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Sapula SA, Hart BJ, Siderius NL, Amsalu A, Blaikie JM, Venter H. Multidrug-resistant Stenotrophomonas maltophilia in residential aged care facilities: An emerging threat. Microbiologyopen 2024; 13:e1409. [PMID: 38682784 PMCID: PMC11057060 DOI: 10.1002/mbo3.1409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 03/20/2024] [Accepted: 04/16/2024] [Indexed: 05/01/2024] Open
Abstract
Stenotrophomonas maltophilia is a multidrug-resistant (MDR), Gram-negative bacterium intrinsically resistant to beta-lactams, including last-resort carbapenems. As an opportunistic pathogen, it can cause serious healthcare-related infections. This study assesses the prevalence, resistance profiles, and genetic diversity of S. maltophilia isolated from residential aged care facilities (RACFs). RACFs are known for their overuse and often inappropriate use of antibiotics, creating a strong selective environment that favors the development of bacterial resistance. The study was conducted on 73 S. maltophilia isolates recovered from wastewater and facility swab samples obtained from three RACFs and a retirement village. Phenotypic and genotypic assessments of the isolates revealed high carbapenem resistance, exemplifying their intrinsic beta-lactam resistance. Alarmingly, 49.3% (36/73) of the isolates were non-wild type for colistin, with minimum inhibitory concentration values of > 4 mg/L, and 11.0% (8/73) were resistant to trimethoprim-sulfamethoxazole. No resistance mechanisms were detected for either antimicrobial. Genotypic assessment of known lineages revealed isolates clustering with Sm17 and Sm18, lineages not previously reported in Australia, suggesting the potential ongoing spread of MDR S. maltophilia. Lastly, although only a few isolates were biocide tolerant (2.7%, 2/73), their ability to grow in high concentrations (64 mg/L) of triclosan is concerning, as it may be selecting for their survival and continued dissemination.
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Affiliation(s)
- Sylvia A. Sapula
- Health and Biomedical Innovation, UniSA Clinical and Health SciencesUniversity of South AustraliaAdelaideSouth AustraliaAustralia
| | - Bradley J. Hart
- Health and Biomedical Innovation, UniSA Clinical and Health SciencesUniversity of South AustraliaAdelaideSouth AustraliaAustralia
| | - Naomi L. Siderius
- Health and Biomedical Innovation, UniSA Clinical and Health SciencesUniversity of South AustraliaAdelaideSouth AustraliaAustralia
| | - Anteneh Amsalu
- Health and Biomedical Innovation, UniSA Clinical and Health SciencesUniversity of South AustraliaAdelaideSouth AustraliaAustralia
- Department of Medical MicrobiologyUniversity of GondarGondarEthiopia
| | - Jack M. Blaikie
- Health and Biomedical Innovation, UniSA Clinical and Health SciencesUniversity of South AustraliaAdelaideSouth AustraliaAustralia
| | - Henrietta Venter
- Health and Biomedical Innovation, UniSA Clinical and Health SciencesUniversity of South AustraliaAdelaideSouth AustraliaAustralia
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2
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Jeong BG, Kim MY, Jeong CS, Do H, Hwang J, Lee JH, Cha SS. Characterization of the extended substrate spectrum of the class A β-lactamase CESS-1 from Stenotrophomonas sp. and structure-based investigation into its substrate preference. Int J Antimicrob Agents 2024; 63:107171. [PMID: 38588869 DOI: 10.1016/j.ijantimicag.2024.107171] [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: 04/03/2023] [Revised: 03/10/2024] [Accepted: 04/03/2024] [Indexed: 04/10/2024]
Abstract
OBJECTIVES Stenotrophomonas spp. intrinsically resistant to many β-lactam antibiotics are found throughout the environment. CESS-1 identified in Stenotrophomonas sp. KCTC 12332 is an uncharacterized class A β-lactamase. The goal of this study was to reveal biochemical and structural characteristics of CESS-1. METHODS The hydrolytic activities of CESS-1 towards penicillins (penicillin G and ampicillin), cephalosporins (cephalexin, cefaclor, and cefotaxime), and carbapenems (imipenem and meropenem) was spectrophotometrically monitored. Structural information on E166Q mutants of CESS-1 acylated by cefaclor, cephalexin, or ampicillin were determined by X-ray crystallography. RESULTS CESS-1 displayed hydrolytic activities toward penicillins and cephalosporins, with negligible activity toward carbapenems. Although cefaclor, cephalexin, and ampicillin have similar structures with identical R1 side chains, the catalytic parameters of CESS-1 toward them were distinct. The kcat values for cefaclor, cephalexin, and ampicillin were 1249.6 s-1, 204.3 s-1, and 69.8 s-1, respectively, with the accompanying KM values of 287.6 μM, 236.7 μM, and 28.8 μM, respectively. CONCLUSIONS CESS-1 was able to discriminate between cefaclor and cephalexin with a single structural difference at C3 position: -Cl (cefaclor) and -CH3 (cephalexin). Structural comparisons among three E166Q mutants of CESS-1 acylated by cefaclor, cephalexin, or ampicillin, revealed that cooperative positional changes in the R1 side chain of substrates and their interaction with the β5-β6 loop affect the distance between Asn170 and the deacylating water at the acyl-enzyme intermediate state. This is directly associated with the differential hydrolytic activities of CESS-1 toward the three structurally similar β-lactam antibiotics.
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Affiliation(s)
- Bo-Gyeong Jeong
- Department of Chemistry & Nanoscience, Ewha Womans University, Seoul, Republic of Korea
| | - Myeong-Yeon Kim
- Department of Chemistry & Nanoscience, Ewha Womans University, Seoul, Republic of Korea
| | - Chang-Sook Jeong
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon, Republic of Korea
| | - Hackwon Do
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon, Republic of Korea
| | - Jisub Hwang
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon, Republic of Korea
| | - Jun Hyuck Lee
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon, Republic of Korea.
| | - Sun-Shin Cha
- Department of Chemistry & Nanoscience, Ewha Womans University, Seoul, Republic of Korea.
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Zhu Y, Gu J, Zhao Z, Chan AWE, Mojica MF, Hujer AM, Bonomo RA, Haider S. Deciphering the Coevolutionary Dynamics of L2 β-Lactamases via Deep Learning. J Chem Inf Model 2024; 64:3706-3717. [PMID: 38687957 PMCID: PMC11094718 DOI: 10.1021/acs.jcim.4c00189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/10/2024] [Accepted: 04/09/2024] [Indexed: 05/02/2024]
Abstract
L2 β-lactamases, serine-based class A β-lactamases expressed by Stenotrophomonas maltophilia, play a pivotal role in antimicrobial resistance (AMR). However, limited studies have been conducted on these important enzymes. To understand the coevolutionary dynamics of L2 β-lactamase, innovative computational methodologies, including adaptive sampling molecular dynamics simulations, and deep learning methods (convolutional variational autoencoders and BindSiteS-CNN) explored conformational changes and correlations within the L2 β-lactamase family together with other representative class A enzymes including SME-1 and KPC-2. This work also investigated the potential role of hydrophobic nodes and binding site residues in facilitating the functional mechanisms. The convergence of analytical approaches utilized in this effort yielded comprehensive insights into the dynamic behavior of the β-lactamases, specifically from an evolutionary standpoint. In addition, this analysis presents a promising approach for understanding how the class A β-lactamases evolve in response to environmental pressure and establishes a theoretical foundation for forthcoming endeavors in drug development aimed at combating AMR.
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Affiliation(s)
- Yu Zhu
- Pharmaceutical
and Biological Chemistry, UCL School of
Pharmacy, London WC1N 1AX, U.K.
| | - Jing Gu
- Pharmaceutical
and Biological Chemistry, UCL School of
Pharmacy, London WC1N 1AX, U.K.
| | - Zhuoran Zhao
- Pharmaceutical
and Biological Chemistry, UCL School of
Pharmacy, London WC1N 1AX, U.K.
| | - A. W. Edith Chan
- Division
of Medicine, UCL School of Pharmacy, London WC1E 6BT, U.K.
| | - Maria F. Mojica
- Department
of Molecular Biology and Microbiology, Case
Western Reserve University School of Medicine, Cleveland, Ohio 44106-5029, United
States
- Research
Service, Department of Veterans Affairs Medical Center, Louis Stokes Cleveland, Cleveland, Ohio 44106-1702, United States
- CWRU-Cleveland
VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA
CARES), Cleveland, Ohio 44106-5029, United States
| | - Andrea M. Hujer
- Research
Service, Department of Veterans Affairs Medical Center, Louis Stokes Cleveland, Cleveland, Ohio 44106-1702, United States
- Department
of Medicine, Case Western Reserve University
School of Medicine, Cleveland, Ohio 44106-5029, United States
| | - Robert A. Bonomo
- Research
Service, Department of Veterans Affairs Medical Center, Louis Stokes Cleveland, Cleveland, Ohio 44106-1702, United States
- CWRU-Cleveland
VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA
CARES), Cleveland, Ohio 44106-5029, United States
- Clinician
Scientist Investigator, Department of Veterans Affairs Medical Center, Louis Stokes Cleveland, Cleveland, Ohio 44106-1702, United States
- Departments
of Pharmacology, Biochemistry, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106-5029, United
States
- Departments
of Molecular Biology and Microbiology, Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106-5029, United
States
| | - Shozeb Haider
- Pharmaceutical
and Biological Chemistry, UCL School of
Pharmacy, London WC1N 1AX, U.K.
- UCL
Centre for Advanced Research in Computing, University College London, London WC1H 9RL, U.K.
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Bhaumik R, Aungkur NZ, Anderson GG. A guide to Stenotrophomonas maltophilia virulence capabilities, as we currently understand them. Front Cell Infect Microbiol 2024; 13:1322853. [PMID: 38274738 PMCID: PMC10808757 DOI: 10.3389/fcimb.2023.1322853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/20/2023] [Indexed: 01/27/2024] Open
Abstract
The Gram-negative pathogen Stenotrophomonas maltophilia causes a wide range of human infections. It causes particularly serious lung infections in individuals with cystic fibrosis, leading to high mortality rates. This pathogen is resistant to most known antibiotics and harbors a plethora of virulence factors, including lytic enzymes and serine proteases, that cause acute infection in host organisms. S. maltophilia also establishes chronic infections through biofilm formation. The biofilm environment protects the bacteria from external threats and harsh conditions and is therefore vital for the long-term pathogenesis of the microbe. While studies have identified several genes that mediate S. maltophilia's initial colonization and biofilm formation, the cascade of events initiated by these factors is poorly understood. Consequently, understanding these and other virulence factors can yield exciting new targets for novel therapeutics.
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Affiliation(s)
| | | | - Gregory G. Anderson
- Department of Biology, Purdue School of Science, Indiana University Purdue University Indianapolis, Indianapolis, IN, United States
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5
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Oelschlaeger P, Kaadan H, Dhungana R. Strategies to Name Metallo-β-Lactamases and Number Their Amino Acid Residues. Antibiotics (Basel) 2023; 12:1746. [PMID: 38136780 PMCID: PMC10740994 DOI: 10.3390/antibiotics12121746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/12/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Metallo-β-lactamases (MBLs), also known as class B β-lactamases (BBLs), are Zn(II)-containing enzymes able to inactivate a broad range of β-lactams, the most commonly used antibiotics, including life-saving carbapenems. They have been known for about six decades, yet they have only gained much attention as a clinical problem for about three decades. The naming conventions of these enzymes have changed over time and followed various strategies, sometimes leading to confusion. We are summarizing the naming strategies of the currently known MBLs. These enzymes are quite diverse on the amino acid sequence level but structurally similar. Problems trying to describe conserved residues, such as Zn(II) ligands and other catalytically important residues, which have different numbers in different sequences, have led to the establishment of a standard numbering scheme for BBLs. While well intended, the standard numbering scheme is not trivial and has not been applied consistently. We revisit this standard numbering scheme and suggest some strategies for how its implementation could be made more accessible to researchers. Standard numbering facilitates the comparison of different enzymes as well as their interaction with novel antibiotics and BBL inhibitors.
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Affiliation(s)
- Peter Oelschlaeger
- Department of Biotechnology and Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, CA 91766, USA; (H.K.)
| | - Heba Kaadan
- Department of Biotechnology and Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, CA 91766, USA; (H.K.)
| | - Rinku Dhungana
- Department of Biotechnology and Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, CA 91766, USA; (H.K.)
