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Genomic surveillance of Pseudomonas aeruginosa in the Philippines, 2013-2014. Western Pac Surveill Response J 2021; 12:4-18. [PMID: 34540307 PMCID: PMC8421739 DOI: 10.5365/wpsar.2020.11.1.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that often causes nosocomial infections resistant to treatment. Rates of antimicrobial resistance (AMR) are increasing, as are rates of multidrug-resistant (MDR) and possible extensively drug-resistant (XDR) infections. Our objective was to characterize the molecular epidemiology and AMR mechanisms of this pathogen. We sequenced the whole genome for each of 176 P. aeruginosa isolates collected in the Philippines in 2013–2014; derived the multilocus sequence type (MLST), presence of AMR determinants and relatedness between isolates; and determined concordance between phenotypic and genotypic resistance. Carbapenem resistance was associated with loss of function of the OprD porin and acquisition of the metallo-β-lactamase (MBL) gene blaVIM. Concordance between phenotypic and genotypic resistance was 93.27% overall for six antibiotics in three classes, but varied among aminoglycosides. The population of P. aeruginosa was diverse, with clonal expansions of XDR genomes belonging to MLSTs ST235, ST244, ST309 and ST773. We found evidence of persistence or reintroduction of the predominant clone ST235 in one hospital, and of transfer between hospitals. Most of the ST235 genomes formed a distinct lineage from global genomes, thus raising the possibility that they may be unique to the Philippines. In addition, long-read sequencing of one representative XDR ST235 isolate identified an integron carrying multiple resistance genes (including blaVIM-2), with differences in gene composition and synteny from the P. aeruginosa class 1 integrons described previously. The survey bridges the gap in genomic data from the Western Pacific Region and will be useful for ongoing surveillance; it also highlights the importance of curtailing the spread of ST235 within the Philippines.
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Hajikhani B, Goudarzi M, Kakavandi S, Amini S, Zamani S, van Belkum A, Goudarzi H, Dadashi M. The global prevalence of fusidic acid resistance in clinical isolates of Staphylococcus aureus: a systematic review and meta-analysis. Antimicrob Resist Infect Control 2021; 10:75. [PMID: 33933162 PMCID: PMC8088720 DOI: 10.1186/s13756-021-00943-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 04/23/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND AND AIM Staphylococcus aureus (S. aureus) is one of the most common pathogens causing nosocomial and community-acquired infections with high morbidity and mortality rates. Fusidic acid has been increasingly used for the treatment of infections due to methicillin-susceptible S. aureus (MSSA) and methicillin-resistant S. aureus (MRSA). The present study aimed to determine the precise prevalence of fusidic acid resistant MRSA (FRMRSA), fusidic acid resistant MSSA (FRMSSA), and total fusidic acid resistant S. aureus (FRSA) on a global scale. METHODS Several international databases including Medline, Embase, and the Web of Sciences were searched (2000-2020) to discern studies addressing the prevalence of FRSA, FRMRSA, and FRMSSA. STATA (version14) software was used to interpret the data. RESULTS Of the 1446 records identified from the databases, 215 studies fulfilled the eligibility criteria for the detection of FRSA (208 studies), FRMRSA (143 studies), and FRMSSA (71 studies). The analyses manifested that the global prevalence of FRSA, FRMRSA, and FRMSSA was 0.5%, 2.6% and 6.7%, respectively. CONCLUSION This meta-analysis describes an increasing incidence of FRSA, FRMSSA, and FRMRSA. These results indicate the need for prudent prescription of fusidic acid to stop or diminish the incidence of fusidic acid resistance as well as the development of strategies for monitoring the efficacy of fusidic acid use.
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Affiliation(s)
- Bahareh Hajikhani
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehdi Goudarzi
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sareh Kakavandi
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sana Amini
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Samira Zamani
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Alex van Belkum
- Data Analytics Unit, bioMérieux 3, Route de Port Michaud, La Balme Les Grottes, France
| | - Hossein Goudarzi
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoud Dadashi
- Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran.
