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Haque A, Chowdhury A, Islam Bhuiyan MN, Bhowmik B, Afrin S, Sarkar R, Haque MM. Molecular characterization, antibiotic resistant pattern and biofilm forming potentiality of bacterial community associated with Ompok pabda fish farming in southwestern Bangladesh. Microb Pathog 2024; 194:106818. [PMID: 39047804 DOI: 10.1016/j.micpath.2024.106818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 07/15/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024]
Abstract
Ompok pabda is gaining popularity in the aquaculture industry due to its increasing demand; however research on microbial diversity and antibiotic susceptibility remains limited. The present study was designed to identify the bacterial pathogens commonly found in the pabda farming system with their biofilm forming potential and antibiotic susceptibility. Different bacterial strains were isolated from water, sediments and gut, gill of pabda fish and the isolates were identified based on their morphological traits, biochemical and molecular analysis. Antibiotic susceptibilities, antibiotic resistance gene determination and biofilm formation capabilities were evaluated by disc diffusion method, PCR amplification and Microtiter plate (MTP) assay, respectively. The respective isolates of gill and gut of pabda aquaculture and their environments were: Exiguobacterium spp. (25 %), Enterococcus spp. (20 %), Bacillus spp. (10 %), Acinetobacter spp. (10 %), Enterobacter spp. (10 %), Aeromonas spp. (10 %), Lactococcus spp. (5 %), Klebsiella spp. (5 %) and Kurthia spp. (5 %). Antibiotic resistance frequencies were found to be relatively high, especially for trimethoprim (95 %), sulfafurazole (75 %), ampicillin (60 %), amoxicillin-clavulanic acid (55 %), and cephradine (50 %). 30 % isolates were categorized as DR bacteria followed by 30 % isolates were MDR bacteria and 40 % were classified as XDR bacteria. Moreover, 4 antibiotic resistant genes were detected with sul1 (30 %), dfrA1 (10 %), tetC (40 %), and qnrA (5 %) of isolates. Based on the microtiter plate method, 20 %, 25 %, and 30 % of isolates were found to produce strong, moderate, and weak biofilms, respectively. The findings suggest that biofilm forming bacterial strains found in O. pabda fish farm may be a potential source of numerous antibiotic-resistant bacteria. The study sheds new light on antibiotic resistance genes, which are typically inherited by bacteria and play an important role in developing effective treatments or control strategies.
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Affiliation(s)
- Afrina Haque
- Department of Zoology, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - Abhijit Chowdhury
- Institute of Food Science and Technology (IFST), Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, 1205, Bangladesh; Central Analytical & Research Facilities (CARF), Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, 1205, Bangladesh.
| | - Mohammad Nazrul Islam Bhuiyan
- Institute of Food Science and Technology (IFST), Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, 1205, Bangladesh
| | - Banasree Bhowmik
- Institute of Food Science and Technology (IFST), Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, 1205, Bangladesh
| | - Sadia Afrin
- Institute of Food Science and Technology (IFST), Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, 1205, Bangladesh
| | - Rajib Sarkar
- Institute of Food Science and Technology (IFST), Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, 1205, Bangladesh
| | - Md Mansurul Haque
- Department of Zoology, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
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Kherroubi L, Bacon J, Rahman KM. Navigating fluoroquinolone resistance in Gram-negative bacteria: a comprehensive evaluation. JAC Antimicrob Resist 2024; 6:dlae127. [PMID: 39144447 PMCID: PMC11323783 DOI: 10.1093/jacamr/dlae127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 07/04/2024] [Indexed: 08/16/2024] Open
Abstract
Since the introduction of quinolone and fluoroquinolone antibiotics to treat bacterial infections in the 1960s, there has been a pronounced increase in the number of bacterial species that have developed resistance to fluoroquinolone treatment. In 2017, the World Health Organization established a priority list of the most critical Gram-negative resistant pathogens. These included Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Escherichia coli. In the last three decades, investigations into the mechanisms of fluoroquinolone resistance have revealed that mutations in the target enzymes of fluoroquinolones, DNA gyrase or topoisomerase IV, are the most prevalent mechanism conferring high levels of resistance. Alterations to porins and efflux pumps that facilitate fluoroquinolone permeation and extrusion across the bacterial cell membrane also contribute to the development of resistance. However, there is a growing observation of novel mutants with newer generations of fluoroquinolones, highlighting the need for novel treatments. Currently, steady progress has been made in the development of novel antimicrobial agents that target DNA gyrase or topoisomerase IV through different avenues than current fluoroquinolones to prevent target-mediated resistance. Therefore, an updated review of the current understanding of fluoroquinolone resistance within the literature is imperative to aid in future investigations.
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Affiliation(s)
- Linda Kherroubi
- School of Cancer and Pharmaceutical Science, King’s College London, London SE1 9NH, UK
| | - Joanna Bacon
- Discovery Group, Vaccine Development and Evaluation Centre, UK Health Security Agency, Porton Down, Salisbury SP4 0JG, UK
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Tobin LA, Jarocki VM, Kenyon J, Drigo B, Donner E, Djordjevic SP, Hamidian M. Genomic analysis of diverse environmental Acinetobacter isolates identifies plasmids, antibiotic resistance genes, and capsular polysaccharides shared with clinical strains. Appl Environ Microbiol 2024; 90:e0165423. [PMID: 38206028 PMCID: PMC10885009 DOI: 10.1128/aem.01654-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 11/30/2023] [Indexed: 01/12/2024] Open
Abstract
Acinetobacter baumannii, an important pathogen known for its widespread antibiotic resistance, has been the focus of extensive research within its genus, primarily involving clinical isolates. Consequently, data on environmental A. baumannii and other Acinetobacter species remain limited. Here, we utilized Illumina and Nanopore sequencing to analyze the genomes of 10 Acinetobacter isolates representing 6 different species sourced from aquatic environments in South Australia. All 10 isolates were phylogenetically distinct compared to clinical and other non-clinical Acinetobacter strains, often tens of thousands of single-nucleotide polymorphisms from their nearest neighbors. Despite the genetic divergence, we identified pdif modules (sections of mobilized DNA) carrying clinically important antimicrobial resistance genes in species other than A. baumannii, including carbapenemase oxa58, tetracycline resistance gene tet(39), and macrolide resistance genes msr(E)-mph(E). These pdif modules were located on plasmids with high sequence identity to those circulating in globally distributed A. baumannii ST1 and ST2 clones. The environmental A. baumannii isolate characterized here (SAAb472; ST350) did not possess any native plasmids; however, it could capture two clinically important plasmids (pRAY and pACICU2) with high transfer frequencies. Furthermore, A. baumannii SAAb472 possessed virulence genes and a capsular polysaccharide type analogous to clinical strains. Our findings highlight the potential for environmental Acinetobacter species to acquire and disseminate clinically important antimicrobial resistance genes, underscoring the need for further research into the ecology and evolution of this important genus.IMPORTANCEAntimicrobial resistance (AMR) is a global threat to human, animal, and environmental health. Studying AMR in environmental bacteria is crucial to understand the emergence and dissemination of resistance genes and pathogens, and to identify potential reservoirs and transmission routes. This study provides novel insights into the genomic diversity and AMR potential of environmental Acinetobacter species. By comparing the genomes of aquatic Acinetobacter isolates with clinical and non-clinical strains, we revealed that they are highly divergent yet carry pdif modules that encode resistance to antibiotics commonly used in clinical settings. We also demonstrated that an environmental A. baumannii isolate can acquire clinically relevant plasmids and carries virulence factors similar to those of hospital-associated strains. These findings suggest that environmental Acinetobacter species may serve as reservoirs and vectors of clinically important genes. Consequently, further research is warranted to comprehensively understand the ecology and evolution of this genus.
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Affiliation(s)
- Liam A. Tobin
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Veronica M. Jarocki
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, New South Wales, Australia
- The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, Australia
| | - Johanna Kenyon
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Barbara Drigo
- Future Industries Institute, University of South Australia, Mawson Lakes, SA, Australia
- UniSA STEM, University of South Australia, Mawson Lakes, SA, Australia
| | - Erica Donner
- Future Industries Institute, University of South Australia, Mawson Lakes, SA, Australia
- Cooperative Research Centre for Solving Antimicrobial Resistance in Agribusiness, Food, and Environments (CRC SAAFE), Adelaide, SA, Australia
| | - Steven P. Djordjevic
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, New South Wales, Australia
- The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, Australia
| | - Mehrad Hamidian
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, New South Wales, Australia
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Aboelenin AM, El-Mowafy M, Saleh NM, Shaaban MI, Barwa R. Ciprofloxacin- and levofloxacin-loaded nanoparticles efficiently suppressed fluoroquinolone resistance and biofilm formation in Acinetobacter baumannii. Sci Rep 2024; 14:3125. [PMID: 38326515 PMCID: PMC10850473 DOI: 10.1038/s41598-024-53441-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 01/31/2024] [Indexed: 02/09/2024] Open
Abstract
The spread of fluoroquinolone (FQ) resistance in Acinetobacter baumannii represents a critical health threat. This study aims to overcome FQ resistance in A. baumannii via the formulation of polymeric nanoFQs. Herein, 80 A. baumannii isolates were obtained from diverse clinical sources. All A. baumannii isolates showed high resistance to most of the investigated antimicrobials, including ciprofloxacin (CIP) and levofloxacin (LEV) (97.5%). FQ resistance-determining regions of the gyrA and parC genes were the most predominant resistant mechanism, harbored by 69 (86.3%) and 75 (93.8%) of the isolates, respectively. Additionally, plasmid-mediated quinolone resistance genes aac(6')-Ib and qnrS were detected in 61 (76.3%) and 2 (2.5%) of the 80 isolates, respectively. The CIP- and LEV-loaded poly ε-caprolactone (PCL) nanoparticles, FCIP and FLEV, respectively, showed a 1.5-6- and 6-12-fold decrease in the MIC, respectively, against the tested isolates. Interestingly, the time kill assay demonstrated that MICs of FCIP and FLEV completely killed A. baumannii isolates after 5-6 h of treatment. Furthermore, FCIP and FLEV were found to be efficient in overcoming the FQ resistance mediated by the efflux pumps in A. baumannii isolates as revealed by decreasing the MIC four-fold lower than that of free CIP and LEV, respectively. Moreover, FCIP and FLEV at 1/2 and 1/4 MIC significantly decreased biofilm formation by 47-93% and 69-91%, respectively. These findings suggest that polymeric nanoparticles can restore the effectiveness of FQs and represent a paradigm shift in the fight against A. baumannii isolates.
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Affiliation(s)
- Alaa M Aboelenin
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, PO Box 35516, Mansoura, Egypt
| | - Mohammed El-Mowafy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, PO Box 35516, Mansoura, Egypt
| | - Noha M Saleh
- Department of Pharmaceutics, Faculty of Pharmacy, Mansoura University, PO Box 35516, Mansoura, Egypt
| | - Mona I Shaaban
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, PO Box 35516, Mansoura, Egypt.
| | - Rasha Barwa
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, PO Box 35516, Mansoura, Egypt.
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Stegmüller J, Rodríguez Estévez M, Shu W, Gläser L, Myronovskyi M, Rückert-Reed C, Kalinowski J, Luzhetskyy A, Wittmann C. Systems metabolic engineering of the primary and secondary metabolism of Streptomyces albidoflavus enhances production of the reverse antibiotic nybomycin against multi-resistant Staphylococcus aureus. Metab Eng 2024; 81:123-143. [PMID: 38072358 DOI: 10.1016/j.ymben.2023.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/17/2023] [Accepted: 12/01/2023] [Indexed: 01/23/2024]
Abstract
Nybomycin is an antibiotic compound with proven activity against multi-resistant Staphylococcus aureus, making it an interesting candidate for combating these globally threatening pathogens. For exploring its potential, sufficient amounts of nybomycin and its derivatives must be synthetized to fully study its effectiveness, safety profile, and clinical applications. As native isolates only accumulate low amounts of the compound, superior producers are needed. The heterologous cell factory S. albidoflavus 4N24, previously derived from the cluster-free chassis S. albidoflavus Del14, produced 860 μg L-1 of nybomycin, mainly in the stationary phase. A first round of strain development modulated expression of genes involved in supply of nybomycin precursors under control of the common Perm* promoter in 4N24, but without any effect. Subsequent studies with mCherry reporter strains revealed that Perm* failed to drive expression during the product synthesis phase but that use of two synthetic promoters (PkasOP* and P41) enabled strong constitutive expression during the entire process. Using PkasOP*, several rounds of metabolic engineering successively streamlined expression of genes involved in the pentose phosphate pathway, the shikimic acid pathway, supply of CoA esters, and nybomycin biosynthesis and export, which more than doubled the nybomycin titer to 1.7 mg L-1 in the sixth-generation strain NYB-6B. In addition, we identified the minimal set of nyb genes needed to synthetize the molecule using single-gene-deletion strains. Subsequently, deletion of the regulator nybW enabled nybomycin production to begin during the growth phase, further boosting the titer and productivity. Based on RNA sequencing along the created strain genealogy, we discovered that the nyb gene cluster was unfavorably downregulated in all advanced producers. This inspired removal of a part and the entire set of the four regulatory genes at the 3'-end nyb of the cluster. The corresponding mutants NYB-8 and NYB-9 exhibited marked further improvement in production, and the deregulated cluster was combined with all beneficial targets from primary metabolism. The best strain, S. albidoflavus NYB-11, accumulated up to 12 mg L-1 nybomycin, fifteenfold more than the basic strain. The absence of native gene clusters in the host and use of a lean minimal medium contributed to a selective production process, providing an important next step toward further development of nybomycin.
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Affiliation(s)
- Julian Stegmüller
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | | | - Wei Shu
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Lars Gläser
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Maksym Myronovskyi
- Department of Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | | | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Andriy Luzhetskyy
- Department of Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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Tawfick MM, Adulall AK, El-Kholy AA, Manakhly ARE. Mutation-based fluoroquinolone resistance in carbapenem-resistant Acinetobacter baumannii and Escherichia coli isolates causing catheter-related bloodstream infections. Int J Health Sci (Qassim) 2023; 17:18-25. [PMID: 37151743 PMCID: PMC10155246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023] Open
Abstract
Objective We studied the presence of mutations in the chromosomal quinolone resistance-determining regions (QRDRs) of the fluoroquinolone targets gyrA and parC genes and detected the carbapenem resistance (CR) encoding genes among Acinetobacter baumannii and Escherichia coli isolates from catheter-related bloodstream infections (CRBSIs). Methods The study included 39 non-duplicate isolates of A. baumannii (14/39, 35.9%) and E. coli (25/39, 64.1%) isolated from 128 confirmed CRBSIs cases. Antimicrobial susceptibility testing was performed, followed by an evaluation of biofilm formation using the tissue culture plate method. The carbapenemase encoding genes were detected by multiplex polymerase chain reaction (PCR). The mutations in QRDRs of gyrA and parC genes were determined by singleplex PCR amplification followed by DNA sequencing and BlastN analysis in the GenBank database. DNA and the translated amino acid sequences were analyzed using the Mega7 bioinformatics tool. Results Multidrug-resistant (MDR) E. coli and A. baumannii isolates harbored CR encoding genes and combined gyrA and parC genes mutation. The specific substitutions observed in GyrA were Cys173Arg, Cys174Gly, Asp80Val, Tyr178ASP, Tyr84Gly, Glu85Lys, Ser172Leu, and Asp176Asn, while the specific substitutions observed in the ParC amino acid sequence were point mutation 62 Arg, Phe60Leu, Ils66Val, and Gln76Lys. Point mutation 62Arg was detected in two A. baumannii isolates, whereas Ser172Leu mutation was observed in two E. coli isolates. Conclusion The presence of new single and multiple mutations in QRDR causes the emergence of MDR E. coli and A. baumannii infections in carbapenem-resistant Enterobacteriaceae in Egypt, requiring further investigation in Gram-negative bacteria.
