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Gurung A, Napit R, Shrestha B, Lekhak B. Carbapenem Resistance in Acinetobacter calcoaceticus-baumannii Complex Isolates From Kathmandu Model Hospital, Nepal, Is Attributed to the Presence of bla OXA-23-like and bla NDM-1 Genes. BIOMED RESEARCH INTERNATIONAL 2024; 2024:8842625. [PMID: 39161641 PMCID: PMC11333142 DOI: 10.1155/2024/8842625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 04/28/2024] [Accepted: 06/11/2024] [Indexed: 08/21/2024]
Abstract
The Acinetobacter calcoaceticus-baumannii (ACB) complex, also known as ACB complex, consists of four bacterial species that can cause opportunistic infections in humans, especially in hospital settings. Conventional therapies for susceptible strains of the ACB complex include broad-spectrum cephalosporins, β-lactam/β-lactamase inhibitors, and carbapenems. Unfortunately, the effectiveness of these antibiotics has declined due to increasing rates of resistance. The predominant resistance mechanisms identified in the ACB complex involve carbapenem-resistant (CR) oxacillinases and metallo-β-lactamases (MBLs). This research, conducted at Kathmandu Model Hospital in Nepal, sought to identify genes associated with CR, specifically blaNDM-1, blaOXA-23-like, and blaOXA-24-like genes in carbapenem-resistant Acinetobacter calcoaceticus-baumannii (CR-ACB) complex. Additionally, the study is aimed at identifying the ACB complex through the sequencing of the 16s rRNA gene. Among the 992 samples collected from hospitalized patients, 43 (approximately 4.334%) tested positive for the ACB complex. These positive samples were mainly obtained from different hospital units, including intensive care units (ICUs); cabins; and neonatal, general, and maternity wards. The prevalence of infection was higher among males (58.14%) than females (41.86%), with the 40-50 age group showing the highest infection rate. In susceptibility testing, colistin and polymyxin B exhibited a susceptibility rate of 100%, whereas all samples showed resistance to third-generation cephalosporins. After polymyxins, gentamicin (30.23%) and amikacin (34.88%) demonstrated the highest susceptibility. A substantial majority (81.45%) of ACB complex isolates displayed resistance to carbapenems, with respiratory and pus specimens being the primary sources. Polymerase chain reaction (PCR) revealed that the primary CR gene within the ACB complex at this hospital was bla OXA-23-like, followed by bla NDM-1. To ensure the accuracy of the phenotypic assessment, 12 samples were chosen for 16s rRNA sequencing using Illumina MiSeq™ to confirm that they are Acinetobacter species. QIIME 2.0 analysis confirmed all 12 isolates to be Acinetobacter species. In the hospital setting, a substantial portion of the ACB complex carries CR genes, rendering carbapenem ineffective for treatment.
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Affiliation(s)
- Anupama Gurung
- Central Department of MicrobiologyTribhuvan University, Kirtipur, Nepal
| | - Rajindra Napit
- Central Department of BiotechnologyTribhuvan University, Kirtipur, Nepal
| | - Basudha Shrestha
- Department of MicrobiologyKathmandu Model Hospital, Putalisadak, Kathmandu, Nepal
| | - Binod Lekhak
- Central Department of MicrobiologyTribhuvan University, Kirtipur, Nepal
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Rodrigues DCS, Silveira MC, Pribul BR, Karam BRS, Picão RC, Kraychete GB, Pereira FM, de Lima RM, de Souza AKG, Leão RS, Marques EA, Rocha-de-Souza CM, Carvalho-Assef APD. Genomic study of Acinetobacter baumannii strains co-harboring bla OXA-58 and bla NDM-1 reveals a large multidrug-resistant plasmid encoding these carbapenemases in Brazil. Front Microbiol 2024; 15:1439373. [PMID: 39086650 PMCID: PMC11288812 DOI: 10.3389/fmicb.2024.1439373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 07/01/2024] [Indexed: 08/02/2024] Open
Abstract
Introduction Acinetobacter baumannii contributes significantly to the global issue of multidrug-resistant (MDR) nosocomial infections. Often, these strains demonstrate resistance to carbapenems (MDR-CRAB), the first-line treatment for infections instigated by MDR A. baumannii. Our study focused on the antimicrobial susceptibility and genomic sequences related to plasmids from 12 clinical isolates of A. baumannii that carry both the blaOXA-58 and bla NDM-1 carbapenemase genes. Methods Whole-genome sequencing with long-read technology was employed for the characterization of an A. baumannii plasmid that harbors the bla OXA-58 and blaNDM-1 genes. The location of the bla OXA-58 and bla NDM-1 genes was confirmed through Southern blot hybridization assays. Antimicrobial susceptibility tests were conducted, and molecular characterization was performed using PCR and PFGE. Results Multilocus Sequence Typing analysis revealed considerable genetic diversity among bla OXA-58 and bla NDM-1 positive strains in Brazil. It was confirmed that these genes were located on a plasmid larger than 300 kb in isolates from the same hospital, which also carry other antimicrobial resistance genes. Different genetic contexts were observed for the co-occurrence of these carbapenemase-encoding genes in Brazilian strains. Discussion The propagation of bla OXA-58 and bla NDM-1 genes on the same plasmid, which also carries other resistance determinants, could potentially lead to the emergence of bacterial strains resistant to multiple classes of antimicrobials. Therefore, the characterization of these strains is of paramount importance for monitoring resistance evolution, curbing their rapid global dissemination, averting outbreaks, and optimizing therapy.
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Affiliation(s)
- Daiana Cristina Silva Rodrigues
- Laboratório de Bacteriologia Aplicada à Saúde Única e Resistência Antimicrobiana (LabSUR), Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
| | - Melise Chaves Silveira
- Laboratório de Bacteriologia Aplicada à Saúde Única e Resistência Antimicrobiana (LabSUR), Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
| | - Bruno Rocha Pribul
- Laboratório de Bacteriologia Aplicada à Saúde Única e Resistência Antimicrobiana (LabSUR), Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
| | - Bruna Ribeiro Sued Karam
- Laboratório de Bacteriologia Aplicada à Saúde Única e Resistência Antimicrobiana (LabSUR), Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
| | - Renata Cristina Picão
- Laboratório de Investigação em Microbiologia Médica (LIMM), Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Gabriela Bergiante Kraychete
- Laboratório de Investigação em Microbiologia Médica (LIMM), Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | | | - Rildo Mendes de Lima
- Laboratório Central de Saúde Pública da Fundação de Vigilância em Saúde do Amazonas (LACEN-AM/FVS-RCP), Amazonas, Brazil
| | | | - Robson Souza Leão
- Departamento de Microbiologia, Imunologia e Parasitologia (DMIP), Faculdade de Ciências Médicas (FCM), Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Elizabeth Andrade Marques
- Departamento de Microbiologia, Imunologia e Parasitologia (DMIP), Faculdade de Ciências Médicas (FCM), Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Cláudio Marcos Rocha-de-Souza
- Laboratório de Bacteriologia Aplicada à Saúde Única e Resistência Antimicrobiana (LabSUR), Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
| | - Ana Paula D'Alincourt Carvalho-Assef
- Laboratório de Bacteriologia Aplicada à Saúde Única e Resistência Antimicrobiana (LabSUR), Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
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Raddaoui A, Mabrouk A, Chebbi Y, Frigui S, Salah Abbassi M, Achour W, Thabet L. Co-occurrence of blaNDM-1 and blaOXA-23 in carbapenemase-producing Acinetobacter baumannii belonging to high-risk lineages isolated from burn patients in Tunisia. J Appl Microbiol 2024; 135:lxae039. [PMID: 38346864 DOI: 10.1093/jambio/lxae039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 01/10/2024] [Accepted: 02/09/2024] [Indexed: 03/21/2024]
Abstract
AIMS Carbapenem-resistant Acinetobacter baumannii (CR-Ab) is an important cause of infections in burn patients. This study aimed to characterize the antimicrobial susceptibility pattern of CR-Ab isolated from burns in Burn Intensive Care Unit (BICU) of the Trauma and Burn Centre of Ben Arous, to determine the prevalence of β-lactamase-encoding genes and to search eventual genetic relatedness of CR-Ab strains. METHODS AND RESULTS From 15 December 2016 to 2 April 2017, all nonduplicated CR-Ab isolated in burn patients in the BICU were screened by simplex Polymerase Chain Reaction (PCR) for the class A, B, C, and D β-lactamase genes. Sequencing was performed for NDM gene only. Genetic relatedness was determined by using pulsed field gel electrophoresis (PFGE) and by multilocus sequence typing. During the study period, 34 strains of CR-Ab were isolated in burns, mainly in blood culture (n = 14) and central vascular catheter (n = 10). CR-Ab strains were susceptible to colistin but resistant to amikacin (91%), ciprofloxacin (100%), rifampicin (97%), and trimethoprim-sulfamethoxazole (100%). All strains harbored blaOXA-51-like and blaOXA-23 genes, only or associated to blaGES (n = 26; 76%), blaADC (n = 20; 59%), blaPER-1 (n = 6; 18%) or/and blaNDM-1 (n = 3; 9%). PFGE identified 16 different clusters and revealed that most strains belonged to one major cluster A (n = 15; 44.1%). Among NDM-1 isolates, two were clonally related in PFGE and belonged to two single locus variant sequence type ST-6 and ST-85. CONCLUSIONS This is the first description of clonally related NDM-1 and OXA-23-producing A. baumannii strains in the largest Tunisian BICU associated with two single locus variant sequence types ST6 and ST85.
