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Yamada N, Kamoshida G, Shiraishi T, Yamaguchi D, Matsuoka M, Yamauchi R, Kanda N, Kamioka R, Takemoto N, Morita Y, Fujimuro M, Yokota SI, Yahiro K. PmrAB, the two-component system of Acinetobacter baumannii, controls the phosphoethanolamine modification of lipooligosaccharide in response to metal ions. J Bacteriol 2024; 206:e0043523. [PMID: 38661375 PMCID: PMC11112996 DOI: 10.1128/jb.00435-23] [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: 12/18/2023] [Accepted: 04/03/2024] [Indexed: 04/26/2024] Open
Abstract
Acinetobacter baumannii is highly resistant to antimicrobial agents, and XDR strains have become widespread. A. baumannii has developed resistance to colistin, which is considered the last resort against XDR Gram-negative bacteria, mainly caused by lipooligosaccharide (LOS) phosphoethanolamine (pEtN) and/or galactosamine (GalN) modifications induced by mutations that activate the two-component system (TCS) pmrAB. Although PmrAB of A. baumannii has been recognized as a drug resistance factor, its function as TCS, including its regulatory genes and response factors, has not been fully elucidated. In this study, to clarify the function of PmrAB as TCS, we elucidated the regulatory genes (regulon) of PmrAB via transcriptome analysis using pmrAB-activated mutant strains. We discovered that PmrAB responds to low pH, Fe2+, Zn2+, and Al3+. A. baumannii selectively recognizes Fe2+ rather than Fe3+, and a novel region ExxxE, in addition to the ExxE motif sequence, is involved in the environmental response. Furthermore, PmrAB participates in the phosphoethanolamine modification of LOS on the bacterial surface in response to metal ions such as Al3+, contributing to the attenuation of Al3+ toxicity and development of resistance to colistin and polymyxin B in A. baumannii. This study demonstrates that PmrAB in A. baumannii not only regulates genes that play an important role in drug resistance but is also involved in responses to environmental stimuli such as metal ions and pH, and this stimulation induces LOS modification. This study reveals the importance of PmrAB in the environmental adaptation and antibacterial resistance emergence mechanisms of A. baumannii. IMPORTANCE Antimicrobial resistance (AMR) is a pressing global issue in human health. Acinetobacter baumannii is notably high on the World Health Organization's list of bacteria for which new antimicrobial agents are urgently needed. Colistin is one of the last-resort drugs used against extensively drug-resistant (XDR) Gram-negative bacteria. However, A. baumannii has become increasingly resistant to colistin, primarily by modifying its lipooligosaccharide (LOS) via activating mutations in the two-component system (TCS) PmrAB. This study comprehensively elucidates the detailed mechanism of drug resistance of PmrAB in A. baumannii as well as its biological functions. Understanding the molecular biology of these molecules, which serve as drug resistance factors and are involved in environmental recognition mechanisms in bacteria, is crucial for developing fundamental solutions to the AMR problem.
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Affiliation(s)
- Noriteru Yamada
- Laboratory of Microbiology and Infection Control, Kyoto Pharmaceutical University, Kyoto, Japan
- Laboratory of Cell Biology, Kyoto Pharmaceutical University, Kyoto, Japan
| | - Go Kamoshida
- Laboratory of Microbiology and Infection Control, Kyoto Pharmaceutical University, Kyoto, Japan
- Department of Infection Control Science, Meiji Pharmaceutical University, Tokyo, Japan
| | - Tsukasa Shiraishi
- Department of Microbiology, Sapporo Medical University School of Medicine, Hokkaido, Japan
| | - Daiki Yamaguchi
- Laboratory of Microbiology and Infection Control, Kyoto Pharmaceutical University, Kyoto, Japan
| | - Momoko Matsuoka
- Laboratory of Microbiology and Infection Control, Kyoto Pharmaceutical University, Kyoto, Japan
| | - Reika Yamauchi
- Laboratory of Microbiology and Infection Control, Kyoto Pharmaceutical University, Kyoto, Japan
| | - Nana Kanda
- Laboratory of Microbiology and Infection Control, Kyoto Pharmaceutical University, Kyoto, Japan
| | - Roku Kamioka
- Laboratory of Microbiology and Infection Control, Kyoto Pharmaceutical University, Kyoto, Japan
| | - Norihiko Takemoto
- Pathogenic Microbe Laboratory, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yuji Morita
- Department of Infection Control Science, Meiji Pharmaceutical University, Tokyo, Japan
| | - Masahiro Fujimuro
- Laboratory of Cell Biology, Kyoto Pharmaceutical University, Kyoto, Japan
| | - Shin-ichi Yokota
- Department of Microbiology, Sapporo Medical University School of Medicine, Hokkaido, Japan
| | - Kinnosuke Yahiro
- Laboratory of Microbiology and Infection Control, Kyoto Pharmaceutical University, Kyoto, Japan
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Lucidi M, Imperi F, Artuso I, Capecchi G, Spagnoli C, Visaggio D, Rampioni G, Leoni L, Visca P. Phage-mediated colistin resistance in Acinetobacter baumannii. Drug Resist Updat 2024; 73:101061. [PMID: 38301486 DOI: 10.1016/j.drup.2024.101061] [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: 10/02/2023] [Revised: 01/24/2024] [Accepted: 01/24/2024] [Indexed: 02/03/2024]
Abstract
AIMS Antimicrobial resistance is a global threat to human health, and Acinetobacter baumannii is a paradigmatic example of how rapidly bacteria become resistant to clinically relevant antimicrobials. The emergence of multidrug-resistant A. baumannii strains has forced the revival of colistin as a last-resort drug, suddenly leading to the emergence of colistin resistance. We investigated the genetic and molecular basis of colistin resistance in A. baumannii, and the mechanisms implicated in its regulation and dissemination. METHODS Comparative genomic analysis was combined with genetic, biochemical, and phenotypic assays to characterize Φ19606, an A. baumannii temperate bacteriophage that carries a colistin resistance gene. RESULTS Ф19606 was detected in 41% of 523 A. baumannii complete genomes and demonstrated to act as a mobile vehicle of the colistin resistance gene eptA1, encoding a functional lipid A phosphoethanolamine transferase. The eptA1 gene is coregulated with its chromosomal homolog pmrC via the PmrAB two-component system and confers colistin resistance when induced by low calcium and magnesium levels. Resistance selection assays showed that the eptA1-harbouring phage Ф19606 promotes the emergence of spontaneous colistin-resistant mutants. CONCLUSIONS Φ19606 is an unprecedented example of a self-transmissible phage vector implicated in the dissemination of colistin resistance.