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Affiliation(s)
- Mahmoud M. Tawfick
- Department of Microbiology and Immunology, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Nasr City, Egypt
- Department of Microbiology and Immunology, Faculty of Pharmacy, Heliopolis University, Cairo, Egypt
| | - Abeer K. Adulall
- Department of Microbiology and Immunology, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
| | - Amani A. El-Kholy
- Department of Clinical Pathology, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Arwa Ramadan El Manakhly
- Department of Microbiology and Immunology, Faculty of Pharmacy, Modern University for Technology and Information (MTI), Cairo, Egypt
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Wunderlich A, Xanthopoulou K, Wille J, Wohlfarth E, Gerson S, Kaase M, Seifert H, Higgins PG. Carbapenem resistance in Acinetobacter pittii isolates mediated by metallo-β-lactamases. J Antimicrob Chemother 2023; 78:488-496. [PMID: 36537203 DOI: 10.1093/jac/dkac418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 11/20/2022] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVES To characterize the genetic environment of metallo-β-lactamases (MBL) in carbapenem-resistant clinical Acinetobacter pittii isolates. METHODS Seventeen carbapenem-resistant A. pittii isolates harbouring an MBL were collected between 2010 and 2015 in Germany. Antimicrobial susceptibility testing was performed using agar dilution. Presence of MBLs was confirmed by PCR and their genetic location determined by S1-pulsed-field gel electrophoresis followed by Southern blot hybridization. Whole-genome sequencing was performed using the Miseq and MinION platforms. Isolates were typed using an ad hoc core genome MLST scheme. Conjugation into A. baumannii was tested by broth mating. RESULTS In 10 isolates the MBL was plasmid-encoded and in seven isolates chromosomally encoded. blaGIM-1 and blaVIM-2 were plasmid-encoded, blaVIM-4 was chromosomally encoded, while blaNDM-1 was chromosomally encoded in four and plasmid-encoded in three isolates. Seven of ten plasmids were conjugative into A. baumannii. Although most isolates were unrelated, the backbones of the MBL-encoding plasmid showed >99% similarity and only differed in the MBL-encoding area. blaNDM-1-harbouring plasmids were highly similar to other plasmids from Acinetobacter isolates worldwide while the blaVIM-2- and blaGIM-1-encoding plasmids have not been described. CONCLUSIONS These data show the existence of a promiscuous plasmid circulating in A. pittii isolates in Germany that differs only in the MBL-encoding region. Its plasmid backbone has been found globally among multiple Acinetobacter spp. These data should raise awareness of an epidemic conjugative plasmid that has independently acquired MBLs. We should also consider that future comparative plasmid analysis will look beyond solely the resistome and include the mobile elements carrying the resistance genes.
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Affiliation(s)
- Alexander Wunderlich
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Kyriaki Xanthopoulou
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Julia Wille
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | | | - Stefanie Gerson
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Martin Kaase
- Institute for Medical Microbiology, Ruhr-University Bochum, Bochum, Germany
| | - Harald Seifert
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Paul G Higgins
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
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8
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Rafei R, Koong J, Osman M, Al Atrouni A, Hamze M, Hamidian M. Analysis of pCl107 a large plasmid carried by an ST25 Acinetobacter baumannii strain reveals a complex evolutionary history and links to multiple antibiotic resistance and metabolic pathways. FEMS MICROBES 2022; 3:xtac027. [PMID: 37332503 PMCID: PMC10117892 DOI: 10.1093/femsmc/xtac027] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/13/2022] [Accepted: 11/14/2022] [Indexed: 09/14/2023] Open
Abstract
Acinetobacter baumannii has successfully spread during the last decades as one of the main critically important pathogens. However, many aspects including plasmids, are still under-investigated. Here, we report the complete sequence of an Acinetobacter baumannii strain, belonging to the ST25IP (Institut Pasteur) sequence type recovered in 2012 in Lebanon, using a combination of Illumina MiSeq and Oxford Nanopore sequencing and a hybrid assembly approach. This strain (Cl107) carries a 198 kb plasmid called pCl107 that encodes the MPFI conjugative transfer system. The plasmid carries the aacA1, aacC2, sul2, strAB, and tetA(B) antibiotic resistance genes. pCl107 region encompassing the sul2, strAB, tetA(B) is closely related to AbGRI1 chromosomal resistance islands, which are widespread in A. baumannii strains belonging to Global Clone 2. The resistance region found in pCl107 is one of the missing links in the evolutionary history of the AbGRI1 islands. pCl107 also contains a BREX Type 1 region and represents one of the two main evolution patterns observed in BREX clusters found in plasmids related to pCl107. pCl107 also harbours a ptx phosphonate metabolism module, which plays an ancestral structure compared to other large plasmids in ST25 strains. While the uric acid metabolic module found in pCl107 is incomplete, we identified possible ancestors from plasmids and chromosomes of Acinetobacter spp. Our analyses indicate a complex evolutionary history of plasmids related to pCl107 with many links to multiple antibiotic resistance and metabolic pathways.
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Affiliation(s)
- Rayane Rafei
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science & Technology, Faculty of Public Health, Lebanese University, Tripoli 1300, Lebanon
| | - Jonathan Koong
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo NSW 2007, Australia
| | - Marwan Osman
- Cornell Atkinson Center for Sustainability, Cornell University, Ithaca, NY 14853, United States
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, United States
| | - Ahmad Al Atrouni
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science & Technology, Faculty of Public Health, Lebanese University, Tripoli 1300, Lebanon
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science & Technology, Faculty of Public Health, Lebanese University, Tripoli 1300, Lebanon
| | - Mehrad Hamidian
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo NSW 2007, Australia
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9
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Genetic Resistance Determinants in Clinical Acinetobacter pittii Genomes. Antibiotics (Basel) 2022; 11:antibiotics11050676. [PMID: 35625320 PMCID: PMC9137642 DOI: 10.3390/antibiotics11050676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/10/2022] [Accepted: 05/16/2022] [Indexed: 12/14/2022] Open
Abstract
Antimicrobial-resistant pathogenic bacteria are an increasing problem in public health, especially in the healthcare environment, where nosocomial infection microorganisms find their niche. Among these bacteria, the genus Acinetobacter which belongs to the ESKAPE pathogenic group harbors different multi-drug resistant (MDR) species that cause human nosocomial infections. Although A. baumannii has always attracted more interest, the close-related species A. pittii is the object of more study due to the increase in its isolation and MDR strains. In this work, we present the genomic analysis of five clinically isolated A. pittii strains from a Spanish hospital, with special attention to their genetic resistance determinants and plasmid structures. All the strains harbored different genes related to β-lactam resistance, as well as different MDR efflux pumps. We also found and described, for the first time in this species, point mutations that seem linked with colistin resistance, which highlights the relevance of this comparative analysis among the pathogenic species isolates.
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Vuillemenot JB, Bour M, Beyrouthy R, Bonnet R, Laaberki MH, Charpentier X, Ruimy R, Plésiat P, Potron A. Genomic analysis of CTX-M-115 and OXA-23/-72 co-producing Acinetobacter baumannii, and their potential to spread resistance genes by natural transformation. J Antimicrob Chemother 2022; 77:1542-1552. [PMID: 35412620 DOI: 10.1093/jac/dkac099] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 02/16/2022] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVES To characterize Acinetobacter baumannii strains co-producing the ESBL CTX-M-115 and carbapenem-hydrolysing class D β-lactamases (CHDLs), and to assess the potential diffusion of their resistance genes by horizontal transfer. METHODS Nineteen CTX-M-115/CHDL-positive A. baumannii were collected between 2015 and 2019 from patients hospitalized in France. Their whole-genome sequences were determined on Illumina and Oxford Nanopore platforms and were compared through core-genome MLST (cgMLST) and SNP analyses. Transferability of resistance genes was investigated by natural transformation assays. RESULTS Eighteen strains were found to harbour CHDL OXA-72, and another one CHDL OXA-23, in addition to CTX-M-115, narrow-spectrum β-lactamases and aminoglycoside resistance determinants including ArmA. cgMLST typing, as well as Oxford Scheme ST and K locus typing, confirmed that 17 out of the 18 CTX-M-115/OXA-72 isolates belonged to new subclades within clonal complex 78 (CC78). The chromosomal region carrying the blaCTX-M-115 gene appeared to vary greatly both in gene content and in length (from 20 to 79 kb) among the strains, likely because of IS26-mediated DNA rearrangements. The blaOXA-72 gene was localized on closely related plasmids showing structural variations that occurred between pdif sites. Transfer of all the β-lactamase genes, as well as aminoglycoside resistance determinants to a drug-susceptible A. baumannii recipient, was easily obtained in vitro by natural transformation. CONCLUSIONS This work highlights the propensity of CC78 isolates to collect multiple antibiotic resistance genes, to rearrange and to pass them to other A. baumannii strains via natural transformation. This process, along with mobile genetic elements, likely contributes to the considerable genomic plasticity of clinical strains, and to the diversity of molecular mechanisms sustaining their multidrug resistance.
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Affiliation(s)
- Jean-Baptiste Vuillemenot
- Centre National de Référence de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire de Besançon, France.,Laboratoire de Bactériologie, UMR 6249 Chrono-Environnement, UFR Santé, Université Bourgogne Franche-Comté, Besançon, France
| | - Maxime Bour
- Centre National de Référence de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire de Besançon, France
| | - Racha Beyrouthy
- UMR INSERM 1071 USC INRA2018, Université Clermont Auvergne, Clermont-Ferrand, France.,Laboratoire associé Centre National de Référence de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire de Clermont-Ferrand, France
| | - Richard Bonnet
- UMR INSERM 1071 USC INRA2018, Université Clermont Auvergne, Clermont-Ferrand, France.,Laboratoire associé Centre National de Référence de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire de Clermont-Ferrand, France
| | - Maria-Halima Laaberki
- CIRI, Centre International de Recherche en Infectiologie, INSERM U1111, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Xavier Charpentier
- CIRI, Centre International de Recherche en Infectiologie, INSERM U1111, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Raymond Ruimy
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Nice, UMR INSERM C3M, Université Côte d'Azur, Nice, France
| | - Patrick Plésiat
- Centre National de Référence de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire de Besançon, France.,Laboratoire de Bactériologie, UMR 6249 Chrono-Environnement, UFR Santé, Université Bourgogne Franche-Comté, Besançon, France
| | - Anaïs Potron
- Centre National de Référence de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire de Besançon, France.,Laboratoire de Bactériologie, UMR 6249 Chrono-Environnement, UFR Santé, Université Bourgogne Franche-Comté, Besançon, France
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11
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Variants of Tn 6924, a Novel Tn 7 Family Transposon Carrying the blaNDM Metallo-β-Lactamase and 14 Copies of the aphA6 Amikacin Resistance Genes Found in Acinetobacter baumannii. Microbiol Spectr 2022; 10:e0174521. [PMID: 35019774 PMCID: PMC8754128 DOI: 10.1128/spectrum.01745-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Carbapenem resistance in Acinetobacter baumannii is primarily due to the global spread of two main clones that carry oxa23, oxa24, and oxa58. However, new carbapenem-resistant clones are emerging that are also resistant to a wide range of antibiotics. Strains belonging to ST85IP (Institut Pasteur) carry the blaNDM metallo-β-lactamase carbapenem resistance gene. Here, we completed the genome sequence of an ST85IP strain, Cl300, recovered in 2015 in Lebanon, using a combination of Illumina MiSeq and Oxford Nanopore sequencing and a hybrid assembly approach. Cl300 is highly resistant to meropenem and amikacin, and consistent with this, a copy of the blaNDM carbapenem and 14 copies of the aphA6 amikacin resistance genes were found in the genome. Cl300 also contains the sul2 sulfonamide and the msr(E) macrolide resistance genes. All aphA6 copies and blaNDM are in a novel 76-kb Tn7 family transposon designated Tn6924. Like Tn7, Tn6924 is bounded by 29-bp inverted repeats with additional TnsB binding sites at each end. Several variants of Tn6924 were found in a set of diverse strains, including ST85IP strains as well as members of global clones 1 and 2. sul2 and msr(E) are in a 13.0-kb pseudocompound transposon (PCT) bounded by IS1008. ST85s represent a diverse group of strains, particularly in their antibiotic resistance gene content and the K and OC surface polysaccharide loci. Acquisition of Tn6924 by members of global clones indicates the significance of this transposon in spreading two clinically significant resistance genes, blaNDM and aphA6. IMPORTANCE To date, efforts to study the resistance mechanisms of carbapenem-resistant Acinetobacter baumannii have been largely focused on the two major globally distributed clones (GC1 and GC2). ST85 is an emerging sequence type, and unlike other clones, it is associated with the carriage of the blaNDM gene. Here, we completed the genome sequence of an ST85 strain and showed that blaNDM and 14 copies of the aphA6 amikacin resistance genes are in Tn6924, a novel Tn7 family transposon. Analysis of all publicly available ST85s predicted that all strains in the main lineage carry a variant of Tn6924. Variants of Tn6924 were also found in other clones, including GC1 and GC2. Tn6924 is an important mobile element given that it carries two clinically important resistance genes (blaNDM and aphA6) and has spread to other clones. Therefore, outbreaks caused by ST85s should be studied and tracked.
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12
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Characterization of Amino Acid Substitutions in the Two-Component Regulatory System AdeRS Identified in Multidrug-Resistant Acinetobacter baumannii. mSphere 2021; 6:e0070921. [PMID: 34817237 PMCID: PMC8612257 DOI: 10.1128/msphere.00709-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Acinetobacter baumannii, resistance-nodulation-cell division (RND)-type efflux is a resistance mechanism of great importance since it contributes to reduced susceptibility to multiple antimicrobial compounds. Some mutations within the genes encoding the two-component regulatory system AdeRS appear to play a major role in increased expression of the RND efflux pump AdeABC and, consequently, in reduced antimicrobial susceptibility, as they are commonly observed in multidrug-resistant (MDR) A. baumannii. In the present study, the impact of frequently identified amino acid substitutions, namely, D21V and D26N in AdeR and T156M in AdeS, on adeB expression, efflux activity, and antimicrobial susceptibility was investigated. Reverse transcription-quantitative PCR (qRT-PCR) studies revealed significantly increased adeB expression caused by D26N (AdeR) and T156M (AdeS). In addition, accumulation assays have shown that these mutations induce increased efflux activity. Subsequently, antimicrobial susceptibility testing via agar dilution and broth microdilution confirmed the importance of these substitutions for the MDR phenotype, as the MICs for various antimicrobials of different classes were increased. In contrast, the amino acid substitution D21V in AdeR did not lead to increased adeB expression and did not reduce antimicrobial susceptibility. This study demonstrates the impact of the D26N (AdeR) and T156M (AdeS) amino acid substitutions, highlighting that these regulators represent promising targets for interfering with efflux activity to restore antimicrobial susceptibility. IMPORTANCE The active efflux of antimicrobials by bacteria can lead to antimicrobial resistance and persistence and can affect multiple different classes of antimicrobials. Efflux pumps are tightly regulated, and their overexpression can be mediated by changes in their regulators. Identifying these changes is one step in the direction of resistance prediction, but it also opens the possibility of targeting efflux pump regulation as a strategy to overcome antimicrobial resistance. Here, we have investigated commonly found changes in the regulators of the main efflux pumps in Acinetobacter baumannii.