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Affiliation(s)
- Anis Raddaoui
- Laboratory Ward, National Bone Marrow Transplant Center, 1006 Tunis, Tunisia
- Faculty of Medicine of Tunis, LR18ES39, University of Tunis El Manar, 1006 Tunis, Tunisia
| | - Aymen Mabrouk
- Laboratory Ward, National Bone Marrow Transplant Center, 1006 Tunis, Tunisia
- Faculty of Medicine of Tunis, LR18ES39, University of Tunis El Manar, 1006 Tunis, Tunisia
| | - Yosra Chebbi
- Laboratory Ward, National Bone Marrow Transplant Center, 1006 Tunis, Tunisia
- Faculty of Medicine of Tunis, LR18ES39, University of Tunis El Manar, 1006 Tunis, Tunisia
| | - Siwar Frigui
- Laboratory Ward, National Bone Marrow Transplant Center, 1006 Tunis, Tunisia
- Faculty of Medicine of Tunis, LR18ES39, University of Tunis El Manar, 1006 Tunis, Tunisia
| | - Mohamed Salah Abbassi
- Faculty of Medicine of Tunis, Laboratory of Antibiotic Resistance LR99ES09, University of Tunis El Manar, 1006 Tunis, Tunisia
- Institute of Veterinary Research of Tunisia, University of Tunis El Manar, 1006 Tunis, Tunisia
| | - Wafa Achour
- Laboratory Ward, National Bone Marrow Transplant Center, 1006 Tunis, Tunisia
- Faculty of Medicine of Tunis, LR18ES39, University of Tunis El Manar, 1006 Tunis, Tunisia
| | - Lamia Thabet
- Laboratory Ward, Traumatology and Great Burned Center, 2074 Ben Arous, Tunisia
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C SK, Khanal S, Joshi TP, Khadka D, Tuladhar R, Joshi DR. Antibiotic resistance determinants among carbapenemase producing bacteria isolated from wastewaters of Kathmandu, Nepal. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 343:123155. [PMID: 38114055 DOI: 10.1016/j.envpol.2023.123155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 12/09/2023] [Accepted: 12/11/2023] [Indexed: 12/21/2023]
Abstract
The emergence of carbapenem resistant bacteria (CRB) possesses a remarkable threat to the health of humans. CRB and carbapenem resistance genes (CRGs) have frequently been reported in clinical isolates from hospitals, however, their occurrence and distribution in wastewaters from various sources and river water have not been emphasized in Nepal. So, this study aimed to detect carbapenem resistant bacterial isolates and their resistance determinants in river water and different types of wastewaters. River water and both untreated and treated wastewater samples from hospitals, pharmaceutical industries, and municipal sewage were collected in summer and winter seasons. From 68 grab wastewater samples, CRB were detected only in 16 samples, which included eight hospital wastewater, and four each from untreated municipal sewage and river water. A total of 25 CRB isolates were detected with dominance of E. coli (44.0%) and K. pneumoniae (24.0%). The majority of the isolates harbored blaNDM-1 (76.0%), followed by blaOXA (36.0%) and blaKPC (20.0%) genes. Hospital wastewater majorly contributed to the presence of blaNDM-1, blaKPC, and blaOXA along with intI1 genes compared to river water and untreated municipal sewage, especially during the winter season. However, CRB were not detected in treated effluents of hospitals and municipal sewage, and both influents and effluents from pharmaceutical industries. The combined presence of each blaNDM-1 & blaOXA and blaKPC & blaOXA occurred in 16.0% of the bacterial isolates. The increased minimum inhibitory concentration (MIC) of meropenem was significantly associated with the presence of CRGs. The results of this study highlight the significance of carbapenem resistance in bacteria isolated from wastewater and river water, and underscore the necessity for efficient monitoring and control strategies to prevent the dispersion of carbapenem resistance in the environment and its potential consequences on human health.
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Affiliation(s)
- Sudeep K C
- Central Department of Microbiology, Tribhuvan University, Kirtipur, Nepal; Environment Research Laboratory, Faculty of Science, Nepal Academy of Science and Technology (NAST), Lalitpur, Nepal
| | - Santosh Khanal
- Central Department of Microbiology, Tribhuvan University, Kirtipur, Nepal; Environment Research Laboratory, Faculty of Science, Nepal Academy of Science and Technology (NAST), Lalitpur, Nepal; Department of Microbiology, Tri-Chandra Multiple Campus, Tribhuvan University, Kathmandu, Nepal
| | - Tista Prasai Joshi
- Environment Research Laboratory, Faculty of Science, Nepal Academy of Science and Technology (NAST), Lalitpur, Nepal
| | - Deegendra Khadka
- Molecular Biotechnology, Faculty of Science, Nepal Academy of Science and Technology (NAST), Lalitpur, Nepal
| | - Reshma Tuladhar
- Central Department of Microbiology, Tribhuvan University, Kirtipur, Nepal
| | - Dev Raj Joshi
- Central Department of Microbiology, Tribhuvan University, Kirtipur, Nepal.
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Beig M, Badmasti F, Solgi H, Nikbin VS, Sholeh M. Carbapenemase genes distribution in clonal lineages of Acinetobacter baumannii: a comprehensive study on plasmids and chromosomes. Front Cell Infect Microbiol 2023; 13:1283583. [PMID: 38106472 PMCID: PMC10722191 DOI: 10.3389/fcimb.2023.1283583] [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: 08/26/2023] [Accepted: 11/14/2023] [Indexed: 12/19/2023] Open
Abstract
Background The global spread of plasmids carrying carbapenemase genes within carbapenem resistant Acinetobacter baumannii (CRAB) strains poses a worldwide public health issue. In this study, we conducted a comprehensive genetic analysis of plasmids and chromosomes harboring the major carbapenemase genes (bla NDM, bla KPC, bla VIM, bla IMP, bla GES, bla OXA-58-like, bla OXA-24/40-like, bla OXA-143-like, and bla OXA-23-like) in CRAB strains using bioinformatic tools. Methods We retrieved plasmids and chromosomes carrying the major carbapenemase genes from GenBank. The size, replicon type, and conjugal apparatus of the plasmids were also determined. Furthermore, allele types, co-existence of other antimicrobial resistance genes alongside carbapenemases in plasmids or chromosomes, co-occurrence of carbapenemase genes, gene repetition, and sequence types (ST) of whole genomes were characterized. Results The database contained 113 plasmids and 38 chromosomes harboring carbapenemase genes. This investigation revealed that bla NDM and bla OXA-58-like were the predominant allele types in both the plasmids and chromosomes. Nine (7.96%) plasmids with bla NDM-1 were potentially conjugative. The most common replicon types of the plasmids were R3-T1, R3-T8, R3-T2, R3-T23, and RP-T1. The analysis revealed that bla NDM-1 and bla OXA-58-like genes possessed the highest variety of co-existence with other antibiotic resistance genes. The co-occurrence of dual carbapenemases was identified in 12 plasmids and 19 chromosomes. Carbapenemase gene repetitions were identified in 10 plasmids and one chromosome. Circular alignment revealed that the plasmids carrying the co-occurrence of bla NDM-1 and bla OXA-58 were more homogeneous. However, there was heterogeneity in certain regions of these plasmids. According to the minimum spanning tree (MST) results, the majority of the plasmids belonged to the genomes of ST2Pas, ST1Pas, ST422Pas, ST622Pas, and ST85Pas. Conclusion A. baumannii appears to have a strong ability for genome plasticity to incorporate carbapenemase genes on its plasmids and chromosomes to develop resistance against carbapenems. Mobilizable plasmids harboring carbapenemases significantly contribute to the dissemination of these genes. The genetic structure of the plasmids revealed a strong associations of class I integrons, ISAba-like structures, Tn4401 elements, and aac (6')-Ib with carbapenemases. Furthermore, gene repetition may also be associated with carbapenem heteroresistance.
