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Antonelli A, Coppi M, Bonaiuto C, Giovacchini N, Vaggelli G, Farese A, Pollini S, Rossolini GM. Novel resistance ICEs carrying the blaFIM-1 metallo-β-lactamase gene from an ST235 Pseudomonas aeruginosa sublineage. Antimicrob Agents Chemother 2024; 68:e0120523. [PMID: 38206043 PMCID: PMC10848763 DOI: 10.1128/aac.01205-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 11/29/2023] [Indexed: 01/12/2024] Open
Abstract
FIM-1 is an acquired metallo-β-lactamase identified in a multidrug-resistant Pseudomonas aeruginosa (index strain FI-14/157) of clinical origin isolated in 2007 in Florence, Italy. Here we report on a second case of infection by FIM-1-positive P. aeruginosa (FI-17645), which occurred in 2020 in the same hospital. Both FIM-1-positive strains exhibited resistance to all anti-Pseudomonas antibiotics except colistin and cefiderocol. Comparative genomic characterization revealed that the two FIM-positive strains were closely related [core genome difference, 16 single nucleotide polymorphisms (SNPs)], suggesting a local circulation of similar strains. In the FI-14/157 index strain, the blaFIM-1 gene was associated with an ISCR19-like element that likely contributed to its capture downstream an integron platform inserted aboard a Tn21-like transposon, named Tn7703.1, which was associated with a large integrative and conjugative element (ICE) named ICE7705.1, integrated into an att site located within the 3'-end of tRNAGly CCC gene of the P. aeruginosa chromosome. In strain FI-17645, blaFIM-1 was associated with a closely related ICE, named ICE7705.2, integrated in the same chromosomal site. Similar ICE platforms, lacking the blaFIM-1-containing region, were detected in other ST235 P. aeruginosa strains from different geographic areas, suggesting a common ancestry and underscoring the role of these elements in the dissemination of resistance genes in P. aeruginosa. Sequence database mining revealed two draft P. aeruginosa genomes, one from Italy and one from the USA (both isolated in 2012), including a contig with blaFIM-1, suggesting that this resistance gene could have a broader distribution than originally anticipated.
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Affiliation(s)
- Alberto Antonelli
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy
| | - Marco Coppi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy
| | - Chiara Bonaiuto
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy
| | - Nicla Giovacchini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Guendalina Vaggelli
- Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy
| | - Alberto Farese
- Infectious and Tropical Diseases Unit, Florence Careggi University Hospital, Florence, Italy
| | - Simona Pollini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy
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Dos Santos PAS, Silva MJA, Gouveia MIM, Lima LNGC, Quaresma AJPG, De Lima PDL, Brasiliense DM, Lima KVB, Rodrigues YC. The Prevalence of Metallo-Beta-Lactamese-(MβL)-Producing Pseudomonas aeruginosa Isolates in Brazil: A Systematic Review and Meta-Analysis. Microorganisms 2023; 11:2366. [PMID: 37764210 PMCID: PMC10534863 DOI: 10.3390/microorganisms11092366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/12/2023] [Accepted: 08/19/2023] [Indexed: 09/29/2023] Open
Abstract
The purpose of the current study is to describe the prevalence of Pseudomonas aeruginosa (PA)-producing MβL among Brazilian isolates and the frequency of blaSPM-1 in MβL-PA-producing isolates. From January 2009 to August 2023, we carried out an investigation on this subject in the internet databases SciELO, PubMed, Science Direct, and LILACS. A total of 20 papers that met the eligibility requirements were chosen by comprehensive meta-analysis software v2.2 for data retrieval and analysis by one meta-analysis using a fixed-effects model for the two investigations. The prevalence of MβL-producing P. aeruginosa was 35.8% or 0.358 (95% CI = 0.324-0.393). The studies' differences were significantly different from one another (x2 = 243.15; p < 0.001; I2 = 92.18%), so they were divided into subgroups based on Brazilian regions. There was indication of asymmetry in the meta-analyses' publishing bias funnel plot; so, a meta-regression was conducted by the study's publication year. According to the findings of Begg's test, no discernible publishing bias was found. blaSPM-1 prevalence was estimated at 66.9% or 0.669 in MβL-PA isolates (95% CI = 0.593-0.738). The analysis of this one showed an average heterogeneity (x2 = 90.93; p < 0.001; I2 = 80.20%). According to the results of Begg's test and a funnel plot, no discernible publishing bias was found. The research showed that MβL-P. aeruginosa and SPM-1 isolates were relatively common among individuals in Brazil. P. aeruginosa and other opportunistic bacteria are spreading quickly and causing severe infections, so efforts are needed to pinpoint risk factors, reservoirs, transmission pathways, and the origin of infection.
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Affiliation(s)
- Pabllo Antonny Silva Dos Santos
- Program in Parasitic Biology in the Amazon Region (PPGBPA), State University of Pará (UEPA), Belém 66087-662, PA, Brazil; (P.A.S.D.S.); (L.N.G.C.L.); (P.D.L.D.L.); (D.M.B.); (K.V.B.L.)
- Bacteriology and Mycology Section, Evandro Chagas Institute (SABMI/IEC), Ministry of Health, Ananindeua 67030-000, PA, Brazil; (M.I.M.G.); (A.J.P.G.Q.)
| | - Marcos Jessé Abrahão Silva
- Bacteriology and Mycology Section, Evandro Chagas Institute (SABMI/IEC), Ministry of Health, Ananindeua 67030-000, PA, Brazil; (M.I.M.G.); (A.J.P.G.Q.)
- Program in Epidemiology and Health Surveillance (PPGEVS), Evandro Chagas Institute (IEC), Ministry of Health, Ananindeua 67030-000, PA, Brazil
| | - Maria Isabel Montoril Gouveia
- Bacteriology and Mycology Section, Evandro Chagas Institute (SABMI/IEC), Ministry of Health, Ananindeua 67030-000, PA, Brazil; (M.I.M.G.); (A.J.P.G.Q.)
| | - Luana Nepomuceno Gondim Costa Lima
- Program in Parasitic Biology in the Amazon Region (PPGBPA), State University of Pará (UEPA), Belém 66087-662, PA, Brazil; (P.A.S.D.S.); (L.N.G.C.L.); (P.D.L.D.L.); (D.M.B.); (K.V.B.L.)
- Bacteriology and Mycology Section, Evandro Chagas Institute (SABMI/IEC), Ministry of Health, Ananindeua 67030-000, PA, Brazil; (M.I.M.G.); (A.J.P.G.Q.)
- Program in Epidemiology and Health Surveillance (PPGEVS), Evandro Chagas Institute (IEC), Ministry of Health, Ananindeua 67030-000, PA, Brazil
| | - Ana Judith Pires Garcia Quaresma
- Bacteriology and Mycology Section, Evandro Chagas Institute (SABMI/IEC), Ministry of Health, Ananindeua 67030-000, PA, Brazil; (M.I.M.G.); (A.J.P.G.Q.)
| | - Patrícia Danielle Lima De Lima
- Program in Parasitic Biology in the Amazon Region (PPGBPA), State University of Pará (UEPA), Belém 66087-662, PA, Brazil; (P.A.S.D.S.); (L.N.G.C.L.); (P.D.L.D.L.); (D.M.B.); (K.V.B.L.)
| | - Danielle Murici Brasiliense
- Program in Parasitic Biology in the Amazon Region (PPGBPA), State University of Pará (UEPA), Belém 66087-662, PA, Brazil; (P.A.S.D.S.); (L.N.G.C.L.); (P.D.L.D.L.); (D.M.B.); (K.V.B.L.)
- Bacteriology and Mycology Section, Evandro Chagas Institute (SABMI/IEC), Ministry of Health, Ananindeua 67030-000, PA, Brazil; (M.I.M.G.); (A.J.P.G.Q.)
