51
|
León-Sampedro R, Del Campo R, Rodriguez-Baños M, Lanza VF, Pozuelo MJ, Francés-Cuesta C, Tedim AP, Freitas AR, Novais C, Peixe L, Willems RJL, Corander J, González Candelas F, Baquero F, Coque TM. Phylogenomics of Enterococcus faecalis from wild birds: new insights into host-associated differences in core and accessory genomes of the species. Environ Microbiol 2019; 21:3046-3062. [PMID: 31162871 DOI: 10.1111/1462-2920.14702] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 05/20/2019] [Accepted: 06/01/2019] [Indexed: 11/29/2022]
Abstract
Wild birds have been suggested to be reservoirs of antimicrobial resistant and/or pathogenic Enterococcus faecalis (Efs) strains, but the scarcity of studies and available sequences limit our understanding of the population structure of the species in these hosts. Here, we analysed the clonal and plasmid diversity of 97 Efs isolates from wild migratory birds. We found a high diversity, with most sequence types (STs) being firstly described here, while others were found in other hosts including some predominant in poultry. We found that pheromone-responsive plasmids predominate in wild bird Efs while 35% of the isolates entirely lack plasmids. Then, to better understand the ecology of the species, the whole genome of fivestrains with known STs (ST82, ST170, ST16 and ST55) were sequenced and compared with all the Efs genomes available in public databases. Using several methods to analyse core and accessory genomes (AccNET, PLACNET, hierBAPS and PANINI), we detected differences in the accessory genome of some lineages (e.g. ST82) demonstrating specific associations with birds. Conversely, the genomes of other Efs lineages exhibited divergence in core and accessory genomes, reflecting different adaptive trajectories in various hosts. This pangenome divergence, horizontal gene transfer events and occasional epidemic peaks could explain the population structure of the species.
Collapse
|
52
|
Botelho J, Grosso F, Peixe L. WITHDRAWN: Antibiotic resistance in Pseudomonas aeruginosa – mechanisms, epidemiology and evolution.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]
|
53
|
Ribeiro TG, Novais Â, Rodrigues C, Nascimento R, Freitas F, Machado E, Peixe L. Dynamics of clonal and plasmid backgrounds of Enterobacteriaceae producing acquired AmpC in Portuguese clinical settings over time. Int J Antimicrob Agents 2019; 53:650-656. [PMID: 30878669 DOI: 10.1016/j.ijantimicag.2019.03.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 03/07/2019] [Accepted: 03/09/2019] [Indexed: 01/06/2023]
Abstract
OBJECTIVES The objective of this work was to provide detailed molecular data on clinically acquired AmpC (qAmpC)-producing Enterobacteriaceae from two different periods (2002-2008 and 2010-2013) in order to clarify the contribution of clonal and plasmid genetic platforms for the current epidemiological scenario concerning extended-spectrum beta-lactams resistance. METHODS We analysed 1246 Enterobacteriaceae non-susceptible to third-generation cephalosporins from two hospitals and one community laboratory between 2010 and 2013. Bacterial identification, antibiotic susceptibility, identification of qAmpC and plasmid-mediated quinolone resistance genes, clonal (pulsed-field gel electrophoresis (PFGE), Multilocus sequence typing (MLST)) and plasmid (S1-/I-CeuI-PFGE, replicon typing, hybridization) analysis were performed by standard methods. Whole-genome sequencing (WGS) was performed in two ST11-Klebsiella pneumoniae isolates harbouring DHA-1. RESULTS The occurrence of qAmpC was lower (2.6%) than that observed in a previous survey (7.4%), and varied slightly over time. Isolates produced DHA-1 (53%), CMY-2 (44%) or DHA-6 (3%), but significant epidemiological changes were observed in the two surveys. While DHA-1 persisted in different institutions by selection of a worldwide epidemic IncR plasmid in an ST11 harbouring KL105, CMY-2 rates increased over time linked to IncI1 plasmids (instead of IncK or IncA/C2) in multiple Escherichia coli clones. CONCLUSIONS The higher frequency of DHA-1 qAmpC in these species contrasts with the scenario in most European countries. Furthermore, the different genetic backgrounds associated with either extended-spectrum β-lactamases (ESBLs) or acquired AmpC β-lactamases (qAmpC) in our country might have contributed to their differential expansion.