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Affiliation(s)
- Masoumeh Beig
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Farzad Badmasti
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Hamid Solgi
- Isfahan Endocrine and Metabolism Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | | | - Mohammad Sholeh
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
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Castanheira M, Mendes RE, Gales AC. Global Epidemiology and Mechanisms of Resistance of Acinetobacter baumannii-calcoaceticus Complex. Clin Infect Dis 2023; 76:S166-S178. [PMID: 37125466 PMCID: PMC10150277 DOI: 10.1093/cid/ciad109] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
Acinetobacter baumannii-calcoaceticus complex is the most commonly identified species in the genus Acinetobacter and it accounts for a large percentage of nosocomial infections, including bacteremia, pneumonia, and infections of the skin and urinary tract. A few key clones of A. baumannii-calcoaceticus are currently responsible for the dissemination of these organisms worldwide. Unfortunately, multidrug resistance is a common trait among these clones due to their unrivalled adaptive nature. A. baumannii-calcoaceticus isolates can accumulate resistance traits by a plethora of mechanisms, including horizontal gene transfer, natural transformation, acquisition of mutations, and mobilization of genetic elements that modulate expression of intrinsic and acquired genes.
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Affiliation(s)
| | | | - Ana C Gales
- Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
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Hajikhani B, Sameni F, Ghazanfari K, Abdolali B, Yazdanparast A, Asarehzadegan Dezfuli A, Nasiri MJ, Goudarzi M, Dadashi M. Prevalence of blaNDM-producing Acinetobacter baumannii strains isolated from clinical samples around the world; a systematic review. GENE REPORTS 2023. [DOI: 10.1016/j.genrep.2022.101728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Labid A, Benouagueni S, Mehainaoui A, Gacemi Kirane D, Touati A. Antimicrobial Resistance Among Gram-Negative Bacteria Isolated in the Newborn Intensive Care Unit at ABDERREZAK-BOUHARA Hospital of Skikda, Algeria. Microb Drug Resist 2023. [PMID: 36812465 DOI: 10.1089/mdr.2022.0254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
Background: This study aimed to determine the epidemiology of gram-negative bacteria (GNB) isolated in the newborn intensive care unit (NICU) population, to assess their antibiotic susceptibility patterns and possible associated risk factors. Methods: All neonates admitted to the NICU of ABDERREZAK-BOUHARA hospital (Skikda, Algeria) with a clinical diagnosis of neonatal infections from March to May 2019 were included in the study. The extended-spectrum β-lactamase (ESBLs), plasmidic cephalosporinase (pAmpC), and carbapenemases genes were screened by polymerase chain reaction (PCR) and sequencing. PCR amplification of oprD among carbapenem-resistant Pseudomonas aeruginosa isolates was also performed. The clonal relatedness of the ESBLs isolates was studied using multilocus sequence typing (MLST). Results: Among 148 clinical specimens, 36 (24.3%) GNB strains were isolated from urine (n = 22), wound (n = 8), stool (n = 3), and blood (n = 3) samples. The bacterial species identified were Escherichia coli (n = 13), Klebsiella pneumoniae (n = 5), Enterobacter cloacae (n = 3), Serratia marcescens (n = 3), Salmonella spp. (n = 3), Proteus mirabilis (n = 1), P. aeruginosa (n = 5), and Acinetobacter baumannii (n = 3). PCR and sequencing showed that eleven Enterobacterales isolates harbored the blaCTX-M-15 gene, two E. coli isolates harbored the blaCMY-2 gene, and three A. baumannii isolates harbored both blaOXA-23 and blaOXA-51 genes. Also, five strains of P. aeruginosa were found to harbor mutations in the oprD gene. MLST showed that the K. pneumoniae strains belonged to ST13 and ST189, E. coli belonged to ST69, and E. cloacae belonged to ST214. Different risk factors that could predict positive GNB cultures were found, including female sex, Apgar score <8 at 5 min of life, enteral nutrition, antibiotic use, and extended length of hospitalization. Conclusion: Our study highlights the importance of determining the epidemiology of pathogens causing neonatal infections, their sequence types (ST), and their antibiotic susceptibility patterns to address rapidly a correct antibiotic treatment regimen.
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Affiliation(s)
- Asma Labid
- Research Laboratory of Interactions, Biodiversity, Ecosystems, and Biotechnology, Department of Nature and Life Sciences, University 20 August 1955, Skikda, Algeria
| | - Sarah Benouagueni
- Department of Biochemistry, Badji Mokhtar University, Annaba, Algeria
| | - Aida Mehainaoui
- Department of Biochemistry, Badji Mokhtar University, Annaba, Algeria
| | | | - Abdelaziz Touati
- Laboratoire d'Ecologie Microbienne, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, Bejaia, Algeria
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Zhang DF, Zhang ZF, Li PD, Qu PH. Characterization of carbapenem resistant Acinetobacter baumannii ST540 and Klebsiella pneumoniae ST2237 isolates in a pneumonia case from China. J Appl Microbiol 2022; 133:1434-1445. [PMID: 35652720 DOI: 10.1111/jam.15648] [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: 11/30/2021] [Revised: 05/19/2022] [Accepted: 05/27/2022] [Indexed: 11/28/2022]
Abstract
AIMS This study aimed to characterize the chromosome and plasmid sequences, and determine the transferability of plasmids in carbapenem-resistance Acinetobacter baumannii (A. baumannii) DD520 and Klebsiella pneumoniae (K. pneumoniae) DD521 isolates from the same patient who was co-infected in a hospital in China. METHODS AND RESULTS Both isolates DD520 and DD521 exhibited multi-drug resistance phenotype, especially the former isolate which was resistant to 9 classes of antimicrobials including carbapenems, quinolones, penicillins, cephalosporins, tetracyclines, phenicols, fosfomycins, sulfanilamides, and aminoglycosides. Carbapenem resistance genes of blaOXA-23 and blaOXA-66 were identified on the chromosome of A. baumannii DD520, and blaKPC-2 was found in the plasmid pDD521.2 from K. pneumoniae DD521. Phylogenetic analysis revealed that A. baumannii DD520 belonged to the ST540 clone, and K. pneumoniae DD521 belonged to the ST2237 clone. Plasmid analysis suggested that blaKPC-2 was embedded into plasmid pDD521.2, which might be resulted from IS26- and Tn1721-mediated transposition. Plasmid pDD521.2 carrying blaKPC-2 successfully transferred from K. pneumoniae DD521 into Escherichia coli C600, and carbapenems resistance also transferred in the conjugation. CONCLUSIONS To our knowledge, it was the first report of A. baumannii ST540 and K. pneumoniae ST2237 in the same patient in China. Both these two isolates exhibited resistance to carbapenem, which was likely to be resulted from carbapenem resistance genes blaOXA-23 -blaOXA-66 on the chromosome of A. baumannii ST540, and blaKPC-2 in the plasmid of K. pneumoniae ST2237. SIGNIFICANCE AND IMPACT OF THE STUDY Our study highlighted that effective measures were urgent to prevent and control the co-infection caused by two or more carbapenem-resistance pathogens in the same patient.