- Program in Epidemiology and Health Surveillance (PPGEVS), Evandro Chagas Institute (IEC), Ministry of Health, Ananindeua 67030-000, PA, Brazil
| | - Karla Valéria Batista Lima
- Program in Parasitic Biology in the Amazon Region (PPGBPA), State University of Pará (UEPA), Belém 66087-662, PA, Brazil; (P.A.S.D.S.); (L.N.G.C.L.); (P.D.L.D.L.); (D.M.B.); (K.V.B.L.)
- Bacteriology and Mycology Section, Evandro Chagas Institute (SABMI/IEC), Ministry of Health, Ananindeua 67030-000, PA, Brazil; (M.I.M.G.); (A.J.P.G.Q.)
- Program in Epidemiology and Health Surveillance (PPGEVS), Evandro Chagas Institute (IEC), Ministry of Health, Ananindeua 67030-000, PA, Brazil
| | - Yan Corrêa Rodrigues
- Bacteriology and Mycology Section, Evandro Chagas Institute (SABMI/IEC), Ministry of Health, Ananindeua 67030-000, PA, Brazil; (M.I.M.G.); (A.J.P.G.Q.)
- Program in Epidemiology and Health Surveillance (PPGEVS), Evandro Chagas Institute (IEC), Ministry of Health, Ananindeua 67030-000, PA, Brazil
- Department of Natural Science, State University of Pará (DCNA/UEPA), Belém 66050-540, PA, Brazil
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Kusumoto M, Tamamura-Andoh Y, Hikoda-Kogiku Y, Magome A, Okuhama E, Sato K, Mizuno Y, Arai N, Watanabe-Yanai A, Iwata T, Ogura Y, Gotoh Y, Nakamura K, Hayashi T, Akiba M. Nationwide analysis of antimicrobial resistance in pathogenic Escherichia coli strains isolated from diseased swine over 29 years in Japan. Front Microbiol 2023; 14:1107566. [PMID: 37007495 PMCID: PMC10065406 DOI: 10.3389/fmicb.2023.1107566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 03/06/2023] [Indexed: 03/19/2023] Open
Abstract
Pathogenic Escherichia coli strains are important causes of several swine diseases that result in significant economic losses worldwide. In Japan, the use of antimicrobials in swine is much higher than that in other farm animals every year. Antimicrobial resistance in pathogenic E. coli strains also heavily impacts the swine industry due to the limited treatment options and an increase in the potential risk of the One Health crisis. In 2016, we investigated 684 Japanese isolates of swine pathogenic E. coli belonging to four major serogroups and reported the emergence and increase in the highly multidrug-resistant serogroups O116 and OSB9 and the appearance of colistin-resistant strains. In the present study, by expanding our previous analysis, we determined the serotypes and antimicrobial resistance of 1,708 E. coli strains isolated from diseased swine between 1991 and 2019 in Japan and found recent increases in the prevalences of multidrug-resistant strains and minor serogroup strains. Among the antimicrobials examined in this study that have been approved for animal use, a third-generation cephalosporin was found to be effective against the most isolates (resistance rate: 1.2%) but not against highly multidrug-resistant strains. We also analyzed the susceptibilities of the 1,708 isolates to apramycin and bicozamycin, both which are available for treating swine in Japan, and found that the rates of resistance to apramycin and bicozamycin were low (6.7% and 5.8%, respectively), and both antimicrobials are more effective (resistance rates: 2.7% and 5.4%, respectively) than third-generation cephalosporins (resistance rate: 16.2%) against highly multidrug-resistant strains.
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Affiliation(s)
- Masahiro Kusumoto
- National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Japan
- Graduate School of Veterinary Science, Osaka Metropolitan University, Osaka, Japan
- *Correspondence: Masahiro Kusumoto,
| | - Yukino Tamamura-Andoh
- National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Japan
| | | | - Asami Magome
- Kagoshima Central Livestock Hygiene Service Center, Kagoshima, Japan
| | - Erina Okuhama
- Miyazaki Livestock Hygiene Service Center, Miyazaki, Japan
| | - Keisuke Sato
- Niigata Chuo Livestock Hygiene Service Center, Niigata, Japan
| | - Yoshino Mizuno
- Kumamoto Chuo Livestock Hygiene Service Center, Kumamoto, Japan
| | - Nobuo Arai
- National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Ayako Watanabe-Yanai
- National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Taketoshi Iwata
- National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Yoshitoshi Ogura
- Department of Infectious Medicine, Kurume University School of Medicine, Fukuoka, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Keiji Nakamura
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masato Akiba
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Japan
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Genomic analysis reveals the role of integrative and conjugative elements in plant pathogenic bacteria. Mob DNA 2022; 13:19. [PMID: 35962419 PMCID: PMC9373382 DOI: 10.1186/s13100-022-00275-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 06/22/2022] [Indexed: 11/29/2022] Open
Abstract
Background ICEs are mobile genetic elements found integrated into bacterial chromosomes that can excise and be transferred to a new cell. They play an important role in horizontal gene transmission and carry accessory genes that may provide interesting phenotypes for the bacteria. Here, we seek to research the presence and the role of ICEs in 300 genomes of phytopathogenic bacteria with the greatest scientific and economic impact. Results Seventy-eight ICEs (45 distinct elements) were identified and characterized in chromosomes of Agrobacterium tumefaciens, Dickeya dadantii, and D. solani, Pectobacterium carotovorum and P. atrosepticum, Pseudomonas syringae, Ralstonia solanacearum Species Complex, and Xanthomonas campestris. Intriguingly, the co-occurrence of four ICEs was observed in some P. syringae strains. Moreover, we identified 31 novel elements, carrying 396 accessory genes with potential influence on virulence and fitness, such as genes coding for functions related to T3SS, cell wall degradation and resistance to heavy metals. We also present the analysis of previously reported data on the expression of cargo genes related to the virulence of P. atrosepticum ICEs, which evidences the role of these genes in the infection process of tobacco plants. Conclusions Altogether, this paper has highlighted the potential of ICEs to affect the pathogenicity and lifestyle of these phytopathogens and direct the spread of significant putative virulence genes in phytopathogenic bacteria. Supplementary Information The online version contains supplementary material available at 10.1186/s13100-022-00275-1.
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Andolfo G, Schuster C, Gharsa HB, Ruocco M, Leclerque A. Genomic analysis of the nomenclatural type strain of the nematode-associated entomopathogenic bacterium Providencia vermicola. BMC Genomics 2021; 22:708. [PMID: 34598677 PMCID: PMC8487129 DOI: 10.1186/s12864-021-08027-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 09/20/2021] [Indexed: 12/18/2022] Open
Abstract
Background Enterobacteria of the genus Providencia are mainly known as opportunistic human pathogens but have been isolated from highly diverse natural environments. The species Providencia vermicola comprises insect pathogenic bacteria carried by entomoparasitic nematodes and is investigated as a possible insect biocontrol agent. The recent publication of several genome sequences from bacteria assigned to this species has given rise to inconsistent preliminary results. Results The genome of the nematode-derived P. vermicola type strain DSM_17385 has been assembled into a 4.2 Mb sequence comprising 5 scaffolds and 13 contigs. A total of 3969 protein-encoding genes were identified. Multilocus sequence typing with different marker sets revealed that none of the previously published presumed P. vermicola genomes represents this taxonomic species. Comparative genomic analysis has confirmed a close phylogenetic relationship of P. vermicola to the P. rettgeri species complex. P. vermicola DSM_17385 carries a type III secretion system (T3SS-1) with probable function in host cell invasion or intracellular survival. Potentially antibiotic resistance-associated genes comprising numerous efflux pumps and point-mutated house-keeping genes, have been identified across the P. vermicola genome. A single small (3.7 kb) plasmid identified, pPVER1, structurally belongs to the qnrD-type family of fluoroquinolone resistance conferring plasmids that is prominent in Providencia and Proteus bacteria, but lacks the qnrD resistance gene. Conclusions The sequence reported represents the first well-supported published genome for the taxonomic species P. vermicola to be used as reference in further comparative genomics studies on Providencia bacteria. Due to a striking difference in the type of injectisome encoded by the respective genomes, P. vermicola might operate a fundamentally different mechanism of entomopathogenicity when compared to insect-pathogenic Providencia sneebia or Providencia burhodogranariea. The complete absence of antibiotic resistance gene carrying plasmids or mobile genetic elements as those causing multi drug resistance phenomena in clinical Providencia strains, is consistent with the invertebrate pathogen P. vermicola being in its natural environment efficiently excluded from the propagation routes of multidrug resistance (MDR) carrying genetic elements operating between human pathogens. Susceptibility to MDR plasmid acquisition will likely become a major criterion in the evaluation of P. vermicola for potential applications in biological pest control. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08027-w.