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13
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Koong J, Johnson C, Rafei R, Hamze M, Myers GSA, Kenyon JJ, Lopatkin AJ, Hamidian M. Phylogenomics of two ST1 antibiotic-susceptible non-clinical Acinetobacter baumannii strains reveals multiple lineages and complex evolutionary history in global clone 1. Microb Genom 2021; 7. [PMID: 34874246 PMCID: PMC8767349 DOI: 10.1099/mgen.0.000705] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Acinetobacter baumannii is an opportunistic pathogen that is difficult to treat due to its resistance to extreme conditions, including desiccation and antibiotics. Most strains causing outbreaks around the world belong to two main global lineages, namely global clones 1 and 2 (GC1 and GC2). Here, we used a combination of Illumina short read and MinION (Oxford Nanopore) long-read sequence data with a hybrid assembly approach to complete the genome sequence of two antibiotic-sensitive GC1 strains, Ex003 and Ax270, recovered in Lebanon from water and a rectal swab of a cat, respectively. Phylogenetic analysis of Ax270 and Ex003 with 186 publicly available GC1 genomes revealed two major clades, including five main lineages (L1–L5), and four single-isolate lineages outside of the two clades. Ax270 and Ex003, along with AB307-0294 and MRSN7213 (both predicted antibiotic-susceptible isolates) represent these individual lineages. Antibiotic resistance islands and transposons interrupting the comM gene remain important features in L1–L5, with L1 associated with the AbaR-type resistance islands, L2 with AbaR4, L3 strains containing either AbaR4 or its variants as well as Tn6022::ISAba42, and L4 and L5 associated with Tn6022 or its variants. Analysis of the capsule (KL) and outer core (OCL) polysaccharide loci further revealed a complex evolutionary history probably involving many recombination events. As more genomes become available, more GC1 lineages continue to emerge. However, genome sequence data from more diverse geographical regions are needed to draw a more accurate population structure of this globally distributed clone.
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Affiliation(s)
- Jonathan Koong
- The iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Claire Johnson
- Department of Biology, Barnard College Affiliated Faculty Data Science Institute, Columbia University Affiliated Faculty, Columbia University, Columbia, USA
| | - Rayane Rafei
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science & Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science & Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Garry S A Myers
- The iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Johanna J Kenyon
- Centre for Immunology and Infection Control, School of Biomedical Sciences. Faculty of Health, Queensland University of Technology, Brisbane, Australia
| | - Allison J Lopatkin
- Department of Biology, Barnard College Affiliated Faculty Data Science Institute, Columbia University Affiliated Faculty, Columbia University, Columbia, USA
| | - Mohammad Hamidian
- The iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
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14
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Singh RB, Das S, Chodosh J, Sharma N, Zegans ME, Kowalski RP, Jhanji V. Paradox of complex diversity: Challenges in the diagnosis and management of bacterial keratitis. Prog Retin Eye Res 2021; 88:101028. [PMID: 34813978 DOI: 10.1016/j.preteyeres.2021.101028] [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] [Received: 07/28/2021] [Revised: 11/09/2021] [Accepted: 11/12/2021] [Indexed: 12/12/2022]
Abstract
Bacterial keratitis continues to be one of the leading causes of corneal blindness in the developed as well as the developing world, despite swift progress since the dawn of the "anti-biotic era". Although, we are expeditiously developing our understanding about the different causative organisms and associated pathology leading to keratitis, extensive gaps in knowledge continue to dampen the efforts for early and accurate diagnosis, and management in these patients, resulting in poor clinical outcomes. The ability of the causative bacteria to subdue the therapeutic challenge stems from their large genome encoding complex regulatory networks, variety of unique virulence factors, and rapid secretion of tissue damaging proteases and toxins. In this review article, we have provided an overview of the established classical diagnostic techniques and therapeutics for keratitis caused by various bacteria. We have extensively reported our recent in-roads through novel tools for accurate diagnosis of mono- and poly-bacterial corneal infections. Furthermore, we outlined the recent progress by our group and others in understanding the sub-cellular genomic changes that lead to antibiotic resistance in these organisms. Finally, we discussed in detail, the novel therapies and drug delivery systems in development for the efficacious management of bacterial keratitis.
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Affiliation(s)
- Rohan Bir Singh
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA; Department of Ophthalmology, Leiden University Medical Center, 2333, ZA Leiden, the Netherlands
| | - Sujata Das
- Cornea and Anterior Segment Services, LV Prasad Eye Institute, Bhubaneshwar, India
| | - James Chodosh
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Namrata Sharma
- Dr. Rajendra Prasad Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi, India
| | - Michael E Zegans
- Department of Ophthalmology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Regis P Kowalski
- Department of Ophthalmology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA; The Charles T Campbell Ophthalmic Microbiology Laboratory, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Vishal Jhanji
- Department of Ophthalmology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA; The Charles T Campbell Ophthalmic Microbiology Laboratory, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
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15
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Liepa R, Mann R, Osman M, Hamze M, Gunawan C, Hamidian M. Cl415, a carbapenem-resistant Acinetobacter baumannii isolate containing four AbaR4 and a new variant of AbGRI2, represents a novel global clone 2 strain. J Antimicrob Chemother 2021; 77:345-350. [PMID: 34741594 PMCID: PMC8809195 DOI: 10.1093/jac/dkab399] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 10/06/2021] [Indexed: 11/29/2022] Open
Abstract
Objectives To determine the genetic context of genes conferring antibiotic resistance on the carbapenem-resistant Acinetobacter baumannii Cl415, recovered in 2017 at El Youssef Hospital Centre in Akkar Governorate, North Lebanon. Methods Antibiotic resistance phenotype for 22 antibiotics was determined using disc diffusion or MIC determination. The whole-genome sequence of Cl415 was determined using a combination of the Illumina MiSeq and Oxford Nanopore (MinION) platforms. Complete genome was assembled using Unicycler and antibiotic resistance determinants and ISs were identified using ResFinder and ISFinder, respectively. Results Cl415 is a global clone 2 (GC2) strain and belongs to the most common STs of this clone, ST2IP and ST218OX. Cl415 is resistant to several antibiotics, including aminoglycosides and carbapenems to a high level. Genomic analysis of Cl415 revealed that it carries four chromosomal AbaR4 copies. One copy was found in the comM gene replacing the AbGRI1 island. Cl415 also contains a novel variant of AbGRI2, herein called AbGRI2-15, carrying only the blaTEM and aphA1 resistance genes. Cl415 belongs to a subclade of GC2 strains that appear to have diverged recently with a wide geographical distribution. Conclusions The resistance gene complement of Cl415 was found in the chromosome with four oxa23 located in AbaR4 copies and the remaining genes in a novel variant of the AbGRI2 resistance island. Cl415 was isolated in Lebanon, but phylogenetic analysis suggests that Cl415 represents a new lineage with global distribution within GC2.
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Affiliation(s)
- Rebekah Liepa
- The iThree Institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Riti Mann
- The iThree Institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Marwan Osman
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon.,Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14850, USA
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Cindy Gunawan
- The iThree Institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Mohammad Hamidian
- The iThree Institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
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16
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Nogbou ND, Nkawane GM, Ntshane K, Wairuri CK, Phofa DT, Mokgokong KK, Ramashia M, Nchabeleng M, Obi LC, Musyoki AM. Efflux Pump Activity and Mutations Driving Multidrug Resistance in Acinetobacter baumannii at a Tertiary Hospital in Pretoria, South Africa. Int J Microbiol 2021; 2021:9923816. [PMID: 34659419 PMCID: PMC8516574 DOI: 10.1155/2021/9923816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/13/2021] [Indexed: 12/13/2022] Open
Abstract
Acinetobacter baumannii (A. baumannii) has developed several resistance mechanisms. The bacteria have been reported as origin of multiple outbreaks. This study aims to investigate the use of efflux pumps and quinolone resistance-associated genotypic mutations as mechanisms of resistance in A. baumannii isolates at a tertiary hospital. A total number of 103 A. baumannii isolates were investigated after identification and antimicrobial susceptibility testing by VITEK2 followed by PCR amplification of bla OXA-51 . Conventional PCR amplification of the AdeABC efflux pump (adeB, adeS, and adeR) and quinolone (parC and gyrA) resistance genes were performed, followed by quantitative real-time PCR of AdeABC efflux pump genes. Phenotypic evaluation of efflux pump expression was performed by determining the difference between the MIC of tigecycline before and after exposure to an efflux pump inhibitor. The Sanger sequencing method was used to sequence the parC and gyrA amplicons. A phylogenetic tree was drawn using MEGA 4.0 to evaluate evolutionary relatedness of the strains. All the collected isolates were bla OXA-51 -positive. High resistance to almost all the tested antibiotics was observed. Efflux pump was found in 75% of isolates as a mechanism of resistance. The study detected parC gene mutation in 60% and gyrA gene mutation in 85%, while 37% of isolates had mutations on both genes. A minimal evolutionary distance between the isolates was reported. The use of the AdeABC efflux pump system as an active mechanism of resistance combined with point mutation mainly in gyrA was shown to contribute to broaden the resistance spectrum of A. baumannii isolates.
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Affiliation(s)
- Noel-David Nogbou
- Department of Microbiological Pathology, School of Medicine, Sefako Makgatho Health Sciences University, Pretoria, South Africa
| | - Granny M. Nkawane
- Department of Microbiological Pathology, School of Medicine, Sefako Makgatho Health Sciences University, Pretoria, South Africa
| | - Khanyisa Ntshane
- Department of Microbiological Pathology, School of Medicine, Sefako Makgatho Health Sciences University, Pretoria, South Africa
| | - Charles K. Wairuri
- Department of Microbiological Pathology, School of Medicine, Sefako Makgatho Health Sciences University, Pretoria, South Africa
| | - Dikwata T. Phofa
- Department of Microbiological Pathology, School of Medicine, Sefako Makgatho Health Sciences University, Pretoria, South Africa
| | - Kagiso K. Mokgokong
- Department of Microbiological Pathology, School of Medicine, Sefako Makgatho Health Sciences University, Pretoria, South Africa
| | - Mbudzeni Ramashia
- Department of Microbiological Pathology, School of Medicine, Sefako Makgatho Health Sciences University, Pretoria, South Africa
| | - Maphoshane Nchabeleng
- Department of Microbiological Pathology, School of Medicine, Sefako Makgatho Health Sciences University, Pretoria, South Africa
- Microbiology Unit, National Health Laboratory Services, Dr George Mukhari Academic Hospital, Pretoria, South Africa
| | - Lawrence C. Obi
- School of Science and Technology, Sefako Makgatho Health Sciences University, Pretoria, South Africa
| | - Andrew M. Musyoki
- Department of Microbiological Pathology, School of Medicine, Sefako Makgatho Health Sciences University, Pretoria, South Africa
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17
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Antimicrobial Resistance Determinants in Genomes and Plasmids from Acinetobacter baumannii Clinical Isolates. Antibiotics (Basel) 2021; 10:antibiotics10070753. [PMID: 34206348 PMCID: PMC8300758 DOI: 10.3390/antibiotics10070753] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 06/13/2021] [Indexed: 12/30/2022] Open
Abstract
Acinetobacter baumannii is a Gram-negative coccoid rod species, clinically relevant as a human pathogen, included in the ESKAPE group. Carbapenem-resistant A. baumannii (CRAB) are considered by the World Health Organization (WHO) as a critical priority pathogen for the research and development of new antibiotics. Some of the most relevant features of this pathogen are its intrinsic multidrug resistance and its ability to acquire rapid and effective new resistant determinants against last-resort clinical antibiotics, mostly from other ESKAPE species. The presence of plasmids and mobile genetic elements in their genomes contributes to the acquisition of new antimicrobial resistance determinants. However, although A. baumannii has arisen as an important human pathogen, information about these elements is still not well understood. Current genomic analysis availability has increased our ability to understand the microevolution of bacterial pathogens, including point mutations, genetic dissemination, genomic stability, and pan- and core-genome compositions. In this work, we deeply studied the genomes of four clinical strains from our hospital, and the reference strain ATCC®19606TM, which have shown a remarkable ability to survive and maintain their effective capacity when subjected to long-term stress conditions. With that, our aim was presenting a detailed analysis of their genomes, including antibiotic resistance determinants and plasmid composition.
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18
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Identification of a Novel Ciprofloxacin Tolerance Gene, aciT, Which Contributes to Filamentation in Acinetobacter baumannii. Antimicrob Agents Chemother 2021; 65:AAC.01400-20. [PMID: 33820764 PMCID: PMC8316044 DOI: 10.1128/aac.01400-20] [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: 07/06/2020] [Accepted: 03/20/2021] [Indexed: 01/19/2023] Open
Abstract
Fluoroquinolones are one of the most prescribed broad-spectrum antibiotics. However, their effectiveness is being compromised by high rates of resistance in clinically important organisms, including Acinetobacter baumannii. We sought to investigate the transcriptomic and proteomic responses of the clinical A. baumannii strain AB5075-UW upon exposure to subinhibitory concentrations of ciprofloxacin. Our transcriptomics and proteomics analyses found that the most highly expressed genes and proteins were components of the intact prophage phiOXA. The next most highly expressed gene (and its protein product) under ciprofloxacin stress was a hypothetical gene, ABUW_0098, named here the Acinetobacterciprofloxacin tolerance (aciT) gene. Disruption of this gene resulted in higher susceptibility to ciprofloxacin, and complementation of the mutant with a cloned aciT gene restored ciprofloxacin tolerance to parental strain levels. Microscopy studies revealed that aciT is essential for filamentation during ciprofloxacin stress in A. baumannii. Sequence analysis of aciT indicates the encoded protein is likely to be localized to the cell membrane. Orthologs of aciT are found widely in the genomes of species from the Moraxellaceae family and are well conserved in Acinetobacter species, suggesting an important role. With these findings taken together, this study has identified a new gene conferring tolerance to ciprofloxacin, likely by enabling filamentation in response to the antibiotic.
