201
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Juan C, Torrens G, Barceló IM, Oliver A. Interplay between Peptidoglycan Biology and Virulence in Gram-Negative Pathogens. Microbiol Mol Biol Rev 2018; 82:e00033-18. [PMID: 30209071 PMCID: PMC6298613 DOI: 10.1128/mmbr.00033-18] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The clinical and epidemiological threat of the growing antimicrobial resistance in Gram-negative pathogens, particularly for β-lactams, the most frequently used and relevant antibiotics, urges research to find new therapeutic weapons to combat the infections caused by these microorganisms. An essential previous step in the development of these therapeutic solutions is to identify their potential targets in the biology of the pathogen. This is precisely what we sought to do in this review specifically regarding the barely exploited field analyzing the interplay among the biology of the peptidoglycan and related processes, such as β-lactamase regulation and virulence. Hence, here we gather, analyze, and integrate the knowledge derived from published works that provide information on the topic, starting with those dealing with the historically neglected essential role of the Gram-negative peptidoglycan in virulence, including structural, biogenesis, remodeling, and recycling aspects, in addition to proinflammatory and other interactions with the host. We also review the complex link between intrinsic β-lactamase production and peptidoglycan metabolism, as well as the biological costs potentially associated with the expression of horizontally acquired β-lactamases. Finally, we analyze the existing evidence from multiple perspectives to provide useful clues for identifying targets enabling the future development of therapeutic options attacking the peptidoglycan-virulence interconnection as a key weak point of the Gram-negative pathogens to be used, if not to kill the bacteria, to mitigate their capacity to produce severe infections.
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Affiliation(s)
- Carlos Juan
- Servicio de Microbiología and Unidad de Investigación, Hospital Son Espases, Instituto de Investigación Sanitaria de Baleares (IdISBa), Palma, Spain
| | - Gabriel Torrens
- Servicio de Microbiología and Unidad de Investigación, Hospital Son Espases, Instituto de Investigación Sanitaria de Baleares (IdISBa), Palma, Spain
| | - Isabel Maria Barceló
- Servicio de Microbiología and Unidad de Investigación, Hospital Son Espases, Instituto de Investigación Sanitaria de Baleares (IdISBa), Palma, Spain
| | - Antonio Oliver
- Servicio de Microbiología and Unidad de Investigación, Hospital Son Espases, Instituto de Investigación Sanitaria de Baleares (IdISBa), Palma, Spain
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202
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Manageiro V, Romão R, Moura IB, Sampaio DA, Vieira L, Ferreira E, Caniça M. Molecular Epidemiology and Risk Factors of Carbapenemase-Producing Enterobacteriaceae Isolates in Portuguese Hospitals: Results From European Survey on Carbapenemase-Producing Enterobacteriaceae (EuSCAPE). Front Microbiol 2018; 9:2834. [PMID: 30538682 PMCID: PMC6277554 DOI: 10.3389/fmicb.2018.02834] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 11/05/2018] [Indexed: 12/11/2022] Open
Abstract
In Portugal, the epidemiological stage for the spread of carbapenemase-producing Enterobacteriaceae (CPE) increased from sporadic isolates or single hospital clones (2010–2013), to hospital outbreaks, later. Here we report data from a 6-month study performed under the European Survey on Carbapenemase-Producing Enterobacteriaceae (EuSCAPE). During the study period, 67 isolates (61 Klebsiella pneumoniae and 6 Escherichia coli) non-susceptible to carbapenems were identified in participant hospital laboratories. We detected 37 blaKPC–type (including one new variant: blaKPC–21), 1 blaGES–5, and 1 blaGES–6 plus blaKPC–3, alone or in combination with other bla genes. Bioinformatics analysis of the KPC-21-producing E. coli identified the new variant blaKPC–21 in a 12,748 bp length plasmid. The blaKPC–21 gene was harbored on a non-Tn4401 element, presenting upstream a partial ISKpn6 (ΔISKpn6/ΔtraN) with the related left IR (IRL) and downstream a truncated Tn3 transposon. PFGE and MLST analysis showed an important diversity, as isolates belonged to distinct PFGE and STs profiles. In this study, we highlighted the presence of the high-risk clone E. coli sequence-type (ST) 131 clade C/H30. This worldwide disseminated E. coli lineage was already detected in Portugal among other antibiotic resistance reservoirs. This study highlights the intra- and inter-hospital spread and possible intercontinental circulation of CPE isolates.
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Affiliation(s)
- Vera Manageiro
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal.,Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, University of Oporto, Oporto, Portugal
| | - Raquel Romão
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Inês Barata Moura
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Daniel A Sampaio
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Luís Vieira
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Eugénia Ferreira
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal.,Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, University of Oporto, Oporto, Portugal
| | | | - Manuela Caniça
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal.,Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, University of Oporto, Oporto, Portugal
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203
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Novais Â, Freitas AR, Rodrigues C, Peixe L. Fourier transform infrared spectroscopy: unlocking fundamentals and prospects for bacterial strain typing. Eur J Clin Microbiol Infect Dis 2018; 38:427-448. [DOI: 10.1007/s10096-018-3431-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 11/11/2018] [Indexed: 01/25/2023]
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204
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Transcriptome analysis of extended-spectrum β-lactamase-producing Escherichia coli and methicillin-resistant Staphylococcus aureus exposed to cefotaxime. Sci Rep 2018; 8:16076. [PMID: 30375423 PMCID: PMC6207760 DOI: 10.1038/s41598-018-34191-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 10/11/2018] [Indexed: 12/25/2022] Open
Abstract
Previous studies on bacterial response to antibiotics mainly focused on susceptible strains. Here we characterized the transcriptional responses of distinct cephalosporin-resistant bacteria of public health relevance to cefotaxime (CTX), a cephalosporin widely used in clinical practice. Adaptation to therapeutic concentrations of CTX (30 µg/ml) was investigated by RNA sequencing in mid-exponential phase cultures of a methicillin-resistant Staphylococcus aureus (MRSA) and two genetically diverse E. coli producing CTX-M-15 or CMY-2 β-lactamase following genome sequencing and annotation for each strain. MRSA showed the most notable adaptive changes in the transcriptome after exposure to CTX, mainly associated with cell envelope functions. This reprogramming coincided with a transient reduction in cell growth, which also occurred in the CMY-2-producing E. coli but not in the CTX-M-15-producing strain. Re-establishment of growth in the CMY-2 producer proceeded without any notable adaptive transcriptional response, while limited reprogramming of gene transcription was observed in the CTX-M-15 producer. Our data show that the transcriptional response of CTX-resistant bacteria to CTX depends on the bacterial species, level of resistance and resistance determinant involved. Gene products induced in the presence of CTX may play an essential role for bacterial survival during therapy and merit further investigation as possible targets for potentiating CTX.
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205
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Prevalence of Integrons and Insertion Sequences in ESBL-Producing E. coli Isolated from Different Sources in Navarra, Spain. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15102308. [PMID: 30347800 PMCID: PMC6209886 DOI: 10.3390/ijerph15102308] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/11/2018] [Accepted: 10/18/2018] [Indexed: 11/17/2022]
Abstract
Mobile genetic elements play an important role in the dissemination of antibiotic resistant bacteria among human and environmental sources. Therefore, the aim of this study was to determine the occurrence and patterns of integrons and insertion sequences of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli isolated from different sources in Navarra, northern Spain. A total of 150 isolates coming from food products, farms and feeds, aquatic environments, and humans (healthy people and hospital inpatients), were analyzed. PCRs were applied for the study of class 1, 2, and 3 integrons (intI1, intI2, and intI3), as well as for the determination of insertion sequences (IS26, ISEcp1, ISCR1, and IS903). Results show the wide presence and dissemination of intI1 (92%), while intI3 was not detected. It is remarkable, the prevalence of intI2 among food isolates, as well as the co-existence of class 1 and class 2 (8% of isolates). The majority of isolates have two or three IS elements, with the most common being IS26 (99.4%). The genetic pattern IS26⁻ISEcp1 (related with the pathogen clone ST131) was present in the 22% of isolates (including human isolates). In addition, the combination ISEcp1⁻IS26⁻IS903⁻ISCR1 was detected in 11 isolates being, to our knowledge, the first study that describes this genetic complex. Due to the wide variability observed, no relationship was determined among these mobile genetic elements and β-lactam resistance. More investigations regarding the genetic composition of these elements are needed to understand the role of multiple types of integrons and insertion sequences on the dissemination of antimicrobial resistance genes among different environments.
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206
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Kirtikliene T, Naugzemys D, Steponkiene A, Bogdevic R, Vizuje G, Zvingila D, Kuisiene N. Evaluation of the Inter- and Intrahospital Spread of Multidrug Resistant Gram-Negative Bacteria in Lithuanian Hospitals. Microb Drug Resist 2018; 25:326-335. [PMID: 30339100 DOI: 10.1089/mdr.2018.0160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Spread of multidrug-resistant pathogenic bacteria became one of the greatest threats in healthcare worldwide. It is generally accepted that both inter- and intrahospital transmissions of these bacteria contribute significantly to this problem. The purpose of the current study was the evaluation of the inter- and intrahospital spread of multidrug resistant Gram-negative pathogenic bacteria in Lithuania. Clinical isolates of Acinetobacter sp., Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa were subjected for the screening for extended spectrum β-lactamase, carbapenemase, as well as plasmid-mediated AmpC β-lactamase genes. BOX-PCR genotyping was used for the genotyping of these isolates. Our results show that all four pathogens are involved in the intra- and/or interhospital dissemination between the Lithuanian healthcare institutions. The level of transmissions differed between pathogens, and the worst situation was detected for Acinetobacter sp. followed by E. coli. In almost all cases, transmissible strains had at least one gene conferring β-lactam resistance, thereby contributing to the dissemination of the resistance determinants in and between Lithuanian hospitals. Our study clearly demonstrated that immediate actions, more effective strategy, and surveillance are needed to confine and prevent further spread of multidrug resistant Gram-negative pathogenic bacteria in Lithuanian healthcare institutions.
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Affiliation(s)
- Tatjana Kirtikliene
- 1 Department of Microbiology and Biotechnology, Institute of Biosciences, Life Sciences Center, Vilnius University , Vilnius, Lithuania .,2 Department of Clinical Testing , National Public Health Surveillance Laboratory, Vilnius, Lithuania
| | - Donatas Naugzemys
- 3 Botanical Garden of Vilnius University, Vilnius University , Vilnius, Lithuania
| | - Ana Steponkiene
- 2 Department of Clinical Testing , National Public Health Surveillance Laboratory, Vilnius, Lithuania
| | - Robert Bogdevic
- 2 Department of Clinical Testing , National Public Health Surveillance Laboratory, Vilnius, Lithuania
| | - Greta Vizuje
- 2 Department of Clinical Testing , National Public Health Surveillance Laboratory, Vilnius, Lithuania
| | - Donatas Zvingila
- 4 Department of Botany and Genetics, Institute of Biosciences, Life Sciences Center, Vilnius University , Vilnius, Lithuania
| | - Nomeda Kuisiene
- 1 Department of Microbiology and Biotechnology, Institute of Biosciences, Life Sciences Center, Vilnius University , Vilnius, Lithuania
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207
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Aslam B, Wang W, Arshad MI, Khurshid M, Muzammil S, Rasool MH, Nisar MA, Alvi RF, Aslam MA, Qamar MU, Salamat MKF, Baloch Z. Antibiotic resistance: a rundown of a global crisis. Infect Drug Resist 2018; 11:1645-1658. [PMID: 30349322 PMCID: PMC6188119 DOI: 10.2147/idr.s173867] [Citation(s) in RCA: 1163] [Impact Index Per Article: 193.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The advent of multidrug resistance among pathogenic bacteria is imperiling the worth of antibiotics, which have previously transformed medical sciences. The crisis of antimicrobial resistance has been ascribed to the misuse of these agents and due to unavailability of newer drugs attributable to exigent regulatory requirements and reduced financial inducements. Comprehensive efforts are needed to minimize the pace of resistance by studying emergent microorganisms, resistance mechanisms, and antimicrobial agents. Multidisciplinary approaches are required across health care settings as well as environment and agriculture sectors. Progressive alternate approaches including probiotics, antibodies, and vaccines have shown promising results in trials that suggest the role of these alternatives as preventive or adjunct therapies in future.
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Affiliation(s)
- Bilal Aslam
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Wei Wang
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Muhammad Imran Arshad
- Institute of Microbiology, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Mohsin Khurshid
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan.,College of Allied Health Professionals, Directorate of Medical Sciences, Government College University Faisalabad, Faisalabad, Pakistan
| | - Saima Muzammil
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | | | - Muhammad Atif Nisar
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Ruman Farooq Alvi
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Muhammad Aamir Aslam
- Institute of Microbiology, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Muhammad Usman Qamar
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | | | - Zulqarnain Baloch
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China,
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208
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Ko KS. Antibiotic-resistant clones in Gram-negative pathogens: presence of global clones in Korea. J Microbiol 2018; 57:195-202. [PMID: 30552629 DOI: 10.1007/s12275-019-8491-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 10/01/2018] [Accepted: 10/02/2018] [Indexed: 12/26/2022]
Abstract
Antibiotic resistance is a global concern in public health. Antibiotic-resistant clones can spread nationally, internationally, and globally. This review considers representative antibiotic-resistant Gram-negative bacterial clones-CTX-M- 15-producing ST131 in Escherichia coli, extended-spectrum ß-lactamase-producing ST11 and KPC-producing ST258 in Klebsiella pneumoniae, IMP-6-producing, carbapenem-resistant ST235 in Pseudomonas aeruginosa, and OXA-23-producing global clone 2 in Acinetobacter baumannii-that have disseminated worldwide, including in Korea. The findings highlight the urgency for systematic monitoring and international cooperation to suppress the emergence and propagation of antibiotic resistance.
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Affiliation(s)
- Kwan Soo Ko
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea.