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Affiliation(s)
- Dao-Feng Zhang
- Institute of Marine Biotechnology and Bio-Resource Utilization, College of Oceanography, Hohai University, Nanjing, China.,Department of Food Science & Technology, School of Agriculture & Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Zeng-Feng Zhang
- Department of Food Science & Technology, School of Agriculture & Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Pan-Dong Li
- Lushi County People's Hospital, Sanmenxia, China
| | - Ping-Hua Qu
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
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Lin H, Feng C, Zhu T, Li A, Liu S, Zhang L, Li Q, Zhang X, Lin L, Lu J, Lin X, Li K, Zhang H, Xu T, Li C, Bao Q. Molecular Mechanism of the β-Lactamase Mediated β-Lactam Antibiotic Resistance of Pseudomonas aeruginosa Isolated From a Chinese Teaching Hospital. Front Microbiol 2022; 13:855961. [PMID: 35572664 PMCID: PMC9096163 DOI: 10.3389/fmicb.2022.855961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 04/08/2022] [Indexed: 01/03/2023] Open
Abstract
Pseudomonas aeruginosa can cause infections in the blood, lungs (pneumonia), or other parts of the body after surgery. To investigate the molecular characteristics of β-lactam antibiotic resistance of P. aeruginosa isolated from a hospital population between 2015 and 2017, in this study, the antimicrobial susceptibility and the resistance gene profile of the bacteria were determined. The Pulsed-field gel electrophoresis (PFGE) was used to characterize the clonal relatedness and sequencing and comparative genomic analysis were performed to analyze the structure of the resistance gene-related sequences. As a result, of the 260 P. aeruginosa strains analyzed, the resistance rates for 6 β-lactam antibiotics ranged from 4.6 to 9.6%. A total of 7 genotypes of 44 β-lactamase genes were identified in 23 isolates (8.9%, 23/260). Four transconjugants from different donors carrying blaCARB-3 exhibited a phenotype of reduced susceptibility to piperacillin–tazobactam, ceftazidime, and cefepime, and 2 transconjugants harboring blaIMP-45 exhibited a phenotype of reduced susceptibility to carbapenems. blaCARB positive isolates (n = 12) presented six PFGE patterns, designated groups A to F. Two bla genes (blaIMP-45 and blaOXA-1) in PA1609 related to a class 1 integron (intI1-blaIMP-45-blaOXA-1-aac(6′)-Ib7-catB3-qacE∆1-sul1) were encoded on a plasmid (pPA1609-475), while the blaCARB-3 gene of PA1616 also related to a class 1 integron was located on the chromosome. The results suggest that β-lactam antibiotic resistance and clonal dissemination exist in this hospital population. It indicates the necessity for molecular surveillance in tracking β-lactamase-producing strains and emphasizes the need for epidemiological monitoring.
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Affiliation(s)
- Hailong Lin
- Department of Infectious Disease, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Chunlin Feng
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Tingting Zhu
- Department of Pediatric Respiratory Disease, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China
| | - Anqi Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Shuang Liu
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Lei Zhang
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Qiaoling Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Department of Pediatric Respiratory Disease, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China
| | - Xueya Zhang
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Department of Pediatric Respiratory Disease, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China
| | - Li Lin
- Department of Pediatric Respiratory Disease, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China
| | - Junwan Lu
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
| | - Xi Lin
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Kewei Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Hailin Zhang
- Department of Pediatric Respiratory Disease, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China
| | - Teng Xu
- Institute of Translational Medicine, Baotou Central Hospital, Baotou, China
| | - Changchong Li
- Department of Pediatric Respiratory Disease, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China
| | - Qiyu Bao
- Department of Infectious Disease, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Department of Pediatric Respiratory Disease, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
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11
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Nabti LZ, Sahli F, Olowo-Okere A, Benslama A, Harrar A, Lupande-Mwenebitu D, Diene SM, Rolain JM. Molecular Characterization of Clinical Carbapenem-Resistant Enterobacteriaceae Isolates from Sétif, Algeria. Microb Drug Resist 2021; 28:274-279. [PMID: 34860598 DOI: 10.1089/mdr.2021.0123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
This study aimed to determine the incidence and the molecular mechanisms of carbapenem-resistant Enterobacteriaceae in patients from the Sétif University Hospital, Algeria. Nonduplicate clinical bacterial isolates recovered from patients attending the University Hospital of Sétif were collected between April and October 2018. Species identification was performed by MALDI-TOF/MS (matrix-assisted laser desorption ionization-time of flight mass spectrometry) method. The susceptibility of the isolates to carbapenems was determined using the disc diffusion method. The carbapenem resistant isolates were screened for the presence of common carbapenemase genes (blaKPC, blaOXA-48, blaVIM, blaIMP, and blaNDM) and extended-spectrum β-lactamase (blaCTX, blaTEM, and blaSHV) using PCR and sequencing technique. A total of 123 nonrepetitive Enterobacteriaceae isolates were obtained. Klebsiella pneumoniae (n = 52/42.28%), Escherichia coli (n = 24/19.51%), and Enterobacter cloacae (n = 19/15.45%) were the most prevalent species. The Carba-NP test showed that 6 out of 123 isolates carried carbapenemase enzymes. OXA-48 was found in five isolates (four K. pneumoniae and one E. coli) and NDM-5 in one E. cloacae isolate. We reported for the first time in Algeria the presence of NDM-5 carbapenemase enzyme in a clinical E. cloacae isolate.
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Affiliation(s)
- Larbi Zakaria Nabti
- Department of Biochemistry and Microbiology, Faculty of Sciences, University of M'sila, M'sila, Algeria.,Laboratoire de Microbiologie, Centre Hospitalier Universitaire (CHU) de Sétif, Sétif, Algérie.,Aix Marseille Univ, IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Marseille, France
| | - Farida Sahli
- Laboratoire de Microbiologie, Centre Hospitalier Universitaire (CHU) de Sétif, Sétif, Algérie
| | - Ahmed Olowo-Okere
- Department of Pharmaceutical Microbiology, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Abderrahim Benslama
- Department of Biochemistry and Microbiology, Faculty of Sciences, University of M'sila, M'sila, Algeria
| | - Abdenassar Harrar
- Department of Biochemistry and Microbiology, Faculty of Sciences, University of M'sila, M'sila, Algeria
| | - David Lupande-Mwenebitu
- Aix Marseille Univ, IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Marseille, France
| | - Seydina M Diene
- Aix Marseille Univ, IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - Jean-Marc Rolain
- Aix Marseille Univ, IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Marseille, France.,IHU Méditerranée Infection, Marseille, France
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12
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Ragheb SM, Govinden U, Osei Sekyere J. Genetic support of carbapenemases: a One Health systematic review and meta-analysis of current trends in Africa. Ann N Y Acad Sci 2021; 1509:50-73. [PMID: 34753206 DOI: 10.1111/nyas.14703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 09/06/2021] [Accepted: 09/26/2021] [Indexed: 11/28/2022]
Abstract
Antimicrobial resistance (AMR) is a public health threat globally. Carbapenems are β-lactam antibiotics used as last-resort agents for treating antibiotic-resistant infections. Mobile genetic elements (MGEs) play an important role in the dissemination and expression of antimicrobial resistance genes (ARGs), including the mobilization of ARGs within and between species. The presence of MGEs around carbapenem-hydrolyzing enzymes, called carbapenemases, in bacterial isolates in Africa is concerning. The association between MGEs and carbapenemases is described herein. Specific plasmid replicons, integrons, transposons, and insertion sequences were found flanking specific and different carbapenemases across the same and different clones and species isolated from humans, animals, and the environment. Notably, similar genetic contexts have been reported in non-African countries, supporting the importance of MGEs in driving the intra- and interclonal and species transmission of carbapenemases in Africa and globally. Technical and budgetary limitations remain challenges for epidemiological analysis of carbapenemases in Africa, as studies undertaken with whole-genome sequencing remained relatively few. Characterization of MGEs in antibiotic-resistant infections can deepen our understanding of carbapenemase epidemiology and facilitate the control of AMR in Africa. Investment in genomic epidemiology will facilitate faster clinical interventions and containment of outbreaks.