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19
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Jia J, Guan Y, Li X, Fan X, Zhu Z, Xing H, Wang Z. Phenotype profiles and adaptive preference of Acinetobacter johnsonii isolated from Ba River with different environmental backgrounds. ENVIRONMENTAL RESEARCH 2021; 196:110913. [PMID: 33639142 DOI: 10.1016/j.envres.2021.110913] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/02/2021] [Accepted: 02/17/2021] [Indexed: 06/12/2023]
Abstract
Acinetobacter johnsonii is a potentially opportunistic pathogen widely distributed in nosocomial and natural environments, but little attention has been paid to this bacillus. Here A. johnsonii strains from Ba River with different pollution levels were isolated. In this study, we found that the increasing anthropogenic contaminants accounted for the emergence of multidrug-resistant (MDR) A. johnsonii strains. Correlation analysis results showed that the resistance phenotype of strains could be generated by co-selection of heavy metals or non-corresponding antibiotics. The whole genome sequence analysis showed that the relative heavy pollution of water selects strains containing more survival-relevant genes. We found that only some genes like blaOXA-24 were responsible for its corresponding resistance profile. Additionally, the tolerance profiles toward heavy metals also attribute to the expression of efflux pumps rather than corresponding resistance genes. In summary, our finding revealed that the resistance profiles of A. johnsonii could be generated by cross or co-selection of anthropogenic contaminants and mediated by efflux pumps instead of corresponding resistance determinants. Our study also has deep-sight into the adaptive preference of bacteria in natural environments, and contributes to surveillance studies and MDR- A. johnsonii monitoring worldwide.
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Affiliation(s)
- Jia Jia
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yongjing Guan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiangju Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiaoteng Fan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zeliang Zhu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Haoran Xing
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zaizhao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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20
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Martínez-Puchol S, Riveros M, Ruidias K, Granda A, Ruiz-Roldán L, Zapata-Cachay C, Ochoa TJ, Pons MJ, Ruiz J. Dissemination of a multidrug resistant CTX-M-65 producer Salmonella enterica serovar Infantis clone between marketed chicken meat and children. Int J Food Microbiol 2021; 344:109109. [PMID: 33677191 DOI: 10.1016/j.ijfoodmicro.2021.109109] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 02/03/2021] [Accepted: 02/15/2021] [Indexed: 02/07/2023]
Abstract
The objective of the present study was to characterize Salmonella enterica serovar Infantis isolated from chicken meat determining their clonal relationships with S. Infantis isolated from children with diarrhea. Fifteen meat-recovered S. Infantis were analyzed. Susceptibility levels to 14 antibacterial agents, the presence of ESBL and that of inducible plasmid-mediated AmpC (i-pAmpC) were determined by phenotypical methods. The presence of ESBL and pAmpC was confirmed by PCR, and detected ESBL-encoding genes were sequenced and their transferability tested by conjugation. The presence of gyrA mutations as well as Class 1 integrons was determined by PCR. Clonal relationships were established by REP-PCR and RAPD. In addition, 25 clinical isolates of S. Infantis were included in clonality studies. All meat-recovered S. Infantis were MDR, showing resistance to ampicillin, nitrofurans and quinolones, while none was resistant to azithromycin, ceftazidime or imipenem. ESBL (blaCTX-M-65) and i-pAmpC (blaDHA) were detected in 2 and 5 isolates respectively (in one case concomitantly), with blaCTX-M-65 being transferable through conjugation. In addition, 1 isolate presented a blaSHV gene. All isolates presented D87Y at GyrA, nalidixic acid active efflux pump and a Class 1 integron of ~1000 bp (aadA1). Clonal analysis showed that all isolates were related. Further they were identical to MDR blaCTX-M-65-producing S. Infantis isolates causing children diarrhea in Lima. The dissemination of MDR blaCTX-M-65-producing S. Infantis between marketed meat and children highlights a public health problem which needs be controlled at livestock level.
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Affiliation(s)
| | - Maribel Riveros
- Facultad de Medicina, Universidad Peruana Cayetano Heredia, Lima, Peru; Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Kenny Ruidias
- Universidad Nacional Federico Villarreal, Lima, Peru
| | - Ana Granda
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Lidia Ruiz-Roldán
- ISGlobal Hospital Clinic - Universitat de Barcelona, Barcelona, Spain
| | - Cristhian Zapata-Cachay
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Theresa J Ochoa
- Facultad de Medicina, Universidad Peruana Cayetano Heredia, Lima, Peru; University of Texas, Houston, TX, USA
| | - Maria J Pons
- ISGlobal Hospital Clinic - Universitat de Barcelona, Barcelona, Spain; Universidad Científica del Sur, Lima, Peru
| | - Joaquim Ruiz
- ISGlobal Hospital Clinic - Universitat de Barcelona, Barcelona, Spain; Universidad Científica del Sur, Lima, Peru.
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21
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Systematic Investigation of Resistance Evolution to Common Antibiotics Reveals Conserved Collateral Responses across Common Human Pathogens. Antimicrob Agents Chemother 2020; 65:AAC.01273-20. [PMID: 33106260 PMCID: PMC7927859 DOI: 10.1128/aac.01273-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 10/06/2020] [Indexed: 12/22/2022] Open
Abstract
As drug resistance continues to grow, treatment strategies that turn resistance into a disadvantage for the organism will be increasingly relied upon to treat infections and to lower the rate of multidrug resistance. The majority of work in this area has investigated how resistance evolution toward a single antibiotic effects a specific organism’s collateral response to a wide variety of antibiotics. The results of these studies have been used to identify networks of drugs which can be used to drive resistance in a particular direction. As drug resistance continues to grow, treatment strategies that turn resistance into a disadvantage for the organism will be increasingly relied upon to treat infections and to lower the rate of multidrug resistance. The majority of work in this area has investigated how resistance evolution toward a single antibiotic effects a specific organism’s collateral response to a wide variety of antibiotics. The results of these studies have been used to identify networks of drugs which can be used to drive resistance in a particular direction. However, little is known about the extent of evolutionary conservation of these responses across species. We sought to address this knowledge gap by performing a systematic resistance evolution study of the ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter cloacae) under uniform growth conditions using five clinically relevant antibiotics with diverse modes of action. Evolved lineages were analyzed for collateral effects and the molecular mechanisms behind the observed phenotypes. Fourteen universal cross-resistance and two global collateral sensitivity relationships were found among the lineages. Genomic analyses revealed drug-dependent divergent and conserved evolutionary trajectories among the pathogens. Our findings suggest that collateral responses may be preserved across species. These findings may help extend the contribution of previous collateral network studies in the development of treatment strategies to address the problem of antibiotic resistance.
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22
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Lin D, Chen K, Guo J, Ye L, Li R, Chan EWC, Chen S. Contribution of biofilm formation genetic locus, pgaABCD, to antibiotic resistance development in gut microbiome. Gut Microbes 2020; 12:1-12. [PMID: 33190591 PMCID: PMC7671071 DOI: 10.1080/19490976.2020.1842992] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The human gut microbiome is the presumed site in which the emergence and evolution of antibiotic-resistant organisms constantly take place. To delineate the genetic basis of resistance formation in gut microbiome strains, we investigated the changes in the subpopulation structure of Escherichia coli in rat intestine before and after antimicrobial treatment. We observed that antibiotic treatment was selected for an originally minor subpopulation E. coli carrying the biofilm-forming genetic locus pgaABCD and the toxin-antitoxin system HipAB. Such strains possessed dramatically enhanced ability to withstand the detrimental effects of antibiotics, becoming a dominant subspecies upon antibiotic treatment and eventually evolving into resistant mutants. In contrast, E. coli strains that did not carry pgaABCD and HipAB were eradicated upon antibiotic treatment. Our findings, therefore, suggested that genes encoding biofilm-forming ability played an important role in conferring specific gut E. coli strains the ability to evolve into resistant strains upon a prolonged antibiotic treatment, and that such strains may therefore be considered bacterial antibiotic resistance progenitor cells in the gut microbiome.
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Affiliation(s)
- Dachuan Lin
- Guangdong Provincial Key Laboratory of Regional Immunity and Disease, Department of Pathology Biology, School of Medicine, Shenzhen University, Shenzhen, China,State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Kaichao Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Jiubiao Guo
- Guangdong Provincial Key Laboratory of Regional Immunity and Disease, Department of Pathology Biology, School of Medicine, Shenzhen University, Shenzhen, China,State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Lianwei Ye
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Ruichao Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, People’s Republic of China
| | - Edward Wai Chi Chan
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Sheng Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong,CONTACT : Sheng Chen Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, Room B1730, Yeung Kin Man Academic Building (Nam Shan Chuen Entrance), City University of Hong Kong, Tat Chee Road, Kowloon, Hong Kong
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23
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Wang X, Du Z, Huang W, Zhang X, Zhou Y. Outbreak of Multidrug-Resistant Acinetobacter baumannii ST208 Producing OXA-23-Like Carbapenemase in a Children's Hospital in Shanghai, China. Microb Drug Resist 2020; 27:816-822. [PMID: 33185494 DOI: 10.1089/mdr.2019.0232] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Aims: Acinetobacter baumannii is notorious for acquiring antibiotic resistance and causing nosocomial infections worldwide. This study aimed to investigate the prevalence and molecular characteristics of A. baumannii isolates obtained from inpatients and the intensive care unit (ICU) environment of a pediatric hospital in Shanghai, China. Methods: Between July 2017 and January 2018, a total of 88 A. baumannii isolates, including three obtained from ICU environmental specimens, were characterized by antibiotic susceptibility, multilocus sequence typing, and resistance genes. Results: Carbapenem-resistant A. baumannii (CRAB) isolates, which were resistant to all the antibiotics tested except colistin, accounted for 69.3% (61/88) of all isolates. Three sequence types (STs) were identified among the CRAB isolates, and the predominant clone was ST208 (93.4%, 57/61), which included three environmental isolates and 54 clinical isolates collected from ICU patients. Carbapenem-susceptible isolates, none of which was multidrug resistant (MDR), showed a more diverse genetic background with three known STs and 21 novel STs identified. Intrinsic blaOXA-51-like and blaAmpC were detected in all isolates, while blaOXA-23-like was only detected in all CRAB isolates. ISAba1-blaOXA-23-like, ISAba1-blaOXA-51-like, and ISAba1-blaAmpC were identified in 69.3% (all CRAB isolates), 0%, and 65.9% (58 CRAB isolates) of all isolates, respectively. Conclusions: A nosocomial outbreak of MDR A. baumannii ST208 producing OXA-23-like carbapenemase occurred, highlighting the necessity for strict infection control interventions in the ICU.
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Affiliation(s)
- Xing Wang
- Department of Laboratory Medicine, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, P.R. China
| | - Zhuoying Du
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, P.R. China.,Neurosurgical Institute of Fudan University.,Shanghai Clinical Medical Center of Neurosurgery.,Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration
| | - Weichun Huang
- Department of Laboratory Medicine, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, P.R. China
| | - Xingyu Zhang
- Department of Laboratory Medicine, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, P.R. China
| | - Yun Zhou
- Department of Critical Care Medicine, Huashan Hospital, Fudan University, Shanghai, P.R. China
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24
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Roe C, Williamson CHD, Vazquez AJ, Kyger K, Valentine M, Bowers JR, Phillips PD, Harrison V, Driebe E, Engelthaler DM, Sahl JW. Bacterial Genome Wide Association Studies (bGWAS) and Transcriptomics Identifies Cryptic Antimicrobial Resistance Mechanisms in Acinetobacter baumannii. Front Public Health 2020; 8:451. [PMID: 33014966 PMCID: PMC7493718 DOI: 10.3389/fpubh.2020.00451] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 07/21/2020] [Indexed: 12/14/2022] Open
Abstract
Antimicrobial resistance (AMR) in the nosocomial pathogen, Acinetobacter baumannii, is becoming a serious public health threat. While some mechanisms of AMR have been reported, understanding novel mechanisms of resistance is critical for identifying emerging resistance. One of the first steps in identifying novel AMR mechanisms is performing genotype/phenotype association studies; however, performing these studies is complicated by the plastic nature of the A. baumannii pan-genome. In this study, we compared the antibiograms of 12 antimicrobials associated with multiple drug families for 84 A. baumannii isolates, many isolated in Arizona, USA. in silico screening of these genomes for known AMR mechanisms failed to identify clear correlations for most drugs. We then performed a bacterial genome wide association study (bGWAS) looking for associations between all possible 21-mers; this approach generally failed to identify mechanisms that explained the resistance phenotype. In order to decrease the genomic noise associated with population stratification, we compared four phylogenetically-related pairs of isolates with differing susceptibility profiles. RNA-Sequencing (RNA-Seq) was performed on paired isolates and differentially-expressed genes were identified. In these isolate pairs, five different potential mechanisms were identified, highlighting the difficulty of broad AMR surveillance in this species. To verify and validate differential expression, amplicon sequencing was performed. These results suggest that a diagnostic platform based on gene expression rather than genomics alone may be beneficial in certain surveillance efforts. The implementation of such advanced diagnostics coupled with increased AMR surveillance will potentially improve A. baumannii infection treatment and patient outcomes.
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Affiliation(s)
- Chandler Roe
- Northern Arizona University, Flagstaff, AZ, United States
| | | | | | - Kristen Kyger
- Northern Arizona University, Flagstaff, AZ, United States
| | - Michael Valentine
- Translational Genomics Research Institute, Flagstaff, AZ, United States
| | - Jolene R. Bowers
- Translational Genomics Research Institute, Flagstaff, AZ, United States
| | | | - Veronica Harrison
- Translational Genomics Research Institute, Flagstaff, AZ, United States
| | - Elizabeth Driebe
- Translational Genomics Research Institute, Flagstaff, AZ, United States
| | | | - Jason W. Sahl
- Northern Arizona University, Flagstaff, AZ, United States
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25
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Boyd DA, Mataseje LF, Pelude L, Mitchell R, Bryce E, Roscoe D, Embree J, Katz K, Kibsey P, Lavallee C, Simor AE, Taylor G, Turgeon N, Langley JM, Amaratunga K, Mulvey MR. Results from the Canadian Nosocomial Infection Surveillance Program for detection of carbapenemase-producing Acinetobacter spp. in Canadian hospitals, 2010-16. J Antimicrob Chemother 2020; 74:315-320. [PMID: 30312401 DOI: 10.1093/jac/dky416] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 09/14/2018] [Indexed: 11/13/2022] Open
Abstract
Objectives Globally there is an increased prevalence of carbapenem-resistant Acinetobacter spp. (CRAs) and carbapenemase-producing Acinetobacter spp. (CPAs) in the hospital setting. This increase prompted the Canadian Nosocomial Infection Surveillance Program (CNISP) to conduct surveillance of CRA colonizations and infections identified from patients in CNISP-participating hospitals between 2010 and 2016. Methods Participating acute care facilities across Canada submitted CRAs from 1 January 2010 to 31 December 2016. Patient data were collected from medical records using a standardized questionnaire. WGS was conducted on all CRAs and data underwent single nucleotide variant analysis, resistance gene detection and MLST. Results The 7 year incidence rate of CRA was 0.02 per 10 000 patient days and 0.015 per 1000 admissions, with no significant increase observed over the surveillance period (P > 0.73). Ninety-four CRA isolates were collected from 58 hospitals, of which 93 (98.9%) were CPA. Carbapenemase OXA-235 group (48.4%) was the most common due to two separate clusters, followed by the OXA-23 group (41.9%). Patients with a travel history were associated with 38.8% of CRA cases. The all-cause 30 day mortality rate for infected cases was 24.4 per 100 CRA cases. Colistin was the most active antimicrobial agent (95.8% susceptibility). Conclusions CRA remains uncommon in Canadian hospitals and the incidence did not increase from 2010 to 2016. Almost half of the cases were from two clusters harbouring OXA-235-group enzymes. Previous medical treatment during travel outside of Canada was common.