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209
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Mutation-Driven Evolution of Pseudomonas aeruginosa in the Presence of either Ceftazidime or Ceftazidime-Avibactam. Antimicrob Agents Chemother 2018; 62:AAC.01379-18. [PMID: 30082283 DOI: 10.1128/aac.01379-18] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 07/27/2018] [Indexed: 02/04/2023] Open
Abstract
Ceftazidime-avibactam is a combination of β-lactam/β-lactamase inhibitor, the use of which is restricted to some clinical cases, including cystic fibrosis patients infected with multidrug-resistant Pseudomonas aeruginosa, in which mutation is the main driver of resistance. This study aims to predict the mechanisms of mutation-driven resistance that are selected for when P. aeruginosa is challenged with either ceftazidime or ceftazidime-avibactam. For this purpose, P. aeruginosa PA14 was submitted to experimental evolution in the absence of antibiotics and in the presence of increasing concentrations of ceftazidime or ceftazidime-avibactam for 30 consecutive days. Final populations were analyzed by whole-genome sequencing. All evolved populations reached similar levels of ceftazidime resistance. In addition, they were more susceptible to amikacin and produced pyomelanin. A first event in this evolution was the selection of large chromosomal deletions containing hmgA (involved in pyomelanin production), galU (involved in β-lactams resistance), and mexXY-oprM (involved in aminoglycoside resistance). Besides mutations in mpl and dacB that regulate β-lactamase expression, mutations related to MexAB-OprM overexpression were prevalent. Ceftazidime-avibactam challenge selected mutants in the putative efflux pump PA14_45890 and PA14_45910 and in a two-component system (PA14_45870 and PA14_45880), likely regulating its expression. All populations produced pyomelanin and were more susceptible to aminoglycosides, likely due to the selection of large chromosomal deletions. Since pyomelanin-producing mutants presenting similar deletions are regularly isolated from infections, the potential aminoglycoside hypersusceptiblity and reduced β-lactam susceptibility of pyomelanin-producing P. aeruginosa should be taken into consideration for treating infections caused by these isolates.
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210
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Sultan I, Rahman S, Jan AT, Siddiqui MT, Mondal AH, Haq QMR. Antibiotics, Resistome and Resistance Mechanisms: A Bacterial Perspective. Front Microbiol 2018; 9:2066. [PMID: 30298054 PMCID: PMC6160567 DOI: 10.3389/fmicb.2018.02066] [Citation(s) in RCA: 146] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 08/13/2018] [Indexed: 12/28/2022] Open
Abstract
History of mankind is regarded as struggle against infectious diseases. Rather than observing the withering away of bacterial diseases, antibiotic resistance has emerged as a serious global health concern. Medium of antibiotic resistance in bacteria varies greatly and comprises of target protection, target substitution, antibiotic detoxification and block of intracellular antibiotic accumulation. Further aggravation to prevailing situation arose on observing bacteria gradually becoming resistant to different classes of antibiotics through acquisition of resistance genes from same and different genera of bacteria. Attributing bacteria with feature of better adaptability, dispersal of antibiotic resistance genes to minimize effects of antibiotics by various means including horizontal gene transfer (conjugation, transformation, and transduction), Mobile genetic elements (plasmids, transposons, insertion sequences, integrons, and integrative-conjugative elements) and bacterial toxin-antitoxin system led to speedy bloom of antibiotic resistance amongst bacteria. Proficiency of bacteria to obtain resistance genes generated an unpleasant situation; a grave, but a lot unacknowledged, feature of resistance gene transfer.
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Affiliation(s)
- Insha Sultan
- Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Safikur Rahman
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, South Korea
| | - Arif Tasleem Jan
- School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, India
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211
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Dolejska M, Papagiannitsis CC. Plasmid-mediated resistance is going wild. Plasmid 2018; 99:99-111. [PMID: 30243983 DOI: 10.1016/j.plasmid.2018.09.010] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 09/08/2018] [Accepted: 09/19/2018] [Indexed: 10/28/2022]
Abstract
Multidrug resistant (MDR) Gram-negative bacteria have been increasingly reported in humans, companion animals and farm animals. The growing trend of plasmid-mediated resistance to antimicrobial classes of critical importance is attributed to the emergence of epidemic plasmids, rapidly disseminating resistance genes among the members of Enterobacteriaceae family. The use of antibiotics to treat humans and animals has had a significant impact on the environment and on wild animals living and feeding in human-influenced habitats. Wildlife can acquire MDR bacteria selected in hospitals, community or livestock from diverse sources, including wastewater, sewage systems, landfills, farm facilities or agriculture fields. Therefore, wild animals are considered indicators of environmental pollution by antibiotic resistant bacteria, but they can also act as reservoirs and vectors spreading antibiotic resistance across the globe. The level of resistance and reported plasmid-mediated resistance mechanisms observed in bacteria of wildlife origin seem to correlate well with the situation described in humans and domestic animals. Additionaly, the identification of epidemic plasmids in samples from different human, animal and wildlife sources underlines the role of horizontal gene transfer in the dissemination of resistance genes. The present review focuses on reports of plasmid-mediated resistance to critically important antimicrobial classes such as broad-spectrum beta-lactams and colistin in Enterobacteriaceae isolates from samples of wildlife origin. The role of plasmids in the dissemination of ESBL-, AmpC- and carbapenemase-encoding genes as well as plasmid-mediated colistin resistance determinants in wildlife are discussed, and their similarities to plasmids previously identified in samples of human clinical or livestock origin are highlighted. Furthermore, we present features of completely sequenced plasmids reported from wildlife Enterobacteriaceae isolates, with special focus on genes that could be associated with the plasticity and stable maintenance of these molecules in antibiotic-free environments.
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Affiliation(s)
- Monika Dolejska
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic; CEITEC VFU, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic.
| | - Costas C Papagiannitsis
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic; CEITEC VFU, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic; Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic
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212
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Nagy E, Nagy G, Power CA, Badarau A, Szijártó V. Anti-bacterial Monoclonal Antibodies. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1053:119-153. [PMID: 29549638 DOI: 10.1007/978-3-319-72077-7_7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The failing efficacy of antibiotics and the high mortality rate among high-risk patients calls for new treatment modalities for bacterial infections. Due to the vastly divergent pathogenesis of human pathogens, each microbe requires a tailored approach. The main modes of action of anti-bacterial antibodies are virulence factor neutralization, complement-mediated bacterial lysis and enhancement of opsonophagocytic uptake and killing (OPK). Gram-positive bacteria cannot be lysed by complement and their pathogenesis often involves secreted toxins, therefore typically toxin-neutralization and OPK activity are required to prevent and ameliorate disease. In fact, the success stories in terms of approved products, in the anti-bacterial mAb field are based on toxin neutralization (Bacillus anthracis, Clostridium difficile). In contrast, Gram-negative bacteria are vulnerable to antibody-dependent complement-mediated lysis, while their pathogenesis rarely relies on secreted exotoxins, and involves the pro-inflammatory endotoxin (lipopolysaccharide). Given the complexity of bacterial pathogenesis, antibody therapeutics are expected to be most efficient upon targeting more than one virulence factor and/or combining different modes of action. The improved understanding of bacterial pathogenesis combined with the versatility and maturity of antibody discovery technologies available today are pivotal for the design of novel anti-bacterial therapeutics. The intensified research generating promising proof-of-concept data, and the increasing number of clinical programs with anti-bacterial mAbs, indicate that the field is ready to fulfill its promise in the coming years.
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Affiliation(s)
- Eszter Nagy
- Arsanis Biosciences GmbH/Arsanis, Inc, Vienna, Austria.
| | - Gábor Nagy
- Arsanis Biosciences GmbH/Arsanis, Inc, Vienna, Austria
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213
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Branger C, Ledda A, Billard-Pomares T, Doublet B, Fouteau S, Barbe V, Roche D, Cruveiller S, Médigue C, Castellanos M, Decré D, Drieux-Rouze L, Clermont O, Glodt J, Tenaillon O, Cloeckaert A, Arlet G, Denamur E. Extended-spectrum β-lactamase-encoding genes are spreading on a wide range of Escherichia coli plasmids existing prior to the use of third-generation cephalosporins. Microb Genom 2018; 4. [PMID: 30080134 PMCID: PMC6202452 DOI: 10.1099/mgen.0.000203] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
To understand the evolutionary dynamics of extended-spectrum β-lactamase (ESBL)-encoding genes in Escherichia coli, we undertook a comparative genomic analysis of 116 whole plasmid sequences of human or animal origin isolated over a period spanning before and after the use of third-generation cephalosporins (3GCs) using a gene-sharing network approach. The plasmids included 82 conjugative, 22 mobilizable and 9 non-transferable plasmids and 3 P-like bacteriophages. ESBL-encoding genes were found on 64 conjugative, 6 mobilizable, 2 non-transferable plasmids and 2 P1-like bacteriophages, indicating that these last three types of mobile elements also play a role, albeit modest, in the diffusion of the ESBLs. The network analysis showed that the plasmids clustered according to their genome backbone type, but not by origin or period of isolation or by antibiotic-resistance type, including type of ESBL-encoding gene. There was no association between the type of plasmid and the phylogenetic history of the parental strains. Finer scale analysis of the more abundant clusters IncF and IncI1 showed that ESBL-encoding plasmids and plasmids isolated before the use of 3GCs had the same diversity and phylogenetic history, and that acquisition of ESBL-encoding genes had occurred during multiple independent events. Moreover, the blaCTX-M-15 gene, unlike other CTX-M genes, was inserted at a hot spot in a blaTEM-1-Tn2 transposon. These findings showed that ESBL-encoding genes have arrived on wide range of pre-existing plasmids and that the successful spread of blaCTX-M-15 seems to be favoured by the presence of well-adapted IncF plasmids that carry a Tn2-blaTEM-1 transposon.
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Affiliation(s)
- Catherine Branger
- 1IAME, UMR1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, UFR de Medecine, 16 Rue Henri Huchard, Paris 75018, France
| | - Alice Ledda
- 2Department of Infectious Disease Epidemiology, Imperial College, London, W2 1PG, UK
| | | | - Benoît Doublet
- 4ISP, INRA, Université François Rabelais de Tours, UMR 1282, 37380 Nouzilly, France
| | - Stéphanie Fouteau
- 5Laboratoire de Biologie Moléculaire pour l'Etude des Génomes, (LBioMEG), CEA, Genoscope, Institut de Biologie François-Jacob, 9100, Evry, France
| | - Valérie Barbe
- 5Laboratoire de Biologie Moléculaire pour l'Etude des Génomes, (LBioMEG), CEA, Genoscope, Institut de Biologie François-Jacob, 9100, Evry, France
| | - David Roche
- 6UMR8030, CNRS, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, CEA, Institut de Génomique - Genoscope, Université Évry-Val-d'Essonne, 91000, Evry, France
| | - Stéphane Cruveiller
- 6UMR8030, CNRS, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, CEA, Institut de Génomique - Genoscope, Université Évry-Val-d'Essonne, 91000, Evry, France
| | - Claudine Médigue
- 6UMR8030, CNRS, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, CEA, Institut de Génomique - Genoscope, Université Évry-Val-d'Essonne, 91000, Evry, France
| | - Miguel Castellanos
- 7IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris13, Sorbonne Paris Cité, 75018, Paris, France
| | - Dominique Decré
- 8CIMI, UMR 1135, INSERM, Université Pierre et Marie Curie Sorbonne Université, 75013, Paris, France
| | - Laurence Drieux-Rouze
- 9APHP, Hôpital de la Pitié-Salpêtrière Service de Bactériologie-Hygiène, 75015, Paris, France
| | - Olivier Clermont
- 7IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris13, Sorbonne Paris Cité, 75018, Paris, France
| | - Jérémy Glodt
- 7IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris13, Sorbonne Paris Cité, 75018, Paris, France
| | - Olivier Tenaillon
- 7IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris13, Sorbonne Paris Cité, 75018, Paris, France
| | - Axel Cloeckaert
- 4ISP, INRA, Université François Rabelais de Tours, UMR 1282, 37380 Nouzilly, France
| | - Guillaume Arlet
- 8CIMI, UMR 1135, INSERM, Université Pierre et Marie Curie Sorbonne Université, 75013, Paris, France
| | - Erick Denamur
- 7IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris13, Sorbonne Paris Cité, 75018, Paris, France
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Activity of RX-04 Pyrrolocytosine Protein Synthesis Inhibitors against Multidrug-Resistant Gram-Negative Bacteria. Antimicrob Agents Chemother 2018; 62:AAC.00689-18. [PMID: 29914946 DOI: 10.1128/aac.00689-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/08/2018] [Indexed: 01/13/2023] Open
Abstract
Pyrrolocytosines RX-04A to -D are designed to bind to the bacterial 50S ribosomal subunit differently from currently used antibiotics. The four analogs had broad anti-Gram-negative activity: RX-04A-the most active analog-inhibited 94.7% of clinical Enterobacteriaceae, Acinetobacter baumannii, and Pseudomonas aeruginosa at 0.5 to 4 μg/ml, with no MICs of >8 μg/ml. MICs for multidrug-resistant (MDR) carbapenemase producers were up to 2-fold higher than those for control strains; values were highest for one Serratia isolate with porin and efflux lesions. mcr-1 did not affect MICs.
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Otter JA, Galletly TJ, Davies F, Hitchcock J, Gilchrist MJ, Dyakova E, Mookerjee S, Holmes AH, Brannigan ET. Planning to halve Gram-negative bloodstream infection: getting to grips with healthcare-associated Escherichia coli bloodstream infection sources. J Hosp Infect 2018; 101:129-133. [PMID: 30059746 DOI: 10.1016/j.jhin.2018.07.033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 07/23/2018] [Indexed: 01/07/2023]
Abstract
BACKGROUND A thorough understanding of the local sources, risks, and antibiotic resistance for Escherichia coli bloodstream infection (BSI) is required to focus prevention initiatives and therapy. AIM To review the sources and antibiotic resistance of healthcare-associated E. coli BSI. METHODS Sources and antibiotic resistance profiles of all 250 healthcare-associated (post 48 h) E. coli BSIs that occurred within our secondary and tertiary care hospital group from April 2014 to March 2017 were reviewed. Epidemiological associations with urinary source, gastrointestinal source, and febrile neutropenia-related BSIs were analysed using univariable and multivariable binary logistic regression models. FINDINGS E. coli BSIs increased 9% from 4.0 to 4.4 per 10,000 admissions comparing the 2014/15 and 2016/17 financial years. Eighty-nine cases (36%) had a urinary source; 30 (34%) of these were classified as urinary catheter-associated urinary tract infections (UTIs). Forty-five (18%) were related to febrile neutropenia, and 38 (15%) had a gastrointestinal source. Cases were rarely associated with surgical procedures (11, 4%) or indwelling vascular devices (seven, 3%). Female gender (odds ratio: 2.3; 95% confidence interval: 1.2-4.6) and older age (1.02; 1.00-1.05) were significantly associated with a urinary source. No significant associations were identified for gastrointestinal source or febrile neutropenia-related BSIs. Forty-seven percent of the isolates were resistant to ciprofloxacin, 37% to third-generation cephalosporins, and 22% to gentamicin. CONCLUSION The gastrointestinal tract and febrile neutropenia together accounted for one-third of E. coli BSI locally but were rare associations nationally. These sources need to be targeted locally to reduce an increasing trend of E. coli BSIs.