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Affiliation(s)
- Giuseppe Andolfo
- Department of Agricultural Sciences, University of Naples "Federico II", Via Università 100, 80055, Portici, Italy.
| | - Christina Schuster
- Department of Biology, Technische Universität Darmstadt, Schnittspahnstraße 10, 64287, Darmstadt, Germany
| | - Haifa Ben Gharsa
- Department of Biology, Technische Universität Darmstadt, Schnittspahnstraße 10, 64287, Darmstadt, Germany
| | - Michelina Ruocco
- Istituto per la Protezione Sostenibile delle Piante (IPSP), Consiglio Nazionale delle Ricerche (CNR), Piazzale Enrico Fermi 1, 80055, Portici, Italy
| | - Andreas Leclerque
- Department of Biology, Technische Universität Darmstadt, Schnittspahnstraße 10, 64287, Darmstadt, Germany. .,Istituto per la Protezione Sostenibile delle Piante (IPSP), Consiglio Nazionale delle Ricerche (CNR), Piazzale Enrico Fermi 1, 80055, Portici, Italy.
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Esposito F, Cardoso B, Fontana H, Fuga B, Cardenas-Arias A, Moura Q, Fuentes-Castillo D, Lincopan N. Genomic Analysis of Carbapenem-Resistant Pseudomonas aeruginosa Isolated From Urban Rivers Confirms Spread of Clone Sequence Type 277 Carrying Broad Resistome and Virulome Beyond the Hospital. Front Microbiol 2021; 12:701921. [PMID: 34539602 PMCID: PMC8446631 DOI: 10.3389/fmicb.2021.701921] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/20/2021] [Indexed: 11/13/2022] Open
Abstract
The dissemination of antibiotic-resistant priority pathogens beyond hospital settings is both a public health and an environmental problem. In this regard, high-risk clones exhibiting a multidrug-resistant (MDR) or extensively drug-resistant (XDR) phenotype have shown rapid adaptation at the human-animal-environment interface. In this study, we report genomic data and the virulence potential of the carbapenemase, São Paulo metallo-β-lactamase (SPM-1)-producing Pseudomonas aeruginosa strains (Pa19 and Pa151) isolated from polluted urban rivers, in Brazil. Bioinformatic analysis revealed a wide resistome to clinically relevant antibiotics (carbapenems, aminoglycosides, fosfomycin, sulfonamides, phenicols, and fluoroquinolones), biocides (quaternary ammonium compounds) and heavy metals (copper), whereas the presence of exotoxin A, alginate, quorum sensing, types II, III, and IV secretion systems, colicin, and pyocin encoding virulence genes was associated with a highly virulent behavior in the Galleria mellonella infection model. These results confirm the spread of healthcare-associated critical-priority P. aeruginosa belonging to the MDR sequence type 277 (ST277) clone beyond the hospital, highlighting that the presence of these pathogens in environmental water samples can have clinical implications for humans and other animals.
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Affiliation(s)
- Fernanda Esposito
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
| | - Brenda Cardoso
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Herrison Fontana
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
| | - Bruna Fuga
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Adriana Cardenas-Arias
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Quézia Moura
- Federal Institute of Education, Science and Technology of Espírito Santo, Vila Velha, Brazil
| | - Danny Fuentes-Castillo
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
- Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Nilton Lincopan
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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Urbanowicz P, Izdebski R, Baraniak A, Żabicka D, Hryniewicz W, Gniadkowski M. Molecular and genomic epidemiology of VIM/IMP-like metallo-β-lactamase-producing Pseudomonas aeruginosa genotypes in Poland. J Antimicrob Chemother 2021; 76:2273-2284. [PMID: 34179963 DOI: 10.1093/jac/dkab188] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/06/2021] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVES To identify key factors of the expansion of metallo-β-lactamase (MBL)-producing Pseudomonas aeruginosa (MPPA) in Poland, focusing on the role of clonal epidemic(s). METHODS MPPA isolates were typed by PFGE, followed by MLST. blaVIM/IMP MBL genes were amplified and sequenced within class 1 integrons. Their location was assessed by S1 nuclease-hybridization assays. Short-read WGS was performed, and genomes were subjected to SNP-based phylogenetic and resistome analyses. RESULTS Of 1314 MPPA isolates collected in 2005-15 from 212 hospitals, 454 representatives were selected. The isolates belonged to 120 pulsotypes and 52 STs, of which ST235 (∼31%), ST111 (∼17%), ST273 (∼16%) and ST654 (∼9%) prevailed, followed by ST244, ST17, ST395, ST175 and ST1567. The isolates produced seven VIM variants (97.5%) and four IMPs encoded by 46 integrons, most of which were observed only or mainly in Poland. Around 60% of the isolates resulted from (inter)regional clonal outbreaks of 10 individual ST235, ST111, ST273 and ST654 genotypes. The phylogenetic analysis of 163 genomes revealed heterogeneity of ST235 and ST111 populations, arising from transnational circulation and on-site differentiation of several clades/branches. Contrarily, ST273 and ST654 formed relatively homogeneous and apparently Poland-specific lineages, and a unique ST273 genotype with integron In249 was the most expansive organism. CONCLUSIONS Together with a previous report on self-transmissible In461-carrying IncP-2-type plasmids, this study revealed the molecular/genomic background of the rapid MPPA increase in Poland in 2001-15, evidencing multi-clonal spread as its leading factor. Numerous novel/specific MPPA characteristics were identified.
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Affiliation(s)
- P Urbanowicz
- Department of Molecular Microbiology, National Medicines Institute, 00-725, Warsaw, Poland
| | - R Izdebski
- Department of Molecular Microbiology, National Medicines Institute, 00-725, Warsaw, Poland
| | - A Baraniak
- Department of Molecular Microbiology, National Medicines Institute, 00-725, Warsaw, Poland
| | - D Żabicka
- Department of Epidemiology and Clinical Microbiology, The National Reference Centre for Susceptibility Testing, National Medicines Institute, 00-725, Warsaw, Poland
| | - W Hryniewicz
- Department of Epidemiology and Clinical Microbiology, The National Reference Centre for Susceptibility Testing, National Medicines Institute, 00-725, Warsaw, Poland
| | - M Gniadkowski
- Department of Molecular Microbiology, National Medicines Institute, 00-725, Warsaw, Poland
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Bahr G, González LJ, Vila AJ. Metallo-β-lactamases in the Age of Multidrug Resistance: From Structure and Mechanism to Evolution, Dissemination, and Inhibitor Design. Chem Rev 2021; 121:7957-8094. [PMID: 34129337 PMCID: PMC9062786 DOI: 10.1021/acs.chemrev.1c00138] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Antimicrobial resistance is one of the major problems in current practical medicine. The spread of genes coding for resistance determinants among bacteria challenges the use of approved antibiotics, narrowing the options for treatment. Resistance to carbapenems, last resort antibiotics, is a major concern. Metallo-β-lactamases (MBLs) hydrolyze carbapenems, penicillins, and cephalosporins, becoming central to this problem. These enzymes diverge with respect to serine-β-lactamases by exhibiting a different fold, active site, and catalytic features. Elucidating their catalytic mechanism has been a big challenge in the field that has limited the development of useful inhibitors. This review covers exhaustively the details of the active-site chemistries, the diversity of MBL alleles, the catalytic mechanism against different substrates, and how this information has helped developing inhibitors. We also discuss here different aspects critical to understand the success of MBLs in conferring resistance: the molecular determinants of their dissemination, their cell physiology, from the biogenesis to the processing involved in the transit to the periplasm, and the uptake of the Zn(II) ions upon metal starvation conditions, such as those encountered during an infection. In this regard, the chemical, biochemical and microbiological aspects provide an integrative view of the current knowledge of MBLs.