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Affiliation(s)
- David A Boyd
- Antimicrobial Resistance and Nosocomial Infections, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Laura F Mataseje
- Antimicrobial Resistance and Nosocomial Infections, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Linda Pelude
- Centre for Communicable Diseases and Infection Control, Public Health Agency of Canada, Ottawa, ON, Canada
| | - Robyn Mitchell
- Centre for Communicable Diseases and Infection Control, Public Health Agency of Canada, Ottawa, ON, Canada
| | - Elizabeth Bryce
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada
| | - Diane Roscoe
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada
| | - Joanne Embree
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada
| | - Kevin Katz
- Department of Infection Prevention and Control, North York General Hospital, Toronto, ON, Canada
| | - Pamela Kibsey
- Department of Laboratory Medicine, Victoria General Hospital, Victoria, BC, Canada
| | | | - Andrew E Simor
- Department of Infectious Diseases, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Geoffrey Taylor
- Division of Infectious Diseases, University of Alberta Hospital, Edmonton, AB, Canada
| | - Nathalie Turgeon
- Department of Médicale Microbiologie, Hôtel-Dieu de Quebec du CHUQ, Quebec City, QC, Canada
| | - Joanne M Langley
- Department of Pediatrics, IWK Health Centre, Halifax, NS, Canada
| | - Kanchana Amaratunga
- Centre for Communicable Diseases and Infection Control, Public Health Agency of Canada, Ottawa, ON, Canada
| | - Michael R Mulvey
- Antimicrobial Resistance and Nosocomial Infections, Public Health Agency of Canada, Winnipeg, MB, Canada
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26
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M Campos JC, Antunes LCM, Ferreira RBR. Global priority pathogens: virulence, antimicrobial resistance and prospective treatment options. Future Microbiol 2020; 15:649-677. [DOI: 10.2217/fmb-2019-0333] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp. and Salmonella spp. are part of a group of pathogens that pose a major threat to human health due to the emergence of multidrug-resistant strains. Moreover, these bacteria have several virulence factors that allow them to successfully colonize their hosts, such as toxins and the ability to produce biofilms, resulting in an urgent need to develop new strategies to fight these pathogens. In this review, we compile the most up-to-date information on the epidemiology, virulence and resistance of these clinically important microorganisms. Additionally, we address new therapeutic alternatives, with a focus on molecules with antivirulence activity, which are considered promising to combat multidrug-resistant bacteria.
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Affiliation(s)
- Juliana C de M Campos
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Luis CM Antunes
- Escola Nacional de Saúde Pública Sergio Arouca, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Instituto Nacional de Ciência e Tecnologia de Inovação em Doenças de Populações Negligenciadas, Centro de Desenvolvimento Tecnológico em Saúde, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Rosana BR Ferreira
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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27
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Palmieri M, D’Andrea MM, Pelegrin AC, Perrot N, Mirande C, Blanc B, Legakis N, Goossens H, Rossolini GM, van Belkum A. Abundance of Colistin-Resistant, OXA-23- and ArmA-Producing Acinetobacter baumannii Belonging to International Clone 2 in Greece. Front Microbiol 2020; 11:668. [PMID: 32425900 PMCID: PMC7212473 DOI: 10.3389/fmicb.2020.00668] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 03/24/2020] [Indexed: 12/14/2022] Open
Abstract
Carbapenem resistant Acinetobacter baumannii (CRAB) represents one of the most challenging pathogens in clinical settings. Colistin is routinely used for treatment of infections by this pathogen, but increasing colistin resistance has been reported. We obtained 122 CRAB isolates from nine Greek hospitals between 2015 and 2017, and those colistin resistant (ColR; N = 40, 32.8%) were whole genome sequenced, also by including two colistin susceptible (ColS) isolates for comparison. All ColR isolates were characterized by a previously described mutation, PmrBA226V, which was associated with low-level colistin resistance. Some isolates were characterized by additional mutations in PmrB (E140V or L178F) or PmrA (K172I or D10N), first described here, and higher colistin minimum inhibitory concentrations (MICs), up to 64 mg/L. Mass spectrometry analysis of lipid A showed the presence of a phosphoethanolamine (pEtN) moiety on lipid A, likely resulting from the PmrA/B-induced pmrC overexpression. Interestingly, also the two ColS isolates had the same lipid A modification, suggesting that not all lipid A modifications lead to colistin resistance or that other factors could contribute to the resistance phenotype. Most of the isolates (N = 37, 92.5%) belonged to the globally distributed international clone (IC) 2 and comprised four different sequence types (STs) as defined by using the Oxford scheme (ST 425, 208, 451, and 436). Three isolates belonged to IC1 and ST1567. All the genomes harbored an intrinsic bla OXA-51 group carbapenemase gene, where bla OXA-66 and bla OXA-69 were associated with IC2 and IC1, respectively. Carbapenem resistance was due to the most commonly reported acquired carbapenemase gene bla OXA-23, with ISAba1 located upstream of the gene and likely increasing its expression. The armA gene, associated with high-level resistance to aminoglycosides, was detected in 87.5% of isolates. Collectively, these results revealed a convergent evolution of different clonal lineages toward the same colistin resistance mechanism, thus limiting the effective therapeutic options for the treatment of CRAB infections.
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Affiliation(s)
- Mattia Palmieri
- bioMérieux, Data Analytics Unit, La Balme-les-Grottes, France
| | - Marco Maria D’Andrea
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | | | - Nadine Perrot
- bioMérieux, R&D Microbiology, La Balme-les-Grottes, France
| | | | | | | | - Herman Goossens
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Clinical Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy
| | - Alex van Belkum
- bioMérieux, Data Analytics Unit, La Balme-les-Grottes, France
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28
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Kakuta N, Nakano R, Nakano A, Suzuki Y, Tanouchi A, Masui T, Horiuchi S, Endo S, Kakuta R, Ono Y, Yano H. A Novel Mismatched PCR-Restriction Fragment Length Polymorphism Assay for Rapid Detection of gyrA and parC Mutations Associated With Fluoroquinolone Resistance in Acinetobacter baumannii. Ann Lab Med 2020; 40:27-32. [PMID: 31432636 PMCID: PMC6713654 DOI: 10.3343/alm.2020.40.1.27] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 03/31/2019] [Accepted: 07/26/2019] [Indexed: 12/05/2022] Open
Abstract
Background Mutations in the quinolone resistance-determining regions (QRDRs) of Acinetobacter baumannii DNA gyrase (gyrA) and topoisomerase IV (parC) are linked to fluoroquinolone (FQ) resistance. We developed a mismatched PCR-restriction fragment length polymorphism (RFLP) assay to detect mutations in the gyrA and parC QRDRs associated with FQ resistance in A. baumannii. Methods Based on the conserved sequences of A. baumanniigyrA and parC, two primer sets were designed for mismatched PCR-RFLP to detect mutations in gyrA (codons 83 and 87) and parC (codons 80 and 84) by introducing an artificial restriction enzyme cleavage site into the PCR products. This assay was evaluated using 58 A. baumannii strains and 37 other Acinetobacter strains that have been identified by RNA polymerase β-subunit gene sequence analysis. Results PCR amplification of gyrA and parC was successful for all A. baumannii strains. In 11 FQ -susceptible strains, the gyrA and parC PCR products were digested by the selected restriction enzymes at the site containing gyrA (codons 83 and 87) and parC (codons 80 and 84). PCR products from 47 FQ-resistant strains containing mutations in gyrA and parC were not digested by the restriction enzymes at the site containing the mutation. As for the non-baumanniiAcinetobacter strains, although amplification products for gyrA were obtained for 28 strains, no parC amplification product was obtained for any strain. Conclusions This assay specifically amplified gyrA and parC from A. baumannii and detected A. baumanniigyrA and parC mutations with FQ resistance.
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Affiliation(s)
- Naoki Kakuta
- Department of Microbiology and Infectious Diseases, Nara Medical University, Nara, Japan
| | - Ryuichi Nakano
- Department of Microbiology and Infectious Diseases, Nara Medical University, Nara, Japan.
| | - Akiyo Nakano
- Department of Microbiology and Infectious Diseases, Nara Medical University, Nara, Japan
| | - Yuki Suzuki
- Department of Microbiology and Infectious Diseases, Nara Medical University, Nara, Japan
| | - Ayako Tanouchi
- Department of Microbiology and Infectious Diseases, Nara Medical University, Nara, Japan
| | - Takashi Masui
- Department of Microbiology and Infectious Diseases, Nara Medical University, Nara, Japan.,Department of Otolaryngology-Head and Neck Surgery, Nara Medical University, Nara, Japan
| | - Saori Horiuchi
- Department of Microbiology and Infectious Diseases, Nara Medical University, Nara, Japan
| | - Shiro Endo
- International University of Health and Welfare, Shioya Hospital, Tochigi, Japan
| | - Risako Kakuta
- Department of Otolaryngology-Head and Neck Surgery, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Yasuo Ono
- Department of Microbiology and Immunology, Teikyo University School of Medicine, Tokyo, Japan
| | - Hisakazu Yano
- Department of Microbiology and Infectious Diseases, Nara Medical University, Nara, Japan
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29
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Kotb DN, Mahdy WK, Mahmoud MS, Khairy RMM. Impact of co-existence of PMQR genes and QRDR mutations on fluoroquinolones resistance in Enterobacteriaceae strains isolated from community and hospital acquired UTIs. BMC Infect Dis 2019; 19:979. [PMID: 31752702 PMCID: PMC6868749 DOI: 10.1186/s12879-019-4606-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 10/30/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Fluoroquinolones are commonly recommended as treatment for urinary tract infections (UTIs). The development of resistance to these agents, particularly in gram-negative microorganisms complicates treatment of infections caused by these organisms. This study aimed to investigate antimicrobial resistance of different Enterobacteriaceae species isolated from hospital- acquired and community-acquired UTIs against fluoroquinolones and correlate its levels with the existing genetic mechanisms of resistance. METHODS A total of 440 Enterobacteriaceae isolates recovered from UTIs were tested for antimicrobial susceptibility. Plasmid-mediated quinolone resistance (PMQR) genes and mutations in the quinolone resistance-determining regions (QRDRs) of gyrA and parC genes were examined in quinolone-resistant strains. RESULTS About (32.5%) of isolates were resistant to quinolones and (20.5%) were resistant to fluoroquinolones. All isolates with high and intermediate resistance phenotypes harbored one or more PMQR genes. QnrB was the most frequent gene (62.9%) of resistant isolates. Co-carriage of 2 PMQR genes was detected in isolates (46.9%) with high resistance to ciprofloxacin (CIP) (MICs > 128 μg/mL), while co-carriage of 3 PMQR genes was detected in (6.3%) of resistant isolates (MICs > 512 μg/mL). Carriage of one gene only was detected in intermediate resistance isolates (MICs of CIP = 1.5-2 μg/mL). Neither qnrA nor qnrC genes were detected. The mutation at code 83 of gyrA was the most frequent followed by Ser80-Ile in parC gene, while Asp-87 Asn mutation of gyrA gene was the least, where it was detected only in high resistant E. coli isolates (MIC ≥128 μg/mL). A double mutation in gyrA (Lys154Arg and Ser171Ala) was observed in high FQs resistant isolates (MIC of CIP < 128 μg/mL). CONCLUSION FQs resistance is caused by interact between PMQR genes and mutations in both gyrA and parC genes while a mutation in one gene only can explain quinolone resistance. Accumulation of PMQR genes and QRDR mutations confers high resistance to FQs.
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Affiliation(s)
- Dalia Nabil Kotb
- Department of Microbiology and Immunology, Faculty of Medicine, Minia University, Minia, 61511, Egypt
| | - Wafaa Khairy Mahdy
- Department of Microbiology and Immunology, Faculty of Medicine, Minia University, Minia, 61511, Egypt
| | - Mahmoud Shokry Mahmoud
- Department of Microbiology and Immunology, Faculty of Medicine, Minia University, Minia, 61511, Egypt
| | - Rasha M M Khairy
- Department of Microbiology and Immunology, Faculty of Medicine, Minia University, Minia, 61511, Egypt.
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30
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Eichenberger EM, Thaden JT. Epidemiology and Mechanisms of Resistance of Extensively Drug Resistant Gram-Negative Bacteria. Antibiotics (Basel) 2019; 8:antibiotics8020037. [PMID: 30959901 PMCID: PMC6628318 DOI: 10.3390/antibiotics8020037] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 03/22/2019] [Accepted: 03/31/2019] [Indexed: 12/13/2022] Open
Abstract
Antibiotic resistance has increased markedly in gram-negative bacteria over the last two decades, and in many cases has been associated with increased mortality and healthcare costs. The adoption of genotyping and next generation whole genome sequencing of large sets of clinical bacterial isolates has greatly expanded our understanding of how antibiotic resistance develops and transmits among bacteria and between patients. Diverse mechanisms of resistance, including antibiotic degradation, antibiotic target modification, and modulation of permeability through the bacterial membrane have been demonstrated. These fundamental insights into the mechanisms of gram-negative antibiotic resistance have influenced the development of novel antibiotics and treatment practices in highly resistant infections. Here, we review the mechanisms and global epidemiology of antibiotic resistance in some of the most clinically important resistance phenotypes, including carbapenem resistant Enterobacteriaceae, extensively drug resistant (XDR) Pseudomonas aeruginosa, and XDR Acinetobacter baumannii. Understanding the resistance mechanisms and epidemiology of these pathogens is critical for the development of novel antibacterials and for individual treatment decisions, which often involve alternatives to β-lactam antibiotics.
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Affiliation(s)
- Emily M Eichenberger
- Department of Medicine, Division of Infectious Diseases, Duke University School of Medicine, Durham, NC 27710, USA.
| | - Joshua T Thaden
- Department of Medicine, Division of Infectious Diseases, Duke University School of Medicine, Durham, NC 27710, USA.