- Department of Biological Sciences, Kenneth P. Dietrich School of Arts & Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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Li Y, Liu X, Chen L, Shen X, Wang H, Guo R, Li X, Yu Z, Zhang X, Zhou Y, Fu L. Comparative genomics analysis of Stenotrophomonas maltophilia strains from a community. Front Cell Infect Microbiol 2023; 13:1266295. [PMID: 38089814 PMCID: PMC10715271 DOI: 10.3389/fcimb.2023.1266295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/07/2023] [Indexed: 12/18/2023] Open
Abstract
Background Stenotrophomonas maltophilia is a multidrug-resistant (MDR) opportunistic pathogen with high resistance to most clinically used antimicrobials. The dissemination of MDR S. maltophilia and difficult treatment of its infection in clinical settings are global issues. Methods To provide more genetic information on S. maltophilia and find a better treatment strategy, we isolated five S. maltophilia, SMYN41-SMYN45, from a Chinese community that were subjected to antibiotic susceptibility testing, biofilm formation assay, and whole-genome sequencing. Whole-genome sequences were compared with other thirty-seven S. maltophilia sequences. Results The five S. maltophilia strains had similar antibiotic resistance profiles and were resistant to β-lactams, aminoglycosides, and macrolides. They showed similar antimicrobial resistance (AMR) genes, including various efflux pumps, β-lactamase resistance genes (blaL1/2), aminoglycoside resistance genes [aac(6'), aph(3'/6)], and macrolide-resistant gene (MacB). Genome sequencing analysis revealed that SMYN41-SMYN45 belonged to sequence type 925 (ST925), ST926, ST926, ST31, and ST928, respectively, and three new STs were identified (ST925, ST926, and ST928). Conclusion This study provides genetic information by comparing genome sequences of several S. maltophilia isolates from a community of various origins, with the aim of optimizing empirical antibiotic medication and contributing to worldwide efforts to tackle antibiotic resistance.
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Affiliation(s)
- Yini Li
- Department of Ultrasound, Affiliated Hospital of Southwest Medical University, Southwest Medical University, Luzhou, China
| | - Xin Liu
- Department of Pathogen Biology, School of Basic Medicine, Public Center of Experimental Technology of Pathogen Biology Technology Platform, Southwest Medical University, Luzhou, China
| | - Lingzhi Chen
- Department of Ultrasound, Affiliated Hospital of Southwest Medical University, Southwest Medical University, Luzhou, China
| | - Xiao Shen
- Department of Pathogen Biology, School of Basic Medicine, Public Center of Experimental Technology of Pathogen Biology Technology Platform, Southwest Medical University, Luzhou, China
| | - Haihong Wang
- Department of Pathogen Biology, School of Basic Medicine, Public Center of Experimental Technology of Pathogen Biology Technology Platform, Southwest Medical University, Luzhou, China
| | - Ruiyu Guo
- Department of Pathogen Biology, School of Basic Medicine, Public Center of Experimental Technology of Pathogen Biology Technology Platform, Southwest Medical University, Luzhou, China
| | - Xiang Li
- Department of Pathogen Biology, School of Basic Medicine, Public Center of Experimental Technology of Pathogen Biology Technology Platform, Southwest Medical University, Luzhou, China
| | - Zehui Yu
- Laboratory Animal Center, Southwest Medical University, Luzhou, China
| | - Xiaoli Zhang
- Department of Allergy, Jiangnan University Medical Center, Wuxi, China
| | - Yingshun Zhou
- Department of Pathogen Biology, School of Basic Medicine, Public Center of Experimental Technology of Pathogen Biology Technology Platform, Southwest Medical University, Luzhou, China
| | - Li Fu
- Affiliated Hospital of Southwest Medical University, Southwest Medical University, Luzhou, China
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7
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Hirai J, Mori N, Sakanashi D, Shibata Y, Asai N, Hagihara M, Mikamo H. Intra-Abdominal Abscess and Bacteremia Due to Stenotrophomonas maltophilia After Total Gastrectomy: A Case Report and Literature Review. Infect Drug Resist 2023; 16:7197-7204. [PMID: 38023400 PMCID: PMC10644874 DOI: 10.2147/idr.s433564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 11/04/2023] [Indexed: 12/01/2023] Open
Abstract
Stenotrophomonas maltophilia (S. maltophilia) is increasingly recognized as a pathogen responsible for nosocomial infections, particularly in immunocompromised patients. The most common types of S. maltophilia infections are pneumonia and catheter-related bloodstream infection, and clinical cases of intra-abdominal abscesses due to S. maltophilia are rare. We present a rare case of intra-abdominal abscess and bacteremia as a surgical site infection (SSI) caused by S. maltophilia in a patient following total gastrectomy. We also reviewed previous literature to elucidate the clinical characteristics of intra-abdominal abscess due to S. maltophilia. The patient, a 75-year-old man with diabetes and polymyositis (treated with prednisolone), developed a fever 17 days after undergoing a total gastrectomy for gastric cancer. Abdominal computed tomography revealed a hypodense solid mass at the esophagojejunostomy site, which appeared to be an intra-abdominal abscess. The culture of both blood and drained abscess pus confirmed only S. maltophilia. Treatment with intravenous trimethoprim-sulfamethoxazole and abscess drainage led to complete resolution. The patient recovered and was discharged and did not experience a recurrence. We reviewed the English literature and found only two additional case reports of intra-abdominal abscesses caused by S. maltophilia. As in our case, the intra-abdominal abscess occurred after abdominal surgery and the source was suspected to be deep SSI. This case highlights the importance of considering S. maltophilia as a potential pathogen in patients with atypical post-surgical abdominal infections. Physicians should be aware that S. maltophilia has the potential to cause intra-abdominal abscesses secondary to SSI, in addition to Enterobacteriaceae, a major causative pathogen of SSI. Further studies are required to elucidate the etiology, epidemiology, and risk factors for SSI caused by S. maltophilia.
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Affiliation(s)
- Jun Hirai
- Department of Clinical Infectious Diseases, Aichi Medical University Hospital, Nagakute, Aichi, Japan
- Department of Infection Control and Prevention, Aichi Medical University Hospital, Nagakute, Aichi, Japan
| | - Nobuaki Mori
- Department of Clinical Infectious Diseases, Aichi Medical University Hospital, Nagakute, Aichi, Japan
- Department of Infection Control and Prevention, Aichi Medical University Hospital, Nagakute, Aichi, Japan
| | - Daisuke Sakanashi
- Department of Infection Control and Prevention, Aichi Medical University Hospital, Nagakute, Aichi, Japan
| | - Yuichi Shibata
- Department of Infection Control and Prevention, Aichi Medical University Hospital, Nagakute, Aichi, Japan
| | - Nobuhiro Asai
- Department of Clinical Infectious Diseases, Aichi Medical University Hospital, Nagakute, Aichi, Japan
- Department of Infection Control and Prevention, Aichi Medical University Hospital, Nagakute, Aichi, Japan
| | - Mao Hagihara
- Department of Molecular Epidemiology and Biomedical Sciences, Aichi Medical University, Nagakute, Aichi, Japan
| | - Hiroshige Mikamo
- Department of Clinical Infectious Diseases, Aichi Medical University Hospital, Nagakute, Aichi, Japan
- Department of Infection Control and Prevention, Aichi Medical University Hospital, Nagakute, Aichi, Japan
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8
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Klimkaitė L, Ragaišis I, Krasauskas R, Ružauskas M, Sužiedėlienė E, Armalytė J. Novel Antibiotic Resistance Genes Identified by Functional Gene Library Screening in Stenotrophomonas maltophilia and Chryseobacterium spp. Bacteria of Soil Origin. Int J Mol Sci 2023; 24:ijms24076037. [PMID: 37047008 PMCID: PMC10094639 DOI: 10.3390/ijms24076037] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/17/2023] [Accepted: 03/19/2023] [Indexed: 04/14/2023] Open
Abstract
As one of the most diverse habitats of microorganisms, soil has been recognised as a reservoir of both antibiotics and the antibiotic resistance genes (ARGs). Bacteria naturally inhabiting soil or water often possess innate ARGs to counteract the chemical compounds produced by competitors living in the same environment. When such bacteria are able to cause infections in immunocompromised patients, their strong innate antibiotic resistance mechanisms make treatment difficult. We generated functional gene libraries using antibiotic-resistant Stenotrophomonas maltophilia and Chryseobacterium spp. bacteria isolated from agricultural soils in Lithuania to select for the genetic determinants responsible for their resistance. We were able to find novel variants of aminoglycoside and β-lactam resistance genes, with β-lactamases isolated from the Chryseobacterium spp. functional gene library, one of which is a variant of IND-like metallo-β-lactamase (MBL) IND-17 and the other of which is a previously uncharacterised MBL we named CHM (Chryseobacterium metallo β-lactamase). Our results indicate that soil microorganisms possess a diversity of ARG variants, which could potentially be transferred to the clinical setting.
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Affiliation(s)
- Laurita Klimkaitė
- Institute of Biosciences, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Ignas Ragaišis
- Institute of Biosciences, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Renatas Krasauskas
- Institute of Biosciences, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Modestas Ružauskas
- Microbiology and Virology Institute, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania
| | - Edita Sužiedėlienė
- Institute of Biosciences, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Julija Armalytė
- Institute of Biosciences, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
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Peykov S, Strateva T. Whole-Genome Sequencing-Based Resistome Analysis of Nosocomial Multidrug-Resistant Non-Fermenting Gram-Negative Pathogens from the Balkans. Microorganisms 2023; 11:microorganisms11030651. [PMID: 36985224 PMCID: PMC10051916 DOI: 10.3390/microorganisms11030651] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023] Open
Abstract
Non-fermenting Gram-negative bacilli (NFGNB), such as Pseudomonas aeruginosa and Acinetobacter baumannii, are among the major opportunistic pathogens involved in the global antibiotic resistance epidemic. They are designated as urgent/serious threats by the Centers for Disease Control and Prevention and are part of the World Health Organization’s list of critical priority pathogens. Also, Stenotrophomonas maltophilia is increasingly recognized as an emerging cause for healthcare-associated infections in intensive care units, life-threatening diseases in immunocompromised patients, and severe pulmonary infections in cystic fibrosis and COVID-19 individuals. The last annual report of the ECDC showed drastic differences in the proportions of NFGNB with resistance towards key antibiotics in different European Union/European Economic Area countries. The data for the Balkans are of particular concern, indicating more than 80% and 30% of invasive Acinetobacter spp. and P. aeruginosa isolates, respectively, to be carbapenem-resistant. Moreover, multidrug-resistant and extensively drug-resistant S. maltophilia from the region have been recently reported. The current situation in the Balkans includes a migrant crisis and reshaping of the Schengen Area border. This results in collision of diverse human populations subjected to different protocols for antimicrobial stewardship and infection control. The present review article summarizes the findings of whole-genome sequencing-based resistome analyses of nosocomial multidrug-resistant NFGNBs in the Balkan countries.
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Affiliation(s)
- Slavil Peykov
- Department of Genetics, Faculty of Biology, Sofia University “St. Kliment Ohridski”, 8, Dragan Tzankov Blvd., 1164 Sofia, Bulgaria
- Department of Medical Microbiology, Faculty of Medicine, Medical University of Sofia, 2, Zdrave Str., 1431 Sofia, Bulgaria
- BioInfoTech Laboratory, Sofia Tech Park, 111, Tsarigradsko Shosse Blvd., 1784 Sofia, Bulgaria
- Correspondence: (S.P.); (T.S.); Tel.: +359-87-6454492 (S.P.); +359-2-9172750 (T.S.)
| | - Tanya Strateva
- Department of Medical Microbiology, Faculty of Medicine, Medical University of Sofia, 2, Zdrave Str., 1431 Sofia, Bulgaria
- Correspondence: (S.P.); (T.S.); Tel.: +359-87-6454492 (S.P.); +359-2-9172750 (T.S.)
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10
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Mojica MF, Humphries R, Lipuma JJ, Mathers AJ, Rao GG, Shelburne SA, Fouts DE, Van Duin D, Bonomo RA. Clinical challenges treating Stenotrophomonas maltophilia infections: an update. JAC Antimicrob Resist 2022; 4:dlac040. [PMID: 35529051 PMCID: PMC9071536 DOI: 10.1093/jacamr/dlac040] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023] Open
Abstract
Stenotrophomonas maltophilia is a non-fermenting, Gram-negative bacillus that has emerged as an opportunistic nosocomial pathogen. Its intrinsic multidrug resistance makes treating infections caused by S. maltophilia a great clinical challenge. Clinical management is further complicated by its molecular heterogeneity that is reflected in the uneven distribution of antibiotic resistance and virulence determinants among different strains, the shortcomings of available antimicrobial susceptibility tests and the lack of standardized breakpoints for the handful of antibiotics with in vitro activity against this microorganism. Herein, we provide an update on the most recent literature concerning these issues, emphasizing the impact they have on clinical management of S. maltophilia infections.