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Affiliation(s)
- Suzan Mohammed Ragheb
- Department of Microbiology and Immunology, Faculty of Pharmacy, Modern University for Technology and Information (MTI), Cairo, Egypt
| | - Usha Govinden
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, KwaZulu-Natal, South Africa
| | - John Osei Sekyere
- Department of Microbiology & Immunology, Indiana University School of Medicine-Northwest, Gary, Indiana.,Department of Dermatology, School of Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
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13
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The Occurrence and Characterization of Class I, II, and III Integrons Among Carbapenemase-Producing Clinical Strains of Acinetobacter baumannii in Tehran, Iran. Jundishapur J Microbiol 2021. [DOI: 10.5812/jjm.117766] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Background: Acinetobacter baumannii has emerged as a critical pathogen with high morbidity and mortality in long-term hospitalized patients who stay in intensive care units. Carbapenemases and integrons are two critical DNA elements that contribute to the emergence of multidrug-resistant (MDR) A. baumannii. Objectives: The current study aimed at characterization and molecular detection of class 1, 2, and 3 integrons among carbapenemase-producing A. baumannii strains recovered from a clinical setting in Tehran, Iran. Methods: A total of 65 non-replicated clinical strains were considered in this study. Class 1, 2, and 3 carbapenemase genes and clonal relatedness of the isolates were investigated by PCR assay. Results: The prevalence of carbapenemases was as follows: blaOXA23 (92.31%), blaVIM (69.23%), and blaNDM (1.54%). In addition, PCR sequencing confirmed the presence of gene cassette arrays consisting of aacA4-catB8-aadA1 (12/46, 26.09%), aadB-aadA1 (26.09%, 12/46), arr2-cm1A5 (30.43%, 14/46), and dfrA1-aadA1 (7.39%, 8/46) in class 1 integron and dfrA1-sat2 (52.94%, 9/17), and sat2-aadA1 (47.06%, 8/17) in class 2 integron. Sequence-based typing of both blaOXA-51-like and ampC revealed the following distribution of three different clone types among isolates: clonal complex (CC) 10 (46.15%, 30/65), CC2 (40%, 26/65), and CC3 (13.85%, 9/65). Statistical analysis showed that the presence of the intI1, blaOXA23, blaVIM, or blaNDM genes can significantly increase the acquiring MDR phenotypes in A. baumannii isolates. Conclusions: High prevalence of carbapenemase-producing A. baumannii harboring integrons is alarming public health. It seems that class 1 integron can be served as a predictive biomarker for the presence of MDR phenotypes in the clinical setting. However, integrons do not carry carbapenemases in these strains.
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14
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First Genome Description of Providencia vermicola Isolate Bearing NDM-1 from Blood Culture. Microorganisms 2021; 9:microorganisms9081751. [PMID: 34442831 PMCID: PMC8398168 DOI: 10.3390/microorganisms9081751] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/05/2021] [Accepted: 08/14/2021] [Indexed: 11/16/2022] Open
Abstract
In this paper, we describe the first complete genome sequence of Providencia vermicola species, a clinical multidrug-resistant strain harboring the New Delhi Metallo-β-lactamase-1 (NDM-1) gene, isolated at the Kinshasa University Teaching Hospital, in Democratic Republic of the Congo. Whole genome sequencing of an imipenem-resistant clinical Gram-negative P. vermicola P8538 isolate was performed using MiSeq and Gridion, and then complete genome analysis, plasmid search, resistome analysis, and comparative genomics were performed. Genome assembly resulted in a circular chromosome sequence of 4,280,811-bp and 40.80% GC and a circular plasmid (pPV8538_NDM-1) of 151,684-bp and 51.93%GC, which was identified in an Escherichia coli P8540 strain isolated in the same hospital. Interestingly, comparative genomic analysis revealed multiple sequences acquisition within the P. vermicola P8538 chromosome, including three complete prophages, a siderophore biosynthesis NRPS cluster, a Type VI secretion system (T6SS), a urease gene cluster, and a complete Type-I-F CRISPR-Cas3 system. Β-lactamase genes, including blaCMY-6 and blaNDM-1, were found on the recombinant plasmid pPV8538_NDM-1, in addition to other antibiotic resistance genes such as rmtC, aac6’-Ib3, aacA4, catA1, sul1, aac6’-Ib-cr, tetA, and tetB. Genome comparison with Providencia species revealed 82.95% of average nucleotide identity (ANI), with P. stuartii species exhibiting 90.79% of proteome similarity. We report the first complete genome of P. vermicola species and for the first time the presence of the blaNDM-1 gene in this species. This work highlights the need to improve surveillance and clinical practices in DR Congo in order to reduce or prevent the spread of such resistance.
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15
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Gheorghe I, Barbu IC, Surleac M, Sârbu I, Popa LI, Paraschiv S, Feng Y, Lazăr V, Chifiriuc MC, Oţelea D, Zhiyong Z. Subtypes, resistance and virulence platforms in extended-drug resistant Acinetobacter baumannii Romanian isolates. Sci Rep 2021; 11:13288. [PMID: 34168184 PMCID: PMC8225882 DOI: 10.1038/s41598-021-92590-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 06/09/2021] [Indexed: 02/05/2023] Open
Abstract
Acinetobacter baumannii has emerged worldwide as a dominant pathogen in a broad range of severe infections, raising an acute need for efficient antibacterials. This is the first report on the resistome and virulome of 33 extended drug-resistant and carbapenem-resistant A. baumannii (XDR CRAB) strains isolated from hospitalized and ambulatory patients in Bucharest, Romania. A total of 33 isolates were collected and analyzed using phenotypic antibiotic susceptibility and conjugation assays, PCR, whole-genome sequencing (WGS), pulsed-field gel electrophoresis (PFGE) and MultiLocus Sequence Typing (MLST). All isolates were extensively drug-resistant (XDR), being susceptible only to colistin. The carbapenem resistance was attributed by PCR mainly to blaOXA-24 and blaOXA-23 genes. PFGE followed by MLST analysis demonstrated the presence of nine pulsotypes and six sequence types. WGS of seven XDR CRAB isolates from healthcare-associated infections demonstrated the high diversity of resistance genes repertoire, as well as of mobile genetic elements, carrying ARGs for aminoglycosides, sulphonamides and macrolides. Our data will facilitate the understanding of resistance, virulence and transmission features of XDR AB isolates from Romanian patients and might be able to contribute to the implementation of appropriate infection control measures and to develop new molecules with innovative mechanisms of action, able to fight effectively against these bugs, for limiting the spread and decreasing the infection rate and mortality.