- Non-Communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran.
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Detection of diverse carbapenem and multidrug resistance genes and high-risk strain types among carbapenem non-susceptible clinical isolates of target gram-negative bacteria in Kenya. PLoS One 2021; 16:e0246937. [PMID: 33617559 PMCID: PMC7899328 DOI: 10.1371/journal.pone.0246937] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 01/29/2021] [Indexed: 11/19/2022] Open
Abstract
Carbapenem-resistant gram-negative bacteria are an increasingly significant clinical threat globally. This risk may be underestimated in Kenya as only four carbapenemase genes in three bacterial species have been described. The study aimed to understand the antibiotic resistance profiles, genes, sequence types, and distribution of carbapenem-resistant gram-negative bacteria from patients in six hospitals across five Kenyan counties by bacterial culture, antibiotic susceptibility testing, and whole-genome sequence analysis. Forty-eight, non-duplicate, carbapenem non-susceptible, clinical isolates were identified across the five counties (predominantly in Nairobi and Kisii): twenty-seven Acinetobacter baumannii, fourteen Pseudomonas aeruginosa, three Escherichia coli, two Enterobacter cloacae, and two Klebsiella pneumoniae. All isolates were non-susceptible to β-lactam drugs with variable susceptibility to tigecycline (66%), minocycline (52.9%), tetracycline (29.4%), and levofloxacin (22.9%). Thirteen P. aeruginosa isolates were resistant to all antibiotics tested. Eleven carbapenemase genes were identified: blaNDM-1, blaOXA-23, -58, -66, -69, and -91 in A. baumannii (STs 1, 2, 164 and a novel ST1475), blaNDM-1 in E. cloacae (STs 25,182), blaNDM-1, blaVIM-1and -6, blaOXA-50 in P. aeruginosa (STs 316, 357, 654, and1203), blaOXA-181, blaNDM-1 in K. pneumoniae (STs 147 and 219), and blaNDM-5 in E. coli (ST164). Five A. baumannii isolates had two carbapenemases, blaNDM-1, and either blaOXA-23 (4) or blaOXA-58 (1). AmpC genes were detected in A. baumannii (blaADC-25), E. cloacae (blaDHA-1 and blaACT-6, 16), and K. pneumoniae (blaCMY). Significant multiple-drug resistant genes were the pan-aminoglycoside resistance16srRNA methyltransferase armA, rmtB, rmtC, and rmtF genes. This study is the first to report blaOXA-420, -58, -181, VIM-6, and blaNDM-5 in Kenyan isolates. High-risk STs of A. baumannii (ST1475, ST2), E. cloacae ST182, K. pneumoniae ST147, P. aeruginosa (ST357, 654), and E. coli ST167, ST648 were identified which present considerable therapeutic danger. The study recommends urgent carbapenem use regulation and containment of high-risk carbapenem-resistant bacteria.