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Affiliation(s)
- Maria F. Mojica
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Case Western Reserve University-Cleveland VA Medical Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH, USA
- Research Service, VA Northeast Ohio Healthcare System, Cleveland, OH, USA
- Grupo de Resistencia Antimicrobiana y Epidemiología Hospitalaria, Universidad El Bosque, Bogotá, Colombia
| | - Romney Humphries
- Department of Pathology, Immunology and Microbiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - John J. Lipuma
- University of Michigan Medical School, Pediatric Infectious Disease, Ann Arbor, MI, USA
| | - Amy J. Mathers
- Division of Infectious Disease and International Health, Department of Medicine, University of Virginia Health System, Charlottesville, VA, USA
- Clinical Microbiology Laboratory, Department of Pathology, University of Virginia Health System, Charlottesville, VA, USA
| | - Gauri G. Rao
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Samuel A. Shelburne
- Department of Infectious Diseases Infection Control and Employee Health, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Science Center McGovern Medical School, Houston, TX, USA
| | - Derrick E. Fouts
- Genomic Medicine, The J. Craig Venter Institute, Rockville, MD, USA
| | - David Van Duin
- Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Robert A. Bonomo
- Case Western Reserve University-Cleveland VA Medical Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH, USA
- Research Service, VA Northeast Ohio Healthcare System, Cleveland, OH, USA
- Senior Clinician Scientist Investigator, Veterans Affairs Northeast Ohio Healthcare System, Cleveland, OH, USA
- Medical Service and Geriatric Research, Education, and Clinical Center (GRECC), Veterans Affairs Northeast Ohio Healthcare System, Cleveland, OH, USA
- Departments of Medicine, Biochemistry, Pharmacology, Molecular Biology and Microbiology, and Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
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11
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Fluit AC, Bayjanov JR, Aguilar MD, Cantón R, Elborn S, Tunney MM, Scharringa J, Benaissa-Trouw BJ, Ekkelenkamp MB. Taxonomic position, antibiotic resistance and virulence factor production by Stenotrophomonas isolates from patients with cystic fibrosis and other chronic respiratory infections. BMC Microbiol 2022; 22:129. [PMID: 35549675 PMCID: PMC9097388 DOI: 10.1186/s12866-022-02466-5] [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] [Received: 05/21/2021] [Accepted: 02/07/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The potential pathogenic role of Stenotrophomonas maltophilia in lung disease and in particular in cystic fibrosis is unclear. To develop further understanding of the biology of this taxa, the taxonomic position, antibiotic resistance and virulence factors of S. maltophilia isolates from patients with chronic lung disease were studied. RESULTS A total of 111 isolates recovered between 2003 and 2016 from respiratory samples from patients in five different countries were included. Based on a cut-off of 95%, analysis of average nucleotide identity by BLAST (ANIb) showed that the 111 isolates identified as S. maltophilia by Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF/MS) belonged to S. maltophilia (n = 65), S. pavanii (n = 6) and 13 putative novel species (n = 40), which each included 1-5 isolates; these groupings coincided with the results of the 16S rDNA analysis, and the L1 and L2 ß-lactamase Neighbor-Joining phylogeny. Chromosomally encoded aminoglycoside resistance was identified in all S. maltophilia and S. pavani isolates, while acquired antibiotic resistance genes were present in only a few isolates. Nevertheless, phenotypic resistance levels against commonly used antibiotics, determined by standard broth microbroth dilution, were high. Although putative virulence genes were present in all isolates, the percentage of positive isolates varied. The Xps II secretion system responsible for the secretion of the StmPr1-3 proteases was mainly limited to isolates identified as S. maltophilia based on ANIb, but no correlation with phenotypic expression of protease activity was found. The RPF two-component quorum sensing system involved in virulence and antibiotic resistance expression has two main variants with one variant lacking 190 amino acids in the sensing region. CONCLUSIONS The putative novel Stenotrophomonas species recovered from patient samples and identified by MALDI-TOF/MS as S. maltophilia, differed from S. maltophilia in resistance and virulence genes, and therefore possibly in pathogenicity. Revision of the Stenotrophomonas taxonomy is needed in order to reliably identify strains within the genus and elucidate the role of the different species in disease.
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Affiliation(s)
- Ad C Fluit
- Department of Medical Microbiology, University Medical Center Utrecht, PO Box 85500, 3508, GA, Utrecht, the Netherlands.
| | - Jumamurat R Bayjanov
- Department of Medical Microbiology, University Medical Center Utrecht, PO Box 85500, 3508, GA, Utrecht, the Netherlands
| | - María Díez Aguilar
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.,Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain.,Present Address: Servicio de Microbiología, Hospital Universitario La Princesa, Madrid, Spain
| | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.,Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain
| | - Stuart Elborn
- Queen's University Belfast, School of Pharmacy, Belfast, UK
| | | | - Jelle Scharringa
- Department of Medical Microbiology, University Medical Center Utrecht, PO Box 85500, 3508, GA, Utrecht, the Netherlands
| | - Barry J Benaissa-Trouw
- Department of Medical Microbiology, University Medical Center Utrecht, PO Box 85500, 3508, GA, Utrecht, the Netherlands
| | - Miquel B Ekkelenkamp
- Department of Medical Microbiology, University Medical Center Utrecht, PO Box 85500, 3508, GA, Utrecht, the Netherlands
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12
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Kullar R, Wenzler E, Alexander J, Goldstein EJC. Overcoming Stenotrophomonas maltophilia Resistance for a More Rational Therapeutic Approach. Open Forum Infect Dis 2022; 9:ofac095. [PMID: 35415194 PMCID: PMC8992361 DOI: 10.1093/ofid/ofac095] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 02/22/2022] [Indexed: 11/14/2022] Open
Abstract
Stenotrophomonas maltophilia is an underappreciated source of morbidity and mortality among gram-negative pathogens. Effective treatment options with acceptable toxicity profiles are limited. Phenotypic susceptibility testing via commercial automated test systems is problematic and no Food and Drug Administration breakpoints are approved for any of the first-line treatment options for S maltophilia. The lack of modern pharmacokinetic/pharmacodynamic data for many agents impedes dose optimization, and the lack of robust efficacy and safety data limits their clinical utility. Levofloxacin has demonstrated similar efficacy to trimethoprim-sulfamethoxazole, although rapid development of resistance is a concern. Minocycline demonstrates the highest rate of in vitro susceptibility, however, evidence to support its clinical use are scant. Novel agents such as cefiderocol have exhibited promising activity in preclinical investigations, though additional outcomes data are needed to determine its place in therapy for S maltophilia. Combination therapy is often employed despite the dearth of adequate supporting data.
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Affiliation(s)
- Ravina Kullar
- Expert Stewardship, Inc, Newport Beach, California, USA
| | - Eric Wenzler
- College of Pharmacy, University of Illinois Chicago, Chicago, Illinois, USA
| | - Jose Alexander
- Department of Microbiology, Virology, and Immunology, AdventHealth Central Florida, Orlando, Florida, USA
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13
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Sanz-García F, Gil-Gil T, Laborda P, Ochoa-Sánchez LE, Martínez JL, Hernando-Amado S. Coming from the Wild: Multidrug Resistant Opportunistic Pathogens Presenting a Primary, Not Human-Linked, Environmental Habitat. Int J Mol Sci 2021; 22:8080. [PMID: 34360847 PMCID: PMC8347278 DOI: 10.3390/ijms22158080] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/22/2021] [Accepted: 07/24/2021] [Indexed: 12/24/2022] Open
Abstract
The use and misuse of antibiotics have made antibiotic-resistant bacteria widespread nowadays, constituting one of the most relevant challenges for human health at present. Among these bacteria, opportunistic pathogens with an environmental, non-clinical, primary habitat stand as an increasing matter of concern at hospitals. These organisms usually present low susceptibility to antibiotics currently used for therapy. They are also proficient in acquiring increased resistance levels, a situation that limits the therapeutic options for treating the infections they cause. In this article, we analyse the most predominant opportunistic pathogens with an environmental origin, focusing on the mechanisms of antibiotic resistance they present. Further, we discuss the functions, beyond antibiotic resistance, that these determinants may have in the natural ecosystems that these bacteria usually colonize. Given the capacity of these organisms for colonizing different habitats, from clinical settings to natural environments, and for infecting different hosts, from plants to humans, deciphering their population structure, their mechanisms of resistance and the role that these mechanisms may play in natural ecosystems is of relevance for understanding the dissemination of antibiotic resistance under a One-Health point of view.
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Affiliation(s)
| | | | | | | | - José L. Martínez
- Centro Nacional de Biotecnología, CSIC, 28049 Madrid, Spain; (F.S.-G.); (T.G.-G.); (P.L.); (L.E.O.-S.); (S.H.-A.)
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14
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Menetrey Q, Sorlin P, Jumas-Bilak E, Chiron R, Dupont C, Marchandin H. Achromobacter xylosoxidans and Stenotrophomonas maltophilia: Emerging Pathogens Well-Armed for Life in the Cystic Fibrosis Patients' Lung. Genes (Basel) 2021; 12:610. [PMID: 33919046 PMCID: PMC8142972 DOI: 10.3390/genes12050610] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/06/2021] [Accepted: 04/19/2021] [Indexed: 02/07/2023] Open
Abstract
In patients with cystic fibrosis (CF), the lung is a remarkable ecological niche in which the microbiome is subjected to important selective pressures. An inexorable colonization by bacteria of both endogenous and environmental origin is observed in most patients, leading to a vicious cycle of infection-inflammation. In this context, long-term colonization together with competitive interactions among bacteria can lead to over-inflammation. While Pseudomonas aeruginosa and Staphylococcus aureus, the two pathogens most frequently identified in CF, have been largely studied for adaptation to the CF lung, in the last few years, there has been a growing interest in emerging pathogens of environmental origin, namely Achromobacter xylosoxidans and Stenotrophomonas maltophilia. The aim of this review is to gather all the current knowledge on the major pathophysiological traits, their supporting mechanisms, regulation and evolutionary modifications involved in colonization, virulence, and competitive interactions with other members of the lung microbiota for these emerging pathogens, with all these mechanisms being major drivers of persistence in the CF lung. Currently available research on A. xylosoxidans complex and S. maltophilia shows that these emerging pathogens share important pathophysiological features with well-known CF pathogens, making them important members of the complex bacterial community living in the CF lung.
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Affiliation(s)
- Quentin Menetrey
- HydroSciences Montpellier, CNRS, IRD, Univ Montpellier, 34093 Montpellier, France; (Q.M.); (P.S.)
| | - Pauline Sorlin
- HydroSciences Montpellier, CNRS, IRD, Univ Montpellier, 34093 Montpellier, France; (Q.M.); (P.S.)
| | - Estelle Jumas-Bilak
- HydroSciences Montpellier, CNRS, IRD, Univ Montpellier, Department d’Hygiène Hospitalière, CHU Montpellier, 34093 Montpellier, France; (E.J.-B.); (C.D.)
| | - Raphaël Chiron
- HydroSciences Montpellier, Université de Montpellier, CNRS, IRD, Centre de Ressources et de Compétences de la Mucoviscidose, CHU de Montpellier, 34093 Montpellier, France;
| | - Chloé Dupont
- HydroSciences Montpellier, CNRS, IRD, Univ Montpellier, Department d’Hygiène Hospitalière, CHU Montpellier, 34093 Montpellier, France; (E.J.-B.); (C.D.)
| | - Hélène Marchandin
- HydroSciences Montpellier, CNRS, IRD, Univ Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, 34093 Nîmes, France
- UMR 5151 HydroSciences Montpellier, Equipe Pathogènes Hydriques Santé Environnements, U.F.R. des Sciences Pharmaceutiques et Biologiques, Université de Montpellier, 15, Avenue Charles Flahault, BP 14491, CEDEX 5, 34093 Montpellier, France
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15
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Activity of Aztreonam in Combination with Avibactam, Clavulanate, Relebactam, and Vaborbactam against Multidrug-Resistant Stenotrophomonas maltophilia. Antimicrob Agents Chemother 2020; 64:AAC.00297-20. [PMID: 32928733 DOI: 10.1128/aac.00297-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 09/04/2020] [Indexed: 12/26/2022] Open
Abstract
The intrinsic L1 metallo- and L2 serine-β-lactamases in Stenotrophomonas maltophilia make it naturally multidrug resistant and difficult to treat. There is a need to identify novel treatment strategies for this pathogen, especially against isolates resistant to first-line agents. Aztreonam in combination with avibactam has demonstrated potential, although data on other aztreonam-β-lactamase inhibitor (BLI) combinations are lacking. Additionally, molecular mechanisms for reduced susceptibility to these combinations have not been explored. The objectives of this study were to evaluate and compare the in vitro activities and to understand the mechanisms of resistance to aztreonam in combination with avibactam, clavulanate, relebactam, and vaborbactam against S. maltophilia A panel of 47 clinical S. maltophilia strains nonsusceptible to levofloxacin and/or trimethoprim-sulfamethoxazole were tested against each aztreonam-BLI combination via broth microdilution, and 6 isolates were then evaluated in time-kill analyses. Three isolates with various aztreonam-BLI MICs were subjected to whole-genome sequencing and quantitative reverse transcriptase PCR. Avibactam restored aztreonam susceptibility in 98% of aztreonam-resistant isolates, compared to 61, 71, and 15% with clavulanate, relebactam, and vaborbactam, respectively. The addition of avibactam to aztreonam resulted in a ≥2-log10-CFU/ml decrease at 24 h versus aztreonam alone against 5/6 isolates compared to 1/6 with clavulanate, 4/6 with relebactam, and 2/6 with vaborbactam. Molecular analyses revealed that decreased susceptibility to aztreonam-avibactam was associated with increased expression of genes encoding L1 and L2, as well as the efflux pump (smeABC). Aztreonam-avibactam is the most promising BLI-combination against multidrug-resistant S. maltophilia Decreased susceptibility may be due to the combination of overexpressed β-lactamases and efflux pumps. Further studies evaluating this combination against S. maltophilia are warranted.