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31
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D'Souza R, Pinto NA, Phuong NL, Higgins PG, Vu TN, Byun JH, Cho YL, Choi JR, Yong D. Phenotypic and Genotypic Characterization of Acinetobacter spp. Panel Strains: A Cornerstone to Facilitate Antimicrobial Development. Front Microbiol 2019; 10:559. [PMID: 30972044 PMCID: PMC6446969 DOI: 10.3389/fmicb.2019.00559] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 03/05/2019] [Indexed: 12/27/2022] Open
Abstract
Acinetobacter spp. have emerged as significant pathogens causing nosocomial infections. Treatment of these pathogens has become a major challenge to clinicians worldwide, due to their increasing tendency to antibiotic resistance. To address this, much revenue and technology are currently being dedicated toward developing novel drugs and antibiotic combinations to combat antimicrobial resistance. To address this issue, we have constructed a panel of Acinetobacter spp. strains expressing different antimicrobial resistance determinants such as narrow spectrum β-lactamases, extended-spectrum β-lactamases, OXA-type-carbapenemase, metallo-beta-lactamase, and over-expressed AmpC β-lactamase. Bacterial strains exhibiting different resistance phenotypes were collected between 2008 and 2013 from Severance Hospital, Seoul. Antimicrobial susceptibility was determined according to the CLSI guidelines using agar dilution method. Selected strains were sequenced using Ion Torrent PGM system, annotated using RAST server and analyzed using Geneious pro 8.0. Genotypic determinants, such as acquired resistance genes, changes in the expression of efflux pumps, mutations, and porin alternations, contributing to the relevant expressed phenotype were characterized. Isolates expressing ESBL phenotype consisted of bla PER-1 gene, the overproduction of intrinsic AmpC beta-lactamase associated with ISAba1 insertion, and carbapenem resistance associated with production of carbapenem-hydrolyzing Ambler class D β-lactamases, such as OXA-23, OXA-66, OXA-120, OXA-500, and metallo-β-lactamase, SIM-1. We have analyzed the relative expression of Ade efflux systems, and determined the sequences of their regulators to correlate with phenotypic resistance. Quinolone resistance-determining regions were analyzed to understand fluoroquinolone-resistance. Virulence factors responsible for pathogenesis were also identified. Due to several mutations, acquisition of multiple resistance genes and transposon insertion, phenotypic resistance decision scheme for for evaluating the resistance proved inaccurate, which highlights the urgent need for modification to this scheme. This complete illustration of mechanism contributing to specific resistance phenotypes can be used as a target for novel drug development. It can also be used as a reference strain in the clinical laboratory and for the evaluation of antibiotic efficacy for specific resistance mechanisms.
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Affiliation(s)
- Roshan D'Souza
- Department of Laboratory Medicine, Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea.,J. Craig Venter Institute, Rockville, MD, United States
| | - Naina A Pinto
- Department of Laboratory Medicine, Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University, Seoul, South Korea
| | - Nguyen Le Phuong
- Department of Laboratory Medicine, Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University, Seoul, South Korea
| | - Paul G Higgins
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany.,German Centre for Infection Research, Partner site Bonn-Cologne, Germany
| | - Thao Nguyen Vu
- Department of Laboratory Medicine, Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University, Seoul, South Korea
| | - Jung-Hyun Byun
- Department of Laboratory Medicine, Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea.,Department of Laboratory Medicine, Gyeongsang National University College of Medicine, Jinju, South Korea
| | - Young Lag Cho
- German Centre for Infection Research, Partner site Bonn-Cologne, Germany
| | - Jong Rak Choi
- Department of Laboratory Medicine, Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
| | - Dongeun Yong
- Department of Laboratory Medicine, Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
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32
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Oinuma KI, Suzuki M, Nakaie K, Sato K, Saeki K, Sakiyama A, Takizawa E, Niki M, Niki M, Yamada K, Shibayama K, Kakeya H, Kaneko Y. Genome-Based Epidemiological Analysis of 13 Acinetobacter Strains Isolated from Blood Cultures of Hospitalized Patients from a University Hospital in Japan. Jpn J Infect Dis 2019; 72:274-280. [PMID: 30814458 DOI: 10.7883/yoken.jjid.2018.403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The genus Acinetobacter comprises many species that can cause infectious diseases. Despite their importance as nosocomial pathogens, the clinical distributions of individual species or clones are not well understood. In this study, we aimed to characterize 13 Acinetobacter strains isolated from blood cultures from Osaka City University Hospital. We conducted whole-genome sequencing to reveal their genetic background. We also performed PCR-based open reading frame typing (POT) and compared the results with those of multilocus sequence typing (MLST) to confirm its reliability as a genotyping method. Although biochemical analysis suggested that most isolates were A. baumannii, genomic analysis revealed that the collection of Acinetobacter isolates comprised six different species, with non-baumannii Acinetobacter species representing the majority. All strains possessed an inherent ADC-type β-lactamase gene, whereas the distribution of OXA-type enzymes was limited to A. baumannii, A. pittii, and A. colistiniresistens. While MLST properly discriminated four A. baumannii strains as different clones, POT failed to distinguish three of the four A. baumannii strains from each other, highlighting a potential pitfall that may be encountered when applying POT to non-epidemiological A. baumannii strains.
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Affiliation(s)
- Ken-Ichi Oinuma
- Department of Bacteriology, Osaka City University Graduate School of Medicine.,Research Center for Infectious Disease Sciences, Osaka City University Graduate School of Medicine
| | - Masato Suzuki
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases
| | - Kiyotaka Nakaie
- Department of Infection Control and Prevention, Osaka City University Hospital.,Department of Infection Control Science, Osaka City University Graduate School of Medicine
| | - Kanako Sato
- Department of Bacteriology, Osaka City University Graduate School of Medicine.,Department of Respiratory Medicine, Osaka City University Graduate School of Medicine
| | - Kozo Saeki
- Department of Bacteriology, Osaka City University Graduate School of Medicine.,Department of Medical Technology, Morinomiya University of Medical Sciences
| | - Arata Sakiyama
- Department of Bacteriology, Osaka City University Graduate School of Medicine
| | - Etsuko Takizawa
- Department of Laboratory Medicine, Osaka City University Hospital
| | - Makoto Niki
- Department of Bacteriology, Osaka City University Graduate School of Medicine.,Department of Laboratory Medicine, Osaka City University Hospital
| | - Mamiko Niki
- Department of Bacteriology, Osaka City University Graduate School of Medicine.,Research Center for Infectious Disease Sciences, Osaka City University Graduate School of Medicine
| | - Koichi Yamada
- Research Center for Infectious Disease Sciences, Osaka City University Graduate School of Medicine.,Department of Infection Control Science, Osaka City University Graduate School of Medicine
| | - Keigo Shibayama
- Department of Bacteriology II, National Institute of Infectious Diseases
| | - Hiroshi Kakeya
- Research Center for Infectious Disease Sciences, Osaka City University Graduate School of Medicine.,Department of Infection Control Science, Osaka City University Graduate School of Medicine
| | - Yukihiro Kaneko
- Department of Bacteriology, Osaka City University Graduate School of Medicine.,Research Center for Infectious Disease Sciences, Osaka City University Graduate School of Medicine
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33
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Meumann EM, Anstey NM, Currie BJ, Piera KA, Kenyon JJ, Hall RM, Davis JS, Sarovich DS. Genomic epidemiology of severe community-onset Acinetobacter baumannii infection. Microb Genom 2019; 5. [PMID: 30806611 PMCID: PMC6487312 DOI: 10.1099/mgen.0.000258] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Acinetobacter baumannii causes severe, fulminant, community-acquired pneumonia (CAP) in tropical and subtropical regions. We compared the population structure, virulence and antimicrobial resistance determinants of northern Australian community-onset A. baumannii strains with local and global strains. We performed whole-genome sequencing on 55 clinical and five throat colonization A. baumannii isolates collected in northern Australia between 1994 and 2016. Clinical isolates included CAP (n=41), healthcare-associated pneumonia (n=7) and nosocomial bloodstream (n=7) isolates. We also included 93 publicly available international A. baumannii genome sequences in the analyses. Patients with A. baumannii CAP were almost all critically unwell; 82 % required intensive care unit admission and 18 % died during their inpatient stay. Whole-genome phylogenetic analysis demonstrated that community-onset strains were not phylogenetically distinct from nosocomial strains. Some non-multidrug-resistant local strains were closely related to multidrug-resistant strains from geographically distant locations. Pasteur sequence type (ST)10 was the dominant ST and accounted for 31/60 (52 %) northern Australian strains; the remainder belonged to a diverse range of STs. The most recent common ancestor for ST10 was estimated to have occurred in 1738 (95 % highest posterior density, 1626–1826), with evidence of multiple introduction events between Australia and Southeast Asia between then and the present day. Virulence genes associated with biofilm formation and the type 6 secretion system (T6SS) were absent in many strains, and were not associated with in-hospital mortality. All strains were susceptible to gentamicin and meropenem; none carried an AbaR resistance island. Our results suggest that international dissemination of A. baumannii is occurring in the community on a contemporary timescale. Genes associated with biofilm formation and the T6SS may not be required for survival in community niches. The relative contributions of host and bacterial factors to the clinical severity of community-onset A. baumannii infection require further investigation.
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Affiliation(s)
- Ella M Meumann
- 1Global and Tropical Health Division, Menzies School of Health Research, Darwin 0810, Australia.,2Department of Infectious Diseases, Royal Darwin Hospital, Darwin 0810, Australia
| | - Nicholas M Anstey
- 1Global and Tropical Health Division, Menzies School of Health Research, Darwin 0810, Australia.,2Department of Infectious Diseases, Royal Darwin Hospital, Darwin 0810, Australia
| | - Bart J Currie
- 1Global and Tropical Health Division, Menzies School of Health Research, Darwin 0810, Australia.,2Department of Infectious Diseases, Royal Darwin Hospital, Darwin 0810, Australia
| | - Kim A Piera
- 1Global and Tropical Health Division, Menzies School of Health Research, Darwin 0810, Australia
| | - Johanna J Kenyon
- 3School of Biomedical Sciences, Queensland University of Technology, Brisbane 4001, Australia
| | - Ruth M Hall
- 4School of Life and Environmental Sciences, The University of Sydney, Sydney 2006, Australia
| | - Joshua S Davis
- 1Global and Tropical Health Division, Menzies School of Health Research, Darwin 0810, Australia.,5Department of Infectious Diseases, John Hunter Hospital and the University of Newcastle, Newcastle 2305, Australia
| | - Derek S Sarovich
- 1Global and Tropical Health Division, Menzies School of Health Research, Darwin 0810, Australia.,6Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs 4072, Australia
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34
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Lari AR, Ardebili A, Hashemi A. AdeR-AdeS mutations & overexpression of the AdeABC efflux system in ciprofloxacin-resistant Acinetobacter baumannii clinical isolates. Indian J Med Res 2018; 147:413-421. [PMID: 29998878 PMCID: PMC6057251 DOI: 10.4103/ijmr.ijmr_644_16] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Background & objectives: Overexpression of efflux pumps is a cause of acquired resistance to fluoroquinolones in Acinetobacter baumannii. The present study was done to investigate the presence and overexpression of AdeABC efflux system and to analyze the sequences of AdeR-AdeS regulatory system in ciprofloxacin-resistant A. baumannii isolates. Methods: Susceptibility of 50 clinical A. baumannii isolates to ciprofloxacin, imipenem, ceftazidime, cefepime and gentamicin antimicrobials was evaluated by agar dilution method. Isolates were screened for the evidence of active efflux pump. Isolates were also examined for adeR-adeS and adeB efflux genes by polymerase chain reaction (PCR). The adeR and adeS regulatory genes were sequenced to detect amino acid substitutions. Expression of adeB was evaluated by quantitative reverse-transcriptase PCR. Results: There were high rates of resistance to ciprofloxacin (88%), ceftazidime (88%), cefepime (74%) and imipenem (72%) and less resistance rate to gentamicin (64%). Phenotypic assay showed involvement of active efflux in decreased susceptibility to ciprofloxacin among 16 isolates. The 12.27-fold increase and 4.25-fold increase were found in adeB expression in ciprofloxacin-full-resistant and ciprofloxacin-intermediate-resistant isolates, respectively. Several effective mutations, including A91V, A136V, L192R, A94V, G103D and G186V, were detected in some domains of AdeR-AdeS regulators in the overexpressed ciprofloxacin-resistant isolates. Interpretation & conclusions: The results of this study indicated that overexpression of the AdeABC efflux pump was important to reduce susceptibility to ciprofloxacin and cefepime in A. baumannii that, in turn, could be triggered by alterations in the AdeR-AdeS two-component system. However, gene expression alone does not seem adequate to explain multidrug resistance phenomenon. These results could help plan improved active efflux pump inhibitors.
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Affiliation(s)
- Abdolaziz Rastegar Lari
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Abdollah Ardebili
- Laboratory Sciences Research Center; Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Ali Hashemi
- Department of Microbiology, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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35
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Bogaty C, Mataseje L, Gray A, Lefebvre B, Lévesque S, Mulvey M, Longtin Y. Investigation of a Carbapenemase-producing Acinetobacter baumannii outbreak using whole genome sequencing versus a standard epidemiologic investigation. Antimicrob Resist Infect Control 2018; 7:140. [PMID: 30479753 PMCID: PMC6249735 DOI: 10.1186/s13756-018-0437-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/12/2018] [Indexed: 11/11/2022] Open
Abstract
Background The standard epidemiologic investigation of outbreaks typically relies on spatiotemporal data and pulsed-field gel electrophoresis (PFGE), but whole genome sequencing (WGS) is becoming increasingly used. This investigation aimed to characterize a carbapenemase-producing Acinetobacter baumannii (CPAb) nosocomial outbreak using WGS compared to a standard outbreak investigation. Methods The CPAb outbreak occurred in a single center between 2012 and 2014. The standard investigation used spatiotemporal data and PFGE to generate a chain of transmission. A separate WGS investigation generated a chain of transmission based solely on WGS and date of sampling and was blinded to all other spatiotemporal data and PFGE. Core single nucleotide variant (SNV) phylogenetic analysis was performed on WGS data generated using the Illumina MiSeq platform. The chains of transmission were compared quantitatively and qualitatively to assess the concordance between both methods. Results 28 colonized and infected cases were included. Of the 27 transmission events identified using the standard investigation, 12 (44%) were identical to the transmission events using WGS. WGS identified several transmission events that had not been detected by traditional method, and numerous transmission events that had occurred on different hospital wards than suspected by standard methods. The average number (standard deviation [SD]) of SNVs per transmission events was 1.63 (SD, 1.31) by traditional method and 0.63 (SD, 0.79) by WGS (p = 0.001) All isolates harbored the rare carbapenemase blaOXA-237. Conclusions The traditional and WGS investigations had moderate concordance. When used alongside epidemiologic data and clinical information, WGS could help improve the mapping of transmission events.
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Affiliation(s)
| | | | | | - Brigitte Lefebvre
- Laboratoire de santé publique du Québec, Sainte-Anne-de-Bellevue, QC Canada
| | - Simon Lévesque
- Laboratoire de santé publique du Québec, Sainte-Anne-de-Bellevue, QC Canada
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36
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Abstract
ABSTRACT
The nonfermenting bacteria belonging to
Acinetobacter
spp. and
Pseudomonas
spp. are capable of colonizing both humans and animals and can also be opportunistic pathogens. More specifically, the species
Acinetobacter baumannii
and
Pseudomonas aeruginosa
have been recurrently reported as multidrug-resistant and even pandrug-resistant in clinical isolates. Both species were categorized among the ESKAPE pathogens, ESKAPE standing for
Enterococcus faecium
,
Staphylococcus aureus
,
Klebsiella pneumoniae
,
A. baumannii
,
P. aeruginosa
, and
Enterobacter
species. These six pathogens are the major cause of nosocomial infections in the United States and are a threat all over the world because of their capacity to become increasingly resistant to all available antibiotics.