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Affiliation(s)
- Irina Gheorghe
- grid.5100.40000 0001 2322 497XDepartment of Microbiology and Immunology, Faculty of Biology, University of Bucharest, Bucharest, Romania ,grid.5100.40000 0001 2322 497XResearch Institute of the University of Bucharest (ICUB), Bucharest, Romania
| | - Ilda Czobor Barbu
- grid.5100.40000 0001 2322 497XDepartment of Microbiology and Immunology, Faculty of Biology, University of Bucharest, Bucharest, Romania ,grid.5100.40000 0001 2322 497XResearch Institute of the University of Bucharest (ICUB), Bucharest, Romania
| | - Marius Surleac
- grid.5100.40000 0001 2322 497XResearch Institute of the University of Bucharest (ICUB), Bucharest, Romania ,grid.8194.40000 0000 9828 7548National Institute for Infectious Diseases “Matei Bals”, Bucharest, Romania
| | - Ionela Sârbu
- grid.5100.40000 0001 2322 497XResearch Institute of the University of Bucharest (ICUB), Bucharest, Romania ,grid.5100.40000 0001 2322 497XGenetics Department, Faculty of Biology, University of Bucharest, Bucharest, Romania
| | - Laura Ioana Popa
- grid.5100.40000 0001 2322 497XDepartment of Microbiology and Immunology, Faculty of Biology, University of Bucharest, Bucharest, Romania ,grid.5100.40000 0001 2322 497XResearch Institute of the University of Bucharest (ICUB), Bucharest, Romania ,grid.435400.60000 0004 0369 4845Department of Bioinformatics, National Institute of Research and Development for Biological Sciences, Bucharest, Romania
| | - Simona Paraschiv
- grid.8194.40000 0000 9828 7548National Institute for Infectious Diseases “Matei Bals”, Bucharest, Romania
| | - Yu Feng
- grid.13291.380000 0001 0807 1581Centre of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Veronica Lazăr
- grid.5100.40000 0001 2322 497XDepartment of Microbiology and Immunology, Faculty of Biology, University of Bucharest, Bucharest, Romania ,grid.5100.40000 0001 2322 497XResearch Institute of the University of Bucharest (ICUB), Bucharest, Romania
| | - Mariana Carmen Chifiriuc
- grid.5100.40000 0001 2322 497XDepartment of Microbiology and Immunology, Faculty of Biology, University of Bucharest, Bucharest, Romania ,grid.5100.40000 0001 2322 497XResearch Institute of the University of Bucharest (ICUB), Bucharest, Romania ,grid.435118.aAcademy of Romanian Scientists, 050045 Bucharest, Romania
| | - Dan Oţelea
- grid.8194.40000 0000 9828 7548National Institute for Infectious Diseases “Matei Bals”, Bucharest, Romania
| | - Zong Zhiyong
- grid.13291.380000 0001 0807 1581Centre of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
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16
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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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17
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Slimene K, El Salabi AA, Dziri O, Mabrouk A, Miniaoui D, Gharsa H, Shokri SA, Alhubge AM, Achour W, Rolain JM, Chouchani C. High Carbapenem Resistance Caused by VIM and NDM Enzymes and OprD Alteration in Nonfermenter Bacteria Isolated from a Libyan Hospital. Microb Drug Resist 2021; 27:1546-1554. [PMID: 34029121 DOI: 10.1089/mdr.2020.0175] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Acinetobacter baumannii and Pseudomonas aeruginosa are among the most prevalent pathogens causing a wide range of serious infections in hospitalized patients and contaminating intensive care units and inanimate surfaces. The purpose of this study was to investigate the mechanism of carbapenem resistance in clinical and hospital environmental isolates of A. baumannii and P. aeruginosa recovered from a Libyan hospital. From a total of 82 Gram-negative bacteria, 8 isolates of A. baumannii and 3 isolates of P. aeruginosa exhibited resistance to imipenem with minimum inhibitory concentrations ranging from 16 to >32 μg/mL. Five isolates of A. baumannii harbored blaOXA-23 gene, from which three isolates were collected from patients and two from hospital environment. Only one isolate harbored blaNDM-1 gene, which was responsible for carbapenem resistance in A. baumannii. The OprD gene seems to be disturbed by an insertion sequence (IS) in two isolates and affected by polymorphism in one isolate. Pulsed-field gel electrophoresis results showed high genetic diversity among carbapenemase producing A. baumannii. This study highlights the dissemination of blaOXA-23 and blaNDM-1 genes in a Libyan setting. Therefore, infection prevention and control practices, antimicrobial stewardship initiatives, and antimicrobial resistance surveillance systems should be implemented to prevent the wide spread of antimicrobial resistance.
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Affiliation(s)
- Khouloud Slimene
- Microbes Evolution Phylogenie et Infections (MEPHI), Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France.,IHU Méditerranée Infection, Valorisation and Transfer, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France.,Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis El-Manar, Tunis, Tunisie.,Laboratoire de Recherche des Sciences et Technologies de l'Environnement, Institut Supérieur des Sciences et Technologies de l'Environnement de Borj-Cedria, Université de Carthage, Borj-Cedria, Tunisie
| | - Allaaeddin Ali El Salabi
- Department of Environmental Health, Faculty of Public Health, University of Benghazi, Benghazi, Libya
| | - Olfa Dziri
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis El-Manar, Tunis, Tunisie.,Laboratoire de Recherche des Sciences et Technologies de l'Environnement, Institut Supérieur des Sciences et Technologies de l'Environnement de Borj-Cedria, Université de Carthage, Borj-Cedria, Tunisie
| | - Aymen Mabrouk
- Faculté de Médecine de Tunis, LR18ES39, Centre National de Greffe de Moelle Osseuse, Université Tunis El Manar, Tunis, Tunisie
| | - Dhouha Miniaoui
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis El-Manar, Tunis, Tunisie.,Laboratoire de Recherche des Sciences et Technologies de l'Environnement, Institut Supérieur des Sciences et Technologies de l'Environnement de Borj-Cedria, Université de Carthage, Borj-Cedria, Tunisie
| | - Haythem Gharsa
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis El-Manar, Tunis, Tunisie.,Institut Supérieur des Sciences Biologiques et Appliqués de Tunis, Université Tunis El Manar, Tunis, Tunisie
| | - Salah A Shokri
- Department of Microbiology, Faculty of Science, Misurata University, Misurata, Libya
| | - Altaher M Alhubge
- Department of Microbiology, Faculty of Science, Misurata University, Misurata, Libya
| | - Wafa Achour
- Faculté de Médecine de Tunis, LR18ES39, Centre National de Greffe de Moelle Osseuse, Université Tunis El Manar, Tunis, Tunisie
| | - Jean-Marc Rolain
- Microbes Evolution Phylogenie et Infections (MEPHI), Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France.,IHU Méditerranée Infection, Valorisation and Transfer, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
| | - Chedly Chouchani
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis El-Manar, Tunis, Tunisie.,Laboratoire de Recherche des Sciences et Technologies de l'Environnement, Institut Supérieur des Sciences et Technologies de l'Environnement de Borj-Cedria, Université de Carthage, Borj-Cedria, Tunisie
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18
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Xanthopoulou K, Urrutikoetxea-Gutiérrez M, Vidal-Garcia M, Diaz de Tuesta Del Arco JL, Sánchez-Urtaza S, Wille J, Seifert H, Higgins PG, Gallego L. First Report of New Delhi Metallo- β-Lactamase-6 (NDM-6) in a Clinical Acinetobacter baumannii Isolate From Northern Spain. Front Microbiol 2020; 11:589253. [PMID: 33240245 PMCID: PMC7683408 DOI: 10.3389/fmicb.2020.589253] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/15/2020] [Indexed: 12/29/2022] Open
Abstract
The objective of this study was the phenotypic and genotypic characterization of a carbapenem resistant Acinetobacter baumannii (CRAB) isolate. The isolate, recovered in Northern Spain in 2019, was identified by MALDI-TOF to the species level. Antimicrobial susceptibility testing was performed using the Phoenix BD NMIC-502 Panel, E-test, and broth microdilution methods. The presence of a metallo-β-lactamase (MBL) was verified by PCR and immunochromatographic assays. The genetic location of the MBL was confirmed using S1-pulsed-field gel electrophoresis (S1-PFGE) followed by Southern blot hybridization. Whole genome sequencing (WGS) was completed using the Miseq and MinION platforms, followed by core-genome MLST (cgMLST) and seven-locus MLST analysis. The CRAB was assigned ST85 (Pasteur scheme) and ST957 (Oxford scheme) representing international clone (IC) 9 and harbored the intrinsic β-lactamase OXA-94 with ISAba1 upstream of it, and the MBL bla NDM-6. Hybridization experiments revealed that the bla NDM-6 was encoded on the chromosome. Using WGS the bla NDM-6 environment could be identified arranged in the following order: ISAba14, aphA6, ISAba125, bla NDM-6, ble MBL, trpF, dsbC, cutA, and ISAba14. Downstream, a 10,462 bp duplication was identified, including a second copy of bla NDM-6 in the following genetic composition: ISAba125, bla NDM-6, ble MBL, trpF, dsbC, cutA, and ISAba14. To our knowledge, this is the first description of bla NDM-6 in A. baumannii. The MBL was present in two copies in the chromosome in a new genetic environment associated with IS elements highlighting the contribution of mobile genetic elements in the dissemination of this gene.