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Affiliation(s)
- Guillermo Bahr
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Lisandro J. González
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Alejandro J. Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
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Yaeger LN, Coles VE, Chan DCK, Burrows LL. How to kill Pseudomonas-emerging therapies for a challenging pathogen. Ann N Y Acad Sci 2021; 1496:59-81. [PMID: 33830543 DOI: 10.1111/nyas.14596] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/08/2021] [Accepted: 03/11/2021] [Indexed: 12/16/2022]
Abstract
As the number of effective antibiotics dwindled, antibiotic resistance (AR) became a pressing concern. Some Pseudomonas aeruginosa isolates are resistant to all available antibiotics. In this review, we identify the mechanisms that P. aeruginosa uses to evade antibiotics, including intrinsic, acquired, and adaptive resistance. Our review summarizes many different approaches to overcome resistance. Antimicrobial peptides have potential as therapeutics with low levels of resistance evolution. Rationally designed bacteriophage therapy can circumvent and direct evolution of AR and virulence. Vaccines and monoclonal antibodies are highlighted as immune-based treatments targeting specific P. aeruginosa antigens. This review also identifies promising drug combinations, antivirulence therapies, and considerations for new antipseudomonal discovery. Finally, we provide an update on the clinical pipeline for antipseudomonal therapies and recommend future avenues for research.
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Affiliation(s)
- Luke N Yaeger
- Department of Biochemistry and Biomedical Sciences and M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Victoria E Coles
- Department of Biochemistry and Biomedical Sciences and M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Derek C K Chan
- Department of Biochemistry and Biomedical Sciences and M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Lori L Burrows
- Department of Biochemistry and Biomedical Sciences and M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
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10
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Pseudomonas aeruginosa epidemic high-risk clones and their association with horizontally-acquired β-lactamases: 2020 update. Int J Antimicrob Agents 2020; 56:106196. [DOI: 10.1016/j.ijantimicag.2020.106196] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 07/30/2020] [Accepted: 09/26/2020] [Indexed: 01/17/2023]
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11
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Botelho J, Schulenburg H. The Role of Integrative and Conjugative Elements in Antibiotic Resistance Evolution. Trends Microbiol 2020; 29:8-18. [PMID: 32536522 DOI: 10.1016/j.tim.2020.05.011] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 05/07/2020] [Accepted: 05/14/2020] [Indexed: 02/07/2023]
Abstract
Mobile genetic elements (MGEs), such as plasmids and integrative and conjugative elements (ICEs), are main drivers for the spread of antibiotic resistance (AR). Coevolution between bacteria and plasmids shapes the transfer and stability of plasmids across bacteria. Although ICEs outnumber conjugative plasmids, the dynamics of ICE-bacterium coevolution, ICE transfer rates, and fitness costs are as yet largely unexplored. Conjugative plasmids and ICEs are both transferred by type IV secretion systems, but ICEs are typically immune to segregational loss, suggesting that the evolution of ICE-bacterium associations varies from that of plasmid-bacterium associations. Considering the high abundance of ICEs among bacteria, ICE-bacterium dynamics represent a promising challenge for future research that will enhance our understanding of AR spread in human pathogens.
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Affiliation(s)
- João Botelho
- Antibiotic Resistance Evolution Group, Max-Planck-Institute for Evolutionary Biology, Plön, Germany; Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts University, Kiel, Germany.
| | - Hinrich Schulenburg
- Antibiotic Resistance Evolution Group, Max-Planck-Institute for Evolutionary Biology, Plön, Germany; Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts University, Kiel, Germany
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12
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Vrancianu CO, Popa LI, Bleotu C, Chifiriuc MC. Targeting Plasmids to Limit Acquisition and Transmission of Antimicrobial Resistance. Front Microbiol 2020; 11:761. [PMID: 32435238 PMCID: PMC7219019 DOI: 10.3389/fmicb.2020.00761] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 03/30/2020] [Indexed: 12/19/2022] Open
Abstract
Antimicrobial resistance (AMR) is a significant global threat to both public health and the environment. The emergence and expansion of AMR is sustained by the enormous diversity and mobility of antimicrobial resistance genes (ARGs). Different mechanisms of horizontal gene transfer (HGT), including conjugation, transduction, and transformation, have facilitated the accumulation and dissemination of ARGs in Gram-negative and Gram-positive bacteria. This has resulted in the development of multidrug resistance in some bacteria. The most clinically significant ARGs are usually located on different mobile genetic elements (MGEs) that can move intracellularly (between the bacterial chromosome and plasmids) or intercellularly (within the same species or between different species or genera). Resistance plasmids play a central role both in HGT and as support elements for other MGEs, in which ARGs are assembled by transposition and recombination mechanisms. Considering the crucial role of MGEs in the acquisition and transmission of ARGs, a potential strategy to control AMR is to eliminate MGEs. This review discusses current progress on the development of chemical and biological approaches for the elimination of ARG carriers.
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Affiliation(s)
- Corneliu Ovidiu Vrancianu
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania
- The Research Institute of the University of Bucharest, Bucharest, Romania
| | - Laura Ioana Popa
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania
- The Research Institute of the University of Bucharest, Bucharest, Romania
- The National Institute of Research and Development for Biological Sciences, Bucharest, Romania
| | - Coralia Bleotu
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania
- The Research Institute of the University of Bucharest, Bucharest, Romania
- Stefan S. Nicolau Institute of Virology, Bucharest, Romania
| | - Mariana Carmen Chifiriuc
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania
- The Research Institute of the University of Bucharest, Bucharest, Romania
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13
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Silveira MC, Rocha-de-Souza CM, Albano RM, de Oliveira Santos IC, Carvalho-Assef APD. Exploring the success of Brazilian endemic clone Pseudomonas aeruginosa ST277 and its association with the CRISPR-Cas system type I-C. BMC Genomics 2020; 21:255. [PMID: 32293244 PMCID: PMC7092672 DOI: 10.1186/s12864-020-6650-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/04/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The Brazilian endemic clone Pseudomonas aeruginosa ST277 carries important antibiotic resistance determinants, highlighting the gene coding for SPM-1 carbapenemase. However, the resistance and persistence of this clone is apparently restricted to the Brazilian territory. To understand the differences between Brazilian strains from those isolated in other countries, we performed a phylogenetic analysis of 47 P. aeruginosa ST277 genomes as well as analyzed the virulence and resistance gene profiles. Furthermore, we evaluated the distribution of genomic islands and assessed in detail the characteristics of the CRISPR-Cas immunity system in these isolates. RESULTS The Brazilian genomes presented a typical set of resistance and virulence determinants, genomic islands and a high frequency of the CRISPR-Cas system type I-C. Even though the ST277 genomes are closely related, the phylogenetic analysis showed that the Brazilian strains share a great number of exclusively SNPs when compared to other ST277 genomes. We also observed a standard CRISPR spacers content for P. aeruginosa ST277, confirming a strong link between sequence type and spacer acquisition. Most CRISPR spacer targets were phage sequences. CONCLUSIONS Based on our findings, P. aeruginosa ST277 strains circulating in Brazil characteristically acquired In163 and PAGI-25, which can distinguish them from strains that do not accumulate resistance mechanisms and can be found on the Asian, European and North American continents. The distinctive genetic elements accumulated in Brazilian samples can contribute to the resistance, pathogenicity and transmission success that characterize the ST277 in this country.