Collapse
|
54
|
Perovic S, Ksiezarek M, Rocha J, Vale L, Silva C, Dinis P, Antunes Lopes T, Peixe L. Time to change microbiological approach to overactive bladder. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/s1569-9056(19)30077-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
55
|
Mendes AC, Novais Â, Campos J, Rodrigues C, Santos C, Antunes P, Ramos H, Peixe L. mcr-1 in Carbapenemase-Producing Klebsiella pneumoniae with Hospitalized Patients, Portugal, 2016-2017. Emerg Infect Dis 2019; 24:762-766. [PMID: 29553327 PMCID: PMC5875258 DOI: 10.3201/eid2404.171787] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
We describe a hospital-based outbreak caused by multidrug-resistant, Klebsiella pneumoniae carbapenemase 3–producing, mcr-1–positive K. pneumoniae sequence type 45 in Portugal. mcr-1 was located in an IncX4 plasmid. Our data highlight the urgent need for systematic surveillance of mcr-1 to support adequate therapeutic choices in the nosocomial setting.
Collapse
|
56
|
Campos J, Mourão J, Peixe L, Antunes P. Non-typhoidal Salmonella in the Pig Production Chain: A Comprehensive Analysis of Its Impact on Human Health. Pathogens 2019; 8:E19. [PMID: 30700039 PMCID: PMC6470815 DOI: 10.3390/pathogens8010019] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 01/21/2019] [Accepted: 01/24/2019] [Indexed: 11/17/2022] Open
Abstract
Salmonellosis remains one of the most frequent foodborne zoonosis, constituting a worldwide major public health concern. The most frequent sources of human infections are food products of animal origin, being pork meat one of the most relevant. Currently, particular pig food production well-adapted and persistent Salmonella enterica serotypes (e.g., Salmonella Typhimurium, Salmonella 1,4,[5],12:i:-, Salmonella Derby and Salmonella Rissen) are frequently reported associated with human infections in diverse industrialized countries. The dissemination of those clinically-relevant Salmonella serotypes/clones has been related to the intensification of pig production chain and to an increase in the international trade of pigs and pork meat. Those changes that occurred over the years along the food chain may act as food chain drivers leading to new problems and challenges, compromising the successful control of Salmonella. Among those, the emergence of antibiotic resistance in non-typhoidal Salmonella associated with antimicrobials use in the pig production chain is of special concern for public health. The transmission of pig-related multidrug-resistant Salmonella serotypes, clones and/or genetic elements carrying clinically-relevant antibiotic resistance genes, frequently associated with metal tolerance genes, from pigs and pork meat to humans, has been reported and highlights the contribution of different drivers to the antibiotic resistance burden. Gathered data strengthen the need for global mandatory interventions and strategies for effective Salmonella control and surveillance across the pig production chain. The purpose of this review was to provide an overview of the role of pig and pork meat in human salmonellosis at a global scale, highlighting the main factors contributing to the persistence and dissemination of clinically-relevant pig-related Salmonella serotypes and clones.
Collapse
|
57
|
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.