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Affiliation(s)
- Massimiliano Lucidi
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, Italy; NBFC, National Biodiversity Future Center, piazza Marina 61, 90133 Palermo, Italy.
| | - Francesco Imperi
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, Italy; NBFC, National Biodiversity Future Center, piazza Marina 61, 90133 Palermo, Italy; Santa Lucia Foundation IRCCS, Via Ardeatina 306/354, 00179 Rome, Italy
| | - Irene Artuso
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, Italy
| | - Giulia Capecchi
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, Italy
| | - Cinzia Spagnoli
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, Italy
| | - Daniela Visaggio
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, Italy; NBFC, National Biodiversity Future Center, piazza Marina 61, 90133 Palermo, Italy; Santa Lucia Foundation IRCCS, Via Ardeatina 306/354, 00179 Rome, Italy
| | - Giordano Rampioni
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, Italy; Santa Lucia Foundation IRCCS, Via Ardeatina 306/354, 00179 Rome, Italy
| | - Livia Leoni
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, Italy
| | - Paolo Visca
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, Italy; NBFC, National Biodiversity Future Center, piazza Marina 61, 90133 Palermo, Italy; Santa Lucia Foundation IRCCS, Via Ardeatina 306/354, 00179 Rome, Italy.
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Vijayakumar S, Swetha RG, Bakthavatchalam YD, Vasudevan K, Abirami Shankar B, Kirubananthan A, Walia K, Ramaiah S, Biswas I, Veeraraghavan B, Anbarasu A. Genomic investigation unveils colistin resistance mechanism in carbapenem-resistant Acinetobacter baumannii clinical isolates. Microbiol Spectr 2024; 12:e0251123. [PMID: 38214512 PMCID: PMC10846133 DOI: 10.1128/spectrum.02511-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 11/29/2023] [Indexed: 01/13/2024] Open
Abstract
Colistin resistance in Acinetobacter baumannii is mediated by multiple mechanisms. Recently, mutations within pmrABC two-component system and overexpression of eptA gene due to upstream insertion of ISAba1 have been shown to play a major role. Thus, the aim of our study is to characterize colistin resistance mechanisms among the clinical isolates of A. baumannii in India. A total of 207 clinical isolates of A. baumannii collected from 2016 to 2019 were included in this study. Mutations within lipid A biosynthesis and pmrABC genes were characterized by whole-genome shotgun sequencing. Twenty-eight complete genomes were further characterized by hybrid assembly approach to study insertional inactivation of lpx genes and the association of ISAba1-eptA. Several single point mutations (SNPs), like M12I in pmrA, A138T and A444V in pmrB, and E117K in lpxD, were identified. We are the first to report two novel SNPs (T7I and V383I) in the pmrC gene. Among the five colistin-resistant A. baumannii isolates where complete genome was available, the analysis showed that three of the five isolates had ISAba1 insertion upstream of eptA. No mcr genes were identified among the isolates. We mapped the SNPs on the respective protein structures to understand the effect on the protein activity. We found that majority of the SNPs had little effect on the putative protein function; however, some SNPs might destabilize the local structure. Our study highlights the diversity of colistin resistance mechanisms occurring in A. baumannii, and ISAba1-driven eptA overexpression is responsible for colistin resistance among the Indian isolates.IMPORTANCEAcinetobacter baumannii is a Gram-negative, emerging and opportunistic bacterial pathogen that is often associated with a wide range of nosocomial infections. The treatment of these infections is hindered by increase in the occurrence of A. baumannii strains that are resistant to most of the existing antibiotics. The current drug of choice to treat the infection caused by A. baumannii is colistin, but unfortunately, the bacteria started to show resistance to the last-resort antibiotic. The loss of lipopolysaccharides and mutations in lipid A biosynthesis genes are the main reasons for the colistin resistance. The present study characterized 207 A. baumannii clinical isolates and constructed complete genomes of 28 isolates to recognize the mechanisms of colistin resistance. We showed the mutations in the colistin-resistant variants within genes essential for lipid A biosynthesis and that cause these isolates to lose the ability to produce lipopolysaccharides.
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Affiliation(s)
- Saranya Vijayakumar
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Rayapadi G. Swetha
- Medical and Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | | | - Karthick Vasudevan
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
- Department of Biotechnology, School of Applied Sciences, REVA University, Bangalore, India
| | - Baby Abirami Shankar
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | | | - Kamini Walia
- Division of Epidemiology and Communicable Diseases, Indian Council for Medical Research, New Delhi, India
| | - Sudha Ramaiah
- Medical and Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Indranil Biswas
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas, USA
| | - Balaji Veeraraghavan
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Anand Anbarasu
- Medical and Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
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Wang Y, Luo Q, Chen T, Chi X, Zhou Y, Fu H, Lu P, Xiong L, Xiao T, Zheng B, Shen P, Xiao Y. Clinical, biological and genome-wide comparison of carbapenem-resistant Klebsiella pneumoniae with susceptibility transformation to polymyxin B during therapy. Clin Microbiol Infect 2023; 29:1336.e1-1336.e8. [PMID: 37423426 DOI: 10.1016/j.cmi.2023.06.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 06/07/2023] [Accepted: 06/29/2023] [Indexed: 07/11/2023]
Abstract
OBJECTIVES The emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) is a major clinical concern, and polymyxin B (PMB) is a 'last resort' antibiotic for its treatment. Understanding the effects of drug susceptibility transformation in CRKP-infected patients undergoing PMB treatment would be beneficial to optimize PMB treatment strategies. METHODS We retrospectively collected data from patients infected with CRKP and treated with PMB from January 2018 to December 2020. CRKPs were collected before and after PMB therapy, and patients were classified into the 'transformation' group (TG) and 'non-transformation' group (NTG) by the shift of susceptibility to PMB. We compared clinical characteristics between these groups, and further analysed the phenotypic and genome variation of CRKP after PMB susceptibility transformation. RESULTS A total of 160 patients (37 in the TG and 123 in the NTG) were included in this study. The duration of PMB treatment before PMB-resistant K. pneumoniae (PRKP) appearance in TG was even longer than the whole duration of PMB treatment in NTG (8 [8] vs. 7 [6] days; p 0.0496). Compared with isogenic PMB-susceptible K. pneumoniae (PSKP), most PRKP strains had missense mutations in mgrB (12 isolates), yciC (10 isolates) and pmrB (7 isolates). The competition index of 82.4% (28/34) of PRKP/PSKP pairs was <67.6% (23/34), and 73.5% (25/34) of PRKP strains showed a higher 7-day lethality in Galleria mellonella and a greater ability to resist complement-dependent killing than their corresponding PSKP, respectively. CONCLUSION Low dose with longer PMB treatment durations may be associated with the emergence of polymyxin resistance. The evolution of PRKP is predominantly mediated by an accumulation of mutations, including those in mgrB, yciC, and pmrB. Lastly, PRKP exhibited reduced growth and increased virulence compared with parental PSKP.
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Affiliation(s)
- Yuan Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Qixia Luo
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China; Department of Structure and Morphology, Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Shandong, China
| | - Tao Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaohui Chi
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yanzi Zhou
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Hao Fu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Ping Lu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Luying Xiong
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Tingting Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Beiwen Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China; Department of Structure and Morphology, Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Shandong, China
| | - Ping Shen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China; Department of Structure and Morphology, Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Shandong, China
| | - Yonghong Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China; Department of Structure and Morphology, Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Shandong, China.