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Karampatakis T, Antachopoulos C, Tsakris A, Roilides E. Molecular epidemiology of carbapenem-resistant Pseudomonas aeruginosa in an endemic area: comparison with global data. Eur J Clin Microbiol Infect Dis 2018; 37:1211-1220. [PMID: 29644540 DOI: 10.1007/s10096-018-3244-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 03/26/2018] [Indexed: 12/15/2022]
Abstract
Carbapenem-resistant Pseudomonas aeruginosa (CRPA) is an endemic problem in certain countries including Greece. CRPA and multidrug-resistant P. aeruginosa (MDRPA) firstly emerged in our region during the 80s, right after the launch of imipenem and meropenem as therapeutic agents against P. aeruginosa infections. The role of outer membrane protein (Opr) inactivation has been known to contribute to imipenem resistance since many years, while efflux overexpression systems have been mainly associated with meropenem resistance. Among carbapenemases, metallo-β-lactamases (MBL) and mostly Verona integron-mediated (VIM) MBL's have played the most crucial role in CRPA emergence. VIM-2 and VIM-4 producing CRPA, usually belonging to clonal complexes (CC) 111 and 235 respectively, have most frequently been isolated. BlaVIM-2 and blaVIM-4 are usually associated with a class 1 integron. VIM-17 also has appeared in Greece. On the other hand, other VIM subtypes detected in a global level, such as VIM-3, VIM-5, VIM-6, VIM-7, VIM-11, VIM-14, VIM-15, VIM-16 and VIM-18 have not yet emerged in Greece. However, new VIM subtypes will probably emerge in the future. In addition, MBL carbapenemases other than VIM, detected worldwide have not yet appeared. A single CRPA isolate producing KPC has emerged in our region several years ago. The study of the molecular basis of Opr deficiency and efflux overexpression remains a challenge for the future. In this article, we review the molecular epidemiology of CRPA in an endemic area, compared to global data.
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Affiliation(s)
- Theodoros Karampatakis
- Infectious Diseases Unit, 3rd Department of Pediatrics, Medical Faculty, School of Health Sciences, Hippokration General Hospital, Konstantinoupoleos 49, GR-546 42, Thessaloniki, Greece
| | - Charalampos Antachopoulos
- Infectious Diseases Unit, 3rd Department of Pediatrics, Medical Faculty, School of Health Sciences, Hippokration General Hospital, Konstantinoupoleos 49, GR-546 42, Thessaloniki, Greece
| | - Athanassios Tsakris
- Microbiology Department, National and Kapodistrian University School of Medicine, Athens, Greece
| | - Emmanuel Roilides
- Infectious Diseases Unit, 3rd Department of Pediatrics, Medical Faculty, School of Health Sciences, Hippokration General Hospital, Konstantinoupoleos 49, GR-546 42, Thessaloniki, Greece.
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Wright LL, Turton JF, Hopkins KL, Livermore DM, Woodford N. Genetic environment of metallo-β-lactamase genes in Pseudomonas aeruginosa isolates from the UK. J Antimicrob Chemother 2015; 70:3250-8. [PMID: 26318194 DOI: 10.1093/jac/dkv263] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 07/29/2015] [Indexed: 01/01/2023] Open
Abstract
OBJECTIVES We sought to characterize the genetic environment of blaVIM and blaIMP genes in Pseudomonas aeruginosa isolates from the UK; these included members of six previously described prevalent complexes, A-F, which correspond to international 'high-risk clones', along with diverse strains. METHODS Metallo-β-lactamase (MBL)-encoding class 1 integrons were amplified by PCR from 218 P. aeruginosa isolates producing VIM-type (n = 196) or IMP-type (n = 22) enzymes, referred from UK hospital laboratories between 2003 and 2012. The variable regions of selected integrons were sequenced using a primer walking method. RESULTS One-hundred-and-nineteen isolates had an MBL-encoding integron with the 3' conserved sequence (3'CS), 65 had Tn5090-like 3' regions and 17 had the sul1 gene, but lacked the qacEΔ1 gene; the 3' region could not be amplified using any primer combinations for the remaining 17 isolates. Six integron profiles were each seen in more than five isolates. Predominant integron types were seen amongst isolates belonging to STs 111, 233, 654/964 and 773 (complexes A, C, D and F, respectively), whereas diverse integron profiles were seen in isolates belonging to ST235 (complex B) and ST357 (complex E). CONCLUSIONS In UK P. aeruginosa isolates, MBL genes occur in diverse class 1 integron structures, though commonly with 3' regions containing the classical 3'CS or Tn5090-like regions. Four of the six main clonal complexes, referred from multiple laboratories, carried a predominant integron type, whereas the remaining two had more diverse types.