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Affiliation(s)
- Melise Chaves Silveira
- Laboratório de Pesquisa em Infecção Hospitalar, Oswaldo Cruz Institute, Fiocruz, Avenida Brasil 4365, Manguinhos, Rio de Janeiro, Rio de Janeiro, 21040-360, Brazil
| | - Cláudio Marcos Rocha-de-Souza
- Laboratório de Pesquisa em Infecção Hospitalar, Oswaldo Cruz Institute, Fiocruz, Avenida Brasil 4365, Manguinhos, Rio de Janeiro, Rio de Janeiro, 21040-360, Brazil
| | - Rodolpho Mattos Albano
- Departamento de Bioquímica, Universidade do Estado do Rio de Janeiro, Boulevard Vinte e Oito de Setembro, 87, fundos, andar 4, Vila Isabel, Rio de Janeiro, Rio de Janeiro, 20551-030, Brazil
| | - Ivson Cassiano de Oliveira Santos
- Laboratório de Pesquisa em Infecção Hospitalar, Oswaldo Cruz Institute, Fiocruz, Avenida Brasil 4365, Manguinhos, Rio de Janeiro, Rio de Janeiro, 21040-360, Brazil
| | - Ana Paula D'Alincourt Carvalho-Assef
- Laboratório de Pesquisa em Infecção Hospitalar, Oswaldo Cruz Institute, Fiocruz, Avenida Brasil 4365, Manguinhos, Rio de Janeiro, Rio de Janeiro, 21040-360, Brazil.
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Ogawara H. Comparison of Antibiotic Resistance Mechanisms in Antibiotic-Producing and Pathogenic Bacteria. Molecules 2019; 24:E3430. [PMID: 31546630 PMCID: PMC6804068 DOI: 10.3390/molecules24193430] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/18/2019] [Accepted: 09/20/2019] [Indexed: 12/13/2022] Open
Abstract
Antibiotic resistance poses a tremendous threat to human health. To overcome this problem, it is essential to know the mechanism of antibiotic resistance in antibiotic-producing and pathogenic bacteria. This paper deals with this problem from four points of view. First, the antibiotic resistance genes in producers are discussed related to their biosynthesis. Most resistance genes are present within the biosynthetic gene clusters, but some genes such as paromomycin acetyltransferases are located far outside the gene cluster. Second, when the antibiotic resistance genes in pathogens are compared with those in the producers, resistance mechanisms have dependency on antibiotic classes, and, in addition, new types of resistance mechanisms such as Eis aminoglycoside acetyltransferase and self-sacrifice proteins in enediyne antibiotics emerge in pathogens. Third, the relationships of the resistance genes between producers and pathogens are reevaluated at their amino acid sequence as well as nucleotide sequence levels. Pathogenic bacteria possess other resistance mechanisms than those in antibiotic producers. In addition, resistance mechanisms are little different between early stage of antibiotic use and the present time, e.g., β-lactam resistance in Staphylococcus aureus. Lastly, guanine + cytosine (GC) barrier in gene transfer to pathogenic bacteria is considered. Now, the resistance genes constitute resistome composed of complicated mixture from divergent environments.
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Affiliation(s)
- Hiroshi Ogawara
- HO Bio Institute, 33-9, Yushima-2, Bunkyo-ku, Tokyo 113-0034, Japan.
- Department of Biochemistry, Meiji Pharmaceutical University, 522-1, Noshio-2, Kiyose, Tokyo 204-8588, Japan.
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15
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Antibiotic resistance in Pseudomonas aeruginosa - Mechanisms, epidemiology and evolution. Drug Resist Updat 2019; 44:100640. [PMID: 31492517 DOI: 10.1016/j.drup.2019.07.002] [Citation(s) in RCA: 252] [Impact Index Per Article: 50.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/11/2019] [Accepted: 07/12/2019] [Indexed: 12/13/2022]
Abstract
Antibiotics are powerful drugs used in the treatment of bacterial infections. The inappropriate use of these medicines has driven the dissemination of antibiotic resistance (AR) in most bacteria. Pseudomonas aeruginosa is an opportunistic pathogen commonly involved in environmental- and difficult-to-treat hospital-acquired infections. This species is frequently resistant to several antibiotics, being in the "critical" category of the WHO's priority pathogens list for research and development of new antibiotics. In addition to a remarkable intrinsic resistance to several antibiotics, P. aeruginosa can acquire resistance through chromosomal mutations and acquisition of AR genes. P. aeruginosa has one of the largest bacterial genomes and possesses a significant assortment of genes acquired by horizontal gene transfer (HGT), which are frequently localized within integrons and mobile genetic elements (MGEs), such as transposons, insertion sequences, genomic islands, phages, plasmids and integrative and conjugative elements (ICEs). This genomic diversity results in a non-clonal population structure, punctuated by specific clones that are associated with significant morbidity and mortality worldwide, the so-called high-risk clones. Acquisition of MGEs produces a fitness cost in the host, that can be eased over time by compensatory mutations during MGE-host coevolution. Even though plasmids and ICEs are important drivers of AR, the underlying evolutionary traits that promote this dissemination are poorly understood. In this review, we provide a comprehensive description of the main strategies involved in AR in P. aeruginosa and the leading drivers of HGT in this species. The most recently developed genomic tools that allowed a better understanding of the features contributing for the success of P. aeruginosa are discussed.
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Botelho J, Grosso F, Peixe L. WITHDRAWN: Antibiotic resistance in Pseudomonas aeruginosa – mechanisms, epidemiology and evolution. Drug Resist Updat 2019. [DOI: 10.1016/j.drup.2019.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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17
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Galetti R, Andrade LN, Varani AM, Darini ALC. SPM-1-producing Pseudomonas aeruginosa ST277 carries a chromosomal pack of acquired resistance genes: An example of high-risk clone associated with 'intrinsic resistome'. J Glob Antimicrob Resist 2018; 16:183-186. [PMID: 30586621 DOI: 10.1016/j.jgar.2018.12.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 11/14/2018] [Accepted: 12/17/2018] [Indexed: 11/27/2022] Open
Abstract
OBJECTIVES The purpose of this study was to investigate the resistome of an SPM-1-producing Pseudomonas aeruginosa ST277 isolate (HC84) from Brazil. METHODS Whole-genome sequencing of P. aeruginosa HC84 was performed using an Ion Proton™ System. De novo assembly was carried out using CLC Genomics Workbench 8.0, and gene prediction was performed using the Prokka pipeline. RESULTS AND CONCLUSION Here we describe the resistome of SPM-1-producing P. aeruginosa ST277 (HC84) consisting of 13 different antimicrobial resistance genes [blaSPM-1, rmtD, aacA4, aadA7, blaOXA-56, blaOXA-396, blaPAO, aph(3')-IIb, aac(6')-Ib-cr, crpP, catB7, cmx and fosA). This particular chromosomal pack of resistance genes is strongly associated with clonal dissemination and suggests an important role in the persistence of this clone in Brazilian nosocomial infections. For that reason, could we already consider the 'chromosomal pack of acquired resistance genes' like an 'ST277 intrinsic resistome'? This is an example of chromosomal accumulation of acquired resistance genes as well as integrative and conjugative elements into a successful bacterial pathogen and calls attention to the evolution of other species driving to insertion and persistence of multiple acquired resistance genes in the bacterial chromosome.
