion and Etest methods. Carbapenemase activity was detected using microbiological tests and PCR. Genetic transfer of the blaNDM-1 gene was performed by conjugation using sodium azide-resistant Escherichia coli J53 as recipient strain. Clonal relationships were studied by multilocus sequence typing (MLST) using partial sequences of the csuE and blaOXA-51 genes. All 43 A. baumannii isolates were resistant to imipenem with high minimum inhibitory concentrations (MICs) (>32μg/mL). The strains harboured blaOXA-23, blaNDM-1, blaOXA-58 and/or blaOXA-24 genes. Co-existence of blaNDM-1 and blaOXA-23 or blaOXA-58 was detected in two isolates and one isolate, respectively. NDM-1 plasmid transfer to E. coli J53 was successful only for one of the three strains harbouring both blaNDM-1 and blaOXA-23 or blaOXA-58. The phylogenetic tree obtained from concatenation of the partial sequences of csuE and blaOXA-51 showed that there was no genetic relationship between the isolates and the blaNDM-1 resistance gene. Here we report for the first time the co-occurrence of blaNDM-1 along with blaOXA-23 or blaOXA-58 in recent clinical isolates of A. baumannii from Northeast Algeria. These findings re-emphasise the dissemination and rapid spread of blaNDM-1 carbapenemase genes in multidrug-resistant clinical A. baumannii isolates in Algeria.
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Affiliation(s)
- Abir Ramoul
- 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; Département de biochimie, Université Badji Mokhtar, Annaba 23000, Algeria; Laboratoire central de microbiologie, CHU Dr Dorban, Annaba, Algeria
| | - Lotfi Loucif
- 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; Laboratoire de biotechnologie des molécules bioactives et de la physiopathologie cellulaire (LBMBPC), Faculté des sciences de la nature et de la vie, Université de Batna 2, Batna, Algeria
| | - 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
| | - Sabrina Amiri
- Laboratoire central de microbiologie, CHU Dr Dorban, Annaba, Algeria
| | - Mazouz Dekhil
- Laboratoire central de microbiologie, CHU Dr Dorban, Annaba, Algeria
| | - 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.
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