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16
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Klimkaitė L, Armalytė J, Skerniškytė J, Sužiedėlienė E. The Toxin-Antitoxin Systems of the Opportunistic Pathogen Stenotrophomonas maltophilia of Environmental and Clinical Origin. Toxins (Basel) 2020; 12:E635. [PMID: 33019620 PMCID: PMC7650669 DOI: 10.3390/toxins12100635] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/22/2020] [Accepted: 09/25/2020] [Indexed: 12/16/2022] Open
Abstract
Stenotrophomonas maltophilia is a ubiquitous environmental bacterium that has recently emerged as a multidrug-resistant opportunistic pathogen causing bloodstream, respiratory, and urinary tract infections. The connection between the commensal environmental S. maltophilia and the opportunistic pathogen strains is still under investigation. Bacterial toxin-antitoxin (TA) systems have been previously associated with pathogenic traits, such as biofilm formation and resistance to antibiotics, which are important in clinical settings. The same species of the bacterium can possess various sets of TAs, possibly influencing their overall stress response. While the TA systems of other important opportunistic pathogens have been researched, nothing is known about the TA systems of S. maltophilia. Here, we report the identification and characterization of S. maltophilia type II TA systems and their prevalence in the isolates of clinical and environmental origins. We found 49 putative TA systems by bioinformatic analysis in S. maltophilia genomes. Despite their even spread in sequenced S. maltophilia genomes, we observed that relBE, hicAB, and previously undescribed COG3832-ArsR operons were present solely in clinical S. maltophilia isolates collected in Lithuania, while hipBA was more frequent in the environmental ones. The kill-rescue experiments in Escherichia coli proved higBA, hicAB, and relBE systems to be functional TA modules. Together with different TA profiles, the clinical S. maltophilia isolates exhibited stronger biofilm formation, increased antibiotic, and serum resistance compared to environmental isolates. Such tendencies suggest that certain TA systems could be used as indicators of virulence traits.
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Affiliation(s)
| | - Julija Armalytė
- Institute of Biosciences, Life Sciences Center, Vilnius University, LT-1025 Vilnius, Lithuania; (L.K.); (J.S.)
| | | | - Edita Sužiedėlienė
- Institute of Biosciences, Life Sciences Center, Vilnius University, LT-1025 Vilnius, Lithuania; (L.K.); (J.S.)
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17
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Blanco P, Corona F, Martinez JL. Mechanisms and phenotypic consequences of acquisition of tigecycline resistance by Stenotrophomonas maltophilia. J Antimicrob Chemother 2020; 74:3221-3230. [PMID: 31369109 DOI: 10.1093/jac/dkz326] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 06/17/2019] [Accepted: 07/02/2019] [Indexed: 01/05/2023] Open
Abstract
OBJECTIVES To elucidate the potential mutation-driven mechanisms involved in the acquisition of tigecycline resistance by the opportunistic pathogen Stenotrophomonas maltophilia. The mutational trajectories and their effects on bacterial fitness, as well as cross-resistance and/or collateral susceptibility to other antibiotics, were also addressed. METHODS S. maltophilia populations were submitted to experimental evolution in the presence of increasing concentrations of tigecycline for 30 days. The genetic mechanisms involved in the acquisition of tigecycline resistance were determined by WGS. Resistance was evaluated by performing MIC assays. Fitness of the evolved populations and individual clones was assessed by measurement of the maximum growth rates. RESULTS All the tigecycline-evolved populations attained high-level resistance to tigecycline following different mutational trajectories, yet with some common elements. Among the mechanisms involved in low susceptibility to tigecycline, mutations in the SmeDEF efflux pump negative regulator smeT, changes in proteins involved in the biogenesis of the ribosome and modifications in the LPS biosynthesis pathway seem to play a major role. Besides tigecycline resistance, the evolved populations presented cross-resistance to other antibiotics, such as aztreonam and quinolones, and they were hypersusceptible to fosfomycin, suggesting a possible combination treatment. Further, we found that the selected resistance mechanisms impose a relevant fitness cost when bacteria grow in the absence of antibiotic. CONCLUSIONS Mutational resistance to tigecycline was easily selected during exposure to this antibiotic. However, the fitness cost may compromise the maintenance of S. maltophilia tigecycline-resistant populations in the absence of antibiotic.
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Affiliation(s)
- Paula Blanco
- Centro Nacional de Biotecnología, CSIC, Madrid, Spain
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18
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Menetrey Q, Dupont C, Chiron R, Marchandin H. [Emerging bacteria in cystic fibrosis and non-cystic fibrosis bronchiectasis from a microbiologist's perspective]. Rev Mal Respir 2020; 37:561-571. [PMID: 32684338 DOI: 10.1016/j.rmr.2020.06.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 03/25/2020] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Common major pathogens like Pseudomonas aeruginosa are identified in the airways of patients with cystic fibrosis (CF) and non-CF bronchiectasis. However, other opportunistic bacterial pathogens like Achromobacter xylosoxidans complex, Stenotrophomonas maltophilia and non-tuberculous mycobacteria are currently emerging in CF and are also reported in non-CF bronchiectasis. BACKGROUND The emergence of opportunistic bacterial pathogens has been recognized in CF through annual national reports of sputum microbiology data. Despite common factors driving the emergence of bacteria identified in CF and non-CF bronchiectasis patients, bronchiectasis registries have been created more recently and no longitudinal analysis of recorded microbiological data is currently available in the literature, thereby preventing the recognition of emerging bacteria in patients with non-CF bronchiectasis. OUTLOOK A longitudinal follow-up of microbiological data is still needed in non-CF bronchiectasis to identify emerging opportunistic bacterial pathogens. Homogeneity in practice of sputum microbiological examination is also required to allow comparative analysis of data in CF and non-CF bronchiectasis. CONCLUSION Bacterial pathogens recognized as emerging in CF have to be more carefully monitored in non-CF bronchiectasis in view of their association with deterioration of the lung disease.
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Affiliation(s)
- Q Menetrey
- HydroSciences Montpellier, CNRS, IRD, université de Montpellier, Montpellier, France
| | - C Dupont
- HydroSciences Montpellier, CNRS, IRD, laboratoire d'écologie microbienne hospitalière, université de Montpellier, CHU de Montpellier, Montpellier, France
| | - R Chiron
- HydroSciences Montpellier, CNRS, IRD, centre de ressources et de compétences de la mucoviscidose, université de Montpellier, CHU de Montpellier, Montpellier, France
| | - H Marchandin
- HydroSciences Montpellier, CNRS, IRD, département de microbiologie, université de Montpellier, CHU de Nîmes, Nîmes, France.
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19
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Peters DL, McCutcheon JG, Dennis JJ. Characterization of Novel Broad-Host-Range Bacteriophage DLP3 Specific to Stenotrophomonas maltophilia as a Potential Therapeutic Agent. Front Microbiol 2020; 11:1358. [PMID: 32670234 PMCID: PMC7326821 DOI: 10.3389/fmicb.2020.01358] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/27/2020] [Indexed: 01/04/2023] Open
Abstract
A novel Siphoviridae phage specific to the bacterial species Stenotrophomonas maltophilia was isolated from a pristine soil sample and characterized as a second member of the newly established Delepquintavirus genus. Phage DLP3 possesses one of the broadest host ranges of any S. maltophilia phage yet characterized, infecting 22 of 29 S. maltophilia strains. DLP3 has a genome size of 96,852 bp and a G+C content of 58.4%, which is significantly lower than S. maltophilia host strain D1571 (G+C content of 66.9%). The DLP3 genome encodes 153 coding domain sequences covering 95% of the genome, including five tRNA genes with different specificities. The DLP3 lysogen exhibits a growth rate increase during the exponential phase of growth as compared to the wild type strain. DLP3 also encodes a functional erythromycin resistance protein, causing lysogenic conversion of the host D1571 strain. Although a temperate phage, DLP3 demonstrates excellent therapeutic potential because it exhibits a broad host range, infects host cells through the S. maltophilia type IV pilus, and exhibits lytic activity in vivo. Undesirable traits, such as its temperate lifecycle, can be eliminated using genetic techniques to produce a modified phage useful in the treatment of S. maltophilia bacterial infections.
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Affiliation(s)
- Danielle L Peters
- Department of Biological Sciences, Faculty of Science, University of Alberta, Edmonton, AB, Canada
| | - Jaclyn G McCutcheon
- Department of Biological Sciences, Faculty of Science, University of Alberta, Edmonton, AB, Canada
| | - Jonathan J Dennis
- Department of Biological Sciences, Faculty of Science, University of Alberta, Edmonton, AB, Canada
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20
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Elufisan TO, Luna ICR, Oyedara OO, Varela AS, García VB, Oluyide BO, Treviño SF, López MAV, Guo X. Antimicrobial susceptibility pattern of Stenotrophomonas species isolated from Mexico. Afr Health Sci 2020; 20:168-181. [PMID: 33402905 PMCID: PMC7750080 DOI: 10.4314/ahs.v20i1.22] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Stenotrophomonas species are multi-resistant bacteria with ability to cause opportunistic infections. OBJECTIVE We isolated 45 Stenotrophomonas species from soil, sewage and the clinic with the aim of investigating their susceptibility to commonly used antimicrobial agents. METHODOLOGY The identities of isolates were confirmed with 16S rRNA gene sequence and MALDI-TOF analysis. Anti-microbial resistance, biofilm production and clonal diversity were also evaluated. The minimum inhibitory concentration technique as described by Clinical & Laboratory Standards Institute: CLSI Guidelines (CLSI) was employed for the evaluation of isolate susceptibility to antibiotics. RESULT Forty-five Stenotrophomonas species which include 36 environmental strains and 9 clinical strains of S. maltophilia were considered in this study. 32 (88.9 %) environmental strains were identified to be S. maltophilia, 2 (5.6 %) were Stenotrophomonas nitritireducens, and 2 (5.6 %) cluster as Stenotrophomonas spp. Stenotrophomonas isolates were resistant to at least six of the antibiotics tested, including Trimethoprim/Sulfamethoxazole (SXT). CONCLUSION Environmental isolates from this study were resistant to SXT which is commonly used for the treatment of S. maltophilia infections. This informs the need for good public hygiene as the environment could be a reservoir of multi-resistant bacteria. It also buttresses the importance of surveillance study in the management of bacterial resistance.
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Affiliation(s)
- Temidayo O Elufisan
- Instituto Politécnico Nacional, Centro de Biotecnología Genómica, Reynosa, Tamaulipas 88710, México
- National Center for Technology Management (An agency of the Federal Ministry of Science and Technology (FMST), Nigeria, Obafemi Awolowo University, Ile-Ife)
| | | | - Omotayo O Oyedara
- Department of Biological Sciences, College of Science, Engineering and Technology, Faculty of Basic and Applied Science, Osun State University, Osogbo, Osun State, Nigeria
| | - Alejandro Sanchez Varela
- Instituto Politécnico Nacional, Centro de Biotecnología Genómica, Reynosa, Tamaulipas 88710, México
| | | | - Busayo O Oluyide
- Ekiti State College of Science and Health Technology, Ijero Ekiti, Ekiti State, Nigeria
| | - Samantha Flores Treviño
- Departamento de Medicina, Autonomous University of Nuevo León (UANL), Interna San Nicolás de los Garza, Mexico
| | - Miguel Angel Villalobos López
- Instituto Politécnico Nacional, Centro de Investigación en Biotecnología Aplicada, Tepetitla, Tlaxcala 90700, México
| | - Xianwu Guo
- Instituto Politécnico Nacional, Centro de Biotecnología Genómica, Reynosa, Tamaulipas 88710, México
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Abstract
β-Lactam antibiotics have been widely used as therapeutic agents for the past 70 years, resulting in emergence of an abundance of β-lactam-inactivating β-lactamases. Although penicillinases in Staphylococcus aureus challenged the initial uses of penicillin, β-lactamases are most important in Gram-negative bacteria, particularly in enteric and nonfermentative pathogens, where collectively they confer resistance to all β-lactam-containing antibiotics. Critical β-lactamases are those enzymes whose genes are encoded on mobile elements that are transferable among species. Major β-lactamase families include plasmid-mediated extended-spectrum β-lactamases (ESBLs), AmpC cephalosporinases, and carbapenemases now appearing globally, with geographic preferences for specific variants. CTX-M enzymes include the most common ESBLs that are prevalent in all areas of the world. In contrast, KPC serine carbapenemases are present more frequently in the Americas, the Mediterranean countries, and China, whereas NDM metallo-β-lactamases are more prevalent in the Indian subcontinent and Eastern Europe. As selective pressure from β-lactam use continues, multiple β-lactamases per organism are increasingly common, including pathogens carrying three different carbapenemase genes. These organisms may be spread throughout health care facilities as well as in the community, warranting close attention to increased infection control measures and stewardship of the β-lactam-containing drugs in an effort to control selection of even more deleterious pathogens.