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5
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Colistin Resistance in Acinetobacter baumannii: Molecular Mechanisms and Epidemiology. Antibiotics (Basel) 2023; 12:antibiotics12030516. [PMID: 36978383 PMCID: PMC10044110 DOI: 10.3390/antibiotics12030516] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/17/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Acinetobacter baumannii is recognized as a clinically significant pathogen causing a wide spectrum of nosocomial infections. Colistin was considered a last-resort antibiotic for the treatment of infections caused by multidrug-resistant A. baumannii. Since the reintroduction of colistin, a number of mechanisms of colistin resistance in A. baumannii have been reported, including complete loss of LPS by inactivation of the biosynthetic pathway, modifications of target LPS driven by the addition of phosphoethanolamine (PEtN) moieties to lipid A mediated by the chromosomal pmrCAB operon and eptA gene-encoded enzymes or plasmid-encoded mcr genes and efflux of colistin from the cell. In addition to resistance to colistin, widespread heteroresistance is another feature of A. baumannii that leads to colistin treatment failure. This review aims to present a critical assessment of relevant published (>50 experimental papers) up-to-date knowledge on the molecular mechanisms of colistin resistance in A. baumannii with a detailed review of implicated mutations and the global distribution of colistin-resistant strains.
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Kabic J, Novovic K, Kekic D, Trudic A, Opavski N, Dimkic I, Jovcic B, Gajic I. Comparative genomics and molecular epidemiology of colistin-resistant Acinetobacter baumannii. Comput Struct Biotechnol J 2022; 21:574-585. [PMID: 36659926 PMCID: PMC9816908 DOI: 10.1016/j.csbj.2022.12.045] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/27/2022] [Accepted: 12/27/2022] [Indexed: 12/29/2022] Open
Abstract
This study aimed to investigate the prevalence and resistance mechanisms of colistin-resistant Acinetobacter baumannii (ColRAB) isolates in Serbia, assess their genetic relatedness to other circulating A. baumannii isolates in the neighbouring European countries, and analyse the global genomic epidemiology of ColRAB isolates. A total of 784 isolates of A. baumannii were recovered from hospitalised patients in Serbia between 2018 and 2021. The antimicrobial susceptibility testing was performed using disk diffusion and broth microdilution. All ColRAB isolates were subjected to DNA isolation and whole-genome sequencing (WGS). Overall, 3.94 % (n = 30) isolates were confirmed as ColRAB. Results of mutational and transcriptional analysis of genes associated with colistin resistance indicate the central role of the two-component regulating system, PmrAB, and increased expression of the pmrC gene in ColRAB. Most of the isolates (n = 29, 96.6 %) belonged to international clone II, with the most common sequence type being STPas2 (n = 23, 76.6 %). Based on the WGS analysis, ColRAB isolates belonging to the same ST isolated in various countries were grouped into the same clusters, indicating the global dissemination of several high-risk clonal lineages. Phylogenomic analysis of ColRAB isolates, together with all previously published A. baumannii genomes from South-Eastern European countries, showed that colistin resistance arose independently in several clonal lineages. Comparative genomic analysis revealed multiple genes with various roles (transcriptional regulation, transmembrane transport, outer membrane assembly, etc.), which might be associated with colistin resistance in A. baumannii. The obtained findings serve as the basis for further studies, contributing to a better understanding of colistin resistance mechanisms in A. baumannii.
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Affiliation(s)
- Jovana Kabic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, 11000, Belgrade, Serbia
| | - Katarina Novovic
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000, Belgrade, Serbia
| | - Dusan Kekic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, 11000, Belgrade, Serbia
| | - Anika Trudic
- Department of Microbiology, Faculty of Medicine, University of Novi Sad, 21000, Novi Sad, Serbia
- Institute for Pulmonary Diseases of Vojvodina, 21204, Sremska Kamenica, Serbia
| | - Natasa Opavski
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, 11000, Belgrade, Serbia
| | - Ivica Dimkic
- Faculty of Biology, University of Belgrade, 11000, Belgrade, Serbia
| | - Branko Jovcic
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000, Belgrade, Serbia
- Faculty of Biology, University of Belgrade, 11000, Belgrade, Serbia
- Correspondence to: Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Faculty of Biology, University of Belgrade Studentski trg 16, 11000 Belgrade, Serbia.
| | - Ina Gajic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, 11000, Belgrade, Serbia
- Correspondence to: Institute of Microbiology and Immunology, Medical Faculty, University of Belgrade Dr Subotica 1, 11000 Belgrade, Serbia.
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Kamoshida G, Yamada N, Nakamura T, Yamaguchi D, Kai D, Yamashita M, Hayashi C, Kanda N, Sakaguchi M, Morimoto H, Sawada T, Okada T, Kaya Y, Takemoto N, Yahiro K. Preferential Selection of Low-Frequency, Lipopolysaccharide-Modified, Colistin-Resistant Mutants with a Combination of Antimicrobials in Acinetobacter baumannii. Microbiol Spectr 2022; 10:e0192822. [PMID: 36173297 PMCID: PMC9602988 DOI: 10.1128/spectrum.01928-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/13/2022] [Indexed: 12/31/2022] Open
Abstract
Colistin, which targets lipopolysaccharide (LPS), is used as a last-resort drug against severe infections caused by drug-resistant Acinetobacter baumannii. However, A. baumannii possesses two colistin-resistance mechanisms. LPS modification caused by mutations in pmrAB genes is often observed in clinical isolates of multidrug-resistant Gram-negative pathogens. In addition to LPS modification, A. baumannii has a unique colistin resistance mechanism, a complete loss of LPS due to mutations in the lpxACD genes, which are involved in LPS biosynthesis. This study aimed to elucidate the detailed mechanism of the emergence of colistin-resistant A. baumannii using strains with the same genetic background. Various colistin-resistant strains were generated experimentally using colistin alone and in combination with other antimicrobials, such as meropenem and ciprofloxacin, and the mutation spectrum was analyzed. In vitro selection of A. baumannii in the presence of colistin led to the emergence of strains harboring mutations in lpxACD genes, resulting in LPS-deficient colistin-resistant strains. However, combination of colistin with other antimicrobials led to the selection of pmrAB mutant strains, resulting in strains with modified LPS (LPS-modified strains). Further, the LPS-deficient strains showed decreased fitness and increased susceptibility to many antibiotics and disinfectants. As LPS-deficient strains have a higher biological cost than LPS-modified strains, our findings suggested that pmrAB mutants are more likely to be isolated in clinical settings. We provide novel insights into the mechanisms of resistance to colistin and provide substantial solutions along with precautions for facilitating current research and treatment of colistin-resistant A. baumannii infections. IMPORTANCE Acinetobacter baumannii has developed resistance to various antimicrobial drugs, and its drug-resistant strains cause nosocomial infections. Controlling these infections has become a global clinical challenge. Carbapenem antibiotics are the frontline treatment drugs for infectious diseases caused by A. baumannii. For patients with infections caused by carbapenem-resistant A. baumannii, colistin-based therapy is often the only treatment option. However, A. baumannii readily acquires resistance to colistin. Many patients infected with colistin-resistant A. baumannii undergo colistin treatment before isolation of the colistin-resistant strain, and it is hypothesized that colistin resistance predominantly emerges under selective pressure during colistin therapy. Although the concomitant use of colistin and carbapenems has been reported to have a synergistic effect in vitro against carbapenem-resistant A. baumannii strains, our observations strongly suggest the need for attention to the emergence of strains with a modified lipopolysaccharide during treatment.