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Affiliation(s)
- J A Otter
- National Institute for Healthcare Research Health Protection Research Unit in HCAI and AMR, Imperial College London, London, UK; Public Health England, Hammersmith Hospital, London, UK; Imperial College Healthcare NHS Trust, St Mary's Hospital, London, UK.
| | - T J Galletly
- National Institute for Healthcare Research Health Protection Research Unit in HCAI and AMR, Imperial College London, London, UK; Public Health England, Hammersmith Hospital, London, UK; Imperial College Healthcare NHS Trust, St Mary's Hospital, London, UK
| | - F Davies
- National Institute for Healthcare Research Health Protection Research Unit in HCAI and AMR, Imperial College London, London, UK; Public Health England, Hammersmith Hospital, London, UK; Imperial College Healthcare NHS Trust, St Mary's Hospital, London, UK
| | - J Hitchcock
- Imperial College Healthcare NHS Trust, St Mary's Hospital, London, UK
| | - M J Gilchrist
- Imperial College Healthcare NHS Trust, St Mary's Hospital, London, UK
| | - E Dyakova
- Imperial College Healthcare NHS Trust, St Mary's Hospital, London, UK
| | - S Mookerjee
- Imperial College Healthcare NHS Trust, St Mary's Hospital, London, UK
| | - A H Holmes
- National Institute for Healthcare Research Health Protection Research Unit in HCAI and AMR, Imperial College London, London, UK; Public Health England, Hammersmith Hospital, London, UK; Imperial College Healthcare NHS Trust, St Mary's Hospital, London, UK
| | - E T Brannigan
- National Institute for Healthcare Research Health Protection Research Unit in HCAI and AMR, Imperial College London, London, UK; Public Health England, Hammersmith Hospital, London, UK; Imperial College Healthcare NHS Trust, St Mary's Hospital, London, UK
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216
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Engelmann C, Berg T. Management of Infectious Complications Associated with Acute-on-Chronic Liver Failure. Visc Med 2018; 34:261-268. [PMID: 30345283 DOI: 10.1159/000491107] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Introduction Acute-on-chronic liver failure (ACLF) is associated with a high susceptibility to infections leading to complications and poor prognosis. The sensitized immune system overwhelmingly responds to invading bacteria leading to organ damage. After resolution of infection or prolonged disease duration, the phagocytic system becomes irresponsive with a reduced bacterial clearance capacity promoting secondary infection. Methods This review focuses on the best management strategies for patients with ACLF and infections. Using the following terms, an extensive literature research on the Medline database was performed: 'acute-on-chronic liver failure', 'infection', 'ACLF', 'bacteria', 'multi-resistance'. Results Analysis of the literature confirmed that delayed diagnosis and treatment of infections in patients with ACLF results in a poor prognosis. Patients with ACLF should be considered as having a potential infection and should undergo a complete screening for sepsis. Once biochemical analysis indicates a potential infection, such as abnormal levels of C-reactive protein and procalcitonin, antibiotic treatment should be initiated immediately without microbiological culture results. For community-acquired infections third-generation cephalosporins are still the first choice, whereas in the nosocomial setting antibiotics with broader spectrum, such as piperacillin/combactam or carbapenems ± glycopeptides, are preferred. The patient should be re-assessed 48 h after treatment initiation in order to tailor the treatment. Non-response is suspicious, likely due to bacterial resistance or fungal infection, which should be considered when choosing further treatment strategies. Albumin substitution to prevent hepatorenal syndrome and to improve patients' outcome is mandatory in patients with spontaneous bacterial peritonitis. Prophylactic antibiotic therapy is suitable to prevent infections in high-risk patients. Conclusion The screening for infections and its treatment is an essential part of managing patients with ACLF. In order to improve patients' prognosis, antibiotic treatment should be initiated once an infection is suspected. However, preventive strategies are already established and should be applied according to the guidelines.
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Affiliation(s)
- Cornelius Engelmann
- Section Hepatology, Department of Gastroenterology and Rheumatology, University Hospital Leipzig, Leipzig, Germany
| | - Thomas Berg
- Section Hepatology, Department of Gastroenterology and Rheumatology, University Hospital Leipzig, Leipzig, Germany
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217
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Bardin EE, Cameron SJS, Perdones-Montero A, Hardiman K, Bolt F, Alton EWFW, Bush A, Davies JC, Takáts Z. Metabolic Phenotyping and Strain Characterisation of Pseudomonas aeruginosa Isolates from Cystic Fibrosis Patients Using Rapid Evaporative Ionisation Mass Spectrometry. Sci Rep 2018; 8:10952. [PMID: 30026575 PMCID: PMC6053451 DOI: 10.1038/s41598-018-28665-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 06/22/2018] [Indexed: 01/16/2023] Open
Abstract
Rapid evaporative ionisation mass spectrometry (REIMS) is a novel technique for the real-time analysis of biological material. It works by conducting an electrical current through a sample, causing it to rapidly heat and evaporate, with the analyte containing vapour channelled to a mass spectrometer. It was used to characterise the metabolome of 45 Pseudomonas aeruginosa (P. aeruginosa) isolates from cystic fibrosis (CF) patients and compared to 80 non-CF P. aeruginosa. Phospholipids gave the highest signal intensity; 17 rhamnolipids and 18 quorum sensing molecules were detected, demonstrating that REIMS has potential for the study of virulence-related metabolites. P. aeruginosa isolates obtained from respiratory samples showed a higher diversity, which was attributed to the chronic nature of most respiratory infections. The analytical sensitivity of REIMS allowed the detection of a metabolome that could be used to classify individual P. aeruginosa isolates after repeated culturing with 81% accuracy, and an average 83% concordance with multilocus sequence typing. This study underpins the capacities of REIMS as a tool with clinical applications, such as metabolic phenotyping of the important CF pathogen P. aeruginosa, and highlights the potential of metabolic fingerprinting for fine scale characterisation at a sub-species level.
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Affiliation(s)
- Emmanuelle E Bardin
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Simon J S Cameron
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | | | - Kate Hardiman
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Frances Bolt
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Eric W F W Alton
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Andrew Bush
- National Heart and Lung Institute, Imperial College London, London, United Kingdom.,Department of Paediatric Respiratory Medicine, Royal Brompton and Harefield NHS Foundation Trust, London, United Kingdom
| | - Jane C Davies
- National Heart and Lung Institute, Imperial College London, London, United Kingdom.,Department of Paediatric Respiratory Medicine, Royal Brompton and Harefield NHS Foundation Trust, London, United Kingdom
| | - Zoltan Takáts
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom.
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218
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Chen L, Wang L, Yassin AK, Zhang J, Gong J, Qi K, Ganta RR, Zhang Y, Yang Y, Han X, Wang C. Genetic characterization of extraintestinal Escherichia coli isolates from chicken, cow and swine. AMB Express 2018; 8:117. [PMID: 30019301 PMCID: PMC6049849 DOI: 10.1186/s13568-018-0646-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 07/10/2018] [Indexed: 02/07/2023] Open
Abstract
Phenotypic determination of antimicrobial resistance in bacteria is very important for diagnosis and treatment, but sometimes this procedure needs further genetic evaluation. Whole-genome sequencing plays a critical role in deciphering and advancing our understanding of bacterial evolution, transmission, and surveillance of antimicrobial resistance. In this study, whole-genome sequencing was performed on nineteen clinically extraintestinal Escherichia coli isolates from chicken, cows and swine and showing different antimicrobial susceptibility. A total of 44 different genes conferring resistance to 11 classes of antimicrobials were detected in 15 of 19 E. coli isolates (78.9%), and 22 types of plasmids were detected in 15/19 (78.9%) isolates. In addition, whole-genome sequencing of these 19 isolates identified 111 potential virulence factors, and 53 of these VFDB-annotated genes were carried by all these 19 isolates. Twelve different virulence genes were identified while the most frequent ones were gad (glutamate decarboxylase), iss (increased serum survival) and lpfA (long polar fimbriae). All isolates harbored at least one of the virulence genes. The findings from comparative genomic analyses of the 19 diverse E. coli isolates in this study provided insights into molecular basis of the rising multi-drug resistance in E. coli.
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Affiliation(s)
- Li Chen
- grid.268415.cCollege of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009 China
| | - Leyi Wang
- 0000 0004 1936 9991grid.35403.31Department of Veterinary Clinical Medicine and the Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL 61802 USA
| | - Afrah Kamal Yassin
- grid.268415.cCollege of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009 China
- 0000 0001 0674 6207grid.9763.bDepartment of Food Hygiene and Safety, Faculty of Public and Environmental Health, University of Khartoum, Khartoum, 11115 Sudan
| | - Jilei Zhang
- grid.268415.cCollege of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009 China
| | - Jiansen Gong
- 0000 0001 0526 1937grid.410727.7Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu 225009 China
| | - Kezong Qi
- 0000 0004 1760 4804grid.411389.6Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei, 230036 China
| | - Roman R. Ganta
- 0000 0001 0737 1259grid.36567.31Center of Excellence for Vector-Borne Diseases (CEVBD), Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506 USA
| | - Yuanyuan Zhang
- grid.268415.cCollege of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009 China
| | - Yi Yang
- grid.268415.cCollege of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009 China
| | - Xiangan Han
- 0000 0001 0526 1937grid.410727.7Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Chengming Wang
- 0000 0001 2297 8753grid.252546.2College of Veterinary Medicine, Auburn University, Auburn, AL USA
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Paskova V, Medvecky M, Skalova A, Chudejova K, Bitar I, Jakubu V, Bergerova T, Zemlickova H, Papagiannitsis CC, Hrabak J. Characterization of NDM-Encoding Plasmids From Enterobacteriaceae Recovered From Czech Hospitals. Front Microbiol 2018; 9:1549. [PMID: 30042758 PMCID: PMC6048247 DOI: 10.3389/fmicb.2018.01549] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 06/21/2018] [Indexed: 01/11/2023] Open
Abstract
The aim of the present study was to characterize sporadic cases and an outbreak of NDM-like-producing Enterobacteriaceae recovered from hospital settings, in Czechia. During 2016, 18 Entrobacteriaceae isolates including 10 Enterobacter cloacae complex (9 E. xiangfangensis and 1 E. asburiae), 4 Escherichia coli, 1 Kluyvera intermedia, 1 Klebsiella pneumoniae, 1 Klebsiella oxytoca, and 1 Raoultella ornithinolytica that produced NDM-like carbapenemases were isolated from 15 patients. Three of the patients were colonized or infected by two different NDM-like producers. Moreover, an NDM-4-producing isolate of E. cloacae complex, isolated in 2012, was studied for comparative purposes. All isolates of E. cloacae complex, except the E. asburiae, recovered from the same hospital, were assigned to ST182. Additionally, two E. coli belonged to ST167, while the remaining isolates were not clonally related. Thirteen isolates carried blaNDM-4, while six isolates carried blaNDM-1 (n = 3) or blaNDM-5 (n = 3). Almost all isolates carried blaNDM-like-carrying plasmids being positive for the IncX3 allele, except ST58 E. coli and ST14 K. pneumoniae isolates producing NDM-1. Analysis of plasmid sequences revealed that all IncX3 blaNDM-like-carrying plasmids exhibited a high similarity to each other and to previously described plasmids, like pNDM-QD28, reported from worldwide. However, NDM-4-encoding plasmids differed from other IncX3 plasmids by the insertion of a Tn3-like transposon. On the other hand, the ST58 E. coli and ST14 K. pneumoniae isolates carried two novel NDM-1-encoding plasmids, pKpn-35963cz, and pEsco-36073cz. Plasmid pKpn-35963cz that was an IncFIB(K) molecule contained an acquired sequence, encoding NDM-1 metallo-β-lactamase (MβL), which exhibited high similarity to the mosaic region of pS-3002cz from an ST11 K. pneumoniae from Czechia. Finally, pEsco-36073cz was a multireplicon A/C2+R NDM-1-encoding plasmid. Similar to other type 1 A/C2 plasmids, the blaNDM-1 gene was located within the ARI-A resistance island. These findings underlined that IncX3 plasmids have played a major role in the dissemination of blaNDM-like genes in Czech hospitals. In combination with further evolvement of NDM-like-encoding MDR plasmids through reshuffling, NDM-like producers pose an important public threat.