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Gil-Gil T, Martínez JL, Blanco P. Mechanisms of antimicrobial resistance in Stenotrophomonas maltophilia: a review of current knowledge. Expert Rev Anti Infect Ther 2020; 18:335-347. [PMID: 32052662 DOI: 10.1080/14787210.2020.1730178] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Introduction: Stenotrophomonas maltophilia is a prototype of bacteria intrinsically resistant to antibiotics. The reduced susceptibility of this microorganism to antimicrobials mainly relies on the presence in its chromosome of genes encoding efflux pumps and antibiotic inactivating enzymes. Consequently, the therapeutic options for treating S. maltophilia infections are limited.Areas covered: Known mechanisms of intrinsic, acquired and phenotypic resistance to antibiotics of S. maltophilia and the consequences of such resistance for treating S. maltophilia infections are discussed. Acquisition of some genes, mainly those involved in co-trimoxazole resistance, contributes to acquired resistance. Mutation, mainly in the regulators of chromosomally-encoded antibiotic resistance genes, is a major cause for S. maltophilia acquisition of resistance. The expression of some of these genes is triggered by specific signals or stressors, which can lead to transient phenotypic resistance.Expert opinion: Treatment of S. maltophilia infections is difficult because this organism presents low susceptibility to antibiotics. Besides, it can acquire resistance to antimicrobials currently in use. Particularly problematic is the selection of mutants overexpressing efflux pumps since they present a multidrug resistance phenotype. The use of novel antimicrobials alone or in combination, together with the development of efflux pumps' inhibitors may help in fighting S. maltophilia infections.
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Affiliation(s)
| | | | - Paula Blanco
- Molecular Basis of Adaptation Laboratory, Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
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Blanco P, Corona F, Martínez JL. Involvement of the RND efflux pump transporter SmeH in the acquisition of resistance to ceftazidime in Stenotrophomonas maltophilia. Sci Rep 2019; 9:4917. [PMID: 30894628 PMCID: PMC6426872 DOI: 10.1038/s41598-019-41308-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 02/19/2019] [Indexed: 01/19/2023] Open
Abstract
The emergence of antibiotic resistant Gram-negative bacteria has become a serious global health issue. In this study, we have employed the intrinsically resistant opportunistic pathogen Stenotrophomonas maltophilia as a model to study the mechanisms involved in the acquisition of mutation-driven resistance to antibiotics. To this aim, laboratory experimental evolution studies, followed by whole-genome sequencing, were performed in the presence of the third-generation cephalosporin ceftazidime. Using this approach, we determined that exposure to increasing concentrations of ceftazidime selects high-level resistance in S. maltophilia through a novel mechanism: amino acid substitutions in SmeH, the transporter protein of the SmeGH RND efflux pump. The recreation of these mutants in a wild-type background demonstrated that, in addition to ceftazidime, the existence of these substitutions provides bacteria with cross-resistance to other beta-lactam drugs. This acquired resistance does not impose relevant fitness costs when bacteria grow in the absence of antibiotics. Structural prediction of both amino acid residues points that the observed resistance phenotype could be driven by changes in substrate access and recognition.
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Affiliation(s)
- Paula Blanco
- Centro Nacional de Biotecnología, CSIC, 28049, Madrid, Spain
| | - Fernando Corona
- Centro Nacional de Biotecnología, CSIC, 28049, Madrid, Spain
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Abstract
Bacteria of the genus Stenotrophomonas are found throughout the environment, in close association with soil, sewage, and plants. Stenotrophomonas maltophilia, the first member of this genus, is the predominant species, observed in soil, water, plants, animals, and humans. It is also an opportunistic pathogen associated with the increased number of infections in both humans and animals in recent years. In this article, we summarize all Stenotrophomonas species (mainly S. maltophilia) isolated from animals and food products of animal origin and further distinguish all isolates based on antimicrobial susceptibility and resistance phenotypes. The various mechanisms of both intrinsic and acquired antimicrobial resistance, which were mainly identified in S. maltophilia isolates of nosocomial infections, have been classified as follows: multidrug efflux pumps; resistance to β-lactams, aminoglycosides, quinolones, trimethoprim-sulfamethoxazole, and phenicols; and alteration of lipopolysaccharide and two-component regulatory systems. The dissemination, coselection, and persistence of resistance determinants among S. maltophilia isolates have also been elaborated.
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25
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Marathe NP, Janzon A, Kotsakis SD, Flach CF, Razavi M, Berglund F, Kristiansson E, Larsson DGJ. Functional metagenomics reveals a novel carbapenem-hydrolyzing mobile beta-lactamase from Indian river sediments contaminated with antibiotic production waste. ENVIRONMENT INTERNATIONAL 2018; 112:279-286. [PMID: 29316517 DOI: 10.1016/j.envint.2017.12.036] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 12/21/2017] [Accepted: 12/24/2017] [Indexed: 05/28/2023]
Abstract
Evolution has provided environmental bacteria with a plethora of genes that give resistance to antibiotic compounds. Under anthropogenic selection pressures, some of these genes are believed to be recruited over time into pathogens by horizontal gene transfer. River sediment polluted with fluoroquinolones and other drugs discharged from bulk drug production in India constitute an environment with unprecedented, long-term antibiotic selection pressures. It is therefore plausible that previously unknown resistance genes have evolved and/or are promoted here. In order to search for novel resistance genes, we therefore analyzed such river sediments by a functional metagenomics approach. DNA fragments providing resistance to different antibiotics in E. coli were sequenced using Sanger and PacBio RSII platforms. We recaptured the majority of known antibiotic resistance genes previously identified by open shot-gun metagenomics sequencing of the same samples. In addition, seven novel resistance gene candidates (six beta-lactamases and one amikacin resistance gene) were identified. Two class A beta-lactamases, blaRSA1 and blaRSA2, were phylogenetically close to clinically important ESBLs like blaGES, blaBEL and blaL2, and were further characterized for their substrate spectra. The blaRSA1 protein, encoded as an integron gene cassette, efficiently hydrolysed penicillins, first generation cephalosporins and cefotaxime, while blaRSA2 was an inducible class A beta-lactamase, capable of hydrolyzing carbapenems albeit with limited efficiency, similar to the L2 beta-lactamase from Stenotrophomonas maltophilia. All detected novel genes were associated with plasmid mobilization proteins, integrons, and/or other resistance genes, suggesting a potential for mobility. This study provides insight into a resistome shaped by an exceptionally strong and long-term antibiotic selection pressure. An improved knowledge of mobilized resistance factors in the external environment may make us better prepared for the resistance challenges that we may face in clinics in the future.
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Affiliation(s)
- Nachiket P Marathe
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 46 Gothenburg, Sweden
| | - Anders Janzon
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 46 Gothenburg, Sweden
| | - Stathis D Kotsakis
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 46 Gothenburg, Sweden
| | - Carl-Fredrik Flach
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 46 Gothenburg, Sweden
| | - Mohammad Razavi
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 46 Gothenburg, Sweden
| | - Fanny Berglund
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden; Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
| | - Erik Kristiansson
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden; Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
| | - D G Joakim Larsson
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 46 Gothenburg, Sweden.
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26
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Bernardini A, Martínez JL. Genome-wide analysis shows that RNase G plays a global role in the stability of mRNAs in Stenotrophomonas maltophilia. Sci Rep 2017; 7:16016. [PMID: 29167539 PMCID: PMC5700063 DOI: 10.1038/s41598-017-16091-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 11/07/2017] [Indexed: 11/28/2022] Open
Abstract
Gene expression is determined by critical processes such as RNA synthesis and degradation. Ribonucleases participate in the coordinated and differential decay of messenger RNAs. We describe a suitable method of normalization and calculation of mRNAs half-life values quantified by RNA-Seq. We determined the mRNA half-lives of more than 2000 genes in Stenotrophomonas maltophilia D457 and in an isogenic RNase G deficient mutant. Median half-lives were 2,74 and 3 min in the wild-type and the rng-deficient strain, respectively. The absence of RNase G resulted in an overall enhancement of mRNA half-life times, showing that many RNAs are targets of RNase G in S. maltophilia. Around 40 genes are likely to be regulated directly by RNase G since their half-lives were more than two-fold higher in the rng-deficient mutant. Gene length, GC content or expression levels did not correlate with mRNAs lifetimes, although groups of genes with different functions showed different RNA half-lives. Further, we predicted 1542 gene pairs to be part of the same operons in S. maltophilia. In contrast to what was described for other bacteria, our data indicate that RNase G has a global role in mRNA stability and consequently in the regulation of S. maltophilia gene expression.
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Affiliation(s)
| | - José L Martínez
- Centro Nacional de Biotecnología, CSIC, Darwin 3, 28049, Madrid, Spain.
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Calvopiña K, Hinchliffe P, Brem J, Heesom KJ, Johnson S, Cain R, Lohans CT, Fishwick CWG, Schofield CJ, Spencer J, Avison MB. Structural/mechanistic insights into the efficacy of nonclassical β-lactamase inhibitors against extensively drug resistantStenotrophomonas maltophiliaclinical isolates. Mol Microbiol 2017; 106:492-504. [DOI: 10.1111/mmi.13831] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2017] [Indexed: 01/23/2023]
Affiliation(s)
- Karina Calvopiña
- School of Cellular & Molecular Medicine; University of Bristol; Bristol UK
| | - Philip Hinchliffe
- School of Cellular & Molecular Medicine; University of Bristol; Bristol UK
| | - Jürgen Brem
- Department of Chemistry; University of Oxford; Oxford UK
| | | | - Samar Johnson
- School of Cellular & Molecular Medicine; University of Bristol; Bristol UK
| | - Ricky Cain
- School of Chemistry; University of Leeds; Leeds UK
| | | | | | | | - James Spencer
- School of Cellular & Molecular Medicine; University of Bristol; Bristol UK
| | - Matthew B. Avison
- School of Cellular & Molecular Medicine; University of Bristol; Bristol UK
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28
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Successful Treatment of Bloodstream Infection Due to Metallo-β-Lactamase-Producing Stenotrophomonas maltophilia in a Renal Transplant Patient. Antimicrob Agents Chemother 2016; 60:5130-4. [PMID: 27551008 DOI: 10.1128/aac.00264-16] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Stenotrophomonas maltophilia is an emerging multidrug-resistant (MDR) opportunistic pathogen for which new antibiotic options are urgently needed. We report our clinical experience treating a 19-year-old renal transplant recipient who developed prolonged bacteremia due to metallo-β-lactamase-producing S. maltophilia refractory to conventional treatment. The infection recurred despite a prolonged course of colistimethate sodium (colistin) but resolved with the use of a novel drug combination with clinical efficacy against the patient's S. maltophilia isolate.
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Sideromimic Modification of Lactivicin Dramatically Increases Potency against Extensively Drug-Resistant Stenotrophomonas maltophilia Clinical Isolates. Antimicrob Agents Chemother 2016; 60:4170-5. [PMID: 27139464 DOI: 10.1128/aac.00371-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 04/24/2016] [Indexed: 01/09/2023] Open
Abstract
Acetamido derivatives of the naturally antibacterial non-β-lactam lactivicin (LTV) have improved activity against their penicillin binding protein targets and reduced hydrolysis by β-lactamases, but penetration into Gram-negative bacteria is still relatively poor. Here we report that modification of the LTV lactone with a catechol-type siderophore increases potency 1,000-fold against Stenotrophomonas maltophilia, a species renowned for its insusceptibility to antimicrobials. The MIC90 of modified lactone compound 17 (LTV17) against a global collection of extensively drug-resistant clinical S. maltophilia isolates was 0.063 μg · ml(-1) Sideromimic modification does not reduce the ability of LTVs to induce production of the L1 and L2 β-lactamases in S. maltophilia and does not reduce the rate at which LTVs are hydrolyzed by L1 or L2. We conclude, therefore, that lactivicin modification with a siderophore known to be preferentially used by S. maltophilia substantially increases penetration via siderophore uptake. LTV17 has the potential to be developed as a novel antimicrobial for treatment of infections by S. maltophilia More generally, our work shows that sideromimic modification in a species-targeted manner might prove useful for the development of narrow-spectrum antimicrobials that have reduced collateral effects.
