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Salgueiro V, Manageiro V, Rosado T, Bandarra NM, Botelho MJ, Dias E, Caniça M. Snapshot of resistome, virulome and mobilome in aquaculture. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:166351. [PMID: 37604365 DOI: 10.1016/j.scitotenv.2023.166351] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 07/28/2023] [Accepted: 08/15/2023] [Indexed: 08/23/2023]
Abstract
Aquaculture environments can be hotspots for resistance genes through the surrounding environment. Our objective was to study the resistome, virulome and mobilome of Gram-negative bacteria isolated in seabream and bivalve molluscs, using a WGS approach. Sixty-six Gram-negative strains (Aeromonadaceae, Enterobacteriaceae, Hafniaceae, Morganellaceae, Pseudomonadaceae, Shewanellaceae, Vibrionaceae, and Yersiniaceae families) were selected for genomic characterization. The species and MLST were determined, and antibiotic/disinfectants/heavy metals resistance genes, virulence determinants, MGE, and pathogenicity to humans were investigated. Our study revealed new sequence-types (e.g. Aeromonas spp. ST879, ST880, ST881, ST882, ST883, ST887, ST888; Shewanella spp. ST40, ST57, ST58, ST60, ST61, ST62; Vibrio spp. ST206, ST205). >140 different genes were identified in the resistome of seabream and bivalve molluscs, encompassing genes associated with β-lactams, tetracyclines, aminoglycosides, quinolones, sulfonamides, trimethoprim, phenicols, macrolides and fosfomycin resistance. Disinfectant resistance genes qacE-type, sitABCD-type and formA-type were found. Heavy metals resistance genes mdt, acr and sil stood out as the most frequent. Most resistance genes were associated with antibiotics/disinfectants/heavy metals commonly used in aquaculture settings. We also identified 25 different genes related with increased virulence, namely associated with adherence, colonization, toxins production, red blood cell lysis, iron metabolism, escape from the immune system of the host. Furthermore, 74.2 % of the strains analysed were considered pathogenic to humans. We investigated the genetic environment of several antibiotic resistance genes, including blaTEM-1B, blaFOX-18, aph(3″)-Ib, dfrA-type, aadA1, catA1-type, tet(A)/(E), qnrB19 and sul1/2. Our analysis also focused on identifying MGE in proximity to these genes (e.g. IntI1, plasmids and TnAs), which could potentially facilitate the spread of resistance among bacteria across different environments. This study provides a comprehensive examination of the diversity of resistance genes that can be transferred to both humans and the environment, with the recognition that aquaculture and the broader environment play crucial roles as intermediaries within this complex transmission network.
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Affiliation(s)
- Vanessa Salgueiro
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal; Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, University of Porto, Porto, Portugal; AL4AnimalS, Associate Laboratory for Animal and Veterinary Sciences, Portugal
| | - Vera Manageiro
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal; Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, University of Porto, Porto, Portugal; AL4AnimalS, Associate Laboratory for Animal and Veterinary Sciences, Portugal
| | - Tânia Rosado
- Laboratory of Biology and Ecotoxicology, Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Narcisa M Bandarra
- Division of Aquaculture, Upgrading and Bioprospecting, Portuguese Institute for the Sea and Atmosphere, IPMA, Lisbon, Portugal; CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto, Matosinhos, Portugal
| | - Maria João Botelho
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto, Matosinhos, Portugal; Division of Oceanography and Marine Environment, Portuguese Institute for the Sea and Atmosphere, Lisbon, Portugal
| | - Elsa Dias
- Laboratory of Biology and Ecotoxicology, Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Manuela Caniça
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal; Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, University of Porto, Porto, Portugal; AL4AnimalS, Associate Laboratory for Animal and Veterinary Sciences, Portugal; CIISA, Center for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal.