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Affiliation(s)
- Laura L Wright
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK Norwich Medical School, University of East Anglia, Norwich, Norfolk NR4 7TJ, UK
| | - Jane F Turton
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Katie L Hopkins
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - David M Livermore
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK Norwich Medical School, University of East Anglia, Norwich, Norfolk NR4 7TJ, UK
| | - Neil Woodford
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
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Hong DJ, Bae IK, Jang IH, Jeong SH, Kang HK, Lee K. Epidemiology and Characteristics of Metallo-β-Lactamase-Producing Pseudomonas aeruginosa. Infect Chemother 2015; 47:81-97. [PMID: 26157586 PMCID: PMC4495280 DOI: 10.3947/ic.2015.47.2.81] [Citation(s) in RCA: 160] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Indexed: 12/18/2022] Open
Abstract
Metallo-β-lactamase-producing Pseudomonas aeruginosa (MPPA) is an important nosocomial pathogen that shows resistance to all β-lactam antibiotics except monobactams. There are various types of metallo-β-lactamases (MBLs) in carbapenem-resistant P. aeruginosa including Imipenemase (IMP), Verona integron-encoded metallo-β-lactamase (VIM), Sao Paulo metallo-β-lactamase (SPM), Germany imipenemase (GIM), New Delhi metallo-β-lactamase (NDM), Florence imipenemase (FIM). Each MBL gene is located on specific genetic elements including integrons, transposons, plasmids, or on the chromosome, in which they carry genes encoding determinants of resistance to carbapenems and other antibiotics, conferring multidrug resistance to P. aeruginosa. In addition, these genetic elements are transferable to other Gram-negative species, increasing the antimicrobial resistance rate and complicating the treatment of infected patients. Therefore, it is essential to understand the epidemiology, resistance mechanism, and molecular characteristics of MPPA for infection control and prevention of a possible global health crisis. Here, we highlight the characteristics of MPPA.
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Affiliation(s)
- Duck Jin Hong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Il Kwon Bae
- Department of Dental Hygiene, Silla University, Busan, Korea
| | - In-Ho Jang
- Department of Biomedical Laboratory Science, College of Health Sciences, Sangji University, Wonju, Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Hyun-Kyung Kang
- Department of Dental Hygiene, Silla University, Busan, Korea
| | - Kyungwon Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
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Potron A, Poirel L, Nordmann P. Emerging broad-spectrum resistance in Pseudomonas aeruginosa and Acinetobacter baumannii: Mechanisms and epidemiology. Int J Antimicrob Agents 2015; 45:568-85. [PMID: 25857949 DOI: 10.1016/j.ijantimicag.2015.03.001] [Citation(s) in RCA: 451] [Impact Index Per Article: 50.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 03/05/2015] [Indexed: 02/07/2023]
Abstract
Multidrug resistance is quite common among non-fermenting Gram-negative rods, in particular among clinically relevant species including Pseudomonas aeruginosa and Acinetobacter baumannii. These bacterial species, which are mainly nosocomial pathogens, possess a diversity of resistance mechanisms that may lead to multidrug or even pandrug resistance. Extended-spectrum β-lactamases (ESBLs) conferring resistance to broad-spectrum cephalosporins, carbapenemases conferring resistance to carbapenems, and 16S rRNA methylases conferring resistance to all clinically relevant aminoglycosides are the most important causes of concern. Concomitant resistance to fluoroquinolones, polymyxins (colistin) and tigecycline may lead to pandrug resistance. The most important mechanisms of resistance in P. aeruginosa and A. baumannii and their most recent dissemination worldwide are detailed here.