Collapse
|
58
|
Freitas-Silva J, Inácio ÂS, Mourão J, Antunes P, Mendes Â, de Carvalho AP, Vasconcelos V, Peixe L, da Costa PM. Occurrence of mcr-1 in Escherichia coli from rabbits of intensive farming. Vet Microbiol 2018; 227:78-81. [DOI: 10.1016/j.vetmic.2018.10.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 10/22/2018] [Accepted: 10/23/2018] [Indexed: 02/05/2023]
|
59
|
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]
|
60
|
Antunes P, Campos J, Mourão J, Pereira J, Novais C, Peixe L. Inflow water is a major source of trout farming contamination with Salmonella and multidrug resistant bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 642:1163-1171. [PMID: 30045498 DOI: 10.1016/j.scitotenv.2018.06.143] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 06/11/2018] [Accepted: 06/11/2018] [Indexed: 06/08/2023]
Abstract
The impact of European aquaculture, namely trout farms, in the spread of antibiotic resistance and/or zoonotic pathogens has been scarcely addressed. Moreover, aquaculture contamination sources and bacterial dissemination routes have been barely explored. In this study, we assessed the contribution of Portuguese land-based intensive rainbow trout farms and retailed market trout to the spread of Salmonella and bacteria carrying clinically-relevant antibiotic resistance genes (ARGs) as well as inflow water and feed as possible sources of those contaminants. Cultural and molecular methods were used to analyse 53 fish farm samples (upstream/downstream water and sediments, tanks and trout) and 25 marketed trout. Plasmid-mediated quinolone resistance (PMQR) genes were found in 21% (n = 11/53) of samples (water/sediment/feed/trout), from all collection points (upstream/within/downstream tanks) and seasons, as well as in 12% (n = 3/25) of marketed trout (3 supermarkets). PMQR genes (qnrS1-S2-S3, qnrB7-B19, qnrD1, oqxAB) were detected in Enterobacteriaceae or Aeromonas hydrophila. An E. coli strain producing extended-spectrum-beta-lactamase SHV-12 was detected in all sampled points of a fish farm. Salmonella (4 serotypes, including S. Newport-ST118) was detected in 26% (n = 14/53) of the samples from both farms (water/sediment upstream/within tanks). The clinically-relevant plasmid-mediated colistin resistance mcr genes were not detected. However, colistin resistant S. Abony with new mutations in the chromosomal pmrA and pmrB genes was observed. Identical Salmonella and SHV-12-producing E. coli strains (by PFGE/MLST) in water upstream and within trout tanks points to inflow-water of trout farms as an important source of pathogenic bacteria and ARG contamination. These results highlight the need to define microbiological standards for water supplying fish farms in the EU and to establish surveillance and control strategies to limit bacterial transmission associated with this fastest growing food sector worldwide.
Collapse
|
61
|
Oravcová V, Peixe L, Coque TM, Novais C, Francia MV, Literák I, Freitas AR. Wild corvid birds colonized with vancomycin-resistant Enterococcus faecium of human origin harbor epidemic vanA plasmids. ENVIRONMENT INTERNATIONAL 2018; 118:125-133. [PMID: 29870913 DOI: 10.1016/j.envint.2018.05.039] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/22/2018] [Accepted: 05/22/2018] [Indexed: 06/08/2023]
Abstract
The most prevalent type of acquired vancomycin resistance in Enterococcus faecium (VREfm) is encoded by the vanA transposon Tn1546, mainly located on transferable plasmids. vanA plasmids have been characterized in VREfm from a variety of sources but not wild birds. The aim of this study was to analyse the genetic context of VREfm strains recovered from wild corvid birds and to compare their plasmid and strain characteristics with human strains. To achieve that, 75 VREfm isolates, including strains from wild birds recovered during wide surveillance studies performed in Europe, Canada and the United States (2010-2013), and clinical and wastewater strains from Czech Republic, a region lacking data about vanA plasmids, were analysed. Their population structure, presence of major putative virulence markers and characterization of vanA transposons and plasmids were established. VREfm from wild birds were mainly associated with major human lineages (ST18 and ST78) circulating in hospitals worldwide and were enriched in putative virulence markers that are highly associated with clinical E. faecium from human infections. They also carried plasmids of the same families usually found in the clinical setting [RCR, small theta plasmids, RepA_N (pRUM/pLG1) and Inc18]. The clinically widespread IS1251-carrying Tn1546 type "F" was predominant and Tn1546-vanA was mainly located on pRUM/Axe-Txe (USA) and Inc18- or pLG1-like (Europe) plasmids. VREfm from hospitals and wastewaters carried Tn1546-vanA in different plasmid types including mosaic pRUM-Inc18 plasmids, not identified in wild birds. This is the first characterization of vanA plasmids obtained from wild birds. A similar plasmid pool seems to exist in different clonal E. faecium backgrounds of humans and wild birds. The isolation of VREfm strains from wild birds that belong to human E. faecium adapted lineages and carry virulence genes, Tn1546 and plasmid variants widespread in the clinical setting is of concern and highlight their role as potential drivers of the global dissemination of vancomycin resistance.