A. baumannii
and
P. aeruginosa
are both intrinsically resistant to many antibiotics due to complementary mechanisms, the main ones being the low permeability of their outer membrane, the production of the AmpC beta-lactamase, and the production of several efflux systems belonging to the resistance-nodulation-cell division family. In addition, they are both capable of acquiring multiple resistance determinants, such as beta-lactamases or carbapenemases. Even if such enzymes have rarely been identified in bacteria of animal origin, they may sooner or later spread to this reservoir. The goal of this article is to give an overview of the resistance phenotypes described in these pathogens and to provide a comprehensive analysis of all data that have been reported on
Acinetobacter
spp. and
Pseudomonas
spp. from animal hosts.
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Kimura Y, Harada K, Shimizu T, Sato T, Kajino A, Usui M, Tamura Y, Tsuyuki Y, Miyamoto T, Ohki A, Watarai M. Species distribution, virulence factors, and antimicrobial resistance of Acinetobacter spp. isolates from dogs and cats: a preliminary study. Microbiol Immunol 2018; 62:462-466. [PMID: 29752821 DOI: 10.1111/1348-0421.12601] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 04/30/2018] [Accepted: 05/11/2018] [Indexed: 11/29/2022]
Abstract
We investigated the prevalence of virulence factors and antimicrobial resistance among 67 Acinetobacter spp. isolates, consisting of 21 Acinetobacter baumannii and 46 non-baumannii Acinetobacter from companion animals. The PCR analysis showed that the most prevalent virulence gene was afa/draBC (29.9%), followed by papC (22.4%) and cvaC (20.9%). Antimicrobial susceptibility testing revealed that resistance to gentamicin (14.9%) and ciprofloxacin (11.9%) was relatively prevalent. Five gentamicin- and/or ciprofloxacin-resistant A. baumannii strains were assigned to ST25, ST149, ST164, ST203, and ST1198. All ciprofloxacin-resistant isolates harbored point mutations in gyrA and/or parC. This is the first preliminary monitoring of animal-origin Acinetobacter spp. in Japan.
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Affiliation(s)
- Yui Kimura
- The United Graduate School of Veterinary Science, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8515, Japan
- Miyamoto Animal Hospital, 2265-8 Kurokawa, Yamaguchi 753-0851, Japan
| | - Kazuki Harada
- The United Graduate School of Veterinary Science, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8515, Japan
- Department of Veterinary Internal Medicine, Tottori University, Minami 4-101, Koyama, Tottori 680-8553, Japan
| | - Takae Shimizu
- The United Graduate School of Veterinary Science, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8515, Japan
- Department of Veterinary Internal Medicine, Tottori University, Minami 4-101, Koyama, Tottori 680-8553, Japan
| | - Tomomi Sato
- Laboratory of Food Microbiology and Food Safety, Rakuno Gakuen University, 582 Midori, Bunkyodai, Ebetsu, Hokkaido 069-8501, Japan
| | - Akari Kajino
- Laboratory of Food Microbiology and Food Safety, Rakuno Gakuen University, 582 Midori, Bunkyodai, Ebetsu, Hokkaido 069-8501, Japan
| | - Masaru Usui
- Laboratory of Food Microbiology and Food Safety, Rakuno Gakuen University, 582 Midori, Bunkyodai, Ebetsu, Hokkaido 069-8501, Japan
| | - Yutaka Tamura
- Laboratory of Food Microbiology and Food Safety, Rakuno Gakuen University, 582 Midori, Bunkyodai, Ebetsu, Hokkaido 069-8501, Japan
| | - Yuzo Tsuyuki
- Sanritsu Zelkova Veterinary Laboratory, 2-5-8 Kuji, Takatsu, Kawasaki, Kanagawa 213-0032, Japan
| | - Tadashi Miyamoto
- Miyamoto Animal Hospital, 2265-8 Kurokawa, Yamaguchi 753-0851, Japan
| | - Asami Ohki
- Fujifilm Monoris Co., Ltd., 1-49-18 Nishikoigakubo, Kokubunji, Tokyo 185-0013, Japan
| | - Masahisa Watarai
- The United Graduate School of Veterinary Science, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8515, Japan
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Zaki MES, Abou ElKheir N, Mofreh M. Molecular Study of Quinolone Resistance Determining Regions of gyrA Gene and parC Gene s in Clinical Isolates of Acintobacter baumannii Resistant to Fluoroquinolone. Open Microbiol J 2018; 12:116-122. [PMID: 29785218 PMCID: PMC5958293 DOI: 10.2174/1874285801812010116] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 04/15/2018] [Accepted: 04/16/2018] [Indexed: 12/21/2022] Open
Abstract
Introduction: Acinetobacterb aumannii (A. baumannii) is an important pathogen in health care associated infections. Quinolone resistance has emerged in this pathogen. Aims & Objectives: The aim of the present study was to determine the presence of mutations of gyrA gene and parC genes by Restriction Fragment Length Polymorphism Polymerase Chain Reaction (RFLP-PCR) among clinical isolates of A. baumanii. Materials and Methods: The study was carried out on 140 clinical isolates of A. baumannii. The isolates were subjected to molecular study of mutations of gyrA gene and parC genes by RFLP–PCR beside determination of Minimal Inhibitory Concentration (MIC) by macro dilution tube method. Results: The isolates of A. baumannii were resistant to ciprofloxacine and levofloxacin at MIC >4 µg/ml. The most isolates had MIC >128 µg/ml (42.3%). All resistant strains to ciprofloxacin of A. baumannii had mutations in gyrA and parC. The most frequent mutations were combined mutations in both genes (85.5%) and 5% had single mutation either in gyrA or parC. The most frequently combined mutations were associated with MIC >128 µg/ml (42.3%). Conclusion: From this study we can conclude that resistance to ciprofloxacin was common in clinical isolates of A. baumannii. The most frequent mutations were present in gyrA and parC. However, mutations in parC alone were not uncommon. Further large scale studies are required to elucidate the resistance pattern of A. baumannii and its molecular mechanisms.
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Affiliation(s)
- Maysaa El Sayed Zaki
- Clinical Pathology Department, Mansoura Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Nermen Abou ElKheir
- Clinical Pathology Department, Mansoura Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Mohamed Mofreh
- Clinical Pathology Department, Mansoura Faculty of Medicine, Mansoura University, Mansoura, Egypt
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Zhang YY, Liang ZX, Li CS, Chang Y, Ma XQ, Yu L, Chen LA. Whole-Genome Analysis of an Extensively Drug-Resistant Acinetobacter baumannii Strain XDR-BJ83: Insights into the Mechanisms of Resistance of an ST368 Strain from a Tertiary Care Hospital in China. Microb Drug Resist 2018; 24:1259-1270. [PMID: 29489445 DOI: 10.1089/mdr.2017.0246] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Acinetobacter baumannii is an important pathogen of nosocomial infections. Nosocomial outbreaks caused by antibiotic-resistant A. baumannii remain a significant challenge. Understanding the antibiotic resistance mechanism of A. baumannii is critical for clinical treatment. The purpose of this study was to determine the whole-genome sequence (WGS) of an extensively drug-resistant (XDR) A. baumannii strain, XDR-BJ83, which was associated with a nosocomial outbreak in a tertiary care hospital of China, and to investigate the antibiotic resistance mechanism of this strain. The WGS of XDR-BJ83 was performed using single-molecule real-time sequencing. The complete genome of XDR-BJ83 consisted of a 4,011,552-bp chromosome and a 69,069-bp plasmid. The sequence type of XDR-BJ83 was ST368, which belongs to clonal complex 92 (CC92). The chromosome of XDR-BJ83 carried multiple antibiotic resistance genes, antibiotic efflux pump genes, and mobile genetic elements, including insertion sequences, transposons, integrons, and resistance islands. The plasmid of XDR-BJ83 (pBJ83) was a conjugative plasmid carrying type IV secretion system. These results indicate that the presence of multiple antibiotic resistance genes, efflux pumps, and mobile genetic elements is likely associated with resistance to various antibiotics in XDR-BJ83.
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Affiliation(s)
- Yang-Yang Zhang
- 1 Department of Respiratory Medicine, Chinese PLA General Hospital , Beijing, China .,2 Department of Respiratory Medicine, Affiliated Hospital of Chengde Medical University , Chengde, China
| | - Zhi-Xin Liang
- 1 Department of Respiratory Medicine, Chinese PLA General Hospital , Beijing, China
| | - Chun-Sun Li
- 1 Department of Respiratory Medicine, Chinese PLA General Hospital , Beijing, China
| | - Yan Chang
- 3 Department of Respiratory Medicine, The General Hospital of the PLA Rocket Force , Beijing, China
| | - Xiu-Qing Ma
- 1 Department of Respiratory Medicine, Chinese PLA General Hospital , Beijing, China
| | - Ling Yu
- 1 Department of Respiratory Medicine, Chinese PLA General Hospital , Beijing, China
| | - Liang-An Chen
- 1 Department of Respiratory Medicine, Chinese PLA General Hospital , Beijing, China
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Yilmaz S, Yalcin I, Okten S, Onurdag FK, Aki-Yalcin E. Synthesis and investigation of binding interactions of 1,4-benzoxazine derivatives on topoisomerase IV in Acinetobacter baumannii. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2017; 28:941-956. [PMID: 29206501 DOI: 10.1080/1062936x.2017.1404490] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 11/09/2017] [Indexed: 06/07/2023]
Abstract
Acinetobacter baumannii has emerged as an important pathogen for nosocomial infections having high morbidity and mortality. This pathogen is notorious for antimicrobial resistance to many common antimicrobial agents including fluoroquinolones, which have both intrinsic and acquired resistance mechanisms. Fluoroquinolones targeting the bacterial topoisomerase II (DNA gyrase and Topo IV) show potent broad-spectrum antibacterial activity by the stabilization of the covalent enzyme-DNA complex. However, their efficacy is now being threatened by an increasing prevalence of resistance. Fluoroquinolones cause stepwise mutations in DNA gyrase and Topo IV, having alterations of their binding sites. Furthermore, the water-Mg+2 bridge, which provides enzyme-fluoroquinolone interactions, has a significant role in resistance. In this study, 13 compounds were synthesized as 1,4-benzoxazine derivatives which act as bacterial topoisomerase II inhibitors and their antibacterial activities were determined against multi-drug resistant Acinetobacter strains which have ciprofloxacin (CIP) resistant and GyrA mutation. Afterwards we performed docking studies with Topo IV (pdb:2XKK) of these compounds to comprehend their binding properties in Discovery Studio 3.5. The results of this study show significant conclusions to elucidate the resistance mechanism and lead to the design of new antibacterial agents as bacterial topoisomerase II inhibitors.
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Affiliation(s)
- S Yilmaz
- a Pharmaceutical Chemistry Department, Faculty of Pharmacy , Trakya University , Edirne , Turkey
| | - I Yalcin
- b Pharmaceutical Chemistry Department, Faculty of Pharmacy , Ankara University , Ankara , Turkey
| | - S Okten
- c Pharmaceutical Microbiology Department, Faculty of Pharmacy , Trakya University , Edirne , Turkey
| | - F K Onurdag
- c Pharmaceutical Microbiology Department, Faculty of Pharmacy , Trakya University , Edirne , Turkey
| | - E Aki-Yalcin
- b Pharmaceutical Chemistry Department, Faculty of Pharmacy , Ankara University , Ankara , Turkey
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Singh HN, Rajeswari MR. DNA-triplex Forming Purine Repeat Containing Genes in Acinetobacter baumannii and Their Association with Infection and Adaptation. Front Cell Infect Microbiol 2017; 7:250. [PMID: 28670571 PMCID: PMC5472653 DOI: 10.3389/fcimb.2017.00250] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 05/26/2017] [Indexed: 12/31/2022] Open
Affiliation(s)
- Himanshu N Singh
- Department of Biochemistry, All India Institute of Medical SciencesNew Delhi, India
| | - Moganty R Rajeswari
- Department of Biochemistry, All India Institute of Medical SciencesNew Delhi, India
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Lee CR, Lee JH, Park M, Park KS, Bae IK, Kim YB, Cha CJ, Jeong BC, Lee SH. Biology of Acinetobacter baumannii: Pathogenesis, Antibiotic Resistance Mechanisms, and Prospective Treatment Options. Front Cell Infect Microbiol 2017; 7:55. [PMID: 28348979 PMCID: PMC5346588 DOI: 10.3389/fcimb.2017.00055] [Citation(s) in RCA: 510] [Impact Index Per Article: 72.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 02/13/2017] [Indexed: 12/27/2022] Open
Abstract
Acinetobacter baumannii is undoubtedly one of the most successful pathogens responsible for hospital-acquired nosocomial infections in the modern healthcare system. Due to the prevalence of infections and outbreaks caused by multi-drug resistant A. baumannii, few antibiotics are effective for treating infections caused by this pathogen. To overcome this problem, knowledge of the pathogenesis and antibiotic resistance mechanisms of A. baumannii is important. In this review, we summarize current studies on the virulence factors that contribute to A. baumannii pathogenesis, including porins, capsular polysaccharides, lipopolysaccharides, phospholipases, outer membrane vesicles, metal acquisition systems, and protein secretion systems. Mechanisms of antibiotic resistance of this organism, including acquirement of β-lactamases, up-regulation of multidrug efflux pumps, modification of aminoglycosides, permeability defects, and alteration of target sites, are also discussed. Lastly, novel prospective treatment options for infections caused by multi-drug resistant A. baumannii are summarized.
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Affiliation(s)
- Chang-Ro Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University Yongin, South Korea
| | - Jung Hun Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University Yongin, South Korea
| | - Moonhee Park
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji UniversityYongin, South Korea; DNA Analysis Division, Seoul Institute, National Forensic ServiceSeoul, South Korea
| | - Kwang Seung Park
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University Yongin, South Korea
| | - Il Kwon Bae
- Department of Dental Hygiene, College of Health and Welfare, Silla University Busan, South Korea
| | - Young Bae Kim
- Biotechnology Program, North Shore Community College Danvers, MA, USA
| | - Chang-Jun Cha
- Department of Systems Biotechnology, College of Biotechnology and Natural Resources, Chung-Ang University Anseong, South Korea
| | - Byeong Chul Jeong
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University Yongin, South Korea
| | - Sang Hee Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University Yongin, South Korea
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Draft Genome Sequences of Clinical Isolates of Multidrug-Resistant Acinetobacter baumannii. GENOME ANNOUNCEMENTS 2017; 5:5/5/e01547-16. [PMID: 28153899 PMCID: PMC5289685 DOI: 10.1128/genomea.01547-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report here the draft genome sequences of two clinically isolated Acinetobacter baumannii strains. These samples were obtained from patients at the University of Colorado Hospital in 2007 and 2013 and encode an estimated 20 and 13 resistance genes, respectively.