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Affiliation(s)
- Anaïs Potron
- Laboratoire de Bactériologie, Faculté de Médecine-Pharmacie, Centre Hospitalier Régional Universitaire, Université de Franche-Comté, Besançon, France
| | - Laurent Poirel
- Emerging Antibiotic Resistance Medical and Molecular Microbiology Unit, Department of Medicine, Faculty of Science, University of Fribourg, Fribourg, Switzerland.
| | - Patrice Nordmann
- Emerging Antibiotic Resistance Medical and Molecular Microbiology Unit, Department of Medicine, Faculty of Science, University of Fribourg, Fribourg, Switzerland; HFR - Hôpital Cantonal de Fribourg, Fribourg, Switzerland
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Dissemination of Pseudomonas aeruginosa Producing blaIMP1, blaVIM2, blaSIM1, blaSPM1 in Shiraz, Iran. Jundishapur J Microbiol 2013. [DOI: 10.5812/jjm.6920] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Potency and spectrum of activity of AN3365, a novel boron-containing protein synthesis inhibitor, tested against clinical isolates of Enterobacteriaceae and nonfermentative Gram-negative bacilli. Antimicrob Agents Chemother 2013; 57:2849-57. [PMID: 23507283 DOI: 10.1128/aac.00160-13] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
AN3365 (MIC(50/90), 0.5/1 μg/ml) was active against Enterobacteriaceae, including a subset of Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae strains (MIC(50/90), 1/2 μg/ml). AN3365 inhibited 98.0 and 92.2% of wild-type (MIC(50/90), 2/8 μg/ml) and carbapenem-resistant (MIC(50/90), 4/8 μg/ml) Pseudomonas aeruginosa strains, respectively, at ≤ 8 μg/ml. AN3365 also demonstrated activity against wild-type Acinetobacter baumannii (MIC(50/90), 2/8 μg/ml) and Stenotrophomonas maltophilia (MIC(50/90), 2/4 μg/ml), while it was less active against multidrug-resistant A. baumannii (MIC50/90, 8/16 μg/ml) and Burkholderia cepacia (MIC(50/90), 8/32 μg/ml).
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Zhao WH, Hu ZQ. Epidemiology and genetics of VIM-type metallo-β-lactamases in Gram-negative bacilli. Future Microbiol 2011; 6:317-33. [DOI: 10.2217/fmb.11.13] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Metallo-β-lactamases (MBLs) are a rapidly evolving group of β-lactamases, which hydrolyze most β-lactams including the carbapenems. Of the known MBLs, VIMs are one of the most common families, with 27 variants detected in at least 23 species of Gram-negative bacilli from more than 40 countries/regions. The amino acid similarities of VIM variants range from 72.9 to 99.6% with 1–72 different residues. Most of the bla VIMs are harbored by a class 1 integron, a genetic platform able to acquire and express gene cassettes. The integrons are usually embedded in transposons and, in turn, accommodated on plasmids, making them highly mobile. Integrons display considerable diversity, with at least 110 different structures associated with the gain and spread of the bla VIMs. In most instances, the bla VIMs co-exist with one or more other resistance genes. The processes for the identification of bacteria harboring bla VIMs are also discussed in this article.
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Affiliation(s)
| | - Zhi-Qing Hu
- Department of Microbiology & Immunology, Showa University School of Medicine, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo 142–8555, Japan
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Early dissemination of NDM-1- and OXA-181-producing Enterobacteriaceae in Indian hospitals: report from the SENTRY Antimicrobial Surveillance Program, 2006-2007. Antimicrob Agents Chemother 2010; 55:1274-8. [PMID: 21189345 DOI: 10.1128/aac.01497-10] [Citation(s) in RCA: 271] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Among 39 carbapenem-resistant Enterobacteriaceae (2.7% overall; Escherichia coli, Enterobacter cloacae, and Klebsiella pneumoniae strains) isolated in 2006 and 2007 in India, 15 strains carried bla(NDM-1) and 10 harbored a gene encoding a variant of the carbapenemase OXA-48, named bla(OXA-181). One E. cloacae strain harbored bla(VIM-6), and one K. pneumoniae strain carrying bla(OXA-181) also possessed bla(VIM-5). Multiple pulsed-field gel electrophoresis patterns and clonal dissemination within and among sites were observed. Isolates producing NDM-1 were disseminated in Indian health care facilities as early as 2006.
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