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30
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Proteomic analysis of outer membrane proteins and vesicles of a clinical isolate and a collection strain of Stenotrophomonas maltophilia. J Proteomics 2016; 142:122-9. [PMID: 27185551 DOI: 10.1016/j.jprot.2016.05.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 03/10/2016] [Accepted: 05/03/2016] [Indexed: 01/12/2023]
Abstract
UNLABELLED Stenotrophomonas maltophilia is a Gram-negative pathogen with emerging nosocomial incidence that displays a high genomic diversity, complicating the study of its pathogenicity, virulence and resistance factors. The interaction of bacterial pathogens with host cells is largely mediated by outer membrane proteins (OMPs). Indeed, several OMPs of Gram-negative bacteria have been recognized as important virulence factors and targets for host immune recognition or to be involved in mechanisms of resistance to antimicrobials. OMPs are also present in outer membrane vesicles (OMVs), which bacteria constitutively secrete to the extracellular milieu and are essential for bacterial survival and pathogenesis. Here, we report the characterization of the OMP and native OMV subproteomes of a clinical isolate (M30) and a collection strain (ATCC13637) of S. maltophilia. We had previously shown that the ATCC13637 strain has an attenuated phenotype in a zebrafish model of infection, as well as a distinct susceptibility profile against a panel of antimicrobials. The protein profiles of the OMP and OMV subproteomes of these two strains and their differences consequently point at pathogenesis, virulence or resistance proteins, such as two variants of the quorum-sensing factor Ax21 that are found to be highly abundant in the OMP fraction and exported to OMVs. BIOLOGICAL SIGNIFICANCE Stenotrophomonas maltophilia is rapidly climbing positions in the ranking of multidrug-resistant pathogens that are frequently isolated in hospital environments. Being an emerging human pathogen, the knowledge on the factors determining the pathogenicity, virulence and resistance traits of this microorganism is still scarce. Outer membrane proteins (OMPs) and vesicles (OMVs) are key elements for the interaction of Gram-negative bacteria with their environment -including the host-and have fundamental roles in both infection and resistance processes. The present study sets a first basis for a phenotype-dependent characterisation of the OMP subproteome of S. maltophilia and complements very recent work on the OMV subproteome of this species. The variability found among even two strains demonstrates once more that the analysis of genotypically and phenotypically distinct isolates under various conditions will be required before we can draw a significant picture of the OMP and OMV subproteomes of S. maltophilia.
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31
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Patil PP, Midha S, Kumar S, Patil PB. Genome Sequence of Type Strains of Genus Stenotrophomonas. Front Microbiol 2016; 7:309. [PMID: 27014232 PMCID: PMC4785145 DOI: 10.3389/fmicb.2016.00309] [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: 12/10/2015] [Accepted: 02/25/2016] [Indexed: 11/23/2022] Open
Abstract
Genomic resource of type strains and historically important strains of genus Stenotrophomonas allowed us to reveal the existence of 18 distinct species by applying modern phylogenomic criterions. Apart from Stenotrophomonas maltophilia, S. africana represents another species of clinical importance. Interestingly, Pseudomonas hibsicola, P. beteli, and S. pavani that are of plant origin are closer to S. maltophilia than the majority of the environmental isolates. The genus has an open pan-genome. By providing the case study on genes encoding metallo-β-lactamase and Clustered Regularly Interspaced Short Palindrome Repeats (CRISPR) regions, we have tried to show the importance of this genomic dataset in understanding its ecology.
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Affiliation(s)
- Prashant P Patil
- Bacterial Genomics and Evolution Laboratory, Council of Scientific and Industrial Research - Institute of Microbial Technology Chandigarh, India
| | - Samriti Midha
- Bacterial Genomics and Evolution Laboratory, Council of Scientific and Industrial Research - Institute of Microbial Technology Chandigarh, India
| | - Sanjeet Kumar
- Bacterial Genomics and Evolution Laboratory, Council of Scientific and Industrial Research - Institute of Microbial Technology Chandigarh, India
| | - Prabhu B Patil
- Bacterial Genomics and Evolution Laboratory, Council of Scientific and Industrial Research - Institute of Microbial Technology Chandigarh, India
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32
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In vitroantimicrobial activity of S-649266, a catechol-substituted siderophore cephalosporin, when tested against non-fermenting Gram-negative bacteria. J Antimicrob Chemother 2015; 71:670-7. [DOI: 10.1093/jac/dkv402] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 10/29/2015] [Indexed: 11/14/2022] Open
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33
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Abda EM, Krysciak D, Krohn-Molt I, Mamat U, Schmeisser C, Förstner KU, Schaible UE, Kohl TA, Nieman S, Streit WR. Phenotypic Heterogeneity Affects Stenotrophomonas maltophilia K279a Colony Morphotypes and β-Lactamase Expression. Front Microbiol 2015; 6:1373. [PMID: 26696982 PMCID: PMC4667094 DOI: 10.3389/fmicb.2015.01373] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 11/18/2015] [Indexed: 12/22/2022] Open
Abstract
Phenotypic heterogeneity at the cellular level in response to various stresses, e.g., antibiotic treatment has been reported for a number of bacteria. In a clonal population, cell-to-cell variation may result in phenotypic heterogeneity that is a mechanism to survive changing environments including antibiotic therapy. Stenotrophomonas maltophilia has been frequently isolated from cystic fibrosis patients, can cause numerous infections in other organs and tissues, and is difficult to treat due to antibiotic resistances. S. maltophilia K279a produces the L1 and L2 β-lactamases in response to β-lactam treatment. Here we report that the patient isolate S. maltophilia K279a diverges into cellular subpopulations with distinct but reversible morphotypes of small and big colonies when challenged with ampicillin. This observation is consistent with the formation of elongated chains of bacteria during exponential growth phase and the occurrence of mainly rod-shaped cells in liquid media. RNA-seq analysis of small versus big colonies revealed differential regulation of at least seven genes among the colony morphotypes. Among those, bla L1 and bla L2 were transcriptionally the most strongly upregulated genes. Promoter fusions of bla L1 and bla L2 genes indicated that expression of both genes is also subject to high levels of phenotypic heterogeneous expression on a single cell level. Additionally, the comE homolog was found to be differentially expressed in homogenously versus heterogeneously bla L2 expressing cells as identified by RNA-seq analysis. Overexpression of comE in S. maltophilia K279a reduced the level of cells that were in a bla L2-ON mode to 1% or lower. Taken together, our data provide strong evidence that S. maltophilia K279a populations develop phenotypic heterogeneity in an ampicillin challenged model. This cellular variability is triggered by regulation networks including bla L1, bla L2, and comE.
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Affiliation(s)
- Ebrahim M Abda
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek - University of Hamburg Hamburg, Germany
| | - Dagmar Krysciak
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek - University of Hamburg Hamburg, Germany
| | - Ines Krohn-Molt
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek - University of Hamburg Hamburg, Germany
| | - Uwe Mamat
- Priority Program Asthma and Allergy, Leibniz-Center for Medicine and Biosciences - Research Center Borstel Borstel, Germany
| | - Christel Schmeisser
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek - University of Hamburg Hamburg, Germany
| | - Konrad U Förstner
- Core Unit Systems Medicine, University of Würzburg Würzburg, Germany
| | - Ulrich E Schaible
- Priority Program Infections, Leibniz-Center for Medicine and Biosciences - Research Center Borstel Borstel, Germany
| | - Thomas A Kohl
- Priority Program Infections, Leibniz-Center for Medicine and Biosciences - Research Center Borstel Borstel, Germany
| | - Stefan Nieman
- Priority Program Infections, Leibniz-Center for Medicine and Biosciences - Research Center Borstel Borstel, Germany ; German Center for Infection Research Borstel, Germany
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek - University of Hamburg Hamburg, Germany
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Bernardini A, Corona F, Dias R, Sánchez MB, Martínez JL. The inactivation of RNase G reduces the Stenotrophomonas maltophilia susceptibility to quinolones by triggering the heat shock response. Front Microbiol 2015; 6:1068. [PMID: 26539164 PMCID: PMC4609926 DOI: 10.3389/fmicb.2015.01068] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 09/17/2015] [Indexed: 01/11/2023] Open
Abstract
Quinolone resistance is usually due to mutations in the genes encoding bacterial topoisomerases. However, different reports have shown that neither clinical quinolone resistant isolates nor in vitro obtained Stenotrophomonas maltophilia mutants present mutations in such genes. The mechanisms so far described consist on efflux pumps' overexpression. Our objective is to get information on novel mechanisms of S. maltophilia quinolone resistance. For this purpose, a transposon-insertion mutant library was obtained in S. maltophilia D457. One mutant presenting reduced susceptibility to nalidixic acid was selected. Inverse PCR showed that the inactivated gene encodes RNase G. Complementation of the mutant with wild-type RNase G allele restored the susceptibility to quinolones. Transcriptomic and real-time RT-PCR analyses showed that several genes encoding heat-shock response proteins were expressed at higher levels in the RNase defective mutant than in the wild-type strain. In agreement with this situation, heat-shock reduces the S. maltophilia susceptibility to quinolone. We can then conclude that the inactivation of the RNase G reduces the susceptibility of S. maltophilia to quinolones, most likely by regulating the expression of heat-shock response genes. Heat-shock induces a transient phenotype of quinolone resistance in S. maltophilia.
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Affiliation(s)
- Alejandra Bernardini
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas Madrid, Spain
| | - Fernando Corona
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas Madrid, Spain
| | - Ricardo Dias
- Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon Lisbon, Portugal
| | - Maria B Sánchez
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas Madrid, Spain
| | - Jose L Martínez
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas Madrid, Spain
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Youenou B, Favre-Bonté S, Bodilis J, Brothier E, Dubost A, Muller D, Nazaret S. Comparative Genomics of Environmental and Clinical Stenotrophomonas maltophilia Strains with Different Antibiotic Resistance Profiles. Genome Biol Evol 2015; 7:2484-505. [PMID: 26276674 PMCID: PMC4607518 DOI: 10.1093/gbe/evv161] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Stenotrophomonas maltophilia, a ubiquitous Gram-negative γ-proteobacterium, has emerged as an important opportunistic pathogen responsible for nosocomial infections. A major characteristic of clinical isolates is their high intrinsic or acquired antibiotic resistance level. The aim of this study was to decipher the genetic determinism of antibiotic resistance among strains from different origins (i.e., natural environment and clinical origin) showing various antibiotic resistance profiles. To this purpose, we selected three strains isolated from soil collected in France or Burkina Faso that showed contrasting antibiotic resistance profiles. After whole-genome sequencing, the phylogenetic relationships of these 3 strains and 11 strains with available genome sequences were determined. Results showed that a strain's phylogeny did not match their origin or antibiotic resistance profiles. Numerous antibiotic resistance coding genes and efflux pump operons were revealed by the genome analysis, with 57% of the identified genes not previously described. No major variation in the antibiotic resistance gene content was observed between strains irrespective of their origin and antibiotic resistance profiles. Although environmental strains generally carry as many multidrug resistant (MDR) efflux pumps as clinical strains, the absence of resistance-nodulation-division (RND) pumps (i.e., SmeABC) previously described to be specific to S. maltophilia was revealed in two environmental strains (BurA1 and PierC1). Furthermore the genome analysis of the environmental MDR strain BurA1 showed the absence of SmeABC but the presence of another putative MDR RND efflux pump, named EbyCAB on a genomic island probably acquired through horizontal gene transfer.