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Sanches MS, Silva LC, da Silva CR, Montini VH, de Oliva BHD, Guidone GHM, Nogueira MCL, Menck-Costa MF, Kobayashi RKT, Vespero EC, Rocha SPD. Prevalence of Antimicrobial Resistance and Clonal Relationship in ESBL/AmpC-Producing Proteus mirabilis Isolated from Meat Products and Community-Acquired Urinary Tract Infection (UTI-CA) in Southern Brazil. Antibiotics (Basel) 2023; 12:370. [PMID: 36830280 PMCID: PMC9952622 DOI: 10.3390/antibiotics12020370] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
The present study aimed to evaluate the prevalence of antimicrobial resistance and clonal relationships in Proteus mirabilis isolated from chicken meat, beef, pork, and community-acquired urinary tract infections (UTI-CA). Chicken meat isolates showed the highest multidrug resistance (MDR), followed by those from pork and UTI-CA, whereas beef had relatively few MDR strains. All sources had strains that carried blaCTX-M-65, whereas blaCTX-M-2 and blaCMY-2 were only detected in chicken meat and UTI-CA isolates. This indicates that chicken meat should be considered an important risk factor for the spread of P. mirabilis carrying ESBL and AmpC. Furthermore, ESBL/AmpC producing strains were resistant to a greater number of antimicrobials and possessed more resistance genes than non-producing strains. In addition, the antimicrobial resistance genes qnrD, aac(6')-Ib-cr, sul1, sul2, fosA3, cmlA, and floR were also found. Molecular typing showed a genetic similarity between chicken meat and UTI-CA isolates, including some strains with 100% similarity, indicating that chicken can be a source of P. mirabilis causing UTI-CA. It was concluded that meat, especially chicken meat, can be an important source of dissemination of multidrug-resistant P. mirabilis in the community.
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Affiliation(s)
- Matheus Silva Sanches
- Laboratory of Bacteriology, Center of Biological Sciences, Department of Microbiology, State University of Londrina, Londrina P.O. Box 10.011, Brazil
| | - Luana Carvalho Silva
- Laboratory of Bacteriology, Center of Biological Sciences, Department of Microbiology, State University of Londrina, Londrina P.O. Box 10.011, Brazil
| | - Caroline Rodrigues da Silva
- Microorganism Research Center, Health Sciences Center, Department of Dermatological, Infectious and Parasitic Diseases, Medical School of São José do Rio Preto, São José do Rio Preto P.O. Box 15.090, Brazil
| | - Victor Hugo Montini
- Laboratory of Bacteriology, Center of Biological Sciences, Department of Microbiology, State University of Londrina, Londrina P.O. Box 10.011, Brazil
| | - Bruno Henrique Dias de Oliva
- Laboratory of Bacteriology, Center of Biological Sciences, Department of Microbiology, State University of Londrina, Londrina P.O. Box 10.011, Brazil
| | - Gustavo Henrique Migliorini Guidone
- Laboratory of Bacteriology, Center of Biological Sciences, Department of Microbiology, State University of Londrina, Londrina P.O. Box 10.011, Brazil
| | - Mara Corrêa Lelles Nogueira
- Microorganism Research Center, Health Sciences Center, Department of Dermatological, Infectious and Parasitic Diseases, Medical School of São José do Rio Preto, São José do Rio Preto P.O. Box 15.090, Brazil
| | - Maísa Fabiana Menck-Costa
- Laboratory of Basic and Applied Bacteriology, Center of Biological Sciences, Department of Microbiology, State University of Londrina, Londrina P.O. Box 10.011, Brazil
| | - Renata Katsuko Takayama Kobayashi
- Laboratory of Basic and Applied Bacteriology, Center of Biological Sciences, Department of Microbiology, State University of Londrina, Londrina P.O. Box 10.011, Brazil
| | - Eliana Carolina Vespero
- Department of Pathology, Health Sciences Center, Clinical and Toxicological Analysis, University Hospital of Londrina, State University of Londrina, Londrina P.O. Box 10.011, Brazil
| | - Sergio Paulo Dejato Rocha
- Laboratory of Bacteriology, Center of Biological Sciences, Department of Microbiology, State University of Londrina, Londrina P.O. Box 10.011, Brazil
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Proteus mirabilis isolated from untreated hospital wastewater, Ibadan, Southwestern Nigeria showed low-level resistance to fluoroquinolone and carried qnrD3 on Col3M plasmids. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:47158-47167. [PMID: 36735119 DOI: 10.1007/s11356-023-25618-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 01/25/2023] [Indexed: 02/04/2023]
Abstract
Untreated wastewater emanating from healthcare facilities are risk factors for the spread of antimicrobial resistance (AMR) at the human-environment interface. In this study, we investigated the determinants of resistance in three multidrug resistant strains of Proteus mirabilis isolated from untreated wastewater collected from three government owned hospitals in Ibadan, Nigeria. Despite showing low-level resistance to ciprofloxacin, whole genome sequencing revealed the transferable mechanism of quinolone resistance (TMQR) gene qnrD3 carried on Col3M plasmids in all the isolates. Core genome phylogenetic analysis showed the isolates are closely related differing from each other by ≤ 23 single nucleotide polymorphisms (SNP). Further, they shared the closest evolutionary relationship with isolates from China. Similarly, the Col3M plasmids is most closely related to p3M-2A found in P. vulgaris 3 M isolated from the intestine of shrimps in China. This to the best of our knowledge is the first report of Col3M plasmids carrying qnrD3 in environmental bacterial isolates. Our results indicate a possible silent spread of this important plasmid associated with the dissemination of qnrD3 in Nigeria, and further highlights the important role played by untreated wastewater from healthcare facilities in the spread of AMR in low- and middle-income countries.