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Affiliation(s)
- Go Kamoshida
- Department of Microbiology and Infection Control Sciences, Kyoto Pharmaceutical University, Kyoto, Japan
| | - Noriteru Yamada
- Department of Microbiology and Infection Control Sciences, Kyoto Pharmaceutical University, Kyoto, Japan
| | - Tomoka Nakamura
- Department of Microbiology and Infection Control Sciences, Kyoto Pharmaceutical University, Kyoto, Japan
| | - Daiki Yamaguchi
- Department of Microbiology and Infection Control Sciences, Kyoto Pharmaceutical University, Kyoto, Japan
| | - Daichi Kai
- Department of Microbiology and Infection Control Sciences, Kyoto Pharmaceutical University, Kyoto, Japan
| | - Maho Yamashita
- Department of Microbiology and Infection Control Sciences, Kyoto Pharmaceutical University, Kyoto, Japan
| | - Chiaki Hayashi
- Department of Microbiology and Infection Control Sciences, Kyoto Pharmaceutical University, Kyoto, Japan
| | - Nana Kanda
- Department of Microbiology and Infection Control Sciences, Kyoto Pharmaceutical University, Kyoto, Japan
| | - Moe Sakaguchi
- Department of Microbiology and Infection Control Sciences, Kyoto Pharmaceutical University, Kyoto, Japan
| | - Hitoshi Morimoto
- Department of Microbiology and Infection Control Sciences, Kyoto Pharmaceutical University, Kyoto, Japan
| | - Teppei Sawada
- Department of Microbiology and Infection Control Sciences, Kyoto Pharmaceutical University, Kyoto, Japan
| | - Tomoko Okada
- Department of Microbiology and Infection Control Sciences, Kyoto Pharmaceutical University, Kyoto, Japan
| | - Yuki Kaya
- Department of Microbiology and Infection Control Sciences, Kyoto Pharmaceutical University, Kyoto, Japan
| | - Norihiko Takemoto
- Pathogenic Microbe Laboratory, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kinnosuke Yahiro
- Department of Microbiology and Infection Control Sciences, Kyoto Pharmaceutical University, Kyoto, Japan
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8
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Iovleva A, Mustapha MM, Griffith MP, Komarow L, Luterbach C, Evans DR, Cober E, Richter SS, Rydell K, Arias CA, Jacob JT, Salata RA, Satlin MJ, Wong D, Bonomo RA, van Duin D, Cooper VS, Van Tyne D, Doi Y. Carbapenem-Resistant Acinetobacter baumannii in U.S. Hospitals: Diversification of Circulating Lineages and Antimicrobial Resistance. mBio 2022; 13:e0275921. [PMID: 35311529 PMCID: PMC9040734 DOI: 10.1128/mbio.02759-21] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 02/02/2022] [Indexed: 12/14/2022] Open
Abstract
Carbapenem-resistant Acinetobacter baumannii (CRAb) is a major cause of health care-associated infections. CRAb is typically multidrug resistant, and infection is difficult to treat. Despite the urgent threat that CRAb poses, few systematic studies of CRAb clinical and molecular epidemiology have been conducted. The Study Network of Acinetobacter as a Carbapenem-Resistant Pathogen (SNAP) is designed to investigate the clinical characteristics and contemporary population structure of CRAb circulating in U.S. hospital systems using whole-genome sequencing (WGS). Analysis of the initial 120 SNAP patients from four U.S. centers revealed that CRAb remains a significant threat to hospitalized patients, affecting the most vulnerable patients and resulting in 24% all-cause 30-day mortality. The majority of currently circulating isolates belonged to ST2Pas, a part of clonal complex 2 (CC2), which is the dominant drug-resistant lineage in the United States and Europe. We identified three distinct sublineages within CC2, which differed in their antibiotic resistance phenotypes and geographic distribution. Most concerning, colistin resistance (38%) and cefiderocol resistance (10%) were common within CC2 sublineage C (CC2C), where the majority of isolates belonged to ST2Pas/ST281Ox. Additionally, we identified ST499Pas as the most common non-CC2 lineage in our study. Our findings suggest a shift within the CRAb population in the United States during the past 10 years and emphasize the importance of real-time surveillance and molecular epidemiology in studying CRAb dissemination and clinical impact. IMPORTANCE Carbapenem-resistant Acinetobacter baumannii (CRAb) constitutes a major threat to public health. To elucidate the molecular and clinical epidemiology of CRAb in the United States, clinical CRAb isolates were collected along with data on patient characteristics and outcomes, and bacterial isolates underwent whole-genome sequencing and antibiotic susceptibility phenotyping. Key findings included emergence of new sublineages within the globally predominant clonal complex 2 (CC2), increased colistin and cefiderocol resistance within one of the CC2 sublineages, and emergence of ST499Pas as the dominant non-CC2 CRAb lineage in U.S. hospitals.
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Affiliation(s)
- Alina Iovleva
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Mustapha M. Mustapha
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Marissa P. Griffith
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Lauren Komarow
- The Biostatistics Center, The George Washington University, Rockville, Maryland, USA
| | - Courtney Luterbach
- Division of Pharmacotherapy and Experimental Therapeutics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Daniel R. Evans
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, USA
| | - Eric Cober
- Department of Infectious Diseases, Cleveland Clinic, Cleveland, Ohio, USA
| | - Sandra S. Richter
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Jacksonville, Florida, USA
| | - Kirsten Rydell
- Division of Infectious Diseases, Houston Methodist Hospital, Houston, Texas, USA
- Center for Infectious Diseases Research, Houston Methodist Research Institute, Houston, Texas USA
| | - Cesar A. Arias
- Division of Infectious Diseases, Houston Methodist Hospital, Houston, Texas, USA
- Center for Infectious Diseases Research, Houston Methodist Research Institute, Houston, Texas USA
| | - Jesse T. Jacob
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Robert A. Salata
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Michael J. Satlin
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Darren Wong
- Division of Infectious Diseases, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Robert A. Bonomo
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
- Departments of Biochemistry, Pharmacology, Molecular Biology and Microbiology, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES) Cleveland, OH, USA
| | - David van Duin
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Vaughn S. Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Daria Van Tyne
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Departments of Microbiology and Infectious Diseases, Fujita Health University School of Medicine, Aichi, Japan
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9
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Hahm C, Chung HS, Lee M. Whole-genome sequencing for the characterization of resistance mechanisms and epidemiology of colistin-resistant Acinetobacter baumannii. PLoS One 2022; 17:e0264335. [PMID: 35245298 PMCID: PMC8896714 DOI: 10.1371/journal.pone.0264335] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 02/08/2022] [Indexed: 11/18/2022] Open
Abstract
Background Multidrug-resistant Acinetobacter baumannii is an important causal pathogen of healthcare-associated infections, and colistin-resistant strains have recently emerged owing to the increased use of colistin. Using next-generation sequencing (NGS), a single whole-genome sequencing (WGS) protocol can identify and type pathogens, analyze genetic relationships among different pathogens, predict pathogenic transmissions, and detect antibiotic resistance genes. However, only a few studies have applied NGS in studying the resistance mechanism and epidemiology of colistin-resistant A. baumannii. This study aimed to elucidate the resistance mechanism of colistin-resistant A. baumannii and analyze its molecular epidemiology through WGS. Materials and methods The subjects in this study were patients who visited a university hospital between 2014 and 2018. Thirty colistin-resistant strains with high minimum inhibitory concentrations were selected from various patient samples, and WGS was performed. Comparative genomic analysis was performed for the 27 colistin-resistant A. baumannii strains using a colistin-susceptible strain as the reference genome. Results The WGS analysis found no mutation for lpxA, lpxC, lpx D, pmrA, pmrB, and mcr1, the genes known to be associated with colistin resistance. Fifty-seven coding sequences (CDS) showed differences; they included 13 CDS with known names and functions that contained 21 genes. From the whole-genome multi-locus sequence typing (wgMLST) and single nucleotide polymorphism (SNP) analyses, two major clusters were found for the colistin-resistant A. baumannii strains. However, no differences were observed by the time of detection for each cluster, the samples, the pattern of antibiotic resistance, or the patient characteristics. In the conventional MLST following the Oxford scheme, the typing result showed ST1809, ST451, ST191, ST1837, and ST369 in the global clone 2 (GC2), without any relation with the results of wgMLST and SNP analyses. Conclusion Based on the findings of the resistance gene analysis through WGS and comparative genomic analysis, the potential genes associated with colistin-resistance or CDS were examined. Furthermore, the analysis of molecular epidemiology through WGS regarding colistin-resistant A. baumannii may prove helpful in preventing infection by multidrug-resistant bacteria and controlling healthcare-associated infections.