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Affiliation(s)
- Veronika Paskova
- Department of Microbiology, Faculty of Medicine and University Hospital in Plzen, Charles University, Plzen, Czechia
- Faculty of Medicine, Biomedical Center, Charles University, Plzen, Czechia
| | - Matej Medvecky
- Veterinary Research Institute, Brno, Czechia
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czechia
| | - Anna Skalova
- Department of Microbiology, Faculty of Medicine and University Hospital in Plzen, Charles University, Plzen, Czechia
- Faculty of Medicine, Biomedical Center, Charles University, Plzen, Czechia
| | - Katerina Chudejova
- Department of Microbiology, Faculty of Medicine and University Hospital in Plzen, Charles University, Plzen, Czechia
- Faculty of Medicine, Biomedical Center, Charles University, Plzen, Czechia
| | - Ibrahim Bitar
- Department of Microbiology, Faculty of Medicine and University Hospital in Plzen, Charles University, Plzen, Czechia
- Faculty of Medicine, Biomedical Center, Charles University, Plzen, Czechia
| | - Vladislav Jakubu
- National Reference Laboratory for Antibiotics, National Institute of Public Health, Prague, Czechia
| | - Tamara Bergerova
- Department of Microbiology, Faculty of Medicine and University Hospital in Plzen, Charles University, Plzen, Czechia
- Faculty of Medicine, Biomedical Center, Charles University, Plzen, Czechia
| | - Helena Zemlickova
- National Reference Laboratory for Antibiotics, National Institute of Public Health, Prague, Czechia
- Department of Clinical Microbiology, University Hospital and Faculty of Medicine in Hradec Kralove, Charles University, Hradec Kralove, Czechia
| | - Costas C. Papagiannitsis
- Department of Microbiology, Faculty of Medicine and University Hospital in Plzen, Charles University, Plzen, Czechia
- Faculty of Medicine, Biomedical Center, Charles University, Plzen, Czechia
| | - Jaroslav Hrabak
- Department of Microbiology, Faculty of Medicine and University Hospital in Plzen, Charles University, Plzen, Czechia
- Faculty of Medicine, Biomedical Center, Charles University, Plzen, Czechia
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Hazen TH, Mettus R, McElheny CL, Bowler SL, Nagaraj S, Doi Y, Rasko DA. Diversity among bla KPC-containing plasmids in Escherichia coli and other bacterial species isolated from the same patients. Sci Rep 2018; 8:10291. [PMID: 29980699 PMCID: PMC6035167 DOI: 10.1038/s41598-018-28085-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 06/15/2018] [Indexed: 11/23/2022] Open
Abstract
Carbapenem resistant Enterobacteriaceae are a significant public health concern, and genes encoding the Klebsiella pneumoniae carbapenemase (KPC) have contributed to the global spread of carbapenem resistance. In the current study, we used whole-genome sequencing to investigate the diversity of blaKPC-containing plasmids and antimicrobial resistance mechanisms among 26 blaKPC-containing Escherichia coli, and 13 blaKPC-containing Enterobacter asburiae, Enterobacter hormaechei, K. pneumoniae, Klebsiella variicola, Klebsiella michiganensis, and Serratia marcescens strains, which were isolated from the same patients as the blaKPC-containing E. coli. A blaKPC-containing IncN and/or IncFIIK plasmid was identified in 77% (30/39) of the E. coli and other bacterial species analyzed. Complete genome sequencing and comparative analysis of a blaKPC-containing IncN plasmid from one of the E. coli strains demonstrated that this plasmid is present in the K. pneumoniae and S. marcescens strains from this patient, and is conserved among 13 of the E. coli and other bacterial species analyzed. Interestingly, while both IncFIIK and IncN plasmids were prevalent among the strains analyzed, the IncN plasmids were more often identified in multiple bacterial species from the same patients, demonstrating a contribution of this IncN plasmid to the inter-genera dissemination of the blaKPC genes between the E. coli and other bacterial species analyzed.
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Affiliation(s)
- Tracy H Hazen
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Roberta Mettus
- Division of Infectious Diseases and Center for Innovative Antimicrobial Therapy, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Christi L McElheny
- Division of Infectious Diseases and Center for Innovative Antimicrobial Therapy, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Sarah L Bowler
- Division of Infectious Diseases and Center for Innovative Antimicrobial Therapy, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Sushma Nagaraj
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Yohei Doi
- Division of Infectious Diseases and Center for Innovative Antimicrobial Therapy, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Department of Microbiology, Fujita Health University, Aichi, Japan.
| | - David A Rasko
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
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221
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Characterization of Extensively Drug-Resistant or Pandrug-Resistant Sequence Type 147 and 101 OXA-48-Producing Klebsiella pneumoniae Causing Bloodstream Infections in Patients in an Intensive Care Unit. Antimicrob Agents Chemother 2018; 62:AAC.02457-17. [PMID: 29661874 DOI: 10.1128/aac.02457-17] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 04/04/2018] [Indexed: 01/15/2023] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae causes important health care-associated infections worldwide. An outbreak of sequence type 11 (ST11) OXA-48-producing K. pneumoniae (OXA-48-Kp) isolates occurred in Tzaneio Hospital in 2012 and was contained until 2014, when OXA-48-Kp reemerged. The present study involved 19 bloodstream infection (BSI) OXA-48-Kp isolates recovered from 19 intensive care unit (ICU) patients hospitalized between August 2014 and July 2016. MICs were determined by broth microdilution. Beta-lactamase genes were detected by PCR. All isolates were typed by pulsed-field gel electrophoresis/multilocus sequence typing (PFGE/MLST), and 10 representative isolates were typed by next-generation sequencing (NGS). Of the 19 study patients, 9 had previous hospitalizations, and 10 carried OXA-48-Kp prior to BSI isolation; median time from ICU admission to BSI was 29 days. Four OXA-48-Kp isolates belonged to PFGE profile A (ST147) and were pandrug resistant (PDR), while 15 isolates exhibited PFGE profile B (ST101) and were extensively drug resistant. Genes detected via NGS resistome analysis accounted for most of the resistance phenotypes, except for tigecycline and fosfomycin. Insertional inactivation of mgrB (distinct per clone) conferred colistin resistance in all 19 isolates. NGS single nucleotide polymorphism (SNP) analysis validated the clonal relatedness of the ST147 and ST101 strains and revealed the possible presence of two index ST147 strains and the microevolution of ST101 strains. Distinct, but highly related, IncL OXA-48-encoding plasmid lineages were identified; plasmids of the ST147 strains were identical with the plasmid of ST11 OXA-48-Kp which caused the 2012 outbreak. In conclusion, biclonal circulation of OXA-48-Kp and, alarmingly, emergence of a PDR clone are reported. These observations, along with the challenging phenotypic detection of OXA-48 producers and the high reported transmissibility of blaOXA-48, necessitate intensive efforts to prevent their further spread.
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Bado I, Papa-Ezdra R, Delgado-Blas JF, Gaudio M, Gutiérrez C, Cordeiro NF, García-Fulgueiras V, Araújo Pirez L, Seija V, Medina JC, Rieppi G, Gonzalez-Zorn B, Vignoli R. Molecular Characterization of Carbapenem-Resistant Acinetobacter baumannii in the Intensive Care Unit of Uruguay's University Hospital Identifies the First rmtC Gene in the Species. Microb Drug Resist 2018; 24:1012-1019. [PMID: 29920143 PMCID: PMC6154759 DOI: 10.1089/mdr.2017.0300] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Carbapenem-resistant Acinetobacter baumannii (CRAB) infections are an increasing concern in intensive care units (ICUs) worldwide. The combination of carbapenemases and 16S rRNA-methyltransferases (16S-RMTases) further reduces the therapeutic options. OXA-carbapenemase/A. baumannii clone tandems in Latin America have already been described; however, no information exists in this region regarding the occurrence of 16S-RMTases in this microorganism. In addition, the epidemiology of A. baumannii in ICUs and its associated resistance profiles are poorly understood. Our objectives were as follows: to study the clonal relationship and antibiotic resistance profiles of clinical and digestive colonizing A. baumannii isolates in an ICU, to characterize the circulating carbapenemases, and to detect 16S-RMTases. Patients admitted between August 2010 and July 2011 with a clinically predicted hospital stay > 48 hr were included. Pharyngeal and rectal swabs were obtained during the first fortnight after hospitalization. Resistance profiles were determined with MicroScan® and VITEK2 system. Carbapenemases and 16S-RMTases were identified by PCR and sequencing, and clonality was assessed by pulsed-field gel electrophoresis and multilocus sequence typing. Sixty-nine patients were studied and 63 were diagnosed with bacterial infections. Among these, 29 were CRAB isolates; 49 A. baumannii were isolated as digestive colonizers. These 78 isolates were clustered in 7 pulsetypes, mostly belonging to ST79. The only carbapenemase genes detected were blaOXA-51 (n = 78), blaOXA-23 (n = 62), and blaOXA-58 (n = 3). Interestingly, two clinical isolates harbored the rmtC 16S-RMTase gene. To the best of our knowledge, this is the first description of the presence of rmtC in A. baumannii.
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Affiliation(s)
- Inés Bado
- 1 Departamento de Bacteriología y Virología, Facultad de Medicina, Instituto de Higiene , Universidad de la República, Montevideo, Uruguay
| | - Romina Papa-Ezdra
- 1 Departamento de Bacteriología y Virología, Facultad de Medicina, Instituto de Higiene , Universidad de la República, Montevideo, Uruguay
| | - Jose F Delgado-Blas
- 2 Departamento de Salud Animal y VISAVET, Universidad Complutense de Madrid , Madrid, Spain
| | - Micaela Gaudio
- 1 Departamento de Bacteriología y Virología, Facultad de Medicina, Instituto de Higiene , Universidad de la República, Montevideo, Uruguay .,2 Departamento de Salud Animal y VISAVET, Universidad Complutense de Madrid , Madrid, Spain
| | - Claudia Gutiérrez
- 3 Departamento de Laboratorio Clínico, Área Microbiología, Facultad de Medicina, Hospital de Clínicas , Universidad de la República, Montevideo, Uruguay
| | - Nicolás F Cordeiro
- 1 Departamento de Bacteriología y Virología, Facultad de Medicina, Instituto de Higiene , Universidad de la República, Montevideo, Uruguay
| | - Virginia García-Fulgueiras
- 1 Departamento de Bacteriología y Virología, Facultad de Medicina, Instituto de Higiene , Universidad de la República, Montevideo, Uruguay
| | - Lucía Araújo Pirez
- 1 Departamento de Bacteriología y Virología, Facultad de Medicina, Instituto de Higiene , Universidad de la República, Montevideo, Uruguay
| | - Verónica Seija
- 3 Departamento de Laboratorio Clínico, Área Microbiología, Facultad de Medicina, Hospital de Clínicas , Universidad de la República, Montevideo, Uruguay
| | - Julio C Medina
- 4 Cátedra de Enfermedades Infecciosas, Facultad de Medicina, Instituto de Higiene , Universidad de la República, Montevideo, Uruguay
| | - Gloria Rieppi
- 5 Facultad de Medicina, Unidad de Cuidados Intensivos del Hospital de Clínicas , Universidad de la República, Montevideo, Uruguay
| | - Bruno Gonzalez-Zorn
- 2 Departamento de Salud Animal y VISAVET, Universidad Complutense de Madrid , Madrid, Spain
| | - Rafael Vignoli
- 1 Departamento de Bacteriología y Virología, Facultad de Medicina, Instituto de Higiene , Universidad de la República, Montevideo, Uruguay
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Salto IP, Torres Tejerizo G, Wibberg D, Pühler A, Schlüter A, Pistorio M. Comparative genomic analysis of Acinetobacter spp. plasmids originating from clinical settings and environmental habitats. Sci Rep 2018; 8:7783. [PMID: 29773850 PMCID: PMC5958079 DOI: 10.1038/s41598-018-26180-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 04/27/2018] [Indexed: 12/20/2022] Open
Abstract
Bacteria belonging to the genus Acinetobacter have become of clinical importance over the last decade due to the development of a multi-resistant phenotype and their ability to survive under multiple environmental conditions. The development of these traits among Acinetobacter strains occurs frequently as a result of plasmid-mediated horizontal gene transfer. In this work, plasmids from nosocomial and environmental Acinetobacter spp. collections were separately sequenced and characterized. Assembly of the sequenced data resulted in 19 complete replicons in the nosocomial collection and 77 plasmid contigs in the environmental collection. Comparative genomic analysis showed that many of them had conserved backbones. Plasmid coding sequences corresponding to plasmid specific functions were bioinformatically and functionally analyzed. Replication initiation protein analysis revealed the predominance of the Rep_3 superfamily. The phylogenetic tree constructed from all Acinetobacter Rep_3 superfamily plasmids showed 16 intermingled clades originating from nosocomial and environmental habitats. Phylogenetic analysis of relaxase proteins revealed the presence of a new sub-clade named MOBQAci, composed exclusively of Acinetobacter relaxases. Functional analysis of proteins belonging to this group showed that they behaved differently when mobilized using helper plasmids belonging to different incompatibility groups.
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Affiliation(s)
- Ileana P Salto
- IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900), La Plata, Argentina
| | - Gonzalo Torres Tejerizo
- IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900), La Plata, Argentina
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstr. 27, D-33615, Bielefeld, Germany
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstr. 27, D-33615, Bielefeld, Germany
| | - Alfred Pühler
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstr. 27, D-33615, Bielefeld, Germany
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstr. 27, D-33615, Bielefeld, Germany
| | - Mariano Pistorio
- IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900), La Plata, Argentina.
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224
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Zaman TU, Alrodayyan M, Albladi M, Aldrees M, Siddique MI, Aljohani S, Balkhy HH. Clonal diversity and genetic profiling of antibiotic resistance among multidrug/carbapenem-resistant Klebsiella pneumoniae isolates from a tertiary care hospital in Saudi Arabia. BMC Infect Dis 2018; 18:205. [PMID: 29724185 PMCID: PMC5934806 DOI: 10.1186/s12879-018-3114-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 04/25/2018] [Indexed: 11/10/2022] Open
Abstract
Background The nexus between resistance determinants, plasmid type, and clonality appears to play a crucial role in the dissemination and survival of carbapenem-resistant Klebsiella pneumoniae (CRKP). The incidence of infections involving CRKP in Saudi Arabia is increasing and there is a need for detailed molecular profiling of this pathogen for CRKP surveillance and control. Methods The resistance determinants of 71 non-redundant CRKP isolates were investigated by polymerase chain reaction (PCR) and sequencing. Plasmid typing was performed using PCR-based replicon typing and the clonality of isolates was determined by multilocus sequence typing. Capsular polysaccharide synthesis genes and other virulence factors were examined using multiplex PCR. Diversity was calculated using DIVEIN, clonal relationship was determined using eBURST, and phylogenetic analysis was performed using SplitsTree4. Results A polyclonal OXA-48 gene alone was the most common carbapenemase detected in 48/71 (67.6%) isolates followed by NDM-1 alone in 9/71 (12.7%) isolates. Coproduction of OXA-48 and NDM-1 was observed in 6/71 (8.5%) isolates. Both carbapenemase genes could be transferred into an Escherichia coli recipient. CTX-M-15 was the most abundant extended-spectrum β-lactamase gene detected in 47/71 (66.2%) isolates, whereas clone-specific CTX-M-14 (ST-199 and -709) was found in 15/71 (21%) isolates. Sixty-seven of 71 isolates were positive for one or more plasmid replicons. The replicons detected were: IncFII; IncFIIK; IncFIA; IncFIB; L/M; IncI1; and IncN. FIIK and L/M were predominant, with 69 and 67% positivity, respectively. All isolates were negative for the magA (K1), rmpA, and K2 genes and presented a non-hypermucoviscous phenotype. Conclusion A polyclonal CRKP reservoir of sequence types (STs)-37, − 199, and − 152 was observed and ST-152 appeared to be a “frequent carrier” of the NDM-1 gene. ST-199, a singleton not previously reported, showed a sequence diversity suggestive of positive selection. A significant association was evident between resistance determinants and the clonal types of K. pneumoniae: all ST-152 isolates were positive for NDM-1 but negative for OXA-48; ST-199 isolates were positive for OXA-48 but negative for NDM-1; and ST-709 and -199 isolates were positive for CTX-M-14. The incidence of certain clonal types in large numbers predicts an outbreak-like situation and warrants stringent surveillance and infection control. Electronic supplementary material The online version of this article (10.1186/s12879-018-3114-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Taher Uz Zaman
- Infectious Diseases Section, King Abdullah International Medical Research Center National Guard Health Affairs, P.O. Box 22490, Mail Code 1515, Riyadh, 11426, Kingdom of Saudi Arabia. .,King Saud Bin Abdul-Aziz University of Health Sciences, Riyadh, Kingdom of Saudi Arabia.
