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Campioni F, Gomes CN, Rodrigues DDP, Bergamini AMM, Falcão JP. Phenotypic analyses of Salmonella enterica serovar Enteritidis strains isolated in the pre- and post-epidemic period in Brazil. Braz J Microbiol 2020; 52:173-183. [PMID: 33107010 DOI: 10.1007/s42770-020-00392-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 10/17/2020] [Indexed: 11/26/2022] Open
Abstract
Salmonella Enteritidis has caused, since the 1980s, a sustained epidemic of human infections in many countries. This study analyzed S. Enteritidis strains isolated before and after the epidemic period in Brazil regarding their capacities to survive to acid, oxidative, and high-temperature stresses, and capacity to grow in egg albumen. Moreover, the ability to invade human epithelial cells (Caco-2) and to survive inside human (U937) and chicken (HD11) macrophages was checked. Post-epidemic strains showed a better ability to survive after 10 min under acid stress at 37 °C (P ≤ 0.05). However, both groups of strains showed similar ability to survive after 1 h under acid stress at 37 °C and at 42 °C independently of the time of exposure. Similar ability was verified in both groups of strains regarding oxidative stress, growth in egg albumen, high-temperature stress, invasion to Caco-2 cells, and invasion and survival in macrophages. In conclusion, post-epidemic S. Enteritidis strains showed a better ability to survive under the acid stress found in the stomach, which might be an advantage to reach the intestine and colonize chickens and humans. However, both groups of strains did not differ significantly in the majority of the phenotypic tests analyzed in this study.
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Frazão MR, Cao G, Medeiros MIC, Duque SDS, Allard MW, Falcão JP. Antimicrobial Resistance Profiles and Phylogenetic Analysis of Campylobacter jejuni Strains Isolated in Brazil by Whole Genome Sequencing. Microb Drug Resist 2020; 27:660-669. [PMID: 33021437 DOI: 10.1089/mdr.2020.0184] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Aims: The objectives of this work were to use whole genome sequencing (WGS) to determine the antimicrobial resistance genotypes of 116 Campylobacter jejuni strains isolated in Brazil and to compare it with the results obtained by antimicrobial susceptibility testing (AST). In addition, WGS was used to uncover the phylogenetic relationship among those strains. Results: By AST, the C. jejuni strains resistant to ciprofloxacin, tetracycline, doxycycline, and erythromycin were 51 (44%), 41 (35.3%), 41 (35.3%), and 6 (5.2%), respectively. By WGS, the genes aph(3')III, aadE, blaOXA-449, blaOXA-184, blaOXA-61, and tet(O) were detected in 6 (5.2%), 3 (2.6%), 1 (0.9%), 10 (8.6%), 55 (47.4%), and 44 (38%) strains, respectively. Fifty-four (46.6%) strains showed the mutation T86I in the gyrA gene, and four (3.4%) strains presented the mutation A2075G in the 23S rRNA gene. The correlation between AST and WGS was 100% for ciprofloxacin, 97.5% for tetracyclines, and 66.7% for erythromycin. The whole genome single nucleotide polymorphism (SNP) tree clustered the C. jejuni strains into two clades comprising strains that were highly related from different sources, places, and years. Conclusion: The high rates of C. jejuni strains resistant to ciprofloxacin and tetracyclines are of concern and may represent a public health problem. WGS has a potential to be a powerful tool for the prediction of resistance of antibiotics used to treat campylobacteriosis. The results obtained by whole genome SNP analysis suggested the potential for transmission between clinical and nonclinical sources and between human and animal sources over the course of 20 years in Brazil.