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Affiliation(s)
- Kyriaki Xanthopoulou
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany.,German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Mikel Urrutikoetxea-Gutiérrez
- Servicio de Microbiología y Control de Infección, Hospital Universitario Basurto, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Matxalen Vidal-Garcia
- Servicio de Microbiología y Control de Infección, Hospital Universitario Basurto, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - José-Luis Diaz de Tuesta Del Arco
- Servicio de Microbiología y Control de Infección, Hospital Universitario Basurto, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Sandra Sánchez-Urtaza
- Department of Immunology, Microbiology, and Parasitology, Faculty of Medicine and Nursing, University of the Basque Country UPV/EHU, Bilbao, Spain
| | - Julia Wille
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany.,German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Harald Seifert
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany.,German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Paul G Higgins
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany.,German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Lucía Gallego
- Department of Immunology, Microbiology, and Parasitology, Faculty of Medicine and Nursing, University of the Basque Country UPV/EHU, Bilbao, Spain
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19
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Vijayakumar S, Wattal C, J K O, Bhattacharya S, Vasudevan K, Anandan S, Walia K, Veeraraghavan B. Insights into the complete genomes of carbapenem-resistant Acinetobacter baumannii harbouring bla OXA-23, bla OXA-420 and bla NDM-1 genes using a hybrid-assembly approach. Access Microbiol 2020; 2:acmi000140. [PMID: 32974602 PMCID: PMC7497828 DOI: 10.1099/acmi.0.000140] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 05/10/2020] [Indexed: 12/20/2022] Open
Abstract
Carbapenem resistance in Acinetobacter baumannii is due to blaOXA-23, which is endemic in India. Recently, the sporadic presence of blaOXA-58 as well as the occurrence of dual carbapenemases were observed. The mobility as well as the dissemination of these resistance genes were mainly mediated by various mobile genetic elements. The present study was aimed at characterizing the genetic arrangement of blaOXA-23, blaNDM-1 and blaOXA-58 identified in two complete genomes of carbapenem-resistant A. baumannii (CRAB). Complete genomes obtained using a hybrid-assembly approach revealed the accurate arrangement of Tn2006 with blaOXA-23, ISAba125 with blaNDM and ISAba3 with blaOXA-58. In addition, the association of IntI1 integrase with the blaCARB-2 gene and several virulence factors required for type-IV pili assembly, motility and biofilm formation have been identified. The current study provided deeper insight into the complete characterization of insertion sequences and transposons associated with the carbapenem-resistant genes using short reads of IonTorrent PGM and long reads of MinIon in A. baumannii.
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Affiliation(s)
| | | | - Oberoi J K
- Sir Ganga Ram Hospital, New Delhi, India
| | | | | | | | - Kamini Walia
- Indian Council of Medical Research, New Delhi, India
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20
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Genetic Diversity of OXA Producing Carbapenem-Resistant Acinetobacter baumannii from Environment of Tertiary Hospitals in Central Iran. ARCHIVES OF CLINICAL INFECTIOUS DISEASES 2020. [DOI: 10.5812/archcid.95602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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21
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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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22
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Kumburu HH, Sonda T, van Zwetselaar M, Leekitcharoenphon P, Lukjancenko O, Mmbaga BT, Alifrangis M, Lund O, Aarestrup FM, Kibiki GS. Using WGS to identify antibiotic resistance genes and predict antimicrobial resistance phenotypes in MDR Acinetobacter baumannii in Tanzania. J Antimicrob Chemother 2019; 74:1484-1493. [PMID: 30843063 PMCID: PMC6524488 DOI: 10.1093/jac/dkz055] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 12/11/2018] [Accepted: 01/16/2019] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Reliable phenotypic antimicrobial susceptibility testing can be a challenge in clinical settings in low- and middle-income countries. WGS is a promising approach to enhance current capabilities. AIM To study diversity and resistance determinants and to predict and compare resistance patterns from WGS data of Acinetobacter baumannii with phenotypic results from classical microbiological testing at a tertiary care hospital in Tanzania. METHODS AND RESULTS MLST using Pasteur/Oxford schemes yielded eight different STs from each scheme. Of the eight, two STs were identified to be global clones 1 (n = 4) and 2 (n = 1) as per the Pasteur scheme. Resistance testing using classical microbiology determined between 50% and 92.9% resistance across all drugs. Percentage agreement between phenotypic and genotypic prediction of resistance ranged between 57.1% and 100%, with coefficient of agreement (κ) between 0.05 and 1. Seven isolates harboured mutations at significant loci (S81L in gyrA and S84L in parC). A number of novel plasmids were detected, including pKCRI-309C-1 (219000 bp) carrying 10 resistance genes, pKCRI-43-1 (34935 bp) carrying two resistance genes and pKCRI-49-1 (11681 bp) and pKCRI-28-1 (29606 bp), each carrying three resistance genes. New ampC alleles detected included ampC-69, ampC-70 and ampC-71. Global clone 1 and 2 isolates were found to harbour ISAba1 directly upstream of the ampC gene. Finally, SNP-based phylogenetic analysis of the A. baumannii isolates revealed closely related isolates in three clusters. CONCLUSIONS The validity of the use of WGS in the prediction of phenotypic resistance can be appreciated, but at this stage is not sufficient for it to replace conventional antimicrobial susceptibility testing in our setting.
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Affiliation(s)
- Happiness H Kumburu
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Tolbert Sonda
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | | | | | | | - Blandina T Mmbaga
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Michael Alifrangis
- Centre for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen and Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
| | - Ole Lund
- DTU-Bioinformatics, Technical University of Denmark, Copenhagen, Denmark
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23
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Ory J, Bricheux G, Robin F, Togola A, Forestier C, Traore O. Biofilms in hospital effluents as a potential crossroads for carbapenemase-encoding strains. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 657:7-15. [PMID: 30530220 DOI: 10.1016/j.scitotenv.2018.11.427] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 11/09/2018] [Accepted: 11/28/2018] [Indexed: 06/09/2023]
Abstract
Bacterial resistance to carbapenem, which is mainly due to the successful dissemination of carbapenemase-encoding genes, has become a major health problem. Few studies have aimed to characterize the level of resistance in the environment, notably in hospital wastewater, which is a likely hotspot for exchange of antibiotic resistance genes. In this work, we looked for the presence of imipenem-resistant bacteria and imipenem in the effluent of the teaching hospital of Clermont-Ferrand, France. Selective growth of bacteria from 14-day old biofilms formed in the pipe sewer showed that 22.1% of the isolates were imipenem-resistant and identified as Aeromonas (n = 23), Pseudomonas (n = 10), Stenotrophomonas (n = 4) and Acinetobacter (n = 1). Fifteen of these strains harbored acquired carbapenemase-encoding genes blaVIM (n = 11), blaOXA-48 (n = 2), blaGES (n = 1), blaNDM (n = 1). All isolates also harbored associated resistances to aminoglycosides, fluoroquinolones and/or tetracyclin. S1-nuclease pulsed-field gel electrophoresis analysis of eight selected isolates showed that four of them harbored one to two plasmids of molecular weight between 48.5 Kb and 194 Kb. In vitro transformation assays evidenced the presence of blaVIM and blaNDM on plasmids with the blaVIM harboring 80 Kb plasmid having conjugative capacity. The predicted environmental concentration of imipenem in the hospital effluent was 3.16 μg/L, suggesting that biofilm bacteria are subjected to sub-MICs of imipenem within the effluent. However, no imipenem molecule was detected in the hospital effluent, probably owing to its instability: in vitro assays indicated that imipenem's biological activity was no longer detectable after 45 h of storage. However, the predictive value of the hazard quotient relative to the development of resistance was >1.0 (HQr = 28.9 ± 1.9), which indicates a possible risk. The presence of carbapenemase-encoding genes in hospital effluent biofilm strains and their ability to transfer are therefore a potential hazard that should not be neglected and points to the need for monitoring antibiotic resistance in hospital wastewater.