| | - Maha Alrodayyan
- Infectious Diseases Section, King Abdullah International Medical Research Center National Guard Health Affairs, P.O. Box 22490, Mail Code 1515, Riyadh, 11426, Kingdom of Saudi Arabia.,King Saud Bin Abdul-Aziz University of Health Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Maha Albladi
- Infectious Diseases Section, King Abdullah International Medical Research Center National Guard Health Affairs, P.O. Box 22490, Mail Code 1515, Riyadh, 11426, Kingdom of Saudi Arabia.,King Saud Bin Abdul-Aziz University of Health Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Mohammed Aldrees
- Infectious Diseases Section, King Abdullah International Medical Research Center National Guard Health Affairs, P.O. Box 22490, Mail Code 1515, Riyadh, 11426, Kingdom of Saudi Arabia.,King Saud Bin Abdul-Aziz University of Health Sciences, Riyadh, Kingdom of Saudi Arabia
| | | | - Sameera Aljohani
- King Saud Bin Abdul-Aziz University of Health Sciences, Riyadh, Kingdom of Saudi Arabia.,Microbiology Section- King Abdul-Aziz Medical City, Riyadh, Kingdom of Saudi Arabia
| | - Hanan H Balkhy
- Infectious Diseases Section, King Abdullah International Medical Research Center National Guard Health Affairs, P.O. Box 22490, Mail Code 1515, Riyadh, 11426, Kingdom of Saudi Arabia. .,King Saud Bin Abdul-Aziz University of Health Sciences, Riyadh, Kingdom of Saudi Arabia. .,Infection Prevention and Control Prevention, King Abdul-Aziz Medical City, National Guard Health Affairs, P.O. Box 22490, Riyadh-11426, Riyadh, Kingdom of Saudi Arabia.
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225
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Tang X, Xiao M, Zhuo C, Xu Y, Zhong N. Multi-level analysis of bacteria isolated from inpatients in respiratory departments in China. J Thorac Dis 2018; 10:2666-2675. [PMID: 29997928 DOI: 10.21037/jtd.2018.04.46] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Background With the different situation for clinical antibiotic usage and its management in different regions and medical institutions, the antimicrobial resistance varied in different level. However, the epidemiological data of multi-drug resistant (MDR) strains from the department of respiration is limited. Thus, this study aims to investigate the epidemiology of bacteria isolated from inpatients of respiratory departments, and analyze the distribution variation of major multi-drug resistant bacteria in China. Methods Based on data from China Antimicrobial Resistance Surveillance System (CARSS) in 2015, 50,417 non-duplicate isolates obtained from inpatients of respiratory departments from 91 general hospitals in seven regions of China were enrolled in the study. The distribution of methicillin-resistant Staphylococcus aureus (MRSA), carbapenem-resistant Escherichia coli (CREC) and Klebsiella pneumoniae (CRKP), carbapenem-resistant Pseudomonas aeruginosa (CRPA) and Acinetobacter baumannii (CRAB), extended-spectrum β-lactamases-producing E. coli (ESBL-EC) and K. pneumoniae (ESBL-KP), were further analyzed by geographic regions, age groups, wards and specimen types. Results The major specimens type were sputum (81.6%, 41,131/50,417), followed by blood (5.3%, 2,649/50,417), urine (4.5%, 2,249/50,417) and bronchoalveolar lavage fluid (BALF) (3.2%, 1,620/50,417). The top four bacteria species isolated from sputum and BALF were similar: K. pneumonia (18.9% and 14.8%, respectively), P. aeruginosa (13.6% and 22.2%, respectively), A. baumannii (11.3% and 11.9%, respectively) and S. pneumonia (11.1% and 9.6%, respectively). The four most common bacteria species were K. pneumonia (17.2%), P. aeruginosa (12.1%), A. baumannii (10.4%) and S. pneumonia (10.1%) in tertiary hospitals but K. pneumonia (20.8%), P. aeruginosa (16.3%), E. coli (11.3%) and A. baumannii (6.9%) in secondary hospitals. The top four bacteria species in respiratory intensive care unit (RICU) were A. baumannii (25.8%), P. aeruginosa (13.1%), K. pneumonia (12.2%) and S. aureus (9.2%). The prevalence of CRKP, CRPA and CRAB in tertiary hospitals was significantly higher than that in secondary hospitals (5.2% vs. 2.5%, 23.8% vs. 12.8% and 53.5% vs. 33.9%, respectively) (all P<0.05). However, the prevalence of ESBL-EC in secondary hospitals was higher than in tertiary ones (63.9% vs. 55.0%, P=0.011). The prevalence of MRSA, CRKP, CRAB, CRPA, ESBL-EC, ESBL-KP in RICU were higher than that in non-ICU respiratory departments (76.5% vs. 35.7%, 20.1% vs. 4.1%, 90.6% vs. 45.5%, 64.2% vs. 19.3%, 47.2% vs. 28.3% and 43.0% vs. 11.2%, respectively) (all P<0.01). Among seven regions in China, central area had the highest detection rates of MRSA (70.3%, 237/337), CRPA (30.9%, 376/1,218), CRAB (71.8%, 487/678) and ESBL-KP (38.8%, 241/621). The prevalence of ESBL-EC and ESBL-KP in pediatric group (68.2% and 55.3%, respectively) was higher than that in geriatric group (54.2% and 27.1%, respectively) and adult group (51.1% and 15.1%, respectively) (all P<0.001). Conclusions In China, the predominant bacterial pathogens in the respiratory ward were Enterobacteriaceae and non-fermentative bacteria. High prevalence of ESBL-EC and ESBL-KP isolated from lower respiratory tract (LRT) was revealed in primary hospitals and pediatric patients.
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Affiliation(s)
- Xiang Tang
- State Key Laboratory of Respiratory Diseases, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510230, China
| | - Meng Xiao
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Beijing 100000, China
| | - Chao Zhuo
- State Key Laboratory of Respiratory Diseases, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510230, China
| | - Yingchun Xu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Beijing 100000, China
| | - Nanshan Zhong
- State Key Laboratory of Respiratory Diseases, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510230, China
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226
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Marquez-Ortiz RA, Haggerty L, Olarte N, Duarte C, Garza-Ramos U, Silva-Sanchez J, Castro BE, Sim EM, Beltran M, Moncada MV, Valderrama A, Castellanos JE, Charles IG, Vanegas N, Escobar-Perez J, Petty NK. Genomic Epidemiology of NDM-1-Encoding Plasmids in Latin American Clinical Isolates Reveals Insights into the Evolution of Multidrug Resistance. Genome Biol Evol 2018; 9:1725-1741. [PMID: 28854628 PMCID: PMC5554438 DOI: 10.1093/gbe/evx115] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2017] [Indexed: 12/21/2022] Open
Abstract
Bacteria that produce the broad-spectrum Carbapenem antibiotic New Delhi Metallo-β-lactamase (NDM) place a burden on health care systems worldwide, due to the limited treatment options for infections caused by them and the rapid global spread of this antibiotic resistance mechanism. Although it is believed that the associated resistance gene blaNDM-1 originated in Acinetobacter spp., the role of Enterobacteriaceae in its dissemination remains unclear. In this study, we used whole genome sequencing to investigate the dissemination dynamics of blaNDM-1-positive plasmids in a set of 21 clinical NDM-1-positive isolates from Colombia and Mexico (Providencia rettgeri, Klebsiella pneumoniae, and Acinetobacter baumannii) as well as six representative NDM-1-positive Escherichia coli transconjugants. Additionally, the plasmids from three representative P. rettgeri isolates were sequenced by PacBio sequencing and finished. Our results demonstrate the presence of previously reported plasmids from K. pneumoniae and A. baumannii in different genetic backgrounds and geographically distant locations in Colombia. Three new previously unclassified plasmids were also identified in P. rettgeri from Colombia and Mexico, plus an interesting genetic link between NDM-1-positive P. rettgeri from distant geographic locations (Canada, Mexico, Colombia, and Israel) without any reported epidemiological links was discovered. Finally, we detected a relationship between plasmids present in P. rettgeri and plasmids from A. baumannii and K. pneumoniae. Overall, our findings suggest a Russian doll model for the dissemination of blaNDM-1 in Latin America, with P. rettgeri playing a central role in this process, and reveal new insights into the evolution and dissemination of plasmids carrying such antibiotic resistance genes.
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Affiliation(s)
- Ricaurte Alejandro Marquez-Ortiz
- Bacterial Molecular Genetics Laboratory, Universidad El Bosque, Bogotá, D.C., Colombia.,The ithree Institute, University of Technology Sydney, New South Wales, Australia
| | - Leanne Haggerty
- The ithree Institute, University of Technology Sydney, New South Wales, Australia
| | | | - Carolina Duarte
- Grupo de Microbiología, Instituto Nacional de Salud, Bogotá, Colombia
| | - Ulises Garza-Ramos
- Instituto Nacional de Salud Pública (INSP), CISEI, Cuernavaca, Morelos, México
| | - Jesus Silva-Sanchez
- Instituto Nacional de Salud Pública (INSP), CISEI, Cuernavaca, Morelos, México
| | - Betsy E Castro
- Bacterial Molecular Genetics Laboratory, Universidad El Bosque, Bogotá, D.C., Colombia
| | - Eby M Sim
- The ithree Institute, University of Technology Sydney, New South Wales, Australia
| | - Mauricio Beltran
- Grupo de Microbiología, Instituto Nacional de Salud, Bogotá, Colombia
| | - María V Moncada
- Bacterial Molecular Genetics Laboratory, Universidad El Bosque, Bogotá, D.C., Colombia
| | | | - Jaime E Castellanos
- Grupo de Patogénesis Infecciosa, Universidad Nacional de Colombia, Bogotá, D.C., Colombia
| | - Ian G Charles
- The ithree Institute, University of Technology Sydney, New South Wales, Australia
| | - Natasha Vanegas
- Bacterial Molecular Genetics Laboratory, Universidad El Bosque, Bogotá, D.C., Colombia.,The ithree Institute, University of Technology Sydney, New South Wales, Australia
| | - Javier Escobar-Perez
- Bacterial Molecular Genetics Laboratory, Universidad El Bosque, Bogotá, D.C., Colombia
| | - Nicola K Petty
- The ithree Institute, University of Technology Sydney, New South Wales, Australia
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227
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Zowawi HM, Syrmis MW, Kidd TJ, Balkhy HH, Walsh TR, Al Johani SM, Al Jindan RY, Alfaresi M, Ibrahim E, Al-Jardani A, Al Salman J, Dashti AA, Sidjabat HE, Baz O, Trembizki E, Whiley DM, Paterson DL. Identification of carbapenem-resistant Pseudomonas aeruginosa in selected hospitals of the Gulf Cooperation Council States: dominance of high-risk clones in the region. J Med Microbiol 2018; 67:846-853. [PMID: 29664716 DOI: 10.1099/jmm.0.000730] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
PURPOSE The molecular epidemiology and resistance mechanisms of carbapenem-resistant Pseudomonas aeruginosa (CRPA) were determined in hospitals in the countries of the Gulf Cooperation Council (GCC), namely, Saudi Arabia, the United Arab Emirates, Oman, Qatar, Bahrain and Kuwait. METHODOLOGY Isolates were screened for common carbapenem-resistance genes by PCR. Relatedness between isolates was assessed using previously described genotyping methods: an informative-single nucleotide polymorphism MassARRAY iPLEX assay (iPLEX20SNP) and the enterobacterial repetitive intergenic consensus (ERIC)-PCR assay, with selected isolates being subjected to multilocus sequence typing (MLST). Ninety-five non-repetitive isolates that were found to be resistant to carbapenems were subjected to further investigation.Results/Key findings. The most prevalent carbapenemase-encoding gene, blaVIM-type, was found in 37/95 (39 %) isolates, while only 1 isolate (from UAE) was found to have blaIMP-type. None of the CRPA were found to have blaNDM-type or blaKPC-type. We found a total of 14 sequence type (ST) clusters, with 4 of these clusters being observed in more than 1 country. Several clusters belonged to the previously recognized internationally disseminated high-risk clones ST357, ST235, ST111, ST233 and ST654. We also found the less predominant ST316, ST308 and ST823 clones, and novel MLST types (ST2010, ST2011, ST2012 and ST2013), in our collection. CONCLUSION Overall our data show that 'high-risk' CRPA clones are now detected in the region and highlight the need for strategies to limit further spread of such organisms, including enhanced surveillance, infection control precautions and further promotion of antibiotic stewardship programmes.