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Affiliation(s)
- Chorong Hahm
- Department of Laboratory Medicine, College of Medicine, Ewha Womans University, Seoul, Korea
- Department of Laboratory Medicine, Eone Laboratories, Incheon, Korea
| | - Hae-Sun Chung
- Department of Laboratory Medicine, College of Medicine, Ewha Womans University, Seoul, Korea
- EWHA Education and Research Center for Infection, College of Medicine, Ewha Womans University, Seoul, Korea
| | - Miae Lee
- Department of Laboratory Medicine, College of Medicine, Ewha Womans University, Seoul, Korea
- EWHA Education and Research Center for Infection, College of Medicine, Ewha Womans University, Seoul, Korea
- * E-mail:
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10
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Abstract
Infection by multidrug-resistant (MDR) Acinetobacter baumannii is one of the major causes of hospital-acquired infections worldwide. The ability of A. baumannii to survive in adverse conditions as well as its extensive antimicrobial resistance make it one of the most difficult to treat pathogens associated with high mortality rates. The aim of this study was to investigate MDR A. baumannii that has spread among pediatric cancer patients in the Children’s Cancer Hospital Egypt 57357. Whole-genome sequencing was used to characterize 31 MDR A. baumannii clinical isolates. Phenotypically, the isolates were MDR, with four isolates showing resistance to the last-resort antibiotic colistin. Multilocus sequence typing showed the presence of eight clonal groups, two of which were previously reported to cause outbreaks in Egypt, and one novel sequence type (ST), Oxf-ST2246. Identification of the circulating plasmids showed the presence of two plasmid lineages in the isolates, strongly governed by sequence type. A large number of antimicrobial genes with a range of resistance mechanisms were detected in the isolates, including β-lactamases and antibiotic efflux pumps. Analysis of insertion sequences (ISs) revealed the presence of ISAba1 and ISAba125 in all the samples, which amplify β-lactamase expression, causing extensive carbapenem resistance. Mutation analysis was used to decipher underlying mutations responsible for colistin resistance and revealed novel mutations in several outer membrane proteins, in addition to previously reported mutations in pmrB. Altogether, understanding the transmissibility of A. baumannii as well as its resistance and virulence mechanisms will help develop novel treatment options for better management of hospital-acquired infections. IMPORTANCEAcinetobacter baumannii represents a major health threat, in particular among immunocompromised cancer patients. The rise in carbapenem-resistant A. baumannii, and the development of resistance to the last-resort antimicrobial agent colistin, complicates the management of A. baumannii outbreaks and increases mortality rates. Here, we investigate 31 multidrug resistant A. baumannii isolates from pediatric cancer patients in Children’s Cancer Hospital Egypt (CCHE) 57357 via whole-genome sequencing. Multilocus sequence typing (MLST) showed the presence of eight clonal groups including a novel sequence type. In silico detection of antimicrobial-resistant genes and virulence factors revealed a strong correlation between certain virulence genes and mortality as well as several point mutations in outer membrane proteins contributing to colistin resistance. Detection of CRISPR/Cas sequences in the majority of the samples was strongly correlated with the presence of prophage sequences and associated with failure of bacteriophage therapy. Altogether, understanding the genetic makeup of circulating A. baumannii is essential for better management of outbreaks.
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11
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Palethorpe S, Milton ME, Pesci EC, Cavanagh J. Structure of the Acinetobacter baumannii PmrA receiver domain and insights into clinical mutants affecting DNA-binding and promoting colistin resistance. J Biochem 2021; 170:787-800. [PMID: 34585233 DOI: 10.1093/jb/mvab102] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/22/2021] [Indexed: 11/14/2022] Open
Abstract
Acinetobacter baumannii is an insidious emerging nosocomial pathogen that has developed resistance to all available antimicrobials, including the last resort antibiotic, colistin. Colistin resistance often occurs due to mutations in the PmrAB two component regulatory system. To better understand the regulatory mechanisms contributing to colistin resistance, we have biochemically characterized the A. baumannii PmrA response regulator. Initial DNA-binding analysis shows that A. baumannii PmrA bound to the Klebsiella pneumoniae PmrA box motif. This prompted analysis of the putative A. baumannii PmrAB regulon which indicated that the A. baumannii PmrA consensus box is 5'- HTTAAD N5 HTTAAD. Additionally, we provide the first structural information for the A. baumannii PmrA N-terminal domain through X-ray crystallography, and we present a full-length model using molecular modeling. From these studies, we were able to infer the effects of two critical PmrA mutations, PmrA::I13M and PmrA::P102R, both of which confer increased colistin resistance. Based on these data, we suggest structural and dynamic reasons for how these mutations can affect PmrA function and hence encourage resistive traits. Understanding these mechanisms will aid in the development of new targeted antimicrobial therapies.