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Seribelli AA, Cruz MF, Vilela FP, Frazão MR, Paziani MH, Almeida F, Medeiros MIC, Rodrigues DDP, von Zeska Kress MR, Allard MW, Falcão JP. Correction: Phenotypic and genotypic characterization of Salmonella Typhimurium isolates from humans and foods in Brazil. PLoS One 2020; 15:e0240055. [PMID: 32976526 PMCID: PMC7518603 DOI: 10.1371/journal.pone.0240055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Seribelli AA, Cruz MF, Vilela FP, Frazão MR, Paziani MH, Almeida F, Medeiros MIC, Rodrigues DDP, Kress MRVZ, Allard MW, Falcão JP. Phenotypic and genotypic characterization of Salmonella Typhimurium isolates from humans and foods in Brazil. PLoS One 2020; 15:e0237886. [PMID: 32810191 PMCID: PMC7437471 DOI: 10.1371/journal.pone.0237886] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 08/04/2020] [Indexed: 01/25/2023] Open
Abstract
Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) causes gastroenteritis in many countries. However, in Brazil there are few studies that have conducted a virulence characterization of this serovar. The aim of this study was to evaluate the virulence potential of S. Typhimurium strains isolated in Brazil. Forty S. Typhimurium strains isolated from humans (n = 20) and food (n = 20) from Brazil were studied regarding their invasion and survival in human epithelial cells (Caco-2) and macrophages (U937). Their virulence potential was determined using the Galleria mellonella larvae model combined with the analysis of virulence genes by whole genome sequencing (WGS). A total of 67.5% of the S. Typhimurium studied (32.5% isolated from humans and 35% isolated from food) invaded Caco-2 epithelial cells at levels similar to or greater than the S. Typhimurium SL1344 prototype strain. In addition, 37.5% of the studied strains (25% isolated from humans and 12.5% isolated from food) survived in U937 human macrophages at levels similar to or greater than SL1344. S. Typhimurium strains isolated from humans (40%) and food (25%) showed high or intermediate virulence in G. mellonella larvae after seven days exposure. Approximately, 153 virulence genes of chromosomal and plasmidial origin were detected in the strains studied. In conclusion, the ability of the S. Typhimurium to invade Caco-2 epithelial cells was strain dependent and was not related to the source or the year of isolation. However, S. Typhimurium strains isolated from humans showed greater survival rates in U937 human macrophages, and presented higher proportion of isolates with a virulent profile in G. mellonella in comparison to strains isolated from food suggesting that this difference may be related to the higher frequency of human isolates which contained plasmid genes, such as spvABCDR operon, pefABCD operon, rck and mig-5.
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Gonzales JC, Seribelli AA, Gomes CN, Dos Prazeres Rodrigues D, Campioni F, Passaglia J, da Silva P, Falcão JP. A high number of multidrug-resistant and predominant genetically related cluster of Shigella flexneri strains isolated over 34 years in Brazil. Braz J Microbiol 2020; 51:1563-1571. [PMID: 32710175 DOI: 10.1007/s42770-020-00332-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 06/29/2020] [Indexed: 11/26/2022] Open
Abstract
Shigella flexneri has been a major public health problem in developing countries. This work analyzed the frequency of 16 virulence genes, the genotypic diversity, and the antimicrobial resistance profiles of 130 S. flexneri strains isolated in Brazil. The ipaH gene was found in all the 130 strains. The frequencies of the other genes were variable ial (88.5%), sigA (82.3%), iuc (74.6%), virA (73%), pic (72.3%), virF (57.7%), sat (48.5%), ipaBCD (37%), sen (36%), set1A (35.4%), sepA (30%), set1B (30%), virB (14%), icsA (10%), and ipgD (5.4%). A total of 57 (43.8%) strains were multidrug-resistant. ERIC-PCR grouped 96 of the strains into a single cluster with ≥ 70.4% of similarity, 75 of these strains presented a similarity ≥ 80.9%. PFGE grouped 120 of the strains into a single cluster with 57.4% of similarity and 82 of these strains presented a similarity ≥ 70.6%. In conclusion, the high frequency of some virulence genes reinforces the pathogenic potential of the strains studied. The high rates of MDR strains are alarming once it may lead to failure when antimicrobial treatment is necessary. Genotype techniques reveled a major cluster with high genetic similarity including S. flexneri strains from the different Brazilian states and distinct years of isolation, showing that they probably emerged from a common ancestor.