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Affiliation(s)
- Hosam M Zowawi
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.,The University of Queensland, UQ Centre for Clinical Research, Herston, Queensland, Australia.,King Abdullah International Medical Research Centre, Riyadh, Saudi Arabia.,WHO Collaborating Centre for Infection Prevention and Control, and GCC Center for Infection Control, Riyadh, Saudi Arabia
| | | | - Timothy J Kidd
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia.,Centre for Experimental Medicine, Queen's University Belfast, Belfast BT9 7BL, UK
| | - Hanan H Balkhy
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.,King Abdullah International Medical Research Centre, Riyadh, Saudi Arabia.,WHO Collaborating Centre for Infection Prevention and Control, and GCC Center for Infection Control, Riyadh, Saudi Arabia
| | - Timothy R Walsh
- The University of Queensland, UQ Centre for Clinical Research, Herston, Queensland, Australia.,Department of Medical Microbiology and Infectious Diseases, School of Medicine, Cardiff University, Heath Park, Cardiff, UK
| | - Sameera M Al Johani
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.,Microbiology, Department of Pathology and Lab Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Reem Y Al Jindan
- Department of Microbiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Mubarak Alfaresi
- Pathology and Laboratory Medicine Department at Sheikh Khalifa General Hospital, Umm Al Quwain, UAE.,College of Medicine, University of Sharjah, UAE
| | - Emad Ibrahim
- Clinical Microbiology Department, Hamad Medical Corporation, Doha, Qatar
| | - Amina Al-Jardani
- Medical Microbiology Department, The Royal Hospital, Muscat, Oman
| | - Jameela Al Salman
- Samlaniya Medical Complex, Infectious Diseases Unit, Manama, Bahrain
| | - Ali A Dashti
- Medical Laboratory Department, Faculty of Allied Health Sciences, Health Science Center, Kuwait University, Kuwait City, Kuwait
| | - Hanna E Sidjabat
- The University of Queensland, UQ Centre for Clinical Research, Herston, Queensland, Australia
| | - Omar Baz
- King Abdullah International Medical Research Centre, Riyadh, Saudi Arabia
| | - Ella Trembizki
- The University of Queensland, UQ Centre for Clinical Research, Herston, Queensland, Australia
| | - David M Whiley
- The University of Queensland, UQ Centre for Clinical Research, Herston, Queensland, Australia.,Pathology Queensland, Brisbane, Queensland 4029, Australia
| | - David L Paterson
- The University of Queensland, UQ Centre for Clinical Research, Herston, Queensland, Australia
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228
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Vading M, Nauclér P, Kalin M, Giske CG. Invasive infection caused by Klebsiella pneumoniae is a disease affecting patients with high comorbidity and associated with high long-term mortality. PLoS One 2018; 13:e0195258. [PMID: 29624618 PMCID: PMC5889183 DOI: 10.1371/journal.pone.0195258] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 03/19/2018] [Indexed: 01/03/2023] Open
Abstract
Klebsiella pneumoniae (KP) is after Escherichia coli (EC) the most common gram-negative species causing invasive infections. Herein, we analyzed risk factors and prognosis in invasive infections caused by KP versus EC, in an area with low antimicrobial resistance. Moreover, we compared antimicrobial resistance and relative prevalence of KP and EC (KP/EC-ratio) in different European countries, using EARS-Net data. Adult patients admitted to Karolinska University Hospital 2006–2012 with invasive infection caused by KP (n = 599) were matched regarding sex and age with patients infected by EC. The medical records were retrospectively reviewed. Comorbidity was adjusted for with multivariable analysis. European data were retrieved from the EARS-Net database. No differences were observed in 7- and 30-day mortality between the groups. The 90-day mortality was significantly higher in the KP cohort (26% versus 17%, p<0.001), but not after adjusting for comorbidity. Malignancy was seen in 53% of the patients with KP versus 38% with EC, OR 1.86 (1.34–2.58). A significant increase in the rate of ESBL-production was observed in EC, but not in KP. The KP/EC-ratio remained stable. In contrast, European data showed increasing percentages of isolates non-susceptible to third-generation cephalosporins in EC and KP, and increasing KP/EC-ratio. Invasive infection caused by KP is a disease affecting patients with high comorbidity and associated with high 90-d mortality. The stable KP/EC-ratio and low occurrence of antimicrobial resistance in data from Karolinska University Hospital compared to aggregate data from 20 EARS-Net countries could be related to absence of clonal spread of multidrug-resistant KP.
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Affiliation(s)
- M. Vading
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Danderyds Hospital, Stockholm, Sweden
- * E-mail:
| | - P. Nauclér
- Department of Infectious Diseases, Karolinska University Hospital Solna, Stockholm, Sweden
- Department of Medicine Solna, Infectious Diseases Unit, Karolinska Institutet, Stockholm, Sweden
| | - M. Kalin
- Department of Medicine Solna, Infectious Diseases Unit, Karolinska Institutet, Stockholm, Sweden
| | - C. G. Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Microbiology, Karolinska University Hospital Solna, Stockholm, Sweden
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229
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López-Causapé C, Cabot G, Del Barrio-Tofiño E, Oliver A. The Versatile Mutational Resistome of Pseudomonas aeruginosa. Front Microbiol 2018; 9:685. [PMID: 29681898 PMCID: PMC5897538 DOI: 10.3389/fmicb.2018.00685] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 03/23/2018] [Indexed: 12/11/2022] Open
Abstract
One of the most striking features of Pseudomonas aeruginosa is its outstanding capacity for developing antimicrobial resistance to nearly all available antipseudomonal agents through the selection of chromosomal mutations, leading to the failure of the treatment of severe hospital-acquired or chronic infections. Recent whole-genome sequencing (WGS) data obtained from in vitro assays on the evolution of antibiotic resistance, in vivo monitoring of antimicrobial resistance development, analysis of sequential cystic fibrosis isolates, and characterization of widespread epidemic high-risk clones have provided new insights into the evolutionary dynamics and mechanisms of P. aeruginosa antibiotic resistance, thus motivating this review. Indeed, the analysis of the WGS mutational resistome has proven to be useful for understanding the evolutionary dynamics of classical resistance pathways and to describe new mechanisms for the majority of antipseudomonal classes, including β-lactams, aminoglycosides, fluoroquinolones, or polymixins. Beyond addressing a relevant scientific question, the analysis of the P. aeruginosa mutational resistome is expected to be useful, together with the analysis of the horizontally-acquired resistance determinants, for establishing the antibiotic resistance genotype, which should correlate with the antibiotic resistance phenotype and as such, it should be useful for the design of therapeutic strategies and for monitoring the efficacy of administered antibiotic treatments. However, further experimental research and new bioinformatics tools are still needed to overcome the interpretation limitations imposed by the complex interactions (including those leading to collateral resistance or susceptibility) between the 100s of genes involved in the mutational resistome, as well as the frequent difficulties for differentiating relevant mutations from simple natural polymorphisms.
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Affiliation(s)
- Carla López-Causapé
- Servicio de Microbiología y Unidad de Investigación, Hospital Universitari Son Espases, Institut d'Investigació Sanitaria Illes Balears, Palma de Mallorca, Spain
| | - Gabriel Cabot
- Servicio de Microbiología y Unidad de Investigación, Hospital Universitari Son Espases, Institut d'Investigació Sanitaria Illes Balears, Palma de Mallorca, Spain
| | - Ester Del Barrio-Tofiño
- Servicio de Microbiología y Unidad de Investigación, Hospital Universitari Son Espases, Institut d'Investigació Sanitaria Illes Balears, Palma de Mallorca, Spain
| | - Antonio Oliver
- Servicio de Microbiología y Unidad de Investigación, Hospital Universitari Son Espases, Institut d'Investigació Sanitaria Illes Balears, Palma de Mallorca, Spain
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Badi S, Cremonesi P, Abbassi MS, Ibrahim C, Snoussi M, Bignoli G, Luini M, Castiglioni B, Hassen A. Antibiotic resistance phenotypes and virulence-associated genes in Escherichia coli isolated from animals and animal food products in Tunisia. FEMS Microbiol Lett 2018; 365:4961136. [DOI: 10.1093/femsle/fny088] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 04/03/2018] [Indexed: 12/12/2022] Open
Affiliation(s)
- Souhir Badi
- Université de Tunis El Manar, Institut de la Recherche Vétérinaire de Tunisie, 20 rue Jebel lakhdhar, Bab Saadoun, Tunis 1006, Tunisie
- Laboratoire de Traitement des Eaux Usées, Centre de Recherches et des Technologies des Eaux, Technopôle de Borj-Cédria, BP 901, 2050 Hammam-Lif, Tunisie
| | - Paola Cremonesi
- Institute of Agricultural Biology and Biotechnology, Italian National Research Council (CNR IBBA), Via Einstein s/n, 26 900 Lodi, Italy
| | - Mohamed Salah Abbassi
- Université de Tunis El Manar, Institut de la Recherche Vétérinaire de Tunisie, 20 rue Jebel lakhdhar, Bab Saadoun, Tunis 1006, Tunisie
- Université de Tunis El Manar, Faculté de Médecine de Tunis, Laboratoire de résistance aux antibiotiques LR99ES09, Tunis 1006, Tunisie
| | - Chourouk Ibrahim
- Laboratoire de Traitement des Eaux Usées, Centre de Recherches et des Technologies des Eaux, Technopôle de Borj-Cédria, BP 901, 2050 Hammam-Lif, Tunisie
| | - Majdi Snoussi
- Laboratoire de Traitement des Eaux Usées, Centre de Recherches et des Technologies des Eaux, Technopôle de Borj-Cédria, BP 901, 2050 Hammam-Lif, Tunisie
| | - Giulia Bignoli
- Institute of Agricultural Biology and Biotechnology, Italian National Research Council (CNR IBBA), Via Einstein s/n, 26 900 Lodi, Italy
| | - Mario Luini
- Laboratory of Bacteriology, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, 26 900 Lodi, Italy
| | - Bianca Castiglioni
- Institute of Agricultural Biology and Biotechnology, Italian National Research Council (CNR IBBA), Via Einstein s/n, 26 900 Lodi, Italy
| | - Abdennaceur Hassen
- Laboratoire de Traitement des Eaux Usées, Centre de Recherches et des Technologies des Eaux, Technopôle de Borj-Cédria, BP 901, 2050 Hammam-Lif, Tunisie
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231
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Zogg AL, Simmen S, Zurfluh K, Stephan R, Schmitt SN, Nüesch-Inderbinen M. High Prevalence of Extended-Spectrum β-Lactamase Producing Enterobacteriaceae Among Clinical Isolates From Cats and Dogs Admitted to a Veterinary Hospital in Switzerland. Front Vet Sci 2018; 5:62. [PMID: 29662886 PMCID: PMC5890143 DOI: 10.3389/fvets.2018.00062] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 03/12/2018] [Indexed: 11/13/2022] Open
Abstract
Objectives This study aimed to identify and characterize extended-spectrum β-lactamase (ESBL) producing Enterobacteriaceae among clinical samples of companion animals. Methods A total of 346 non-duplicate Enterobacteriaceae isolates were collected between 2012 and 2016 from diseased cats (n = 115) and dogs (n = 231). The presence of blaESBL, PMQR genes, and the azithromycin resistance gene mph(A) was confirmed by PCR and sequencing of bla genes. Isolates were further characterized by antimicrobial resistance profiling, multilocus sequence typing, phylogenetic grouping, identification of mutations in the QRDR of gyrA and parC, and screening for virulence-associated genes. Results Among the 346 isolates, 72 (20.8%) were confirmed ESBL producers [58 Escherichia coli (E. coli), 11 Klebsiella pneumoniae (K. pneumoniae), and 3 Enterobacter cloacae]. The strains were cultured from urine (n = 45), skin and skin wounds (n = 8), abscesses (n = 6), surgical sites (n = 6), bile (n = 4), and other sites (n = 3). ESBL genes included blaCTX-M-1, 14, 15, 27, 55, and blaSHV-12, predominantly blaCTX-M-15 (54.8%, 40/73), and blaCTX-M-1 (24.7%, 18/73). Further genes included qnrB (4.2%, 3/72), qnrS (9.7%, 7/72), aac(6')-Ib-cr (47.2%, 34/72), and mph(A) (38.9%, 28/72). Seventeen (23.6%) isolates belonged to the major lineages of human pathogenic K. pneumoniae ST11, ST15, and ST147 and E. coli ST131. The most prevalent ST was E. coli ST410 belonging to phylogenetic group C. Conclusion The high prevalence of ESBL producing clinical Enterobacteriaceae from cats and dogs in Switzerland and the presence of highly virulent human-related K. pneumoniae and E. coli clones raises concern about transmission prevention as well as infection management and prevention in veterinary medicine.
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Affiliation(s)
- Anna Lena Zogg
- National Centre for Enteropathogenic Bacteria and Listeria, Vetsuisse Faculty, Institute for Food Safety and Hygiene, University of Zürich, Zürich, Switzerland
| | - Sabrina Simmen
- National Centre for Enteropathogenic Bacteria and Listeria, Vetsuisse Faculty, Institute for Food Safety and Hygiene, University of Zürich, Zürich, Switzerland
| | - Katrin Zurfluh
- National Centre for Enteropathogenic Bacteria and Listeria, Vetsuisse Faculty, Institute for Food Safety and Hygiene, University of Zürich, Zürich, Switzerland
| | - Roger Stephan
- National Centre for Enteropathogenic Bacteria and Listeria, Vetsuisse Faculty, Institute for Food Safety and Hygiene, University of Zürich, Zürich, Switzerland
| | - Sarah N Schmitt
- Vetsuisse Faculty, Institute of Veterinary Bacteriology, University of Zürich, Zürich, Switzerland
| | - Magdalena Nüesch-Inderbinen
- National Centre for Enteropathogenic Bacteria and Listeria, Vetsuisse Faculty, Institute for Food Safety and Hygiene, University of Zürich, Zürich, Switzerland
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232
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High Genetic Plasticity in Multidrug-Resistant Sequence Type 3-IncHI2 Plasmids Revealed by Sequence Comparison and Phylogenetic Analysis. Antimicrob Agents Chemother 2018; 62:AAC.02068-17. [PMID: 29437633 DOI: 10.1128/aac.02068-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 01/31/2018] [Indexed: 12/26/2022] Open
Abstract
We report a novel fusion plasmid, pP2-3T, cointegrating sequence type 3 (ST3)-IncHI2 with an IncFII plasmid backbone mediating multidrug resistance (MDR) and virulence. Phylogenetic analysis and comparative genomics revealed that pP2-3T and other MDR ST3-IncHI2 plasmids clustered together, representing a unique IncHI2 lineage that exhibited high conservation in backbones of plasmids but possessed highly genetic plasticity in various regions by acquiring numerous antibiotic resistance genes and fusing with other plasmids. Surveillance studies should be performed to monitor multiresistance IncHI2 plasmids among Enterobacteriaceae.
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233
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Treepong P, Kos V, Guyeux C, Blanc D, Bertrand X, Valot B, Hocquet D. Global emergence of the widespread Pseudomonas aeruginosa ST235 clone. Clin Microbiol Infect 2018. [DOI: 10.1016/j.cmi.2017.06.018] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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234
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Kukla R, Chudejova K, Papagiannitsis CC, Medvecky M, Habalova K, Hobzova L, Bolehovska R, Pliskova L, Hrabak J, Zemlickova H. Characterization of KPC-Encoding Plasmids from Enterobacteriaceae Isolated in a Czech Hospital. Antimicrob Agents Chemother 2018; 62:e02152-17. [PMID: 29263065 PMCID: PMC5826142 DOI: 10.1128/aac.02152-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 12/02/2017] [Indexed: 12/29/2022] Open
Abstract
Ten Enterobacteriaceae isolates collected in a Czech hospital carried blaKPC-positive plasmids of different sizes (∼30, ∼45, and ∼80 kb). Sequencing revealed three types of plasmids (A to C) with the Tn4401a transposon. Type A plasmids comprised an IncR backbone and a KPC-2-encoding multidrug resistance (MDR) region. Type B plasmids were derivatives of type A plasmids carrying an IncN3-like segment, while type C plasmids were IncP6 plasmids sharing the same KPC-2-encoding MDR region with type A and B plasmids.