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Affiliation(s)
- Renata Galetti
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil.
| | - Leonardo Neves Andrade
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Alessandro M Varani
- Faculdade de Ciencias Agrárias e Veterinárias, Universidade Estadual Paulista 'Julio de Mesquita Filho', Jaboticabal, Brazil
| | - Ana Lúcia Costa Darini
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
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18
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Botelho J, Roberts AP, León-Sampedro R, Grosso F, Peixe L. Carbapenemases on the move: it's good to be on ICEs. Mob DNA 2018; 9:37. [PMID: 30574213 PMCID: PMC6299553 DOI: 10.1186/s13100-018-0141-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 11/29/2018] [Indexed: 12/13/2022] Open
Abstract
Background The evolution and spread of antibiotic resistance is often mediated by mobile genetic elements. Integrative and conjugative elements (ICEs) are the most abundant conjugative elements among prokaryotes. However, the contribution of ICEs to horizontal gene transfer of antibiotic resistance has been largely unexplored. Results Here we report that ICEs belonging to mating-pair formation (MPF) classes G and T are highly prevalent among the opportunistic pathogen Pseudomonas aeruginosa, contributing to the spread of carbapenemase-encoding genes (CEGs). Most CEGs of the MPFG class were encoded within class I integrons, which co-harbour genes conferring resistance to other antibiotics. The majority of the integrons were located within Tn3-like and composite transposons. Conserved attachment site could be predicted for the MPFG class ICEs. MPFT class ICEs carried the CEGs within composite transposons which were not associated with integrons. Conclusions The data presented here provides a global snapshot of the different CEG-harbouring ICEs and sheds light on the underappreciated contribution of these elements to the evolution and dissemination of antibiotic resistance on P. aeruginosa. Electronic supplementary material The online version of this article (10.1186/s13100-018-0141-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- João Botelho
- 1UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia da Universidade do Porto, Rua Jorge Viterbo Ferreira nº 228, 4050-313 Porto, Portugal
| | - Adam P Roberts
- 2Department of Parasitology, Liverpool School of Tropical Medicine, Liverpool, UK.,3Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Ricardo León-Sampedro
- 4Department of Microbiology, University Hospital Ramón y Cajal, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain.,Biomedical Research Networking Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - Filipa Grosso
- 1UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia da Universidade do Porto, Rua Jorge Viterbo Ferreira nº 228, 4050-313 Porto, Portugal
| | - Luísa Peixe
- 1UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia da Universidade do Porto, Rua Jorge Viterbo Ferreira nº 228, 4050-313 Porto, Portugal
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Partridge SR, Kwong SM, Firth N, Jensen SO. Mobile Genetic Elements Associated with Antimicrobial Resistance. Clin Microbiol Rev 2018; 31:e00088-17. [PMID: 30068738 PMCID: PMC6148190 DOI: 10.1128/cmr.00088-17] [Citation(s) in RCA: 1189] [Impact Index Per Article: 198.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Strains of bacteria resistant to antibiotics, particularly those that are multiresistant, are an increasing major health care problem around the world. It is now abundantly clear that both Gram-negative and Gram-positive bacteria are able to meet the evolutionary challenge of combating antimicrobial chemotherapy, often by acquiring preexisting resistance determinants from the bacterial gene pool. This is achieved through the concerted activities of mobile genetic elements able to move within or between DNA molecules, which include insertion sequences, transposons, and gene cassettes/integrons, and those that are able to transfer between bacterial cells, such as plasmids and integrative conjugative elements. Together these elements play a central role in facilitating horizontal genetic exchange and therefore promote the acquisition and spread of resistance genes. This review aims to outline the characteristics of the major types of mobile genetic elements involved in acquisition and spread of antibiotic resistance in both Gram-negative and Gram-positive bacteria, focusing on the so-called ESKAPEE group of organisms (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp., and Escherichia coli), which have become the most problematic hospital pathogens.
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Affiliation(s)
- Sally R Partridge
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Westmead, New South Wales, Australia
| | - Stephen M Kwong
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Neville Firth
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Slade O Jensen
- Microbiology and Infectious Diseases, School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
- Antibiotic Resistance & Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, New South Wales, Australia
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Botelho J, Grosso F, Peixe L. Unravelling the genome of a Pseudomonas aeruginosa isolate belonging to the high-risk clone ST235 reveals an integrative conjugative element housing a blaGES-6 carbapenemase. J Antimicrob Chemother 2018; 73:77-83. [PMID: 29029083 DOI: 10.1093/jac/dkx337] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 08/19/2017] [Indexed: 12/12/2022] Open
Abstract
Objectives In Pseudomonas aeruginosa, the blaGES-6 carbapenemase gene was previously associated with an In1076 class I integron. Here, we conducted a genome-based analysis and explored the genetic platform associated with the mobility of this gene. Methods WGS of a blaGES-6-harbouring P. aeruginosa isolate (FFUP_PS_690) was performed with Illumina HiSeq, de novo assembly was performed using SPAdes and subsequent bioinformatic analysis was performed concerning antibiotic resistance genes, virulence features and mobile genetic elements. Results The FFUP_PS_690 isolate belongs to the ST235 high-risk clone and houses a novel integrative conjugative element (ICE), hereby named ICEPae690. This clc-like ICE comprises the blaGES-6-harbouring In1076 integron and specific modules. An ExoU island A variant was also identified. Conclusions The presence of a 'hitch-hiking' blaGES-6-harbouring In1076 integron in an ICE and an exoU-carrying genomic island highlight the potential spread of these elements through conjugation and/or clonal expansion of the ST235 lineage.
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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
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
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21
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Acquisition of resistance to carbapenem and macrolide-mediated quorum sensing inhibition by Pseudomonas aeruginosa via ICE Tn4371 6385. Commun Biol 2018; 1:57. [PMID: 30271939 PMCID: PMC6123621 DOI: 10.1038/s42003-018-0064-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 05/03/2018] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas aeruginosa can cause life-threatening infections in immunocompromised patients. The first-line agents to treat P. aeruginosa infections are carbapenems. However, the emergence of carbapenem-resistant P. aeruginosa strains greatly compromised the effectiveness of carbapenem treatment, which makes the surveillance on their spreading and transmission important. Here we characterized the full-length genomes of two carbapenem-resistant P. aeruginosa clinical isolates that are capable of producing New Delhi metallo-β-lactamase-1 (NDM-1). We show that blaNDM-1 is carried by a novel integrative and conjugative element (ICE) ICETn43716385, which also carries the macrolide resistance gene msr(E) and the florfenicol resistance gene floR. By exogenously expressing msr(E) in P. aeruginosa laboratory strains, we show that Msr(E) can abolish azithromycin-mediated quorum sensing inhibition in vitro and anti-Pseudomonas effect in vivo. We conclude that ICEs are important in transmitting carbapenem resistance, and that anti-virulence treatment of P. aeruginosa infections using sub-inhibitory concentrations of macrolides can be challenged by horizontal gene transfer. Yichen Ding et al. identify a novel integrative and conjugative element that confers Pseudomonas aeruginosa with resistance to carbapenem, the last-resort drug for susceptable Gram-negative bacterial infections. This study also shows how antivirulence treatment for P. aeruginosainfections can be challenged by horizontal gene transfer.
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22
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Fonseca EL, Andrade BGN, Vicente ACP. The Resistome of Low-Impacted Marine Environments Is Composed by Distant Metallo-β-Lactamases Homologs. Front Microbiol 2018; 9:677. [PMID: 29675014 PMCID: PMC5895761 DOI: 10.3389/fmicb.2018.00677] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 03/22/2018] [Indexed: 01/20/2023] Open
Abstract
The worldwide dispersion and sudden emergence of new antibiotic resistance genes (ARGs) determined the need in uncovering which environment participate most as their source and reservoir. ARGs closely related to those currently found in human pathogens occur in the resistome of anthropogenic impacted environments. However, the role of pristine environment as the origin and source of ARGs remains underexplored and controversy, particularly, the marine environments represented by the oceans. Here, due to the ocean nature, we hypothesized that the resistome of this pristine/low-impacted marine environment is represented by distant ARG homologs. To test this hypothesis we performed an in silico analysis on the Global Ocean Sampling (GOS) metagenomic project dataset focusing on the metallo-β-lactamases (MβLs) as the ARG model. MβLs have been a challenge to public health, since they hydrolyze the carbapenems, one of the last therapeutic choice in clinics. Using Hidden Markov Model (HMM) profiles, we were successful in identifying a high diversity of distant MβL homologs, related to the B1, B2, and B3 subclasses. The majority of them were distributed across the Atlantic, Indian, and Pacific Oceans being related to the chromosomally encoded MβL GOB present in Elizabethkingia genus. It was observed only a reduced number of metagenomic sequence homologs related to the acquired MβL enzymes (VIM, SPM-1, and AIM-1) that currently have impact in clinics. Therefore, low antibiotic impacted marine environment, as the ocean, are unlikely the source of ARGs that have been causing enormous threat to the public health.