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Affiliation(s)
- Benjamin Youenou
- Université de Lyon, France; Research Group on Environmental Multi-Resistance and Efflux Pump, CNRS, Ecole Nationale Vétérinaire de Lyon, and Université Lyon 1, UMR 5557 Ecologie Microbienne, Villeurbanne, France
| | - Sabine Favre-Bonté
- Université de Lyon, France; Research Group on Environmental Multi-Resistance and Efflux Pump, CNRS, Ecole Nationale Vétérinaire de Lyon, and Université Lyon 1, UMR 5557 Ecologie Microbienne, Villeurbanne, France
| | - Josselin Bodilis
- EA4312 Laboratoire de Microbiologie Signaux et Microenvironnement, Université de Rouen, Mont-Saint-Aignan, France
| | - Elisabeth Brothier
- Université de Lyon, France; Research Group on Environmental Multi-Resistance and Efflux Pump, CNRS, Ecole Nationale Vétérinaire de Lyon, and Université Lyon 1, UMR 5557 Ecologie Microbienne, Villeurbanne, France
| | - Audrey Dubost
- Université de Lyon, France; Research Group on Environmental Multi-Resistance and Efflux Pump, CNRS, Ecole Nationale Vétérinaire de Lyon, and Université Lyon 1, UMR 5557 Ecologie Microbienne, Villeurbanne, France
| | - Daniel Muller
- Université de Lyon, France; Research Group on Environmental Multi-Resistance and Efflux Pump, CNRS, Ecole Nationale Vétérinaire de Lyon, and Université Lyon 1, UMR 5557 Ecologie Microbienne, Villeurbanne, France
| | - Sylvie Nazaret
- Université de Lyon, France; Research Group on Environmental Multi-Resistance and Efflux Pump, CNRS, Ecole Nationale Vétérinaire de Lyon, and Université Lyon 1, UMR 5557 Ecologie Microbienne, Villeurbanne, France
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Flores-Treviño S, Gutiérrez-Ferman JL, Morfín-Otero R, Rodríguez-Noriega E, Estrada-Rivadeneyra D, Rivas-Morales C, Llaca-Díaz JM, Camacho-Ortíz A, Mendoza-Olazarán S, Garza-González E. Stenotrophomonas maltophilia in Mexico: antimicrobial resistance, biofilm formation and clonal diversity. J Med Microbiol 2014; 63:1524-1530. [PMID: 25165124 DOI: 10.1099/jmm.0.074385-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Stenotrophomonas maltophilia is an important multidrug-resistant nosocomial pathogen associated with high mortality. Our aim was to examine antimicrobial susceptibility, biofilm production and clonal relatedness of clinical isolates of S. maltophilia. S. maltophilia isolates were collected between 2006 and 2013 from two tertiary care hospitals in Mexico. Antimicrobial susceptibility was evaluated by the broth microdilution method. PCR was used to determine the presence of β-lactamase genes L1 and L2. Biofilm formation was assessed with crystal violet staining. Clonal relatedness was determined by PFGE. Among the 119 collected S. maltophilia isolates, 73 (61.3%) were from the respiratory tract. Resistance levels exceeded 75% for imipenem, meropenem, ampicillin, aztreonam, gentamicin and tobramycin. Resistance to trimethoprim-sulfamethoxazole was 32.8%. L1 and L2 genes were detected in 77.1% (91/118) and 66.9% (79/118) of isolates, respectively. All S. maltophilia strains were able to produce biofilms. Strains were classified as weak (47.9%, 57/119), moderate (38.7%, 46/119), or strong (13.4%, 16/119) biofilm producers. A total of 89 distinct PFGE types were identified and 21.6% (22/102) of the isolates were distributed in nine clusters. This is the first study in Mexico to reveal characteristics of clinical isolates of S. maltophilia. Clonal diversity data indicate low cross-transmission of S. maltophilia in a hospital setting. The high antibiotic resistance underscores the need for continuous surveillance of S. maltophilia in hospital settings in Mexico.
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Affiliation(s)
- Samantha Flores-Treviño
- Servicio de Gastroenterología, Hospital Universitario Dr José Eleuterio González, Universidad Autónoma de Nuevo León, Av. Francisco I. Madero Pte. S/N y Av. Gonzalitos, Col. Mitras Centro, 64460 Monterrey, Nuevo León, Mexico
| | - Jessica Lizzeth Gutiérrez-Ferman
- Laboratorio de Química Analítica, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, México, Pedro de Alba SN, Col. Ciudad Universitaria, 66450 San Nicolás de los Garza, Nuevo León, Mexico
| | - Rayo Morfín-Otero
- Hospital Civil de Guadalajara, Fray Antonio Alcalde y el Instituto de Patología Infecciosa y Experimental, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Sierra Mojada 950, Col. Independencia, 44350 Guadalajara, Jalisco, Mexico
| | - Eduardo Rodríguez-Noriega
- Hospital Civil de Guadalajara, Fray Antonio Alcalde y el Instituto de Patología Infecciosa y Experimental, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Sierra Mojada 950, Col. Independencia, 44350 Guadalajara, Jalisco, Mexico
| | - Diego Estrada-Rivadeneyra
- Hospital Civil de Guadalajara, Fray Antonio Alcalde y el Instituto de Patología Infecciosa y Experimental, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Sierra Mojada 950, Col. Independencia, 44350 Guadalajara, Jalisco, Mexico
| | - Catalina Rivas-Morales
- Laboratorio de Química Analítica, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, México, Pedro de Alba SN, Col. Ciudad Universitaria, 66450 San Nicolás de los Garza, Nuevo León, Mexico
| | - Jorge M Llaca-Díaz
- Departamento de Patología Clínica, Hospital Universitario Dr José Eleuterio González, Universidad Autónoma de Nuevo León, Av. Francisco I. Madero Pte. S/N y José E. González, Col. Mitras Centro, CP 64460 Monterrey, Nuevo León, Mexico
| | - Adrián Camacho-Ortíz
- Servicio de Infectología, Hospital Universitario Dr José Eleuterio González, Universidad Autónoma de Nuevo León, Av. Francisco I. Madero Pte. S/N y José E. González, Col. Mitras Centro, CP 64460 Monterrey, Nuevo León, Mexico
| | - Soraya Mendoza-Olazarán
- Servicio de Gastroenterología, Hospital Universitario Dr José Eleuterio González, Universidad Autónoma de Nuevo León, Av. Francisco I. Madero Pte. S/N y Av. Gonzalitos, Col. Mitras Centro, 64460 Monterrey, Nuevo León, Mexico
| | - Elvira Garza-González
- Departamento de Patología Clínica, Hospital Universitario Dr José Eleuterio González, Universidad Autónoma de Nuevo León, Av. Francisco I. Madero Pte. S/N y José E. González, Col. Mitras Centro, CP 64460 Monterrey, Nuevo León, Mexico.,Servicio de Gastroenterología, Hospital Universitario Dr José Eleuterio González, Universidad Autónoma de Nuevo León, Av. Francisco I. Madero Pte. S/N y Av. Gonzalitos, Col. Mitras Centro, 64460 Monterrey, Nuevo León, Mexico
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Alexander EL, Satlin MJ, Gamaletsou MN, Sipsas NV, Walsh TJ. Worldwide challenges of multidrug-resistant bacteria in patients with hematologic malignancies. Int J Hematol Oncol 2013. [DOI: 10.2217/ijh.13.46] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
SUMMARY The emergence of infections due to multidrug-resistant (MDR) bacteria poses a major public health threat to all patients, but patients with hematologic malignancies are especially at risk. A common thread across all classes of bacteria is that increased reliance on and usage of broad-spectrum antibacterial agents, combined with the intrinsic ability of bacteria to develop and transmit resistance-conferring mutations, has led to the widespread dissemination of MDR organisms. In this article, we summarize the most worrisome MDR bacteria, assess their clinical impact on patients with hematologic malignancies and outline measures that are required to mitigate this impact.
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Affiliation(s)
| | - Michael J Satlin
- Division of Infectious Diseases, Weill Cornell Medical Center, New York, NY, USA
- Transplantation–Oncology Infectious Diseases Program, Department of Medicine, Weill Cornell Medical Center, New York, NY, USA
| | - Maria N Gamaletsou
- University of Athens School of Medicine & Laikon Hospital, Athens, Greece
| | - Nikolaos V Sipsas
- University of Athens School of Medicine & Laikon Hospital, Athens, Greece
| | - Thomas J Walsh
- Department of Pediatrics, Weill Cornell Medical Center, New York, NY, USA
- Department of Microbiology & Immunology, Weill Cornell Medical Center, New York, NY, USA
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Verma D, Jacobs DJ, Livesay DR. Variations within class-A β-lactamase physiochemical properties reflect evolutionary and environmental patterns, but not antibiotic specificity. PLoS Comput Biol 2013; 9:e1003155. [PMID: 23874193 PMCID: PMC3715408 DOI: 10.1371/journal.pcbi.1003155] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 06/10/2013] [Indexed: 11/19/2022] Open
Abstract
The bacterial enzyme β-lactamase hydrolyzes the β-lactam ring of penicillin and chemically related antibiotics, rendering them ineffective. Due to rampant antibiotic overuse, the enzyme is evolving new resistance activities at an alarming rate. Related, the enzyme's global physiochemical properties exhibit various amounts of conservation and variability across the family. To that end, we characterize the extent of property conservation within twelve different class-A β-lactamases, and conclusively establish that the systematic variations therein parallel their evolutionary history. Large and systematic differences within electrostatic potential maps and pairwise residue-to-residue couplings are observed across the protein, which robustly reflect phylogenetic outgroups. Other properties are more conserved (such as residue pKa values, electrostatic networks, and backbone flexibility), yet they also have systematic variations that parallel the phylogeny in a statistically significant way. Similarly, the above properties also parallel the environmental condition of the bacteria they are from in a statistically significant way. However, it is interesting and surprising that the only one of the global properties (protein charge) parallels the functional specificity patterns; meaning antibiotic resistance activities are not significantly constraining the global physiochemical properties. Rather, extended spectrum activities can emerge from the background of nearly any set of electrostatic and dynamic properties.
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Affiliation(s)
- Deeptak Verma
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
| | - Donald J. Jacobs
- Department of Physics and Optical Science, University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
| | - Dennis R. Livesay
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
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Abstract
β-Lactamases can be named on the basis of molecular characteristics or functional properties. Molecular classes A, B, C, and D define an enzyme according to amino acid sequence and conserved motifs. Functional groups 1, 2, and 3 are used to assign a clinically useful description to a family of enzymes, with subgroups designated according to substrate and inhibitor profiles. In addition, other designations are used to define the functionality of specific subgroups, such as extended-spectrum β-lactamases, or ESBLs, and inhibitor-resistant TEM, or IRT, β-lactamases. None of these systems provides an unambiguous description of this versatile set of enzymes. A proposed classification system involving microbiological, molecular, and biochemical properties is described, based on the traditional classes A, B, C, and D and functional groups 1, 2, and 3 designations.
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Affiliation(s)
- Karen Bush
- Department of Molecular and Cellular Biochemistry, Indiana University Bloomington, Simon Hall 102B, 212 S. Hawthorne Dr., Bloomington, IN, 47405, USA.
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40
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Van Oudenhove L, De Vriendt K, Van Beeumen J, Mercuri PS, Devreese B. Differential proteomic analysis of the response of Stenotrophomonas maltophilia to imipenem. Appl Microbiol Biotechnol 2012; 95:717-33. [DOI: 10.1007/s00253-012-4167-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 05/09/2012] [Accepted: 05/10/2012] [Indexed: 11/28/2022]
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41
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Araoka H, Fujii T, Izutsu K, Kimura M, Nishida A, Ishiwata K, Nakano N, Tsuji M, Yamamoto H, Asano-Mori Y, Uchida N, Wake A, Taniguchi S, Yoneyama A. Rapidly progressive fatal hemorrhagic pneumonia caused by Stenotrophomonas maltophilia in hematologic malignancy. Transpl Infect Dis 2012; 14:355-63. [PMID: 22283869 DOI: 10.1111/j.1399-3062.2011.00710.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2011] [Revised: 10/06/2011] [Accepted: 10/19/2011] [Indexed: 11/27/2022]
Abstract
BACKGROUND Pneumonia caused by Stenotrophomonas maltophilia is rare, but can be lethal in severely immunocompromised patients. However, its clinical course remains unclear. PATIENTS AND METHODS Patients with pneumonia caused by S. maltophilia in Toranomon Hospital (890 beds, Tokyo, Japan) were reviewed retrospectively between April 2006 and March 2010. RESULTS During the study period, 10 cases of S. maltophilia pneumonia were identified. Seven patients had acute myeloid leukemia, 2 had myelodysplastic syndrome, and 1 had malignant lymphoma. All patients developed symptoms after allogeneic hematopoietic stem cell transplantation (HSCT). Five patients received first cord blood transplantation (CBT), 4 patients received second CBT, and 1 patient received first peripheral blood stem cell transplantation (PBSCT). The overall incidence of S. maltophilia pneumonia among 508 patients who received HSCT during the period was 2.0%. The incidence was 0% (0/95) in patients after bone marrow transplantation, 0.8% (1/133) after PBSCT, and 3.2% (9/279) after CBT. Pneumonia developed a median of 13.5 days (range, 6-40) after transplantation. At onset, the median white blood cell count was 10/μL (range, 10-1900), and the median neutrophil count was 0/μL (range, 0-1720). In all patients, S. maltophilia bacteremia developed with bloody sputum or hemoptysis. The 28-day mortality rate was 100%; the median survival after onset of pneumonia was 2 days (range, 1-10). CONCLUSIONS Hemorrhagic S. maltophilia pneumonia rapidly progresses and is fatal in patients with hematologic malignancy. Attention should be particularly paid to the neutropenic phase early after HSCT or prolonged neutropenia due to engraftment failure. A prompt trimethoprim-sulfamethoxazole-based multidrug combination regimen should be considered to rescue suspected cases of S. maltophilia pneumonia in these severely immunosuppressed patients.
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Affiliation(s)
- H Araoka
- Department of Infectious Diseases, Toranomon Hospital, Tokyo, Japan.