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Affiliation(s)
- Rudolf Kukla
- Department of Clinical Microbiology, University Hospital and Faculty of Medicine in Hradec Kralove, Charles University, Hradec Kralove, Czech Republic
| | - Katerina Chudejova
- Department of Microbiology, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic
| | - Costas C Papagiannitsis
- Department of Clinical Microbiology, University Hospital and Faculty of Medicine in Hradec Kralove, Charles University, Hradec Kralove, Czech Republic
- Department of Microbiology, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic
| | - Matej Medvecky
- Veterinary Research Institute, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Katerina Habalova
- Department of Clinical Microbiology, University Hospital and Faculty of Medicine in Hradec Kralove, Charles University, Hradec Kralove, Czech Republic
| | - Lenka Hobzova
- Department of Hospital Hygiene, University Hospital, Hradec Kralove, Czech Republic
| | - Radka Bolehovska
- Department of Clinical Biochemistry and Diagnostics, University Hospital, Hradec Kralove, Czech Republic
| | - Lenka Pliskova
- Department of Clinical Biochemistry and Diagnostics, University Hospital, Hradec Kralove, Czech Republic
| | - Jaroslav Hrabak
- Department of Microbiology, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic
| | - Helena Zemlickova
- Department of Clinical Microbiology, University Hospital and Faculty of Medicine in Hradec Kralove, Charles University, Hradec Kralove, Czech Republic
- National Reference Laboratory for Antibiotics, National Institute of Public Health, Prague, Czech Republic
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235
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Campos ACC, Andrade NL, Ferdous M, Chlebowicz MA, Santos CC, Correal JCD, Lo Ten Foe JR, Rosa ACP, Damasco PV, Friedrich AW, Rossen JWA. Comprehensive Molecular Characterization of Escherichia coli Isolates from Urine Samples of Hospitalized Patients in Rio de Janeiro, Brazil. Front Microbiol 2018; 9:243. [PMID: 29503639 PMCID: PMC5821075 DOI: 10.3389/fmicb.2018.00243] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 01/31/2018] [Indexed: 01/09/2023] Open
Abstract
Urinary tract infections (UTIs) are often caused by Escherichia coli. Their increasing resistance to broad-spectrum antibiotics challenges the treatment of UTIs. Whereas, E. coli ST131 is often multidrug resistant (MDR), ST69 remains susceptible to antibiotics such as cephalosporins. Both STs are commonly linked to community and nosocomial infections. E. coli phylogenetic groups B2 and D are associated with virulence and resistance profiles making them more pathogenic. Little is known about the population structure of E. coli isolates obtained from urine samples of hospitalized patients in Brazil. Therefore, we characterized E. coli isolated from urine samples of patients hospitalized at the university and three private hospitals in Rio de Janeiro, using whole genome sequencing. A high prevalence of E. coli ST131 and ST69 was found, but other lineages, namely ST73, ST648, ST405, and ST10 were also detected. Interestingly, isolates could be divided into two groups based on their antibiotic susceptibility. Isolates belonging to ST131, ST648, and ST405 showed a high resistance rate to all antibiotic classes tested, whereas isolates belonging to ST10, ST73, ST69 were in general susceptible to the antibiotics tested. Additionally, most ST69 isolates, normally resistant to aminoglycosides, were susceptible to this antibiotic in our population. The majority of ST131 isolates were ESBL-producing and belonged to serotype O25:H4 and the H30-R subclone. Previous studies showed that this subclone is often associated with more complicated UTIs, most likely due to their high resistance rate to different antibiotic classes. Sequenced isolates could be classified into five phylogenetic groups of which B2, D, and F showed higher resistance rates than groups A and B1. No significant difference for the predicted virulence genes scores was found for isolates belonging to ST131, ST648, ST405, and ST69. In contrast, the phylogenetic groups B2, D and F showed a higher predictive virulence score compared to phylogenetic groups A and B1. In conclusion, despite the diversity of E. coli isolates causing UTIs, clonal groups O25:H4-B2-ST131 H30-R, O1:H6-B2-ST648, and O102:H6-D-ST405 were the most prevalent. The emergence of highly virulent and MDR E. coli in Brazil is of high concern and requires more attention from the health authorities.
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Affiliation(s)
- Ana Carolina C Campos
- Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil.,Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Nathália L Andrade
- Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mithila Ferdous
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Monika A Chlebowicz
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Carla C Santos
- Departamento de Controle de Infecções, Hospital Rio Laranjeiras, Rio de Janeiro, Brazil
| | - Julio C D Correal
- Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil.,Departamento de Controle de Infecções, Hospital Rio Laranjeiras, Rio de Janeiro, Brazil
| | - Jerome R Lo Ten Foe
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Ana Cláudia P Rosa
- Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paulo V Damasco
- Departamento de Doenças Infecciosas e Parasitárias, Universidade Federal do Estado do Rio de Janeiro, Rio de Janeiro, Brazil.,Departamento de Doenças Infecciosas e Parasitárias, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alex W Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - John W A Rossen
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
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236
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Mancini S, Poirel L, Corthesy M, Greub G, Nordmann P. Klebsiella pneumoniae co-producing KPC and RmtG, finally targeting Switzerland. Diagn Microbiol Infect Dis 2018; 90:151-152. [DOI: 10.1016/j.diagmicrobio.2017.10.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 10/23/2017] [Accepted: 10/29/2017] [Indexed: 10/18/2022]
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237
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Affiliation(s)
- Bente Olesen
- Department of Clinical Microbiology, Herlev and Gentofte Hospital, University of Copenhagen, Denmark
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238
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Bevan ER, Jones AM, Hawkey PM. Global epidemiology of CTX-M β-lactamases: temporal and geographical shifts in genotype. J Antimicrob Chemother 2018; 72:2145-2155. [PMID: 28541467 DOI: 10.1093/jac/dkx146] [Citation(s) in RCA: 483] [Impact Index Per Article: 80.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Globally, rates of ESBL-producing Enterobacteriaceae are rising. We undertook a literature review, and present the temporal trends in blaCTX-M epidemiology, showing that blaCTX-M-15 and blaCTX-M-14 have displaced other genotypes in many parts of the world. Explanations for these changes can be attributed to: (i) horizontal gene transfer (HGT) of plasmids; (ii) successful Escherichia coli clones; (iii) ESBLs in food animals; (iv) the natural environment; and (v) human migration and access to basic sanitation. We also provide explanations for the changing epidemiology of blaCTX-M-2 and blaCTX-M-27. Modifiable anthropogenic factors, such as poor access to basic sanitary facilities, encourage the spread of blaCTX-M and other antimicrobial resistance (AMR) genes, such as blaNDM, blaKPC and mcr-1. We provide further justification for novel preventative and interventional strategies to reduce transmission of these AMR genes.
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Affiliation(s)
- Edward R Bevan
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.,Public Health England, West Midlands Public Health Laboratory, Heart of England NHS Foundation Trust, Birmingham B5 9SS, UK
| | - Annie M Jones
- Magus Strategic Communications Ltd, Marr House, Scagglethorpe, Malton YO17?8ED, UK
| | - Peter M Hawkey
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.,Public Health England, West Midlands Public Health Laboratory, Heart of England NHS Foundation Trust, Birmingham B5 9SS, UK
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239
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Botelho J, Grosso F, Quinteira S, Brilhante M, Ramos H, Peixe L. Two decades of blaVIM-2-producing Pseudomonas aeruginosa dissemination: an interplay between mobile genetic elements and successful clones. J Antimicrob Chemother 2018; 73:873-882. [DOI: 10.1093/jac/dkx517] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 12/08/2017] [Indexed: 12/30/2022] Open
Affiliation(s)
- João Botelho
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Filipa Grosso
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Sandra Quinteira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto (CIBIO/UP)/InBio Laboratório Associado, Vairão, Portugal
- Faculdade de Ciências da Universidade do Porto, Departamento de Biologia, Porto, Portugal
- CESPU, Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde, Gandra, PRD, Portugal
| | - Michael Brilhante
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Helena Ramos
- Serviço de Microbiologia, Centro Hospitalar do Porto, Porto, Portugal
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
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240
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Navon-Venezia S, Kondratyeva K, Carattoli A. Klebsiella pneumoniae: a major worldwide source and shuttle for antibiotic resistance. FEMS Microbiol Rev 2018; 41:252-275. [PMID: 28521338 DOI: 10.1093/femsre/fux013] [Citation(s) in RCA: 638] [Impact Index Per Article: 106.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 02/28/2017] [Indexed: 01/15/2023] Open
Abstract
Klebsiella pneumoniae is an important multidrug-resistant (MDR) pathogen affecting humans and a major source for hospital infections associated with high morbidity and mortality due to limited treatment options. We summarize the wide resistome of this pathogen, which encompasses plentiful chromosomal and plasmid-encoded antibiotic resistance genes (ARGs). Under antibiotic selective pressure, K. pneumoniae continuously accumulates ARGs, by de novo mutations, and via acquisition of plasmids and transferable genetic elements, leading to extremely drug resistant (XDR) strains harboring a 'super resistome'. In the last two decades, numerous high-risk (HiR) MDR and XDR K. pneumoniae sequence types have emerged showing superior ability to cause multicontinent outbreaks, and continuous global dissemination. The data highlight the complex evolution of MDR and XDR K. pneumoniae, involving transfer and spread of ARGs, and epidemic plasmids in highly disseminating successful clones. With the worldwide catastrophe of antibiotic resistance and the urgent need to identify the main pathogens that pose a threat on the future of infectious diseases, further studies are warranted to determine the epidemic traits and plasmid acquisition in K. pneumoniae. There is a need for future genomic and translational studies to decipher specific targets in HiR clones to design targeted prevention and treatment.
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Affiliation(s)
- Shiri Navon-Venezia
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Ariel 40700, Israel
| | - Kira Kondratyeva
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Ariel 40700, Israel
| | - Alessandra Carattoli
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome 00161, Italy
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241
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Vila J, Sáez-López E, Johnson JR, Römling U, Dobrindt U, Cantón R, Giske CG, Naas T, Carattoli A, Martínez-Medina M, Bosch J, Retamar P, Rodríguez-Baño J, Baquero F, Soto SM. Escherichia coli: an old friend with new tidings. FEMS Microbiol Rev 2018; 40:437-463. [PMID: 28201713 DOI: 10.1093/femsre/fuw005] [Citation(s) in RCA: 175] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 09/23/2015] [Accepted: 02/04/2016] [Indexed: 12/16/2022] Open
Abstract
Escherichia coli is one of the most-studied microorganisms worldwide but its characteristics are continually changing. Extraintestinal E. coli infections, such as urinary tract infections and neonatal sepsis, represent a huge public health problem. They are caused mainly by specialized extraintestinal pathogenic E. coli (ExPEC) strains that can innocuously colonize human hosts but can also cause disease upon entering a normally sterile body site. The virulence capability of such strains is determined by a combination of distinctive accessory traits, called virulence factors, in conjunction with their distinctive phylogenetic background. It is conceivable that by developing interventions against the most successful ExPEC lineages or their key virulence/colonization factors the associated burden of disease and health care costs could foreseeably be reduced in the future. On the other hand, one important problem worldwide is the increase of antimicrobial resistance shown by bacteria. As underscored in the last WHO global report, within a wide range of infectious agents including E. coli, antimicrobial resistance has reached an extremely worrisome situation that ‘threatens the achievements of modern medicine’. In the present review, an update of the knowledge about the pathogenicity, antimicrobial resistance and clinical aspects of this ‘old friend’ was presented.
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Affiliation(s)
- J Vila
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- Department of Clinical Microbiology, Hospital Clinic, Universitat de Barcelona, Barcelona, Spain
- Spanish Network for Research in Infectious Diseases (REIPI), Instituto de Salud Carlos III, Madrid, Spain
| | - E Sáez-López
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - J R Johnson
- VA Medical Center, Minneapolis, MN, USA, and University of Minnesota, Minneapolis, MN, USA
| | - U Römling
- Karolinska Institute, Stockholm, Sweden
| | - U Dobrindt
- Institute of Hygiene, University of Münster, Münster, Germany
| | - R Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Spanish Network for Research in Infectious Diseases (REIPI), Instituto de Salud Carlos III, Madrid, Spain
| | - C G Giske
- Karolinska Institute, Stockholm, Sweden
| | - T Naas
- Hôpital de Bicêtre, Université Paris Sud, Le Kremlin-Bicêtre, France
| | - A Carattoli
- Department of infectious, parasitic and immune-mediated diseases, Istituto Superiore di Sanità, Rome, Italy
| | - M Martínez-Medina
- Laboratory of Molecular Microbiology, Department of Biology, University of Girona, Girona, Spain
| | - J Bosch
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- Department of Clinical Microbiology, Hospital Clinic, Universitat de Barcelona, Barcelona, Spain
| | - P Retamar
- Unidad Clínica de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospitales Universitarios Virgen Macarena y Virgen del Rocío, Departamento de Medicina, Universidad de Sevilla, Seville, Spain
| | - J Rodríguez-Baño
- Unidad Clínica de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospitales Universitarios Virgen Macarena y Virgen del Rocío, Departamento de Medicina, Universidad de Sevilla, Seville, Spain
- Spanish Network for Research in Infectious Diseases (REIPI), Instituto de Salud Carlos III, Madrid, Spain
| | - F Baquero
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - S M Soto
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
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242
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Skleenova E, Azizov I, Shek Е, Edelstein M, Kozlov R, Dekhnich A. Pseudomonas aeruginosa: the history of one of the most successful
nosocomial pathogens in Russian hospitals. ACTA ACUST UNITED AC 2018. [DOI: 10.36488/cmac.2018.3.164-171] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Pseudomonas aeruginosa is recognized as one of the six most important pathogens in terms of antimicrobial resistance («ESKAPE» pathogens), and included by WHO in the group of microorganisms for which the need for development of new antimicrobial agents is crucial. In 2015, P. aeruginosa was the second (after Klebsiella spp.) most common nosocomial bacterial pathogen in Russia with the following resistance rates: amikacin – 45.2%, imipenem – 51.5%, meropenem – 53.3%, colistin – 2.2%, piperacillin/tazobactam – 61.4%, ceftazidime – 56.8%, ciprofloxacin – 61.2%. The majority of carbapenemase-producing isolates in Russia belong to the two epidemic lineages – CC235 and CC654.