Collapse
|
62
|
Novais Â, Moniz T, Rebelo AR, Silva AM, Rangel M, Peixe L. New fluorescent rosamine chelator showing promising antibacterial activity against Gram-positive bacteria. Bioorg Chem 2018; 79:341-349. [DOI: 10.1016/j.bioorg.2018.05.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 05/08/2018] [Accepted: 05/14/2018] [Indexed: 12/27/2022]
|
63
|
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.
Collapse
|
64
|
Silva L, Mourão J, Grosso F, Peixe L. Uncommon carbapenemase-encoding plasmids in the clinically emergent Acinetobacter pittii. J Antimicrob Chemother 2018; 73:52-56. [PMID: 29069366 DOI: 10.1093/jac/dkx364] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 09/07/2017] [Indexed: 11/12/2022] Open
Abstract
Objectives Two carbapenemase-carrying plasmids, pLS488 (blaOXA-23) and pLS535 (blaOXA-58) from Acinetobacter pittii clinical isolates, were characterized in this study, including their ability to be transferred to Acinetobacter baumannii. Methods The clinical isolates were obtained from drainage fluid of a patient with biliary tract cancer and from an exudate of a patient with a hip infection (Portuguese University Hospital, 2012). Isolate characterization included antimicrobial susceptibility tests, carbapenemase production by Blue-Carba, carbapenem-hydrolysing class D β-lactamase (CHDL) gene search by PCR sequencing, ApaI-PFGE, CHDL genetic location and plasmid size by hybridization and WGS. Plasmid transfer was performed by conjugation or electroporation. Results pLS488 constitutes the first conjugative plasmid reported to carry a carbapenem resistance gene in A. pittii and is part of a potential new incompatibility group that might also account for the dissemination of OXA-23 in A. baumannii. pLS535 belongs to the Acinetobacter GR7 incompatibility group and presents a new scaffold for OXA-58. This plasmid lacked the machinery for conjugation, but was transferable by electroporation to A. baumannii. Both isolates, which displayed the same PFGE pattern, represent the first report of CHDL-carrying A. pittii in Portuguese hospitals. Conclusions Altogether, these results emphasize the importance of A. pittii, or particular A. pittii clones, as a source of resistance genes, facilitating their dissemination among different bacterial species.
Collapse
|
65
|
Campos J, Sousa C, Mourão J, Lopes J, Antunes P, Peixe L. Discrimination of non-typhoid Salmonella serogroups and serotypes by Fourier Transform Infrared Spectroscopy: A comprehensive analysis. Int J Food Microbiol 2018; 285:34-41. [PMID: 30015261 DOI: 10.1016/j.ijfoodmicro.2018.07.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/30/2018] [Accepted: 07/03/2018] [Indexed: 01/11/2023]
Abstract
Simpler, quick and low-cost methods for routine Salmonella enterica typing are required for epidemiologic surveillance of this important zoonotic pathogen. In this study, using a comprehensive isolate collection, we investigated the potential of Fourier transform infrared spectroscopy (FTIRS) to discriminate the most clinically-relevant serogroups and serotypes of non-typhoid Salmonella. Moreover, the role of O-units composition on the FTIRS Salmonella discrimination was also explored. S. enterica isolates (n = 325; 2002-2015; different sources and countries), of 57 serotypes and 15 serogroups [including the most frequent ones, B-n = 122; C-n = 108; D-n = 43 and E-n = 33)] were analysed by FTIRS. Infrared spectra were analysed by Partial Least Square Discriminant Analysis (PLSDA) and/or Principal Component Analysis (PCA). The polysaccharides region provided the spectral sharpest differences being used in the subsequent Salmonella typing. Serogroups (B, C, D and E) discrimination was achieved with high accuracy (99.6% of correct assignments; PLSDA model). Differences in the O-unit structures composition of those serogroups are likely justifying the discrimination achieved. Other serogroups (G, H, K, L, M, N, O, T, U, Y, Z) were correctly predicted as not belonging to serogroups B, C, D nor E, except for 3 isolates of serogroups H (S. Sundsvall, n = 1) and K (S. Cerro, n = 2). In fact, O-unit structure of serogroup H and K shows some similarity with sub-serogroup C1 with the remaining serogroups presenting marked differences in this cellular component. The sub-serogroups discrimination was successfully achieved for C1, C2 and C3 (using PCA), and for E1-E2-E3 and E4 (by PLSDA). Appropriate serotype discrimination was obtained for most of S. Rissen from the remaining C1 serotypes (91.5%-PLSDA), and S. Enteritidis (D1) from the remaining D1/D2 serotypes (93.4%-PLSDA). The lack of available O-unit composition for particular serotypes prevents the elucidation of the role of this cellular component on the discrimination at serotype level obtained. FTIRS was able to discriminate relevant serogroups (B, C, D and E), sub-serogroups (C1, C2 and C3; E1-E2-E3 and E4) and particular important serotypes (S. Enteritidis, S. Rissen and S. Senftenberg). Further studies on O-antigen composition would clarify the fundaments of discrimination obtained by FTIRS.
Collapse
|
66
|
Novais C, Campos J, Freitas AR, Barros M, Silveira E, Coque TM, Antunes P, Peixe L. Water supply and feed as sources of antimicrobial-resistant Enterococcus spp. in aquacultures of rainbow trout (Oncorhyncus mykiss), Portugal. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 625:1102-1112. [PMID: 29996407 DOI: 10.1016/j.scitotenv.2017.12.265] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 12/18/2017] [Accepted: 12/21/2017] [Indexed: 06/08/2023]
Abstract
The role of European fish farms in the spread of antimicrobial-resistance in the environment and food chain, as well as possible sources of their contamination by clinically relevant antimicrobial-resistance bacteria is scarcely known. This study aimed to assess the contribution of Portuguese rural trout farms on dispersion of Enterococcus with antimicrobial-resistance and putative virulence genes in the environment and food chain, as well as to identify farms contamination sources. We also assessed the presence of Enterococcus with low-levels of antimicrobial-resistance using epidemiological cut-offs (ECOFFs). Enterococcus spp. (n=391) from water/sediment recovered upstream, within and downstream trout tanks, feed, trout (2 aquacultures; no antibiotic use) and marketed trout (8 supermarkets) showed variable resistance to tetracycline, erythromycin, ciprofloxacin, chloramphenicol, quinupristin-dalfopristin, nitrofurantoin or aminoglycosides. Antimicrobial-resistance rates were similar among upstream, within and downstream trout tank samples (P>0.05), positioning water-supplying aquacultures as a source of multidrug-resistant (MDR) strains. Nevertheless, predominance of MDR E. faecium in feed, trout tanks and trout comparing to upstream samples, suggests feed as an additional aquaculture contamination source. The observation of E. faecium and E. faecalis susceptible to ampicillin and gentamicin by clinical breakpoints but with low-levels of resistance to those antimicrobials by ECOFFs breakpoints is of concern, as they might evolve throughout secondary genetic events to resistance levels with human clinical impact. Multiple MDR clones carrying copper tolerance (tcrB/cueO), putative virulence or other genes often associated with clinical strains (e.g. E. faecium with IS16/ptsD/sgrA) were observed, some in distinct samples (e.g. upstream and within trout tanks). They included major human and animal Enterococcus lineages, suggesting human and non-aquatic animal origins. The results highlight the need to define the maximum acceptance level of antimicrobial-resistance genes/bacteria to assess water quality and to monitor antimicrobial-resistance strains on feed, essential requirements to maintain a sustainable aquaculture production.