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Frazão MR, de Souza RA, Medeiros MIC, da Silva Duque S, Cao G, Allard MW, Falcão JP. Molecular typing of Campylobacter jejuni strains: comparison among four different techniques. Braz J Microbiol 2020; 51:519-525. [PMID: 31872391 PMCID: PMC7203312 DOI: 10.1007/s42770-019-00218-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 12/17/2019] [Indexed: 11/29/2022] Open
Abstract
This study compared the ability of pulsed-field gel electrophoresis (PFGE), flaA small variable region (SVR) sequencing, analysis of the clustered regularly interspaced short palindromic repeats locus by high resolution melting analysis (CRISPR-HRMA), and multilocus sequence typing (MLST) for typing 111 Campylobacter jejuni strains isolated from diverse sources during 20 years in Brazil. For this, we used previous results obtained by PFGE and flaA-SVR sequencing from our research group and performed CRISPR-HRMA and MLST typing for the first time. Furthermore, the discrimination index (DI) of each method was accessed. The DI for PFGE, flaA-SVR sequencing, CRISPR-HRMA, and MLST was 0.980, 0.932, 0.868, and 0.931, respectively. By PFGE and flaA-SVR sequencing, some strains from clinical and non-clinical sources and from humans and animals presented ≥ 80% similarity. Similarly, some strains from different origins presented the same ST and CRISPR-HRMA types. In conclusion, despite the different DI values, all assays provided the same epidemiological information suggesting that a potential transmission may have occurred between C. jejuni from clinical and non-clinical sources and from animals and humans in Brazil. Furthermore it was demonstrated the suitability of PFGE that should be used preferably together with MLST and/or flaA-SVR sequencing for typing C. jejuni strains.
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Furlan JPR, Gallo IFL, de Campos ACLP, Passaglia J, Falcão JP, Navarro A, Nakazato G, Stehling EG. Molecular characterization of multidrug-resistant Shiga toxin-producing Escherichia coli harboring antimicrobial resistance genes obtained from a farmhouse. Pathog Glob Health 2019; 113:268-274. [PMID: 31757195 DOI: 10.1080/20477724.2019.1693712] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) colonize the gastrointestinal tract of animals; however, STEC may also cause severe diarrheal diseases. Food-producing animals have been acting as reservoirs and disseminators of multidrug-resistant (MDR) bacteria and antimicrobial resistance genes (ARGs); however, there are few studies characterizing molecularly bacterial isolates from sheep. Therefore, this study aimed to characterize E. coli isolates obtained from feces of sheep in a Brazilian farmhouse. A total of 14 MDR E. coli isolates were obtained from 100 feces samples, six of which were classified as non-O157 STEC (stx1, stx2 and ehxA). MDR E. coli isolates presented different ARGs [blaCTX-M-Gp9, blaCMY, blaSHV, qnrS, oqxB, aac(6')-Ib, tet(A), tet(B), tet(C), sul1, sul2, and cmlA] and plasmids (IncI1, IncFrepB, IncFIB, IncFIA, IncHI1, IncK, and ColE-like). In addition, mutations in the quinolone-resistance determining region of GyrA (Ser83Leu; Asp87Asn) and ParC (Glu84Asp) were detected. PFGE showed a high genetic diversity (30.9 to 83.9%) and thirteen STs were detected (ST25, ST48, ST155, ST162, ST642, ST1247, ST1518, ST1725, ST2107, ST2522, ST3270, ST5036, and ST7100). Subtyping of the fimH gene showed seven fimH-type (25, 32, 38, 41, 54, 61, and 366). The results found in the present study showed high genetic diversity among MDR ARGs-producing E. coli obtained from a farmhouse. This study reports for the first time, the presence of MDR STEC and non-STEC belonging to ST25, ST162, ST642, ST1247, ST1518, ST1725, ST2107, ST3270, ST5036, and ST7100 in sheep, and contributes to the surveillance studies associated with One Health concept.