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Affiliation(s)
- E.Yu Skleenova
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University
| | - I.S. Azizov
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University
| | - Е.А. Shek
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University
| | - M.V. Edelstein
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University
| | - R.S. Kozlov
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University
| | - A.V. Dekhnich
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University
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Codjoe FS, Donkor ES. Carbapenem Resistance: A Review. Med Sci (Basel) 2017; 6:medsci6010001. [PMID: 29267233 PMCID: PMC5872158 DOI: 10.3390/medsci6010001] [Citation(s) in RCA: 270] [Impact Index Per Article: 38.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 11/25/2017] [Accepted: 12/05/2017] [Indexed: 12/16/2022] Open
Abstract
Carbapenem resistance is a major and an on-going public health problem globally. It occurs mainly among Gram-negative pathogens such as Klebsiella pneumoniae, Pseudomonas aeruginosa and Acinetobacter baumannii, and may be intrinsic or mediated by transferable carbapenemase-encoding genes. This type of resistance genes are already widespread in certain parts of the world, particularly Europe, Asia and South America, while the situation in other places such as sub-Saharan Africa is not well documented. In this paper, we provide an in-depth review of carbapenem resistance providing up-to-date information on the subject.
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Affiliation(s)
- Francis S Codjoe
- Department of Medical Laboratory Sciences (Microbiology Division), School of Biomedical & Allied Health Sciences, College of Health Sciences, University of Ghana, Korle Bu KB 143 Accra, Ghana.
- Biomolecular Science Research Centre, Sheffield Hallam University, Sheffield S1 1WB, UK.
| | - Eric S Donkor
- Department of Medical Microbiology, School of Biomedical & Allied Health Sciences, College of Health Sciences, University of Ghana, Korle Bu KB 143 Accra, Ghana.
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244
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Parulekar RS, Sonawane KD. Molecular modeling studies to explore the binding affinity of virtually screened inhibitor toward different aminoglycoside kinases from diverse MDR strains. J Cell Biochem 2017; 119:2679-2695. [DOI: 10.1002/jcb.26435] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Accepted: 10/18/2017] [Indexed: 01/17/2023]
Affiliation(s)
| | - Kailas D. Sonawane
- Department of MicrobiologyShivaji UniversityKolhapurMaharashtra (M.S.)India
- Department of Biochemistry, Structural Bioinformatics UnitShivaji UniversityKolhapurMaharashtra (M.S.)India
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245
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Nüesch-Inderbinen MT, Baschera M, Zurfluh K, Hächler H, Nüesch H, Stephan R. Clonal Diversity, Virulence Potential and Antimicrobial Resistance of Escherichia coli Causing Community Acquired Urinary Tract Infection in Switzerland. Front Microbiol 2017; 8:2334. [PMID: 29250044 PMCID: PMC5716990 DOI: 10.3389/fmicb.2017.02334] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/13/2017] [Indexed: 12/30/2022] Open
Abstract
Objectives: The aim of this study was to assess the clonal structure, virulence potential and antibiotic susceptibility of uropathogenic Escherichia coli (UPEC) isolates causing community acquired urinary tract infection (CAUTI) in unselected primary care patients in Switzerland. Methods: We performed multilocus sequence typing, virulence factor determination, and phenotypic and genotypic antimicrobial resistance testing on 44 non-duplicate UPEC isolates. Results: Twenty-seven different sequence types (STs) were identified. Major UPEC clones were represented by 19 (43.2%) of the isolates, including E. coli ST131, ST69 (both 13.6%), ST73 (6.8%), ST10 (4.5%), ST127, ST140, (both 2.3%). Five (11.4%) isolates belonged to ST141. Aggregate virulence factor (VF) scores were highest among isolates belonging to ST127 and ST141. Overall, 50% of the isolates were susceptible to all 12 antimicrobials tested, and all isolates remained susceptible to fosfomycin and nitrofurantoin. Resistance to sulfamethoxazole and ciprofloxacin were found in 31.8, and 15.9% of the isolates, respectively. Plasmid-mediated resistance genes were detected in ST69 and ST131 and included aac(6')-Ib-cr (2.3% of all isolates) blaCTX-M-14 and blaCTX-M-15 (9%), and mph(A) (13.6%). None of the isolates tested positive for mcr-1 or mcr-2. Conclusions: Our results show that CAUTI in Switzerland is caused by a wide variety of UPEC STs for which fosfomycin remains a good treatment option. We suggest that ST141 is an emerging clone associated with UTI in the community, and warrants closer attention. Moreover, the high rate of E. coli harboring mph(A) from patients without a history of antimicrobial therapy or hospitalization indicates that UPEC is an important reservoir for mph(A).
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Affiliation(s)
- Magdalena T. Nüesch-Inderbinen
- National Centre for Enteropathogenic Bacteria and Listeria, Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - Melinda Baschera
- National Centre for Enteropathogenic Bacteria and Listeria, Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - Katrin Zurfluh
- National Centre for Enteropathogenic Bacteria and Listeria, Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - Herbert Hächler
- National Centre for Enteropathogenic Bacteria and Listeria, Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - Hansjakob Nüesch
- Practice for General and Internal Medicine, Seuzach, Switzerland
| | - Roger Stephan
- National Centre for Enteropathogenic Bacteria and Listeria, Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
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246
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Aktaş E, Otlu B, Erdemir D, Ekici H, Bulut E. A First Insight into Escherichia coli ST131 High-Risk Clone Among Extended-Spectrum Beta-Lactamase-Producing Urine Isolates in Istanbul with the Use of Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass-Spectrometry and Real-Time PCR. Microb Drug Resist 2017; 23:1032-1036. [DOI: 10.1089/mdr.2017.0021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Elif Aktaş
- Clinical Microbiology Laboratory, Sisli Hamidiye Etfal Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Barış Otlu
- Department of Medical Microbiology, Inonu University Faculty of Medicine, Malatya, Turkey
| | - Duygu Erdemir
- Clinical Microbiology Laboratory, Sisli Hamidiye Etfal Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Hatice Ekici
- Clinical Microbiology Laboratory, Sisli Hamidiye Etfal Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Emin Bulut
- Clinical Microbiology Laboratory, Sisli Hamidiye Etfal Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
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247
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Papagiannitsis CC, Medvecky M, Chudejova K, Skalova A, Rotova V, Spanelova P, Jakubu V, Zemlickova H, Hrabak J. Molecular Characterization of Carbapenemase-Producing Pseudomonas aeruginosa of Czech Origin and Evidence for Clonal Spread of Extensively Resistant Sequence Type 357 Expressing IMP-7 Metallo-β-Lactamase. Antimicrob Agents Chemother 2017; 61:e01811-17. [PMID: 28993328 PMCID: PMC5700319 DOI: 10.1128/aac.01811-17] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 09/21/2017] [Indexed: 11/20/2022] Open
Abstract
The objective of this study was to perform molecular surveillance for assessing the spread of carbapenemase-producing Pseudomonas aeruginosa in Czech hospitals. One hundred thirty-six carbapenemase-producing isolates were recovered from 22 hospitals located throughout the country. Sequence type 357 (ST357) dominated (n = 120) among carbapenemase producers. One hundred seventeen isolates produced IMP-type (IMP-7 [n = 116] and IMP-1 [n = 1]) metallo-β-lactamases (MβLs), 15 produced the VIM-2 MβL, and the remaining isolates expressed the GES-5 enzyme. The blaIMP-like genes were located in three main integron types, with In-p110-like being the most prevalent (n = 115). The two other IMP-encoding integrons (In1392 and In1393) have not been described previously. blaVIM-2-carrying integrons included In59-like, In56, and a novel element (In1391). blaGES-5 was carried by In717. Sequencing data showed that In-p110-like was associated with a Tn4380-like transposon inserted in genomic island LESGI-3 in the P. aeruginosa chromosome. The other integrons were also integrated into the P. aeruginosa chromosome. These findings indicated the clonal spread of ST357 P. aeruginosa, carrying the IMP-7-encoding integron In-p110, in Czech hospitals. Additionally, the sporadic emergence of P. aeruginosa producing different carbapenemase types, associated with divergent or novel integrons, punctuated the ongoing evolution of these bacteria.
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Affiliation(s)
- Costas C Papagiannitsis
- Department of Microbiology, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic
| | | | - Katerina Chudejova
- Department of Microbiology, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic
| | - Anna Skalova
- Department of Microbiology, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic
| | - Veronika Rotova
- Department of Microbiology, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic
| | - Petra Spanelova
- National Reference Laboratory for Antibiotics, National Institute of Public Health, Prague, Czech Republic
| | - Vladislav Jakubu
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic
- National Reference Laboratory for Antibiotics, National Institute of Public Health, Prague, Czech Republic
| | - Helena Zemlickova
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic
- National Reference Laboratory for Antibiotics, National Institute of Public Health, Prague, Czech Republic
- Department of Clinical Microbiology, University Hospital and Faculty of Medicine in Hradec Kralove, Charles University, Hradec Kralove, Czech Republic
| | - Jaroslav Hrabak
- Department of Microbiology, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic
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248
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Lopatkin AJ, Meredith HR, Srimani JK, Pfeiffer C, Durrett R, You L. Persistence and reversal of plasmid-mediated antibiotic resistance. Nat Commun 2017; 8:1689. [PMID: 29162798 PMCID: PMC5698434 DOI: 10.1038/s41467-017-01532-1] [Citation(s) in RCA: 195] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 09/22/2017] [Indexed: 02/07/2023] Open
Abstract
In the absence of antibiotic-mediated selection, sensitive bacteria are expected to displace their resistant counterparts if resistance genes are costly. However, many resistance genes persist for long periods in the absence of antibiotics. Horizontal gene transfer (primarily conjugation) could explain this persistence, but it has been suggested that very high conjugation rates would be required. Here, we show that common conjugal plasmids, even when costly, are indeed transferred at sufficiently high rates to be maintained in the absence of antibiotics in Escherichia coli. The notion is applicable to nine plasmids from six major incompatibility groups and mixed populations carrying multiple plasmids. These results suggest that reducing antibiotic use alone is likely insufficient for reversing resistance. Therefore, combining conjugation inhibition and promoting plasmid loss would be an effective strategy to limit conjugation-assisted persistence of antibiotic resistance. It is unclear whether the transfer of plasmids carrying antibiotic resistance genes can explain their persistence when antibiotics are not present. Here, Lopatkin et al. show that conjugal plasmids, even when costly, are indeed transferred at sufficiently high rates to be maintained in the absence of antibiotics.
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Affiliation(s)
- Allison J Lopatkin
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Hannah R Meredith
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Jaydeep K Srimani
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Connor Pfeiffer
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Rick Durrett
- Department of Mathematics, Duke University, Durham, NC, 27708, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA. .,Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA. .,Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, 27710, USA.
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249
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Interplay among Resistance Profiles, High-Risk Clones, and Virulence in the Caenorhabditis elegans Pseudomonas aeruginosa Infection Model. Antimicrob Agents Chemother 2017; 61:AAC.01586-17. [PMID: 28923877 DOI: 10.1128/aac.01586-17] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 09/15/2017] [Indexed: 12/22/2022] Open
Abstract
The increasing prevalence of nosocomial infections produced by multidrug-resistant (MDR) or extensively drug-resistant (XDR) Pseudomonas aeruginosa is frequently linked to widespread international strains designated high-risk clones. In this work, we attempted to decipher the interplay between resistance profiles, high-risk clones, and virulence, testing a large (n = 140) collection of well-characterized P. aeruginosa isolates from different sources (bloodstream infections, nosocomial outbreaks, cystic fibrosis, and the environment) in a Caenorhabditis elegans infection model. Consistent with previous data, we documented a clear inverse correlation between antimicrobial resistance and virulence in the C. elegans model. Indeed, the lowest virulence was linked to XDR profiles, which were typically linked to defined high-risk clones. However, virulence varied broadly depending on the involved high-risk clone; it was high for sequence type 111 (ST111) and ST235 but very low for ST175. The highest virulence of ST235 could be attributed to its exoU+ type III secretion system (TTSS) genotype, which was found to be linked with higher virulence in our C. elegans model. Other markers, such as motility or pigment production, were not essential for virulence in the C. elegans model but seemed to be related with the higher values of the statistical normalized data. In contrast to ST235, the ST175 high-risk clone, which is widespread in Spain and France, seems to be associated with a particularly low virulence in the C. elegans model. Moreover, the previously described G154R AmpR mutation, prevalent in ST175, was found to contribute to the reduced virulence, although it was not the only factor involved. Altogether, our results provide a major step forward for understanding the interplay between P. aeruginosa resistance profiles, high-risk clones, and virulence.
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250
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Pires J, Kuenzli E, Hauser C, Tinguely R, Kasraian S, Atkinson A, Rauch A, Furrer H, Perreten V, Marschall J, Hatz C, Endimiani A. Intestinal colonisation with extended-spectrum cephalosporin-resistant Enterobacteriaceae in different populations in Switzerland: prevalence, risk factors and molecular features. J Glob Antimicrob Resist 2017; 12:17-19. [PMID: 29175015 DOI: 10.1016/j.jgar.2017.11.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 11/13/2017] [Accepted: 11/13/2017] [Indexed: 12/11/2022] Open
Affiliation(s)
- João Pires
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Esther Kuenzli
- Swiss Tropical and Public Health Institute, Basel, Switzerland; Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland
| | - Christoph Hauser
- Department of Infectious Diseases, Bern University Hospital and University of Bern, Bern, Switzerland
| | - Regula Tinguely
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Sara Kasraian
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Andrew Atkinson
- Department of Infectious Diseases, Bern University Hospital and University of Bern, Bern, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, Bern University Hospital and University of Bern, Bern, Switzerland
| | - Hansjakob Furrer
- Department of Infectious Diseases, Bern University Hospital and University of Bern, Bern, Switzerland
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jonas Marschall
- Department of Infectious Diseases, Bern University Hospital and University of Bern, Bern, Switzerland
| | - Christoph Hatz
- Swiss Tropical and Public Health Institute, Basel, Switzerland; Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland.
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