Collapse
|
67
|
Freitas AR, Novais C, Duarte B, Pereira AP, Coque TM, Peixe L. High rates of colonisation by ampicillin-resistant enterococci in residents of long-term care facilities in Porto, Portugal. Int J Antimicrob Agents 2018; 51:503-507. [DOI: 10.1016/j.ijantimicag.2017.11.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 11/06/2017] [Accepted: 11/14/2017] [Indexed: 11/15/2022]
|
68
|
Botelho J, Grosso F, Quinteira S, Mabrouk A, Peixe L. The complete nucleotide sequence of an IncP-2 megaplasmid unveils a mosaic architecture comprising a putative novel blaVIM-2-harbouring transposon in Pseudomonas aeruginosa. J Antimicrob Chemother 2018; 72:2225-2229. [PMID: 28505370 DOI: 10.1093/jac/dkx143] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 04/19/2017] [Indexed: 01/01/2023] Open
Abstract
Objectives In Pseudomonas aeruginosa , bla VIM-2 has been mostly associated with a chromosomal location and rarely with a plasmid backbone. Until now, only three complete bla VIM-2 -carrying plasmid sequences have been described in this species. Here we explore the modular structure of pJB37, the first bla VIM-2 -carrying megaplasmid described in P. aeruginosa . Methods The complete nucleotide sequence of plasmid pJB37 was determined with an Illumina HiSeq, with de novo assembly by SPAdes, annotation by RAST and searching for antimicrobial resistance genes and virulence factors. Conjugation assays were conducted. Results Megaplasmid pJB37 (464 804 bp long and GC content of 57.2%) comprised: an IncP-2 repA-oriV-parAB region; a conjugative transfer region ( traF , traG , virD2 and trbBCDEJLFGI genes); Tn 6356 , a new putative bla VIM-2 -carrying transposon; heavy metal (mercury and tellurite) resistance operons; and an arsenal of virulence genes. Plasmid pJB37 was transferable by conjugation to a spontaneous rifampicin-resistant mutant of P. aeruginosa PAO1. Here, a bla VIM-2 -harbouring In58 integron was associated with a new complex transposable structure, herein named Tn 6356 , suggesting that In58 was most likely acquired by insertion of this element. Conclusions The mosaic arrangement exhibited by the pJB37 IncP-2 megaplasmid, which highlights the vast assembly potential of distinct genetic elements in a Pseudomonas widespread plasmid platform, gives new insights into bacterial adaptation and evolution.
Collapse
|
69
|
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
|
70
|
Campos J, Mourão J, Silveira L, Saraiva M, Correia CB, Maçãs AP, Peixe L, Antunes P. Imported poultry meat as a source of extended-spectrum cephalosporin-resistant CMY-2-producing Salmonella Heidelberg and Salmonella Minnesota in the European Union, 2014–2015. Int J Antimicrob Agents 2018; 51:151-154. [DOI: 10.1016/j.ijantimicag.2017.09.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 09/07/2017] [Accepted: 09/10/2017] [Indexed: 11/30/2022]
|
71
|
Freitas AR, Tedim AP, Novais C, Coque TM, Peixe L. Distribution of putative virulence markers in Enterococcus faecium: towards a safety profile review. J Antimicrob Chemother 2017; 73:306-319. [DOI: 10.1093/jac/dkx387] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 09/22/2017] [Indexed: 12/14/2022] Open
|
72
|
Ribeiro TG, Gonçalves BR, da Silva MS, Novais Â, Machado E, Carriço JA, Peixe L. Citrobacter portucalensis sp. nov., isolated from an aquatic sample. Int J Syst Evol Microbiol 2017; 67:3513-3517. [DOI: 10.1099/ijsem.0.002154] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
73
|
Campos J, Cristino L, Peixe L, Antunes P. MCR-1 in multidrug-resistant and copper-tolerant clinically relevant Salmonella 1,4,[5],12:i:- and S. Rissen clones in Portugal, 2011 to 2015. ACTA ACUST UNITED AC 2017; 21:30270. [PMID: 27387036 DOI: 10.2807/1560-7917.es.2016.21.26.30270] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 06/30/2016] [Indexed: 11/20/2022]
Abstract
The mcr-1 gene was found in 11 isolates from a Portuguese Salmonella collection (n = 1,010; 58 serotypes; 2002-15) of clinical samples, foodstuff, food-animals and water. Mcr-1 has been located on different plasmids (IncX4/IncHI2) in pig-associated multidrug-resistant, copper-tolerant S.1,4,[5],12:i:-/ST34 and S. Rissen/ST469 clones from human and pork products since at least 2011. Our data highlight dissemination of mcr-1 by successful resistant clones in Europe and raise questions about the efficacy of copper-based interventions to reduce colistin use.