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Abstract
Stenotrophomonas maltophilia is an emerging multidrug-resistant global opportunistic pathogen. The increasing incidence of nosocomial and community-acquired S. maltophilia infections is of particular concern for immunocompromised individuals, as this bacterial pathogen is associated with a significant fatality/case ratio. S. maltophilia is an environmental bacterium found in aqueous habitats, including plant rhizospheres, animals, foods, and water sources. Infections of S. maltophilia can occur in a range of organs and tissues; the organism is commonly found in respiratory tract infections. This review summarizes the current literature and presents S. maltophilia as an organism with various molecular mechanisms used for colonization and infection. S. maltophilia can be recovered from polymicrobial infections, most notably from the respiratory tract of cystic fibrosis patients, as a cocolonizer with Pseudomonas aeruginosa. Recent evidence of cell-cell communication between these pathogens has implications for the development of novel pharmacological therapies. Animal models of S. maltophilia infection have provided useful information about the type of host immune response induced by this opportunistic pathogen. Current and emerging treatments for patients infected with S. maltophilia are discussed.
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Affiliation(s)
- Joanna S Brooke
- Department of Biological Sciences, DePaul University, Chicago, Illinois, USA.
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Al-Hamad A, Burnie J, Upton M. Enhancement of antibiotic susceptibility ofStenotrophomonas maltophiliausing a polyclonal antibody developed against an ABC multidrug efflux pump. Can J Microbiol 2011; 57:820-8. [DOI: 10.1139/w11-076] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Stenotrophomonas maltophilia is an emerging nosocomial pathogen capable of causing healthcare-associated infections, including pneumonia and bacteremia. Intrinsic resistance in S. maltophilia is exhibited towards many broad-spectrum antibiotics, and treatment recommendations are controversial. One of the major causes of antimicrobial resistance is attributed to a robust array of efflux pumps that extrude drug compounds from the cell. Using checkerboard and growth kinetic assays, we evaluated the in vitro activity of a polyclonal antibody raised against an ATP-binding cassette efflux protein in S. maltophilia. Six clinical strains of S. maltophilia and one type strain were challenged with co-trimoxazole, ticarcillin–clavulanate, and ciprofloxacin, alone and in combination with antibody. One clinical strain was tested by growth curve experiments for each antibiotic–antibody combination. The use of antibody resulted in significantly increased susceptibility in 71.4% (15/21) of treatments tested, with 33.3% displaying synergy and 38.1% an additive effect. In growth kinetic studies, synergy was obtained for each antibiotic–antibody combination. Thus, the use of antibody raised against multidrug efflux pumps for the treatment of multidrug-resistant organisms warrants further investigation. Antibody targeting substrate recognition sites, or other functionally important epitopes, may lead to inhibition of multiple efflux pumps that share the same substrate and is an attractive area that should be explored.
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Affiliation(s)
- Arif Al-Hamad
- Medical Microbiology, School of Medicine, University of Manchester, 2nd Floor Clinical Sciences Building, Manchester Royal Infirmary, Manchester M13 9WL, UK
- Divisions of Clinical Microbiology and Infection Prevention and Control, Qatif Central Hospital, P.O. Box 18476, Qatif 31911, Saudi Arabia
| | - James Burnie
- Medical Microbiology, School of Medicine, University of Manchester, 2nd Floor Clinical Sciences Building, Manchester Royal Infirmary, Manchester M13 9WL, UK
| | - Mathew Upton
- Medical Microbiology, School of Medicine, University of Manchester, 2nd Floor Clinical Sciences Building, Manchester Royal Infirmary, Manchester M13 9WL, UK
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Looney WJ, Narita M, Mühlemann K. Stenotrophomonas maltophilia: an emerging opportunist human pathogen. THE LANCET. INFECTIOUS DISEASES 2009; 9:312-23. [PMID: 19393961 DOI: 10.1016/s1473-3099(09)70083-0] [Citation(s) in RCA: 346] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Stenotrophomonas maltophilia has emerged as an important opportunistic pathogen in the debilitated host. S maltophilia is not an inherently virulent pathogen, but its ability to colonise respiratory-tract epithelial cells and surfaces of medical devices makes it a ready coloniser of hospitalised patients. S maltophilia can cause blood-stream infections and pneumonia with considerable morbidity in immunosuppressed patients. Management of infection is hampered by high-level intrinsic resistance to many antibiotic classes and the increasing occurrence of acquired resistance to the first-line drug co-trimoxazole. Prevention of acquisition and infection depends upon the application of modern infection-control practices, with emphasis on the control of antibiotic use and environmental reservoirs.
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Affiliation(s)
- W John Looney
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
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Hu RM, Chiang KH, Chang YC, Yang TC. Characterization of the charge variants of L2 beta-lactamase in Stenotrophomonas maltophilia. J Med Microbiol 2009; 58:318-321. [PMID: 19208880 DOI: 10.1099/jmm.0.000380-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Stenotrophomonas maltophilia KH has two acid beta-lactamases with isoelectric points (pIs) of 4.6 and 5.4, and several basic beta-lactamases (pIs >7.0) that produce a ladder-shaped pattern by IEF. An isogenic L2 mutant, KHL2(xylE), was constructed by gene replacement. From IEF and native PAGE zymograms of strains KH and KHL2(xylE), it was demonstrated that the basic beta-lactamases and the acid beta-lactamase with pI 5.4 are encoded by the same L2 gene and that the active types of these L2 charge variants were dependent on the buffer pH. The beta-lactamase activities of these L2 charge variants in phosphate buffer at pH 7.0 and 8.0 were 1075+/-29 and 1114+/-81 U mg(-1), respectively. These results indicate that L2 charge variants give S. maltophilia a better chance of adapting and surviving in response to changes in the environment.
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Affiliation(s)
- Rouh-Mei Hu
- Department of Biotechnology and Bioinformatics, Asia University, Taichung 413, Taiwan, ROC
| | - Kai-Hung Chiang
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung 404, Taiwan, ROC
| | - Yi-Chih Chang
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung 404, Taiwan, ROC
| | - Tsuey-Ching Yang
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung 404, Taiwan, ROC
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Salsbury FR, Crowder MW, Kingsmore SF, Huntley JJA. Molecular dynamic simulations of the metallo-beta-lactamase from Bacteroides fragilis in the presence and absence of a tight-binding inhibitor. J Mol Model 2008; 15:133-45. [PMID: 19039608 DOI: 10.1007/s00894-008-0410-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2008] [Accepted: 07/19/2008] [Indexed: 11/28/2022]
Abstract
The beta-lactam-based antibiotics are among the most prescribed and effective antibacterial agents. Widespread use of these antibiotics, however, has created tremendous pressure for the emergence of resistance mechanisms in bacteria. The most common cause of antibiotic resistance is bacterial production of actamases that efficiently degrade antibiotics. The metallo-beta-lactamases are of particular clinical concern due to their transference between bacterial strains. We used molecular dynamics (MD) simulations to further study the conformational changes that occur due to binding of an inhibitor to the dicanzinc metallo-beta-lactamase from Bacteroides fragilis. Our studies confirm previous findings that the major flap is a major source of plasticity within the active site, therefore its dynamic response should be considered in drug development. However, our results also suggest the need for care in using MD simulations in evaluating loop mobility, both due to relaxation times and to the need to accurately model the zinc active site. Our study also reveals two new robust responses to ligand binding. First, there are specific localized changes in the zinc active site--a local loop flip--due to ligand intercalation that may be critical to the function of this enzyme. Second, inhibitor binding perturbs the dynamics throughout the protein, without otherwise perturbing the enzyme structure. These dynamic perturbations radiate outward from the active site and their existence suggests that long-range communication and dynamics may be important in the activity of this enzyme.
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Affiliation(s)
- Freddie R Salsbury
- Department of Physics, Wake Forest University, Winston Salem, NC 27109, USA.
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Sec- and Tat-dependent translocation of beta-lactamases across the Escherichia coli inner membrane. Antimicrob Agents Chemother 2008; 53:242-8. [PMID: 18981261 DOI: 10.1128/aac.00642-08] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
beta-Lactamases represent the major resistance mechanism of gram-negative bacteria against beta-lactam antibiotics. The amino acid sequences of these proteins vary widely, but all are located in the periplasm of bacteria. In this study, we investigated the translocation mechanism of representative beta-lactamases in an Escherichia coli model. N-terminal signal sequence analyses, antibiotic activity assay, and direct measurement of translocation of a green fluorescent protein (GFP) reporter fused to beta-lactamases revealed that most were exported via the Sec pathway. However, the Stenotrophomonas maltophilia L2 beta-lactamase was exported via the E. coli Tat translocase, while the S. maltophilia L1 beta-lactamase was Sec dependent. These results show the possible Tat-dependent translocation of beta-lactamases in the E. coli model system. In addition, the mutation of the cytoskeleton-encoding gene mreB, which may be involved in the spatial organization of penicillin-binding proteins, decreased the MIC of beta-lactams for beta-lactamase-producing E. coli. These findings provide new knowledge about beta-lactamase translocation, a putative new target for addressing beta-lactamase-mediated resistance.
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48
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Lavigne JP, Gaillard JB, Bourg G, Tichit C, Lecaillon E, Sotto A. Étude de souches de Stenotrophomonas maltophilia sécrétrices de BLSE : détection de CTX-M et étude de la virulence. ACTA ACUST UNITED AC 2008; 56:447-53. [DOI: 10.1016/j.patbio.2008.07.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2008] [Accepted: 07/03/2008] [Indexed: 11/29/2022]
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Falagas ME, Valkimadi PE, Huang YT, Matthaiou DK, Hsueh PR. Therapeutic options for Stenotrophomonas maltophilia infections beyond co-trimoxazole: a systematic review. J Antimicrob Chemother 2008; 62:889-94. [PMID: 18662945 DOI: 10.1093/jac/dkn301] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Stenotrophomonas maltophilia has emerged as an important opportunistic pathogen, causing infections whose management is often problematic due to its inherent resistance to many antibiotics, making co-trimoxazole the main therapeutic option. However, there are cases in which either due to antimicrobial resistance or allergic reactions and intolerance to co-trimoxazole this antibiotic cannot be administered. We sought to evaluate the available clinical evidence regarding potentially effective alternative antibiotics for the treatment of S. maltophilia infections. METHODS The literature search was performed in the PubMed and Scopus databases. The search string used was 'Stenotrophomonas maltophilia OR Xanthomonas maltophilia'. RESULTS Thirty-one case reports and 5 case series were retrieved including a total of 49 patients with a variety of infections. Twenty of 49 cases (40.8%) were treated with ciprofloxacin as monotherapy or in combination with other antibiotics; 12 of 49 cases (24.5%) were treated with ceftriaxone- or ceftazidime-based regimens; and 6 of 49 cases (12.2%) were treated with ticarcillin- or ticarcillin/clavulanate-based regimens. The cure or improvement rates were 18 cases (90%), 8 (75%) and 4 (66.7%), respectively. The remaining 11 patients received various antimicrobials including aminoglycoside-based regimens, carbapenems, levofloxacin, chloramphenicol, aztreonam, minocycline and other beta-lactams. CONCLUSIONS The limited available data suggest that ciprofloxacin, ceftazidime or ceftriaxone, and ticarcillin/clavulanate, alone or in combination with other antibiotics, may be considered as alternative options beyond co-trimoxazole.
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Safdar A, Rolston KV. Stenotrophomonas maltophilia: changing spectrum of a serious bacterial pathogen in patients with cancer. Clin Infect Dis 2008; 45:1602-9. [PMID: 18190323 DOI: 10.1086/522998] [Citation(s) in RCA: 142] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Stenotrophomonas maltophilia colonization/infection in patients with cancer has significantly increased over the past 2 decades. Patients with prolonged neutropenia, exposure to broad-spectrum antibiotics, and those requiring mechanical ventilation have higher risk of infection. These micro-organisms are intrinsically resistant to carbapenems, and exposure to these agents has been linked to selection of S. maltophilia. Recently, these infections are being documented in patients without traditional risk factors. The spectrum of infection includes bacteremia, catheter-related infection, pneumonia, complicated biliary and urinary tract infection, and skin and skin-structure infection. Trimethoprim-sulfamethoxazole is the therapeutic agent of choice, but resistance is increasingly being reported. Susceptibility to alternative agents is unpredictable. Combination therapy and alternative routes of drug administration, such as aerosolized aminoglycoside, might be necessary. New insights into the mechanisms of drug resistance might lead to identification of new target sites. Agents that improve outer-membrane permeability and broad-spectrum beta-lactamase inhibitors may favorably impact difficult-to-treat (i.e., multidrug resistant) S. maltophilia infections.
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Affiliation(s)
- Amar Safdar
- Dept. of Infectious Diseases, Infection Control, and Employee Health, 402, The M. D. Anderson Cancer Center, University of Texas, 1515 Holcombe Blvd., Houston, TX 77030, USA.
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