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Affiliation(s)
- J Ory
- Université Clermont Auvergne, CNRS, Laboratoire "Microorganismes: Génome et Environnement", F-63000 Clermont-Ferrand, France; Service d'hygiène hospitalière, CHU de Clermont-Ferrand, Clermont-Ferrand, France
| | - G Bricheux
- Université Clermont Auvergne, CNRS, Laboratoire "Microorganismes: Génome et Environnement", F-63000 Clermont-Ferrand, France
| | - F Robin
- Laboratoire de Bactériologie & CNR de la Résistance aux Antibiotiques, CHU de Clermont-Ferrand, Clermont-Ferrand, France; Université Clermont Auvergne, Inserm, M2ISH, F-63000 Clermont-Ferrand, France
| | - A Togola
- Bureau de recherches géologiques et minières (BRGM), 3 avenue Claude Guillemin, F-45100 Orléans, France
| | - C Forestier
- Université Clermont Auvergne, CNRS, Laboratoire "Microorganismes: Génome et Environnement", F-63000 Clermont-Ferrand, France
| | - O Traore
- Université Clermont Auvergne, CNRS, Laboratoire "Microorganismes: Génome et Environnement", F-63000 Clermont-Ferrand, France; Service d'hygiène hospitalière, CHU de Clermont-Ferrand, Clermont-Ferrand, France.
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24
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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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25
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Leungtongkam U, Thummeepak R, Tasanapak K, Sitthisak S. Acquisition and transfer of antibiotic resistance genes in association with conjugative plasmid or class 1 integrons of Acinetobacter baumannii. PLoS One 2018; 13:e0208468. [PMID: 30521623 PMCID: PMC6283642 DOI: 10.1371/journal.pone.0208468] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 11/16/2018] [Indexed: 12/30/2022] Open
Abstract
Conjugation is a type of horizontal gene transfer (HGT) that serves as the primary mechanism responsible for accelerating the spread of antibiotic resistance genes in Gram-negative bacteria. The present study aimed to elucidate the mechanisms underlying the conjugation-mediated gene transfer from the extensively drug-resistant Acinetobacter baumannii (XDR-AB) and New Delhi Metallo-beta-lactamase-1-producing Acinetobacter baumannii (NDM-AB) to environmental isolates of Acinetobacter spp. Conjugation experiments demonstrated that resistance to ticarcillin and kanamycin could be transferred from four donors to two sodium azide-resistant A. baumannii strains, namely, NU013R and NU015R. No transconjugants were detected on Mueller-Hinton Agar (MHA) plates containing tetracycline. Plasmids obtained from donors as well as successful transconjugants were characterized by PCR-based replicon typing and S1-nuclease pulsed-field gel electrophoresis (S1-PFGE). Detection of antibiotic resistance genes and integrase genes (int) was performed using PCR. Results revealed that the donor AB364 strain can transfer the blaOXA-23 and blaPER-1 genes to both recipients in association with int1. A 240-kb plasmid was successfully transferred from the donor AB364 to recipients. In addition, the aphA6 and blaPER-1 genes were co-transferred with the int1 gene from the donor strains AB352 and AB405. The transfer of a 220-kb plasmid from the donors to recipient was detected. The GR6 plasmid containing the kanamycin resistance gene (aphA6) was successfully transferred from the donor strain AB140 to both recipient strains. However, the blaNDM-1 and tet(B) genes were not detected in all transconjugants. Our study is the first to demonstrate successful in vitro conjugation, which indicated that XDR-AB contained combination mechanisms of the co-transfer of antimicrobial resistance elements with integron cassettes or with the plasmid group GR6. Thus, conjugation could be responsible for the emergence of new types of antibiotic-resistant strains.
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Affiliation(s)
- 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
| | - Kannipa Tasanapak
- 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, Naresuan University, Phitsanulok, Thailand
- * E-mail:
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26
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Peyclit L, Chanteloup A, Hadjadj L, Rolain JM. Role of Institut Hospitalo-Universitaire Méditerranée Infection in the surveillance of resistance to antibiotics and training of students in the Mediterranean basin and in African countries. New Microbes New Infect 2018; 26:S52-S64. [PMID: 30402244 PMCID: PMC6205572 DOI: 10.1016/j.nmni.2018.06.001] [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: 11/29/2022] Open
Abstract
Surveillance of antibiotic resistance has become a public global concern after the rapid worldwide dissemination of several antibiotic resistance genes. Here we report the role of the Institut Hospitalo-Universitaire Méditerranée Infection created in 2011 in the identification and description of multidrug-resistant bacteria thanks to collaborations and training of students from the Mediterranean basin and from African countries. Since the creation of the institute, 95 students and researchers have come from 19 different countries from these areas to characterize 6359 bacterial isolates from 7280 samples from humans (64%), animals (28%) and the environment (8%). Most bacterial isolates studied were Gram-negative bacteria (n = 5588; 87.9%), mostly from Algeria (n = 4190), Lebanon (n = 946), Greece (n = 610), Saudi Arabia (n = 299) and Senegal (n = 278). Antibiotic resistance was diversified with the detection and characterization of extended-spectrum β-lactamases, carbapenemases and resistance to colistin, vancomycin and methicillin. All those studies led to 97 indexed international scientific papers. Over the last 6 years, our institute has created a huge network of collaborations by training students that plays a major role in the surveillance of resistance to antibiotics in these countries.
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Affiliation(s)
| | | | | | - J.-M. Rolain
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
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27
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Hadjadj L, Bakour S, Rolain JM. Co-occurrence of carbapenemase encoding genes in Acinetobacter baumannii, a dream or reality? BMC Microbiol 2018; 18:107. [PMID: 30185164 PMCID: PMC6125877 DOI: 10.1186/s12866-018-1252-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 08/28/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Acinetobacter baumannii is an important opportunistic pathogen that is rapidly evolving towards multidrug resistance and is responsible for life-threatening infections. Carbapenems are commonly used to treat A. baumannii infections but the emergence of carbapenemase encoding genes, such as blaOXA-23-like, blaOXA-24-like, blaOXA-58-like, and blaNDM has been reported. Moreover, several studies have reported the co-occurrence of two distinct carbapenemases in some isolates. The aim of the present study is to demonstrate whether the phenomenon of co-occurrence of two distinct carbapenemase encoding genes in a single isolate still exists. RESULTS We studied six strains of A. baumannii including one harboring blaOXA-23-like and blaOXA-24-like genes and five with blaOXA-23-like and blaNDM genes. One colony of each strain was inoculated in sterile water and diluted ten-fold. Each dilution was cultivated on trypticase soy agar plates for 24 h at 37 °C and the isolated bacteria were analyzed. For two of the six tested strains, we identified two different populations of A. baumannii, each with a different carbapenemase, genes encoding aminoglycoside modifying enzymes, resistance phenotype, and clonal type. In addition, the two different populations had the same aspect on the agar plate. CONCLUSIONS Here, we demonstrate that A. baumannii infections could be linked to multiple clones harboring different carbapenemase encoding genes in the same sample. In addition, we describe an easy method of verifying the presence of co-occurrence of carbapenemase in one isolate.
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Affiliation(s)
- Linda Hadjadj
- 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
| | - Sofiane Bakour
- 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
| | - 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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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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Fagerquist CK. Unlocking the proteomic information encoded in MALDI-TOF-MS data used for microbial identification and characterization. Expert Rev Proteomics 2016; 14:97-107. [DOI: 10.1080/14789450.2017.1260451] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Clifton K. Fagerquist
- United States Department of Agriculture (USDA), Agricultural Research Service, Albany, CA, USA
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