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Affiliation(s)
- Samantha Palethorpe
- Department of Microbiology and Immunology Brody School of Medicine East Carolina University Greenville, NC 27834 United States
| | - Morgan E Milton
- Department of Biochemistry and Molecular Biology Brody School of Medicine East Carolina University Greenville, NC 27834 United States
| | - Everett C Pesci
- Department of Microbiology and Immunology Brody School of Medicine East Carolina University Greenville, NC 27834 United States
| | - John Cavanagh
- Department of Biochemistry and Molecular Biology Brody School of Medicine East Carolina University Greenville, NC 27834 United States
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12
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Colistin and Carbapenem-Resistant Acinetobacter baumannii Aci46 in Thailand: Genome Analysis and Antibiotic Resistance Profiling. Antibiotics (Basel) 2021; 10:antibiotics10091054. [PMID: 34572636 PMCID: PMC8468411 DOI: 10.3390/antibiotics10091054] [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] [Received: 07/29/2021] [Revised: 08/26/2021] [Accepted: 08/27/2021] [Indexed: 12/12/2022] Open
Abstract
Resistance to the last-line antibiotics against invasive Gram-negative bacterial infection is a rising concern in public health. Multidrug resistant (MDR) Acinetobacter baumannii Aci46 can resist colistin and carbapenems with a minimum inhibitory concentration of 512 µg/mL as determined by microdilution method and shows no zone of inhibition by disk diffusion method. These phenotypic characteristics prompted us to further investigate the genotypic characteristics of Aci46. Next generation sequencing was applied in this study to obtain whole genome data. We determined that Aci46 belongs to Pasture ST2 and is phylogenetically clustered with international clone (IC) II as the predominant strain in Thailand. Interestingly, Aci46 is identical to Oxford ST1962 that previously has never been isolated in Thailand. Two plasmids were identified (pAci46a and pAci46b), neither of which harbors any antibiotic resistance genes but pAci46a carries a conjugational system (type 4 secretion system or T4SS). Comparative genomics with other polymyxin and carbapenem-resistant A. baumannii strains (AC30 and R14) identified shared features such as CzcCBA, encoding a cobalt/zinc/cadmium efflux RND transporter, as well as a drug transporter with a possible role in colistin and/or carbapenem resistance in A. baumannii. Single nucleotide polymorphism (SNP) analyses against MDR ACICU strain showed three novel mutations i.e., Glu229Asp, Pro200Leu, and Ala138Thr, in the polymyxin resistance component, PmrB. Overall, this study focused on Aci46 whole genome data analysis, its correlation with antibiotic resistance phenotypes, and the presence of potential virulence associated factors.
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13
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Cha MH, Kim SH, Kim S, Lee W, Kwak HS, Chi YM, Woo GJ. Antimicrobial Resistance Profile of Acinetobacter spp. Isolates from Retail Meat Samples under Campylobacter-Selective Conditions. J Microbiol Biotechnol 2021; 31:733-739. [PMID: 33820890 PMCID: PMC9705846 DOI: 10.4014/jmb.2102.02027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/31/2021] [Accepted: 04/02/2021] [Indexed: 12/15/2022]
Abstract
Acinetobacter strains are widely present in the environment. Some antimicrobial-resistant strains of this genus have been implicated in infections acquired in hospitals. Genetic similarities have been reported between Acinetobacter strains in nosocomial infections and those isolated from foods. However, the antimicrobial resistance of Acinetobacter strains in foods, such as meat, remains unclear. This study initially aimed to isolate Campylobacter strains; instead, strains of the genus Acinetobacter were isolated from meat products, and their antimicrobial resistance was investigated. In total, 58 Acinetobacter strains were isolated from 381 meat samples. Of these, 32 strains (38.6%) were from beef, 22 (26.5%) from pork, and 4 (4.8%) from duck meat. Antimicrobial susceptibility tests revealed that 12 strains were resistant to more than one antimicrobial agent, whereas two strains were multidrug-resistant; both strains were resistant to colistin. Cephalosporin antimicrobials showed high minimal inhibitory concentration against Acinetobacter strains. Resfinder analysis showed that one colistin-resistant strain carried mcr-4.3; this plasmid type was not confirmed, even when analyzed with PlasmidFinder. Analysis of the contig harboring mcr-4.3 using BLAST confirmed that this contig was related to mcr-4.3 of Acinetobacter baumannii. The increase in antimicrobial resistance in food production environments increases the resistance rate of Acinetobacter strains present in meat, inhibits the isolation of Campylobacter strains, and acts as a medium for the transmission of antimicrobial resistance in the environment. Therefore, further investigations are warranted to prevent the spread of antimicrobial resistance in food products.
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Affiliation(s)
- Min-Hyeok Cha
- Laboratory of Food Safety and Evaluation, Department of Biotechnology, Korea University Graduate School, Seoul 02841, Republic of Korea
| | - Sun Hee Kim
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Seokhwan Kim
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea
| | - Woojung Lee
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea
| | - Hyo-Sun Kwak
- Department of Food Science and Biotechnology, Kyung Hee University, Gyeonggi-do 17104, Republic of Korea
| | - Young-Min Chi
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea,
Y.-M. Chi Phone: +82-2-3290-3025 Fax: +82-2-3290-3489 E-mail:
| | - Gun-Jo Woo
- Laboratory of Food Safety and Evaluation, Department of Biotechnology, Korea University Graduate School, Seoul 02841, Republic of Korea,Corresponding authors G.-J. Woo Phone: +82-2-3290-3021 Fax: +82-2-3290-3581 E-mail:
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14
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Jahangiri A, Neshani A, Mirhosseini SA, Ghazvini K, Zare H, Sedighian H. Synergistic effect of two antimicrobial peptides, Nisin and P10 with conventional antibiotics against extensively drug-resistant Acinetobacter baumannii and colistin-resistant Pseudomonas aeruginosa isolates. Microb Pathog 2020; 150:104700. [PMID: 33346078 DOI: 10.1016/j.micpath.2020.104700] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 11/17/2020] [Accepted: 12/05/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND Infections caused by drug-resistant strains of Acinetobacter baumannii and Pseudomonas aeruginosa are now a global problem that requires the immediate development of new antimicrobial drugs. Combination therapy and using antimicrobial peptides are two strategies with high potential to solve this issue. By these strategies, this study aimed to determine the antimicrobial effect of Nisin and P10 antimicrobial peptides on extensively drug-resistant Acinetobacter baumannii and colistin-resistant Pseudomonas aeruginosa isolates, and investigate the most effective combination of an antimicrobial peptide with an antibiotic. MATERIAL AND METHODS This study was performed on five resistant clinical isolates and one standard strain for each kind of bacterium. First, the minimum inhibitory concentrations of two antimicrobial peptides (Nisin and P10) and five common antibiotics for the treatment of Gram-negative bacteria (ceftazidime, tobramycin, ciprofloxacin, doripenem, and colistin) was determined using Scanner-Assisted Colorimetric MIC Method. Then, the combination effect of P10+Nisin, P10+antibiotics, Nisin + antibiotics was investigated using checkerboard method. RESULTS The MIC value of Nisin and P10 against studied pathogens were 64-256 and 8-32 μg/ml, respectively. P10+Nisin combination showed synergistic effect against standard strains and additive effect against drug-resistant clinical isolates. It was also found that the combination effect of P10+ceftazidim, P10+doripenem, and Nisin + colistin was synergistic in most cases. Nisin + tobramycin combination showed synergistic effect in exposure to standard strains, while the synergy is strain-dependent against drug-resistant clinical isolates. CONCLUSION In conclusion, the synergism of Nisin + colistin and P10+ceftazidime/doripenem could be of great therapeutic value as antimicrobial drugs against infections caused by colistin-resistant P.aeruginosa and XDR A. baumannii.
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Affiliation(s)
- Abolfazl Jahangiri
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Alireza Neshani
- Department of Laboratory Sciences, School of Paramedical Sciences, Mashhad University of Medical Sciences, Mashhad, Iran; Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Ali Mirhosseini
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Kiarash Ghazvini
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hosna Zare
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hamid Sedighian
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.