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Vilela FP, Falcão JP, Campioni F. Analysis of Resistance Gene Prevalence in Whole-Genome Sequenced Enterobacteriales from Brazil. Microb Drug Resist 2019; 26:594-604. [PMID: 31746671 DOI: 10.1089/mdr.2019.0370] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Enterobacteriales is an order of bacteria responsible for community and hospital-acquired infections related to high rates of antimicrobial resistance and increased treatment costs, morbidity, and mortality globally. The aims of this study were to analyze the frequency of the resistance genes detected and distribution over the years and sources of isolation in sequenced Enterobacteriales strains isolated in Brazil and available at the Pathogen Detection website. The presence of resistance genes was analyzed in 1,507 whole-genome sequenced strains of 19 Enterobacteriales species. A total of 58.0% of the strains presented resistance genes to at least one antimicrobial class and 684 strains presented a multidrug-resistant (MDR) profile. Resistance genes to 14 classes of antimicrobials were detected. Aminoglycosides presented the most prevalent and diverse resistance genes, while the sulfonamide resistance gene, sul2, was the most prevalent among the strains studied. The presence of resistance genes from 14 different antimicrobial classes, the high levels of MDR strains, and the detection of genes related to clinical and veterinary-used drugs reinforce the necessity of more efficient control measures. Moreover, it warns for the necessity of the rational use of antimicrobials in veterinary and clinical situations in Brazil, since contaminated food may act as a vehicle for human infections.
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Vilela FP, Gomes CN, Passaglia J, Rodrigues DP, Costa RG, Tiba Casas MR, Fernandes SA, Falcão JP, Campioni F. Genotypic Resistance to Quinolone and Tetracycline in Salmonella Dublin Strains Isolated from Humans and Animals in Brazil. Microb Drug Resist 2018; 25:143-151. [PMID: 30222519 DOI: 10.1089/mdr.2017.0329] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Resistance of Salmonella Dublin strains to quinolones and tetracycline has been increasing worldwide. Studies regarding the genotypic resistance traits of strains of this serovar isolated in Brazil are scarce. This study aims to examine the genetic characteristics of Salmonella Dublin strains isolated in Brazil, which are associated with resistance to quinolone and tetracycline. The minimum inhibitory concentrations (MICs) of nalidixic acid, ciprofloxacin, and tetracycline of the 10 strains sensitive and 21 strains resistant to quinolone and tetracycline were determined using Etest.® The mutation profiles of the gyrA, gyrB, parC, and parE genes were accessed by sequencing, while the presence of plasmid-mediated quinolone resistance and tet genes was analyzed by PCR. Quinolone-resistant strains presented the amino acid substitutions Ser96→Tyr, Ser96→Phe, Asp107→Asn, or Asp108→Gly on the gyrA gene, and the Ser224→Phe and Glu231→Asp mutations on the gyrB gene. The qnrA, tet(A), and tet(B) genes were detected in 5, 13, and 6 strains, respectively. Analysis of the MIC values revealed that 1 and 3 strains presented intermediate and resistant MIC profiles to nalidixic acid, respectively; 6 strains presented intermediate MIC profile to ciprofloxacin; and 13 strains presented resistant MIC profile to tetracycline. In the Salmonella Dublin strains studied, quinolone resistance was mainly related to mutation points that led to target alteration in the gyrA and gyrB genes, while tetracycline resistance was associated with the presence of tet(A) and/or tet(B) genes, with the highest resistance levels detected in strains bearing the tet(B) gene. The presence of the aforementioned genotypic resistance traits in Salmonella Dublin strains isolated over 33 years in Brazil indicates that ciprofloxacin or tetracycline therapy against such strains may fail.