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Domitrovic TN, Hujer AM, Perez F, Marshall SH, Hujer KM, Woc-Colburn LE, Parta M, Bonomo RA. Multidrug Resistant Pseudomonas aeruginosa Causing Prosthetic Valve Endocarditis: A Genetic-Based Chronicle of Evolving Antibiotic Resistance. Open Forum Infect Dis 2016; 3:ofw188. [PMID: 29057280 PMCID: PMC5091635 DOI: 10.1093/ofid/ofw188] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 08/30/2016] [Indexed: 11/12/2022] Open
Abstract
A rare case of MDR P. aeruginosa causing PVE is analyzed at the genetic level with the goal of understanding acquired resistance mechanisms. The molecular basis of evolving antibiotic resistance gives clinicians insight into the nature of persistent P. aeruginosa infections. Background. Successful treatment of infections caused by multidrug-resistant (MDR) Pseudomonas aeruginosa is thwarted by the emergence of antibiotic resistance and biofilm formation on prosthetic devices. Our aims were to decipher the molecular basis of resistance in a unique case of prosthetic valve endocarditis (PVE) caused by MDR P. aeruginosa. Methods. Five sequential MDR P. aeruginosa blood isolates collected during a 7-month period were recovered from a patient suffering from PVE previously exposed to β-lactam antibiotics. Minimum inhibitory concentrations (MICs) of several classes of antibiotics were used to indicate clinical resistance characteristics; relatedness of the isolates was determined using multilocus sequence typing and repetitive sequence-based polymerase chain reaction. Amplification and sequencing of regulatory and resistance genes was performed. Results. All isolates belonged to ST 298, possessed blaPDC-16, and were resistant to fluoroquinolones and carbapenems. In the course of therapy, we observed a >2-fold increase in cephalosporin resistance (4 µg/mL to >16 µg/mL). Sequencing of the AmpC regulator, ampR, revealed a D135N point mutation in cephalosporin-resistant isolates. Common carbapenemase genes were not identified. All isolates demonstrated a premature stop codon at amino acid 79 of the outer membrane protein OprD and mutations in the quinolone resistance-determining regions of gyrA and parC. Point mutations in nalC, an efflux pump regulator, were also observed. Conclusions. In this analysis, we chart the molecular evolution of β-lactam resistance in a case of PVE. We show that mutations in regulatory genes controlling efflux and cephalosporinase production contributed to the MDR phenotype.
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Affiliation(s)
- T Nicholas Domitrovic
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center.,Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Andrea M Hujer
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center.,Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Federico Perez
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center.,Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Steven H Marshall
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center
| | - Kristine M Hujer
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center.,Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | | | - Mark Parta
- Baylor College of Medicine, Houston, Texas
| | - Robert A Bonomo
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center.,Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio.,Departments of Pharmacology, Molecular Biology and Microbiology, Biochemistry, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio
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First Occurrence of OXA-72-Producing Acinetobacter baumannii in Serbia. Antimicrob Agents Chemother 2016; 60:5724-30. [PMID: 27431216 DOI: 10.1128/aac.01016-16] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 06/21/2016] [Indexed: 12/11/2022] Open
Abstract
Here, we characterized the first OXA-72-producing Acinetobacter baumannii isolate (designated MAL) recovered from a urine sample from a Serbian patient. Antimicrobial susceptibility testing, plasmid analysis, and whole-genome sequencing (WGS) were performed to fully characterize the resistome of the A. baumannii MAL clinical isolate. The isolate was multidrug resistant and remained susceptible only to colistin and tigecycline. PCR analysis revealed the presence of the carbapenemase OXA-72, an OXA-40 variant. Extraction by the Kieser method revealed the presence of two plasmids, and one of these, a ca. 10-kb plasmid, harbored the blaOXA-72 gene. WGS revealed 206 contigs corresponding to a genome of 3.9 Mbp in size with a G+C content of 38.8%. The isolate belonged to sequence type 492 and to worldwide clone II (WWCII). Naturally occurring β-lactamase-encoding genes (blaADC-25 and blaOXA-66) were also identified. Aminoglycoside resistance genes encoding one aminoglycoside adenyltransferase (aadA2), three aminoglycoside phosphatases (strA, strB, aphA6), and one 16S RNA methylase (armA) conferring resistance to all aminoglycosides were identified. Resistance to fluoroquinolones was likely due to mutations in gyrA, parC, and parE Of note, the resistome matched perfectly with the antibiotic susceptibility testing results.
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Nigro SJ, Hall RM. Loss and gain of aminoglycoside resistance in global clone 2Acinetobacter baumanniiin Australia via modification of genomic resistance islands and acquisition of plasmids. J Antimicrob Chemother 2016; 71:2432-40. [DOI: 10.1093/jac/dkw176] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 04/17/2016] [Indexed: 01/06/2023] Open
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Molecular characterization and antimicrobial susceptibility of Acinetobacter baumannii isolates obtained from two hospital outbreaks in Los Angeles County, California, USA. BMC Infect Dis 2016; 16:194. [PMID: 27146090 PMCID: PMC4857389 DOI: 10.1186/s12879-016-1526-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Accepted: 04/27/2016] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Antibiotic resistant strains of Acinetobacter baumannii have been responsible for an increasing number of nosocomial infections including bacteremia and ventilator-associated pneumonia. In this study, we analyzed 38 isolates of A. baumannii obtained from two hospital outbreaks in Los Angeles County for the molecular epidemiology, antimicrobial susceptibility and resistance determinants. METHODS Pulsed field gel electrophoresis, tri-locus multiplex PCR and multi-locus sequence typing (Pasteur scheme) were used to examine clonal relationships of the outbreak isolates. Broth microdilution method was used to determine antimicrobial susceptibility of these isolates. PCR and subsequent DNA sequencing were employed to characterize antibiotic resistance genetic determinants. RESULTS Trilocus multiplex PCR showed these isolates belong to Global Clones I and II, which were confirmed to ST1 and ST2, respectively, by multi-locus sequence typing. Pulsed field gel electrophoresis analysis identified two clonal clusters, one with 20 isolates (Global Clone I) and the other with nine (Global Clone II), which dominated the two outbreaks. Antimicrobial susceptibility testing using 14 antibiotics indicated that all isolates were resistant to antibiotics belonging to four or more categories of antimicrobial agents. In particular, over three fourth of 38 isolates were found to be resistant to both imipenem and meropenem. Additionally, all isolates were found to be resistant to piperacillin, four cephalosporin antibiotics, ciprofloxacin and levofloxacin. Resistance phenotypes of these strains to fluoroquinolones were correlated with point mutations in gyrA and parC genes that render reduced affinity to target proteins. ISAba1 was detected immediately upstream of the bla OXA-23 gene present in those isolates that were found to be resistant to both carbapenems. Class 1 integron-associated resistance gene cassettes appear to contribute to resistance to aminoglycoside antibiotics. CONCLUSION The two outbreaks were found to be dominated by two clonal clusters of A. baumannii belonging to MLST ST1 and ST2. All isolates were resistant to antibiotics of at least four categories of antimicrobial agents, and their antimicrobial susceptibility profiles correlate well with genetic determinants. The results of this study will facilitate our understanding of the molecular epidemiology, antimicrobial susceptibility and mechanisms of resistance of A. baumannii obtained from Los Angeles hospitals.
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Novel Aminoglycoside Resistance Transposons and Transposon-Derived Circular Forms Detected in Carbapenem-Resistant Acinetobacter baumannii Clinical Isolates. Antimicrob Agents Chemother 2016; 60:1801-18. [PMID: 26824943 PMCID: PMC4776018 DOI: 10.1128/aac.02143-15] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Accepted: 12/16/2015] [Indexed: 12/15/2022] Open
Abstract
Acinetobacter baumannii has emerged as an important opportunistic pathogen equipped with a growing number of antibiotic resistance genes. Our study investigated the molecular epidemiology and antibiotic resistance features of 28 consecutive carbapenem-resistant clinical isolates of A. baumannii collected throughout Sweden in 2012 and 2013. The isolates mainly belonged to clonal complexes (CCs) with an extensive international distribution, such as CC2 (n = 16) and CC25 (n = 7). Resistance to carbapenems was related to blaOXA-23 (20 isolates), blaOXA-24/40-like (6 isolates), blaOXA-467 (1 isolate), and ISAba1-blaOXA-69 (1 isolate). Ceftazidime resistance was associated with blaPER-7 in the CC25 isolates. Two classical point mutations were responsible for resistance to quinolones in all the isolates. Isolates with high levels of resistance to aminoglycosides carried the 16S rRNA methylase armA gene. The isolates also carried a variety of genes encoding aminoglycoside-modifying enzymes. Several novel structures involved in aminoglycoside resistance were identified, including Tn6279, ΔTn6279, Ab-ST3-aadB, and different assemblies of Tn6020 and TnaphA6. Importantly, a number of circular forms related to the IS26 or ISAba125 composite transposons were detected. The frequent occurrence of these circular forms in the populations of several isolates indicates a potential role of these circular forms in the dissemination of antibiotic resistance genes.
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Lean SS, Yeo CC, Suhaili Z, Thong KL. Comparative Genomics of Two ST 195 Carbapenem-Resistant Acinetobacter baumannii with Different Susceptibility to Polymyxin Revealed Underlying Resistance Mechanism. Front Microbiol 2016; 6:1445. [PMID: 26779129 PMCID: PMC4700137 DOI: 10.3389/fmicb.2015.01445] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 12/03/2015] [Indexed: 01/19/2023] Open
Abstract
Acinetobacter baumannii is a Gram-negative nosocomial pathogen of importance due to its uncanny ability to acquire resistance to most antimicrobials. These include carbapenems, which are the drugs of choice for treating A. baumannii infections, and polymyxins, the drugs of last resort. Whole genome sequencing was performed on two clinical carbapenem-resistant A. baumannii AC29 and AC30 strains which had an indistinguishable ApaI pulsotype but different susceptibilities to polymyxin. Both genomes consisted of an approximately 3.8 Mbp circular chromosome each and several plasmids. AC29 (susceptible to polymyxin) and AC30 (resistant to polymyxin) belonged to the ST195 lineage and are phylogenetically clustered under the International Clone II (IC-II) group. An AbaR4-type resistance island (RI) interrupted the comM gene in the chromosomes of both strains and contained the bla OXA-23 carbapenemase gene and determinants for tetracycline and streptomycin resistance. AC29 harbored another copy of bla OXA-23 in a large (~74 kb) conjugative plasmid, pAC29b, but this gene was absent in a similar plasmid (pAC30c) found in AC30. A 7 kb Tn1548::armA RI which encodes determinants for aminoglycoside and macrolide resistance, is chromosomally-located in AC29 but found in a 16 kb plasmid in AC30, pAC30b. Analysis of known determinants for polymyxin resistance in AC30 showed mutations in the pmrA gene encoding the response regulator of the two-component pmrAB signal transduction system as well as in the lpxD, lpxC, and lpsB genes that encode enzymes involved in the biosynthesis of lipopolysaccharide (LPS). Experimental evidence indicated that impairment of LPS along with overexpression of pmrAB may have contributed to the development of polymyxin resistance in AC30. Cloning of a novel variant of the bla AmpC gene from AC29 and AC30, and its subsequent expression in E. coli also indicated its likely function as an extended-spectrum cephalosporinase.
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Affiliation(s)
- Soo-Sum Lean
- Faulty of Science, Institute of Biological Sciences, Universiti Malaya Kuala Lumpur, Malaysia
| | - Chew Chieng Yeo
- Faculty of Medicine, Biomedical Research Centre, Universiti Sultan Zainal Abidin Kuala Terengganu, Malaysia
| | - Zarizal Suhaili
- Faculty of Bioresources and Food Industry, Universiti Sultan Zainal Abidin Kuala Terengganu, Malaysia
| | - Kwai-Lin Thong
- Faulty of Science, Institute of Biological Sciences, Universiti Malaya Kuala Lumpur, Malaysia
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Esterly JS, Richardson CL, Eltoukhy NS, Qi C, Scheetz MH. Genetic Mechanisms of Antimicrobial Resistance of Acinetobacter baumannii. Ann Pharmacother 2015; 45:218-28. [PMID: 21304033 DOI: 10.1345/aph.1p084] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVE To summarize published data identifying known genetic mechanisms of antibiotic resistance in Acinetobacter baumannii and the correlating phenotypic expression of antibiotic resistance. DATA SOURCES MEDLINE databases (1966-July 15, 2010) were searched to identify original reports of genetic mechanisms of antibiotic resistance in A. baumannii. DATA SYNTHESIS Numerous genetic mechanisms of resistance to multiple classes of antibiotics are known to exist in A. baumannii, a gram-negative bacterium increasingly implicated in nosocomial infections. Mechanisms may be constitutive or acquired via plasmids, integrons, and transposons. Methods of resistance include enzymatic modification of antibiotic molecules, modification of antibiotic target sites, expression of efflux pumps, and downregulation of cell membrane porin channel expression. Resistance to β-lactams appears to be primarily caused by β-lactamase production, including extended spectrum β-lactamases (b/aTEM, blaSHV, b/aTX-M,b/aKPC), metallo-β-lactamases (blaMP, blaVIM, bla, SIM), and most commonly, oxacillinases (blaOXA). Antibiotic target site alterations confer resistance to fluoroquinolones (gyrA, parC) and aminoglycosides (arm, rmt), and to a much lesser extent, β-lactams. Efflux pumps (tet, ade, abe) contribute to resistance against β-lactams, tetracyclines, fluoroquinolones, and aminoglycosides. Finally, porin channel deletion (carO, oprD) appears to contribute to β-lactam resistance and may contribute to rarely seen polymyxin resistance. Of note, efflux pumps and porin deletions as solitary mechanisms may not render clinical resistance to A. baumannii. CONCLUSIONS A. baumannii possesses copious genetic resistance mechanisms. Knowledge of local genotypes and expressed phenotypes for A. baumannii may aid clinicians more than phenotypic susceptibilities reported in large epidemiologic studies.
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Affiliation(s)
- John S Esterly
- John S Esterly PharmD BCPS, at time of writing, Infectious Diseases Pharmacotherapy Fellow, Department of Pharmacy Practice, College of Pharmacy, Midwestern University Chicago, Downers Grove, IL; now, Assistant Professor of Pharmacy Practice, College of Pharmacy, Chicago State University, Chicago, IL; Infectious Diseases Pharmacist, Northwestern Memorial Hospital, Chicago
| | - Chad L Richardson
- Chad L Richardson PharmD, at time of writing, Infectious Diseases Pharmacotherapy Resident, Department of Pharmacy Practice, College of Pharmacy, Midwestern University Chicago; now, Solid Organ Transplant Pharmacist, Northwestern Memorial Hospital
| | - Noha S Eltoukhy
- Noha S Eltoukhy PharmD BCPS, at time of writing, Infectious Diseases Pharmacy Resident, Department of Pharmacy Practice, College of Pharmacy, Midwestern University Chicago; Rush University Medical Center, Chicago; now, Infectious DIseases Clinical Pharmacy Specialist, St. Mary Medical Center, Langhorne, PA
| | - Chao Qi
- Chao Qi PhD, Assistant Professor of Pathology, Feinberg School of Medicine, Northwestern University; Assistant Director, Clinical Microbiology Laboratory, Northwestern Memorial Hospital, Chicago
| | - Marc H Scheetz
- Marc H Scheetz PharmD MSc BCPS, Assistant Professor of Pharmacy Practice, College of Pharmacy, Midwestern University Chicago; Infectious Diseases Pharmacist, Northwestern Memorial Hospital
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