Collapse
|
74
|
Ribeiro TG, Clermont D, Branquinho R, Machado E, Peixe L, Brisse S. Citrobacter europaeus sp. nov., isolated from water and human faecal samples. Int J Syst Evol Microbiol 2017; 67:170-173. [PMID: 27902229 DOI: 10.1099/ijsem.0.001606] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strains 97/79T and A121, recovered respectively from human faeces and well water, were compared to currently known species of the genus Citrobacter using genotypic and phenotypic approaches. Multilocus sequence analysis based on housekeeping genes fusA, leuS, pyrG, rpoB and recN, showed that the two strains formed a distinct phylogenetic lineage within the genus Citrobacter. Average nucleotide identity (ANI) between strains 97/79T and A121 was 99.2 %, whereas ANI values of strain 97/79T with the type strains of closely related species of the genus Citrobacter, C. werkmanii, C. braakii, C. freundii, C. youngae and C. pasteurii, were all below 93.0 %. The ability to metabolize different compounds also discriminated strains 97/79T and A121 from other species of the genus Citrobacter. Based on these results, strains 97/79T and A121 represent a novel species of the genus Citrobacter, for which the name Citrobacter europaeus sp. nov. is proposed, with strain 97/79T (=CIP 106467T=DSM 103031T) as the type strain. The DNA G+C content of strain 97/79T is 52.0 %.
Collapse
|
75
|
Rodrigues C, Novais Â, Sousa C, Ramos H, Coque TM, Cantón R, Lopes JA, Peixe L. Elucidating constraints for differentiation of major human Klebsiella pneumoniae clones using MALDI-TOF MS. Eur J Clin Microbiol Infect Dis 2016; 36:379-386. [PMID: 27812805 DOI: 10.1007/s10096-016-2812-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 10/10/2016] [Indexed: 11/29/2022]
Abstract
The establishment of matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF MS) in routine microbial identification boosted many developments towards high-throughput applications, including bacterial typing. However, results are still controversial for different bacterial species. We aim to evaluate the suitability of MALDI-TOF MS for typing clinically relevant multidrug resistant (MDR) Klebsiella pneumoniae subsp. pneumoniae clones using routine conditions and a previously validated chemometric analysis workflow. Mass spectra of 83 K. pneumoniae clinical isolates representing major human MDR clones [11 sequence types (STs), 22 PFGE-types] recovered in Portugal and Spain during outbreaks and non-outbreak situations (2003-2012) were obtained from cell extracts (CE) and intact cells (IC), and analysed with different chemometric tools. We observed a highly consistent peak pattern among isolates from different clones either with CE or IC, suggesting a high degree of conservation of biomolecules analysed (a large part corresponding to ribosomal proteins). Moreover, the low degree of agreement between MALDI-TOF MS and other methods (from 34.9 % to 43.4 % of correct assignments for CE and from 40.8 % to 70.1 % for IC) corroborates the low discriminatory potential of the technique at infraspecies level. Our results suggest a low discriminatory power of MALDI-TOF MS for clinically relevant MDR K. pneumoniae clones and highlight the need of developing tools for high-resolution typing in this species.
Collapse
|