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Almeida F, Seribelli AA, Medeiros MIC, Rodrigues DDP, de MelloVarani A, Luo Y, Allard MW, Falcão JP. Phylogenetic and antimicrobial resistance gene analysis of Salmonella Typhimurium strains isolated in Brazil by whole genome sequencing. PLoS One 2018; 13:e0201882. [PMID: 30102733 PMCID: PMC6089434 DOI: 10.1371/journal.pone.0201882] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 07/24/2018] [Indexed: 12/02/2022] Open
Abstract
Whole genome sequencing (WGS) has been used as a powerful technology for molecular epidemiology, surveillance, identification of species and serotype, identification of the sources of outbreaks, among other purposes. In Brazil, there is relatively few epidemiological data on Salmonella. In this study, 90 Salmonella Typhimurium strains had their genome sequenced to uncover the diversity of Salmonella Typhimurium isolated from humans and food, between 1983 and 2013, from different geographic regions in Brazil based on single nucleotide polymorphism (SNP) analysis. A total of 39 resistance genes were identified, such as aminoglycoside, tetracycline, sulfonamide, trimethoprim, beta-lactam, fluoroquinolone, phenicol and macrolide, as well as the occurrence of point mutations in some of the genes such as gyrA, gyrB, parC and parE. A total of 65 (72.2%) out of 90 S. Typhimurium strains studied were phenotypically resistant to sulfonamides, 44 (48.9%) strains were streptomycin resistant, 27 (30%) strains were resistant to tetracycline, 21 (23.3%) strains were gentamicin resistant, and seven (7.8%) strains were resistant to ceftriaxone. In the gyrA gene, it was observed the following amino acid substitutions: Asp(87)→Gly, Asp(87)→Asn, Ser(83)→Phe, Ser(83)→Tyr. Phylogenetic results placed the 90 S. Typhimurium strains into two major clades suggesting the existence of a prevalent subtype, likely more adapted, among strains isolated from humans, with some diversity in subtypes in foods. The variety and prevalence of resistant genes found in these Salmonella Typhimurium strains reinforces their potential hazard for humans and the risk in foods in Brazil.
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Campioni F, Cao G, Kastanis G, Janies DA, Bergamini AMM, Rodrigues DDP, Stones R, Brown E, Allard MW, Falcão JP. Changing of the Genomic Pattern of Salmonella Enteritidis Strains Isolated in Brazil Over a 48 year-period revealed by Whole Genome SNP Analyses. Sci Rep 2018; 8:10478. [PMID: 29993044 PMCID: PMC6041339 DOI: 10.1038/s41598-018-28844-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 06/28/2018] [Indexed: 11/09/2022] Open
Abstract
Salmonella Enteritidis became the main serovar isolated from gastroenteritis cases in Brazil after the 90's. In this study we used whole genome sequence analysis to determine the phylogenetic relationships among a collection of strains isolated in Brazil to identify possible genomic differences between the strains isolated in the pre and post-epidemic period. Also, we compared our data from strains isolated in Brazil to strains available in the public domain from other South American countries. Illumina technology was used to sequence the genome of 256 Salmonella Enteritidis strains isolated over a 48 year-period in Brazil, comprising the pre- and post-epidemic period. Phylogenetic analyses revealed distinct lineages for strains isolated before and after 1994. Moreover, the phage region SE20 that may be related to the emergence of Salmonella Enteritidis worldwide was present only in strains of the post-epidemic cluster. In conclusion, our results showed that the genomic profile of Salmonella Enteritidis strains isolated in Brazil shifted after 1994, replaced by a global epidemic group of strains. It may be hypothesized that the presence of the prophage SE20 might have conferred to these strains a better ability to colonize chicken and consequently to infect and cause disease in humans, which might better explain the increase in the number of S. Enteritidis cases in Brazil and other South American countries. However, to verify this hypothesis further studies are needed.
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Frazão MR, Medeiros MIC, Duque SDS, Falcão JP. Pathogenic potential and genotypic diversity of Campylobacter jejuni: a neglected food-borne pathogen in Brazil. J Med Microbiol 2017; 66:350-359. [PMID: 28317494 DOI: 10.1099/jmm.0.000424] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Purpose and methodology.Campylobacter jejuni is a major zoonotic pathogen that causes food-borne gastroenteritis worldwide. However, there are only a few studies available that have molecularly characterized C. jejuni strains isolated in Brazil. The aim of this study was to genotype 111 C. jejuni strains isolated from sick humans (43), monkey faeces (19), chicken faeces (14), chicken meat (33) and sewage (2) between 1996 and 2016 in Brazil using flaA-SVR (short variable region) sequencing and PFGE. Furthermore, the presence of 16 virulence genes was analysed by PCR. RESULTS Using PFGE and flaA-SVR sequencing, the 111 C. jejuni strains studied were grouped into three and two clusters, respectively, and some strains of different origin presented a similarity of ≥80 %. In total, 35 flaA-SVR alleles were detected. Alleles gt45, gt49 and gt57 were the most prevalent, in contrast with those frequently described in the PubMLST database. All 111 C. jejuni strains contained the genes flaA, flhA, cadF, docA, cdtA, cdtB, cdtC, iamA, ciaB, sodB, dnaJ, pldA, racR and csrA. The wlaN gene was detected in 11 strains (9.9 %), and the virB11 in just one strain (0.9 %). CONCLUSIONS In conclusion, the pathogenic potential of the C. jejuni strains studied was highlighted by the high frequency of the majority of the virulence genes searched. The flaA-SVR sequencing and PFGE results showed that some of the strains studied presented a high genotypic similarity, suggesting potential for transmission between animal sources and humans in this country. Altogether, the results characterize further C. jejuni isolates from Brazil, an important producer and exporter of chicken meat.