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15
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Sorensen M, Chandler CE, Gardner FM, Ramadan S, Khot PD, Leung LM, Farrance CE, Goodlett DR, Ernst RK, Nilsson E. Rapid microbial identification and colistin resistance detection via MALDI-TOF MS using a novel on-target extraction of membrane lipids. Sci Rep 2020; 10:21536. [PMID: 33299017 PMCID: PMC7725828 DOI: 10.1038/s41598-020-78401-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 11/20/2020] [Indexed: 12/18/2022] Open
Abstract
Rapid infection diagnosis is critical to improving patient treatment and outcome. Recent studies have shown microbial lipids to be sensitive and selective biomarkers for identifying bacterial and fungal species and antimicrobial resistance. Practical procedures for microbial lipid biomarker analysis will therefore improve patient outcomes and antimicrobial stewardship. However, current lipid extraction methods require significant hands-on time and are thus not suited for direct adoption as a clinical assay for microbial identification. Here, we have developed a method for lipid extraction directly on the surface of stainless-steel matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) plates, termed fast lipid analysis technique or FLAT, which facilitates the identification of bacterial and fungal species using a sub-60-minute workflow. Additionally, our method detects lipid A modifications in Gram-negative bacteria that are associated with antimicrobial resistance, including to colistin.
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Affiliation(s)
| | - Courtney E Chandler
- Pataigin, LLC, Seattle, WA, USA
- University of Maryland, Baltimore, Baltimore, MD, 21201, USA
- Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Francesca M Gardner
- Pataigin, LLC, Seattle, WA, USA
- University of Maryland, Baltimore, Baltimore, MD, 21201, USA
| | | | | | - Lisa M Leung
- Maryland Department of Health and Mental Hygiene, Baltimore, MD, 21205, USA
- U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA
| | | | - David R Goodlett
- University of Maryland, Baltimore, Baltimore, MD, 21201, USA
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdańsk, Poland
| | - Robert K Ernst
- University of Maryland, Baltimore, Baltimore, MD, 21201, USA.
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16
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Jovcic B, Novovic K, Dekic S, Hrenovic J. Colistin Resistance in Environmental Isolates of Acinetobacter baumannii. Microb Drug Resist 2020; 27:328-336. [PMID: 32762604 DOI: 10.1089/mdr.2020.0188] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Although the molecular mechanisms of carbapenem resistance of environmental isolates of Acinetobacter baumannii are well described, data on the mechanisms of colistin resistance are scarce. In this study, we report the molecular mechanisms of colistin resistance in environmental isolates of A. baumannii. Seven clinically relevant isolates of A. baumannii belonging to ST-2Pasteur were recovered from hospital wastewater and wastewater treatment plant. The phenotypic resistance to colistin was confirmed by broth microdilution with minimum inhibitory concentration values ranging from 20 to 160 mg/L. Colistin sulfate and colistimethate sodium showed bactericidal activity against two colistin-heteroresistant isolates in vitro, but substantially recovery of population was observed after prolonged incubation. In silico genome analysis revealed nucleotide variations resulting in amino acid changes in LpxC (N286D), LpxD (E117K), PmrB (A138T, R263S, L267W, Q309P, and A444V), and EptA (F166L, I228V, R348K, A370S, and K531T). According to reverse transcription quantitative PCR, all isolates had increased levels of eptA mRNA and decreased levels of lpxA and lpxD mRNA. Isolates expressed low hydrophobicity, biofilm, and pellicle formation, but showed excellent survival in river water during 50 days of monitoring. Colistin- and pandrug-resistant A. baumannii disseminated in the environment could represent the source for the occurrence of serious community-acquired infections.
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Affiliation(s)
- Branko Jovcic
- Faculty of Biology, University of Belgrade, Belgrade, Serbia.,Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Katarina Novovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Svjetlana Dekic
- Division of Microbiology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Jasna Hrenovic
- Division of Microbiology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
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17
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Karakonstantis S. A systematic review of implications, mechanisms, and stability of in vivo emergent resistance to colistin and tigecycline in Acinetobacter baumannii. J Chemother 2020; 33:1-11. [PMID: 32677578 DOI: 10.1080/1120009x.2020.1794393] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The potential of A. baumannii for acquired resistance to last resort antibiotics (colistin and tigecycline) during treatment has important clinical implications, especially when dealing with patients failing to improve despite treatment with an active antimicrobial. However, the relevant literature remains scattered. Therefore, a systematic search was conducted in PubMed and Scopus. Several studies reported emergence of resistance to colistin or tigecycline during treatment, in most cases (86%) resulting in persistent or recurrent infections, especially in cases of emergent resistance without fitness cost. Lipopolysaccharide modification in the case of colistin and overexpression of efflux pumps in the case of tigecycline were the main mechanisms of resistance. Emergent colistin resistance is often associated with fitness cost which may result in re-emergence of the fitter and more virulent colistin susceptible strain after cessation of antibiotic pressure. Prospective studies are needed to determine the frequency of emergent resistance during treatment and its impact on patient outcomes.
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Affiliation(s)
- Stamatis Karakonstantis
- Internal Medicine Department, General Hospital of Heraklion Venizeleio, Heraklion, Crete, Greece.,School of medicine, University of Crete, Heraklion, Crete, Greece
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18
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Karakonstantis S, Saridakis I. Colistin heteroresistance in Acinetobacter spp.: systematic review and meta-analysis of the prevalence and discussion of the mechanisms and potential therapeutic implications. Int J Antimicrob Agents 2020; 56:106065. [PMID: 32599229 DOI: 10.1016/j.ijantimicag.2020.106065] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/30/2020] [Accepted: 06/20/2020] [Indexed: 01/29/2023]
Abstract
BACKGROUND Colistin is one of the few remaining options for carbapenem-resistant Acinetobacter baumannii (A. baumannii); however, emergence of resistance from heteroresistant populations is possible. This review aimed to systematically search and consolidate the literature on the prevalence, mechanisms and therapeutic implications of colistin heteroresistance in Acinetobacter spp. METHODS A systematic search was conducted in PubMed and Scopus. The pooled prevalence of colistin heteroresistance was calculated using meta-analysis of proportions with the Freeman-Tukey transformation and the random-effects (DerSimonian and Laird) method. RESULTS Based on 15 studies the prevalence of colistin heteroresistance was 33% (95% CI 16-53%) but considerable heterogeneity was observed (I2 = 96%, P < 0.001). Prior exposure to colistin was associated with a higher proportion of resistant subpopulations. Colistin heteroresistance may result from chromosomal mutations in resistant subpopulations (predominantly in PmrAB and lpx genes) resulting in lipopolysaccharide modification or loss, or overexpression of efflux pumps. No dosage scheme of colistin monotherapy can prevent the emergence of resistant subpopulations in vitro, but few studies have reported in vivo emergence of resistance from heteroresistant A. baumannii during treatment, and studies examining the correlation between heteroresistance and clinical/microbiological outcomes are lacking. Several colistin-based combinations have been shown in vitro to prevent the emergence of the resistant subpopulations but none have been translated so far into clinical benefit. Reasons for this discrepancy are discussed. CONCLUSIONS Colistin heteroresistance was common but highly variable between studies. The impact of colistin heteroresistance (frequency of emergent resistance during treatment and correlation with treatment outcomes) requires further study.