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Affiliation(s)
- Erica L Fonseca
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Bruno G N Andrade
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Ana C P Vicente
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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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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Martins WMBS, Narciso AC, Cayô R, Santos SV, Fehlberg LCC, Ramos PL, da Cruz JB, Gales AC. SPM-1-producing Pseudomonas aeruginosa ST277 clone recovered from microbiota of migratory birds. Diagn Microbiol Infect Dis 2017; 90:221-227. [PMID: 29224710 DOI: 10.1016/j.diagmicrobio.2017.11.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 11/01/2017] [Accepted: 11/02/2017] [Indexed: 02/02/2023]
Abstract
The production of São Paulo metallo-β-lactamase (SPM-1) is the most common carbapenem resistance mechanism detected among multidrug-resistant Pseudomonas aeruginosa clinical isolates in Brazil. Dissemination of SPM-1-producing P. aeruginosa has been restricted to the nosocomial settings, with sporadic reports of environmental isolates due to contamination by hospital sewage. Herein, we described the detection and molecular characterization of SPM-1-producing P. aeruginosa recovered from the microbiota of migratory birds in Brazil. Three hundred gram-negative bacilli were recovered from cloacal and choanal swabs of Dendrocygna viduata during a surveillance study for detection of carbapenem-resistant isolates. All isolates were identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Molecular typing was performed by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing. MICs were determined by agar dilution, except for polymyxin B. Antibiotic resistance genes were detected by polymerase chain reaction (PCR) followed by DNA sequencing. Transcriptional levels of oprD and efflux system encoding genes were also carried out by quantitative real-time PCR. Nine imipenem-resistant P. aeruginosa isolates were recovered with 7 of them carrying blaSPM-1. Additional resistance genes (rmtD-1, blaOXA-56,aacA4, and aac(6')-Ib-cr) were also detected in all 9 isolates. The SPM-1-producing isolates showed high MICs for all β-lactams, fluoroquinolones, and aminoglycosides, being susceptible only to polymyxin B. Interestingly, all isolates showed the same PFGE pattern and belonged to ST277. Overexpression of MexXY-OprM and MexAB-OprM was observed in those isolates that did not harbor blaSPM-1. Our results suggest that migratory birds might have played a role in the dissemination of SPM-1-producing P. aeruginosa within the Brazilian territory.
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Affiliation(s)
- Willames M B S Martins
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo-UNIFESP, São Paulo, Brazil.
| | - Ana Clara Narciso
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo-UNIFESP, São Paulo, Brazil
| | - Rodrigo Cayô
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo-UNIFESP, São Paulo, Brazil
| | - Stéfanie Vanessa Santos
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo-UNIFESP, São Paulo, Brazil
| | - Lorena C C Fehlberg
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo-UNIFESP, São Paulo, Brazil
| | - Patrícia Locosque Ramos
- Departamento de Pesquisas Aplicadas, Fundação Parque Zoológico de São Paulo, São Paulo, SP, Brazil
| | | | - Ana Cristina Gales
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo-UNIFESP, São Paulo, Brazil
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25
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Escandón-Vargas K, Reyes S, Gutiérrez S, Villegas MV. The epidemiology of carbapenemases in Latin America and the Caribbean. Expert Rev Anti Infect Ther 2016; 15:277-297. [PMID: 27915487 DOI: 10.1080/14787210.2017.1268918] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
INTRODUCTION Enterobacteriaceae, Pseudomonas spp., and Acinetobacter spp. infections are major causes of morbidity and mortality, especially due to the emergence and spread of β-lactamases. Carbapenemases, which are β-lactamases with the capacity to hydrolyze or inactivate carbapenems, have become a serious concern as they have the largest hydrolytic spectrum and therefore limit the utility of most β-lactam antibiotics. Areas covered: Here, we present an update of the current status of carbapenemases in Latin America and the Caribbean. Expert commentary: The increased frequency of reports on carbapenemases in Latin America and the Caribbean shows that they have successfully spread and have even become endemic in some countries. Countries such as Brazil, Colombia, Argentina, and Mexico account for the majority of these reports. Early suspicion and detection along with implementation of antimicrobial stewardship programs in all healthcare settings are crucial for the control and prevention of carbapenemase-producing bacteria.
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Affiliation(s)
- Kevin Escandón-Vargas
- a Bacterial Resistance and Hospital Epidemiology Unit , International Center for Medical Research and Training (CIDEIM) , Cali , Colombia
| | - Sergio Reyes
- a Bacterial Resistance and Hospital Epidemiology Unit , International Center for Medical Research and Training (CIDEIM) , Cali , Colombia
| | - Sergio Gutiérrez
- a Bacterial Resistance and Hospital Epidemiology Unit , International Center for Medical Research and Training (CIDEIM) , Cali , Colombia
| | - María Virginia Villegas
- a Bacterial Resistance and Hospital Epidemiology Unit , International Center for Medical Research and Training (CIDEIM) , Cali , Colombia.,b Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics , Universidad El Bosque , Bogotá , Colombia
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26
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Nascimento APB, Ortiz MF, Martins WMBS, Morais GL, Fehlberg LCC, Almeida LGP, Ciapina LP, Gales AC, Vasconcelos ATR. Intraclonal Genome Stability of the Metallo-β-lactamase SPM-1-producing Pseudomonas aeruginosa ST277, an Endemic Clone Disseminated in Brazilian Hospitals. Front Microbiol 2016; 7:1946. [PMID: 27994579 PMCID: PMC5136561 DOI: 10.3389/fmicb.2016.01946] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 11/21/2016] [Indexed: 01/30/2023] Open
Abstract
Carbapenems represent the mainstay therapy for the treatment of serious P. aeruginosa infections. However, the emergence of carbapenem resistance has jeopardized the clinical use of this important class of compounds. The production of SPM-1 metallo-β-lactamase has been the most common mechanism of carbapenem resistance identified in P. aeruginosa isolated from Brazilian medical centers. Interestingly, a single SPM-1-producing P. aeruginosa clone belonging to the ST277 has been widely spread within the Brazilian territory. In the current study, we performed a next-generation sequencing of six SPM-1-producing P. aeruginosa ST277 isolates. The core genome contains 5899 coding genes relative to the reference strain P. aeruginosa PAO1. A total of 26 genomic islands were detected in these isolates. We identified remarkable elements inside these genomic islands, such as copies of the blaSPM−1 gene conferring resistance to carbapenems and a type I-C CRISPR-Cas system, which is involved in protection of the chromosome against foreign DNA. In addition, we identified single nucleotide polymorphisms causing amino acid changes in antimicrobial resistance and virulence-related genes. Together, these factors could contribute to the marked resistance and persistence of the SPM-1-producing P. aeruginosa ST277 clone. A comparison of the SPM-1-producing P. aeruginosa ST277 genomes showed that their core genome has a high level nucleotide similarity and synteny conservation. The variability observed was mainly due to acquisition of genomic islands carrying several antibiotic resistance genes.