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Almeida F, Seribelli AA, da Silva P, Medeiros MIC, Dos Prazeres Rodrigues D, Moreira CG, Allard MW, Falcão JP. Multilocus sequence typing of Salmonella Typhimurium reveals the presence of the highly invasive ST313 in Brazil. INFECTION GENETICS AND EVOLUTION 2017; 51:41-44. [PMID: 28288927 DOI: 10.1016/j.meegid.2017.03.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Revised: 03/08/2017] [Accepted: 03/10/2017] [Indexed: 10/20/2022]
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Almeida F, Medeiros MIC, Rodrigues DDP, Allard MW, Falcão JP. Molecular characterization of Salmonella Typhimurium isolated in Brazil by CRISPR-MVLST. J Microbiol Methods 2016; 133:55-61. [PMID: 28034696 DOI: 10.1016/j.mimet.2016.12.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 12/20/2016] [Accepted: 12/21/2016] [Indexed: 11/17/2022]
Abstract
CRISPR-multi-locus virulence sequence typing (CRISPR-MVLST) was performed to type 92 S. Typhimurium strains isolated from humans and food sources between 1983 and 2013 in Brazil and assess the suitability of this methodology comparing it with PFGE already used for subtyping the same strains. Among the 92 S. Typhimurium strains studied, we identified 25 CRISPR1 alleles, 27 CRISPR2 alleles, 2 fimH alleles and 3 sseL alleles showing that the genetic variability is much higher in the CRISPRs loci than in the virulence genes. The CRISPR-MVLST analysis provided similar results to the PFGE previously published used to type the same set of strains, demonstrating that CRISPR-MVLST is a very efficient approach for subtyping S. Typhimurium serovar and can be used to complement and validate results obtained by the PFGE methodology.
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Campioni F, Souza RA, Martins VV, Stehling EG, Bergamini AMM, Falcão JP. Prevalence of gyrA Mutations in Nalidixic Acid-Resistant Strains of Salmonella Enteritidis Isolated from Humans, Food, Chickens, and the Farm Environment in Brazil. Microb Drug Resist 2016; 23:421-428. [PMID: 27559761 DOI: 10.1089/mdr.2016.0024] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Salmonella Enteritidis strains that are resistant to nalidixic acid and exhibit reduced susceptibility to fluoroquinolones have been increasing worldwide. In Brazil, few studies have been conducted to elucidate the quinolone resistance mechanisms of S. Enteritidis strains. This study analyzed the profile of gyrA, gyrB, parC, and parE mutations and plasmid-mediated quinolone resistance (PMQR) mechanisms in S. Enteritidis NalR strains isolated in Brazil. Moreover, the minimum inhibitory concentrations (MICs) of ciprofloxacin were evaluated in 84 NalR strains and compared with 20 NalS strains. The mutation profiles of the gyrA gene were accessed by high-resolution melting analysis and gyrB, parC, and parE by quinolone resistance-determining region sequencing. The MICs of ciprofloxacin were accessed with Etest®. The strains were divided into five gyrA melting profiles. The NalR strains exhibited the following amino acid substitutions: Ser97→Pro, Ser83→Phe, Asp87→Asn, or Asp87→Tyr. The average MICs of ciprofloxacin was 0.006 μg/ml in the NalS and 0.09 μg/ml in the NalR strains. No points of mutation were observed in the genes gyrB, parC, and parE. The qnrB gene was found in two strains. In conclusion, the reduced susceptibility to ciprofloxacin observed in NalR strains may cause treatment failures once this drug is commonly used to treat Salmonella infections. Moreover, this reduced susceptibility in these Brazilian strains was provided by target alteration of gene gyrA and not by mobile elements, such as resistance plasmids.