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Affiliation(s)
- Stamatis Karakonstantis
- School of Medicine, University of Crete, Heraklion, Crete, Greece; Internal Medicine Department, General Hospital of Heraklion Venizeleio, Heraklion, Crete, Greece.
| | - Ioannis Saridakis
- Internal Medicine Department, General Hospital of Heraklion Venizeleio, Heraklion, Crete, Greece
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Adams MD, Wright MS, Karichu JK, Venepally P, Fouts DE, Chan AP, Richter SS, Jacobs MR, Bonomo RA. Rapid Replacement of Acinetobacter baumannii Strains Accompanied by Changes in Lipooligosaccharide Loci and Resistance Gene Repertoire. mBio 2019; 10:e00356-19. [PMID: 30914511 PMCID: PMC6437055 DOI: 10.1128/mbio.00356-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 02/19/2019] [Indexed: 12/14/2022] Open
Abstract
The population structure of health care-associated pathogens reflects patterns of diversification, selection, and dispersal over time. Empirical data detailing the long-term population dynamics of nosocomial pathogens provide information about how pathogens adapt in the face of exposure to diverse antimicrobial agents and other host and environmental pressures and can inform infection control priorities. Extensive sequencing of clinical isolates from one hospital spanning a decade and a second hospital in the Cleveland, OH, metropolitan area over a 3-year time period provided high-resolution genomic analysis of the Acinetobacter baumannii metapopulation. Genomic analysis demonstrated an almost complete replacement of the predominant strain groups with a new, genetically distinct strain group during the study period. The new group, termed clade F, differs from other global clone 2 (GC2) strains of A. baumannii in several ways, including its antibiotic resistance and lipooligosaccharide biosynthesis genes. Clade F strains are part of a large phylogenetic group with broad geographic representation. Phylogenetic analysis of single-nucleotide variants in core genome regions showed that although the Cleveland strains are phylogenetically distinct from those isolated from other locations, extensive intermixing of strains from the two hospital systems was apparent, suggesting either substantial exchange of strains or a shared, but geographically restricted, external pool from which infectious isolates were drawn. These findings document the rapid evolution of A. baumannii strains in two hospitals, with replacement of the predominant clade by a new clade with altered lipooligosaccharide loci and resistance gene repertoires.IMPORTANCE Multidrug-resistant (MDR) A. baumannii is a difficult-to-treat health care-associated pathogen. Knowing the resistance genes present in isolates causing infection aids in empirical treatment selection. Furthermore, knowledge of the genetic background can assist in tracking patterns of transmission to limit the spread of infections in hospitals. The appearance of a new genetic background in A. baumannii strains with a different set of resistance genes and cell surface structures suggests that strong selective pressures exist, even in highly MDR pathogens. Because the new strains have levels of antimicrobial resistance similar to those of the strains that were displaced, we hypothesize that other features, including host colonization and infection, may confer additional selective advantages and contribute to their increased prevalence.
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Affiliation(s)
- Mark D Adams
- The J. Craig Venter Institute, La Jolla, California, USA
| | | | - James K Karichu
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | | | | | - Agnes P Chan
- The J. Craig Venter Institute, Rockville, Maryland, USA
| | - Sandra S Richter
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | - Michael R Jacobs
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Robert A Bonomo
- Department of Medicine, Case Western Reserve University and CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology, Cleveland, Ohio, USA
- Department of Pharmacology, Case Western Reserve University and CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology, Cleveland, Ohio, USA
- Department of Molecular Biology and Microbiology, Case Western Reserve University and CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology, Cleveland, Ohio, USA
- Department of Biochemistry, Case Western Reserve University and CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology, Cleveland, Ohio, USA
- Center for Proteomics, Case Western Reserve University and CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology, Cleveland, Ohio, USA
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
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Cafiso V, Stracquadanio S, Lo Verde F, Gabriele G, Mezzatesta ML, Caio C, Pigola G, Ferro A, Stefani S. Colistin Resistant A. baumannii: Genomic and Transcriptomic Traits Acquired Under Colistin Therapy. Front Microbiol 2019; 9:3195. [PMID: 30666237 PMCID: PMC6330354 DOI: 10.3389/fmicb.2018.03195] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 12/10/2018] [Indexed: 12/31/2022] Open
Abstract
Even though colistin-based treatment represents the antimicrobial-regimen backbone for the management of multidrug-resistant Gram-negative infections, colistin resistance is still rare, at least as a full resistance, in Acinetobacter baumannii (Ab). We investigated the genomics and transcriptomics of two clinical Extensively Drug Resistance (XDR) colistin-susceptible/resistant (COL-S/R) Ab strain-pairs in which COL-resistance was developed after exposure to colistin therapy. The molecular characterization of the strains showed that all strains belonged to PFGE-A, ST-281, OXA-23 producers, Global Clone-II, and were resistant to imipenem, meropenem, ampicillin/sulbactam, ciprofloxacin, gentamicin, amikacin, trimethoprim/sulfamethoxazole, and susceptible to tigecycline, in agreement with NGS-acquired resistome. COL-R vs. COL-S Ab comparative genomics, mapping on Ab ATCC 17978 and Ab ACICU Reference Genomes, revealed a closely related genomic phylogeny, especially between strain-pair isolates, and distinctive common genomic non-synonymous SNPs (nsSNPs) in COL-R Ab strains. Furthermore, pmrB and pmrC nsSNPs were found. Notably we recovered, for the first time, lpxC and lpxD nsSNPs previously described only in "in-vitro" mutants and associated with colistin resistance in a clinical COL-R Ab. COL-R vs. COL-S Ab comparative transcriptomics evidenced a strain-dependent response to the colistin resistance onset highly variable among the single COL-R strains vs. their COL-S parents and merely seven common over-expressed transcripts, i.e. the PgaB lipoprotein for biofilm-matrix production, the diacylglycerol kinase for the lipid recycling in the membrane-derived oligosaccharide cycle, a membrane non-ribosomal peptide synthetase, the Lipid A phosphoethanol aminotransferase PmrC, and three hypothetical proteins. The transcript analysis of the "COL-R related genes" and the RNA-seq data confirmed pmrCAB over-expression responsible for a greater positive net cell-charge, and lpxACD under-expression in COL-R causing a decreased LPS production, as main mechanisms of colistin resistance. Our study reports the COL-R Ab genomic and transcriptomic signatures reflecting the interplay between several direct and indirect potential adaptations to antimicrobial pressure, including the occurrence of SNP accumulation hotspot loci in genes related to intrinsic or adaptive colistin resistance, surface adhesion proteins and porins, and over-expressed genes involved in different pathways, i.e. biofilm production, oxidative stress response, extensive drug and COL resistance.
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Affiliation(s)
- Viviana Cafiso
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Stefano Stracquadanio
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Flavia Lo Verde
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Giacoma Gabriele
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Maria Lina Mezzatesta
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Carla Caio
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Giuseppe Pigola
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Alfredo Ferro
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Stefania Stefani
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
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