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Affiliation(s)
- Ana P B Nascimento
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica Petrópolis, Brazil
| | - Mauro F Ortiz
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica Petrópolis, Brazil
| | - Willames M B S Martins
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina, Universidade Federal de São Paulo São Paulo, Brazil
| | - Guilherme L Morais
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica Petrópolis, Brazil
| | - Lorena C C Fehlberg
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina, Universidade Federal de São Paulo São Paulo, Brazil
| | - Luiz G P Almeida
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica Petrópolis, Brazil
| | - Luciane P Ciapina
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica Petrópolis, Brazil
| | - Ana C Gales
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina, Universidade Federal de São Paulo São Paulo, Brazil
| | - Ana T R Vasconcelos
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica Petrópolis, Brazil
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27
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Description of genomic islands associated to the multidrug-resistant Pseudomonas aeruginosa clone ST277. INFECTION GENETICS AND EVOLUTION 2016; 42:60-5. [DOI: 10.1016/j.meegid.2016.04.024] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 04/13/2016] [Accepted: 04/20/2016] [Indexed: 12/11/2022]
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28
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Hopkins KL, Meunier D, Findlay J, Mustafa N, Parsons H, Pike R, Wright L, Woodford N. SPM-1 metallo-β-lactamase-producing Pseudomonas aeruginosa ST277 in the UK. J Med Microbiol 2016; 65:696-697. [DOI: 10.1099/jmm.0.000269] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Katie L. Hopkins
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Danièle Meunier
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Jacqueline Findlay
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Nazim Mustafa
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Helena Parsons
- Sheffield Teaching Hospitals NHS Foundation Trust, Northern General Hospital, Herries Road, Sheffield S5 7AU, UK
| | - Rachel Pike
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Laura Wright
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Neil Woodford
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
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29
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Turano H, Gomes F, Medeiros M, Oliveira S, Fontes LC, Sato MIZ, Lincopan N. Presence of high-risk clones of OXA-23-producing Acinetobacter baumannii (ST79) and SPM-1-producing Pseudomonas aeruginosa (ST277) in environmental water samples in Brazil. Diagn Microbiol Infect Dis 2016; 86:80-2. [PMID: 27342783 DOI: 10.1016/j.diagmicrobio.2016.06.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 06/02/2016] [Accepted: 06/04/2016] [Indexed: 11/30/2022]
Abstract
This study reports the presence of hospital-associated high-risk lineages of OXA-23-producing ST79 Acinetobacter baumannii and SPM-1-producing ST277 Pseudomonas aeruginosa in urban rivers in Brazil. These findings indicate that urban rivers can act as reservoirs of clinically important multidrug-resistant bacteria, which constitute a potential risk to human and animal health.
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Affiliation(s)
- Helena Turano
- Department of Microbiology, Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil
| | - Fernando Gomes
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Universidade de São Paulo, São Paulo, Brazil
| | - Micheli Medeiros
- Department of Clinical Analysis, School of Pharmacy, Universidade de São Paulo, São Paulo, Brazil
| | - Silvane Oliveira
- Department of Microbiology, Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil
| | - Lívia C Fontes
- Department of Microbiology, Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil
| | - Maria I Z Sato
- Environmental Company of São Paulo State (CETESB), São Paulo, Brazil
| | - Nilton Lincopan
- Department of Microbiology, Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil; Department of Clinical Analysis, School of Pharmacy, Universidade de São Paulo, São Paulo, Brazil.
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30
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Fonseca EL, Vicente ACP. Commentary: Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium. Front Microbiol 2016; 7:770. [PMID: 27242778 PMCID: PMC4876116 DOI: 10.3389/fmicb.2016.00770] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 05/06/2016] [Indexed: 11/13/2022] Open
Affiliation(s)
- Erica L Fonseca
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, FIOCRUZ Rio de Janeiro, Brasil
| | - Ana Carolina P Vicente
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, FIOCRUZ Rio de Janeiro, Brasil
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31
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Araujo BF, Ferreira ML, de Campos PA, Royer S, Batistão DWDF, Dantas RCC, Gonçalves IR, Faria ALS, de Brito CS, Yokosawa J, Gontijo-Filho PP, Ribas RM. Clinical and Molecular Epidemiology of Multidrug-Resistant P. aeruginosa Carrying aac(6')-Ib-cr, qnrS1 and blaSPM Genes in Brazil. PLoS One 2016; 11:e0155914. [PMID: 27219003 PMCID: PMC4878783 DOI: 10.1371/journal.pone.0155914] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 05/08/2016] [Indexed: 11/19/2022] Open
Abstract
We described a comprehensive analysis of the molecular epidemiology of multidrug-resistant (MDR) P. aeruginosa. Molecular analysis included typing by Pulsed Field Gel Electrophoresis, identification of genes of interest through PCR-based assays and sequencing of target genes. Case-control study was conducted to better understand the prognostic of patients and the impact of inappropriate therapy in patients with bacteremia, as well as the risk factors of MDR infections. We observed a high rate of MDR isolates (40.7%), and 51.0% of them was independently associated with inappropriate antibiotic therapy. Bacteremia was detected in 66.9% of patients, and prolonged hospital stay was expressive in those resistant to fluoroquinolone. Plasmid-mediated quinolone resistance genes (PMQR), qnrS1 and aac(6')Ib-cr, were detected in two different nosocomial isolates (5.3%), and the aac(6')-Ib7 variant was detected at a high frequency (87.5%) in those negative to PMQR. The presence of mutations in gyrA and parC genes was observed in 100% and 85% of selected isolates, respectively. Isolates harboring PMQR genes or mutations in gyrA and parC were not closely related, except in those containing SPM (São Paulo metallo-β-lactamase) clone. In addition, there is no study published in Brazil to date reporting the presence of Pseudomonas aeruginosa isolates harboring both qnrS1 and aac(6')Ib-cr genes, with alarming frequency of patients with inappropriate therapy.
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Affiliation(s)
- Bruna Fuga Araujo
- Instituto de Ciências Biomédicas (ICBIM), Laboratory of Molecular Microbiology, Universidade Federal de Uberlandia (UFU), Uberlandia, Minas Gerais, Brazil
| | - Melina Lorraine Ferreira
- Instituto de Ciências Biomédicas (ICBIM), Laboratory of Molecular Microbiology, Universidade Federal de Uberlandia (UFU), Uberlandia, Minas Gerais, Brazil
| | - Paola Amaral de Campos
- Instituto de Ciências Biomédicas (ICBIM), Laboratory of Molecular Microbiology, Universidade Federal de Uberlandia (UFU), Uberlandia, Minas Gerais, Brazil
| | - Sabrina Royer
- Instituto de Ciências Biomédicas (ICBIM), Laboratory of Molecular Microbiology, Universidade Federal de Uberlandia (UFU), Uberlandia, Minas Gerais, Brazil
| | - Deivid William da Fonseca Batistão
- Instituto de Ciências Biomédicas (ICBIM), Laboratory of Molecular Microbiology, Universidade Federal de Uberlandia (UFU), Uberlandia, Minas Gerais, Brazil
| | - Raquel Cristina Cavalcanti Dantas
- Instituto de Ciências Biomédicas (ICBIM), Laboratory of Molecular Microbiology, Universidade Federal de Uberlandia (UFU), Uberlandia, Minas Gerais, Brazil
| | - Iara Rossi Gonçalves
- Instituto de Ciências Biomédicas (ICBIM), Laboratory of Molecular Microbiology, Universidade Federal de Uberlandia (UFU), Uberlandia, Minas Gerais, Brazil
| | - Ana Luiza Souza Faria
- Instituto de Ciências Biomédicas (ICBIM), Laboratory of Molecular Microbiology, Universidade Federal de Uberlandia (UFU), Uberlandia, Minas Gerais, Brazil
| | - Cristiane Silveira de Brito
- Instituto de Ciências Biomédicas (ICBIM), Laboratory of Molecular Microbiology, Universidade Federal de Uberlandia (UFU), Uberlandia, Minas Gerais, Brazil
| | - Jonny Yokosawa
- Instituto de Ciências Biomédicas (ICBIM), Laboratory of Virology, Universidade Federal de Uberlandia (UFU), Uberlandia, Minas Gerais, Brazil
| | - Paulo Pinto Gontijo-Filho
- Instituto de Ciências Biomédicas (ICBIM), Laboratory of Molecular Microbiology, Universidade Federal de Uberlandia (UFU), Uberlandia, Minas Gerais, Brazil
| | - Rosineide Marques Ribas
- Instituto de Ciências Biomédicas (ICBIM), Laboratory of Molecular Microbiology, Universidade Federal de Uberlandia (UFU), Uberlandia, Minas Gerais, Brazil
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