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Almeida F, Medeiros MIC, Kich JD, Falcão JP. Virulence-associated genes, antimicrobial resistance and molecular typing of Salmonella Typhimurium strains isolated from swine from 2000 to 2012 in Brazil. J Appl Microbiol 2016; 120:1677-90. [PMID: 26913828 DOI: 10.1111/jam.13110] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 02/02/2016] [Accepted: 02/17/2016] [Indexed: 11/29/2022]
Abstract
AIMS The aims of this study were to assess the pathogenic potential, antimicrobial resistance and genotypic diversity of Salmonella Typhimurium strains isolated in Brazil from swine (22) and the surrounding swine environment (5) from 2000 to 2012 and compare them to the profiles of 43 human strains isolated from 1983 to 2010, which had been previously studied. METHODS AND RESULTS The presence of 12 SPI-1, SPI-2 and plasmid genes was assessed by PCR, the antimicrobial susceptibility to 13 antimicrobials was determined by the disc diffusion assay and genotyping was performed using pulsed-field gel electrophoresis (PFGE), multiple-locus variable-number of tandem repeats analysis (MLVA) and ERIC-PCR. More than 77·8% of the swine strains carried 10 or more of the virulence markers. Ten (37%) strains isolated from swine were multi-drug resistant (MDR). All the molecular typing techniques grouped the strains in two main clusters. Some strains isolated from swine and humans were allocated together in the PFGE-B2, MLVA-A1, MLVA-B and ERIC-A1 clusters. CONCLUSIONS The genotyping results suggest that some strains isolated from swine and humans may descend from a common subtype and may indicate a possible risk of MDR S. Typhimurium with high frequency of virulence genes isolated from swine to contaminate humans in Brazil. SIGNIFICANCE AND IMPACT OF THE STUDY This study provided new information about the pathogenic potential, antimicrobial resistance and genotypic diversity of S. Typhimurium isolates from swine origin in Brazil, the fourth largest producer of pigs worldwide.
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Peres NTDA, Silva LGD, Santos RDS, Jacob TR, Persinoti GF, Rocha LB, Falcão JP, Rossi A, Martinez-Rossi NM. In vitro and ex vivo infection models help assess the molecular aspects of the interaction of Trichophyton rubrum with the host milieu. Med Mycol 2016; 54:420-7. [PMID: 26768373 DOI: 10.1093/mmy/myv113] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 12/14/2015] [Indexed: 12/24/2022] Open
Abstract
Dermatophytes are fungal pathogens that cause cutaneous infections such as onychomycosis and athlete's foot in both healthy and immunocompromised patients.Trichophyton rubrum is the most prevalent dermatophyte causing human nail and skin infections worldwide, and because of its anthropophilic nature, animal infection models are limited. The purpose of this work was to compare the expression profile of T. rubrum genes encoding putative virulence factors during growth in ex vivo and in vitro infection models. The efficiency of the ex vivo skin infection model was confirmed by scanning electron microscopy (SEM), which showed that the conidia had produced hyphae that penetrated into the epidermis. Quantitative RT-PCR (qRT-PCR) analysis showed that the expression of some genes is modulated in response to the infection model used, as compared to that observed in cells grown in glucose-containing media. We concluded that ex vivo infection models help assess the molecular aspects of the interaction of T. rubrum with the host milieu, and thus provide insights into the modulation of genes during infection.
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Almeida F, Medeiros MIC, Rodrigues DDP, Falcão JP. Genotypic diversity, pathogenic potential and the resistance profile of Salmonella Typhimurium strains isolated from humans and food from 1983 to 2013 in Brazil. J Med Microbiol 2015; 64:1395-1407. [DOI: 10.1099/jmm.0.000158] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Souza RA, Imori PFM, Passaglia J, Pitondo-Silva A, Falcão JP. Molecular typing of Yersinia pseudotuberculosis strains isolated from livestock in Brazil. GENETICS AND MOLECULAR RESEARCH 2013; 12:4869-78. [PMID: 24301748 DOI: 10.4238/2013.october.22.6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Yersinia pseudotuberculosis can infect a broad range of animals. In Brazil, this bacterium has been isolated from healthy and sick animals from sporadic cases and outbreaks of hemorrhagic gastroenteritis among livestock. However, the molecular diversity of these isolates is little understood. In this study, we used multilocus sequence typing, enterobacterial repetitive intergenic consensus PCR and pulsed-field gel electrophoresis to genotype 40 Y. pseudotuberculosis strains belonging to bio-serogroups 1/O:1a and 2/O:3 isolated between 1982 and 1990 in the southern region of Brazil. All three methodologies clustered the strains into two main clusters according to their bio-serogroups. Good correlations were observed between the clusters and the pathogenic potential of the strains. No correlation among the strains was observed according to geographical origin, host, place, or year of isolation. The grouping of the Y. pseudotuberculosis isolated in Brazil determined by these assays leads us to suggest that Brazilian livestock harbor two subpopulations of Y. pseudotuberculosis.
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Martins VV, Pitondo-Silva A, Manço LDM, Falcão JP, Freitas SDS, da Silveira WD, Stehling EG. Pathogenic potential and genetic diversity of environmental and clinical isolates of Pseudomonas aeruginosa. APMIS 2013; 122:92-100. [PMID: 23879442 DOI: 10.1111/apm.12112] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 03/19/2013] [Indexed: 12/21/2022]
Abstract
The aim of this study was to investigate the occurrence of virulence genes among clinical and environmental isolates of Pseudomonas aeruginosa and to establish their genetic relationships by Enterobacterial Repetitive Intergenic Consensus PCR (ERIC-PCR). A total of 60 P. aeruginosa isolates from environmental and clinical sources were studied. Of these, 20 bacterial isolates were from soil, 20 from water, and 20 from patients with cystic fibrosis. Analysis of ERIC-PCR demonstrated that the isolates of P. aeruginosa showed a considerable genetic variability, regardless of their habitat. Numerous virulence genes were detected in both clinical and environmental isolates, reinforcing the possible pathogenic potential of soil and water isolates. The results showed that the environmental P. aeruginosa has all the apparatus needed to cause disease in humans and animals.
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Falcão JP, Brocchi M, Proença-Módena JL, Acrani GO, Corrêa EF, Falcão DP. Virulence characteristics and epidemiology of Yersinia enterocolitica and Yersiniae other than Y. pseudotuberculosis and Y. pestis isolated from water and sewage. J Appl Microbiol 2004; 96:1230-6. [PMID: 15139914 DOI: 10.1111/j.1365-2672.2004.02268.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS To determine the species, bio-sero-phagetypes, antimicrobial drug resistance and also the pathogenic potential of 144 strains of Yersinia spp. isolated from water sources and sewage in Brazil. METHODS AND RESULTS The 144 Yersinia strains were characterized biochemically, serologically and had their antibiotic resistance and phenotypic virulence markers determined by microbiological and serological standard techniques. The Y. enterocolitica strains related to human diseases were also tested for the presence of virulence genes, by the PCR technique. The isolates were classified as Y. enterocolitica, Y. intermedia, Y. frederiksenii, Y. kristensenii and Yersinia biochemically atypical. The 144 isolates belonged to various bio-serogroups. Half of the strains showed resistance to three or more drugs. The Y. enterocolitica strains related to human diseases exhibited phenotypic virulence characteristics and virulence genes. CONCLUSIONS Water from various sources and sewage are contaminated with Yersinia spp. in Brasil. Among these bacteria, virulent strains of Y. enterocolitica were found, with biotypes and serogroups related to human diseases. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first documented description of the occurrence of pathogenic Y. enterocolitica in water sources and sewage in Brazil. The occurrence of virulence strains of Y. enterocolitica shows that the environment is a potential source of human infection by this species in this country.
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