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Azargun R, Gholizadeh P, Sadeghi V, Hosainzadegan H, Tarhriz V, Memar MY, Pormohammad A, Eyvazi S. Molecular mechanisms associated with quinolone resistance in Enterobacteriaceae: review and update. Trans R Soc Trop Med Hyg 2021; 114:770-781. [PMID: 32609840 DOI: 10.1093/trstmh/traa041] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 04/09/2020] [Accepted: 05/20/2020] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Quinolones are broad-spectrum antibiotics, which are used for the treatment of different infectious diseases associated with Enterobacteriaceae. During recent decades, the wide use as well as overuse of quinolones against diverse infections has led to the emergence of quinolone-resistant bacterial strains. Herein, we present the development of quinolone antibiotics, their function and also the different quinolone resistance mechanisms in Enterobacteriaceae by reviewing recent literature. METHODS All data were extracted from Google Scholar search engine and PubMed site, using keywords; quinolone resistance, Enterobacteriaceae, plasmid-mediated quinolone resistance, etc. RESULTS AND CONCLUSION The acquisition of resistance to quinolones is a complex and multifactorial process. The main resistance mechanisms consist of one or a combination of target-site gene mutations altering the drug-binding affinity of target enzymes. Other mechanisms of quinolone resistance are overexpression of AcrAB-tolC multidrug-resistant efflux pumps and downexpression of porins as well as plasmid-encoded resistance proteins including Qnr protection proteins, aminoglycoside acetyltransferase (AAC(6')-Ib-cr) and plasmid-encoded active efflux pumps such as OqxAB and QepA. The elucidation of resistance mechanisms will help researchers to explore new drugs against the resistant strains.
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Affiliation(s)
- Robab Azargun
- Department of Microbiology, Faculty of Medicine, Maragheh University of Medical Sciences, Maragheh, Iran
| | - Pourya Gholizadeh
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Vahid Sadeghi
- Faculty of Veterinary Medicine, Islamic Azad University, Urmia, Iran
| | - Hasan Hosainzadegan
- Department of Microbiology, Faculty of Medicine, Maragheh University of Medical Sciences, Maragheh, Iran
| | - Vahideh Tarhriz
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Yousef Memar
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali Pormohammad
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shirin Eyvazi
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Zhang H, Chang M, Zhang X, Cai P, Dai Y, Song T, Wu Z, Xu H, Qiao M. Functional Identification and Evolutionary Analysis of Two Novel Plasmids Mediating Quinolone Resistance in Proteus vulgaris. Microorganisms 2020; 8:microorganisms8071074. [PMID: 32708454 PMCID: PMC7409132 DOI: 10.3390/microorganisms8071074] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/15/2020] [Accepted: 07/16/2020] [Indexed: 01/08/2023] Open
Abstract
Plasmid-mediated quinolone resistance (PMQR) remains one of the main mechanisms of bacterial quinolone resistance and plays an important role in the transmission of antibiotic resistance genes (ARGs). In this study, two novel plasmids, p3M-2A and p3M-2B, which mediate quinolone resistance in Proteus vulgaris strain 3M (P3M) were identified. Of these, only p3M-2B appeared to be a qnrD-carrying plasmid. Both p3M-2A and p3M-2B could be transferred into Escherichia coli, and the latter caused a twofold change in ciprofloxacin resistance, according to the measured minimum inhibitory concentration (MIC). Plasmid curing/complementation and qRT-PCR results showed that p3M-2A can directly regulate the expression of qnrD in p3M-2B under treatment with ciprofloxacin, in which process, ORF1 was found to play an important role. Sequence alignments and phylogenetic analysis revealed the evolutionary relationships of all reported qnrD-carrying plasmids and showed that ORF1–4 in p3M-2B is the most conserved backbone for the normal function of qnrD-carrying plasmids. The identified direct repeats (DR) suggested that, from an evolutionary perspective, p3M-2B may have originated from the 2683-bp qnrD-carrying plasmid and may increase the possibility of plasmid recombination and then of qnrD transfer. To the best of our knowledge, this is the first identification of a novel qnrD-carrying plasmid isolated from a P. vulgaris strain of shrimp origin and a plasmid that plays a regulatory role in qnrD expression. This study also sheds new light on plasmid evolution and on the mechanism of horizontal transfer of ARGs encoded by plasmids.
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Affiliation(s)
- Hongyang Zhang
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China; (H.Z.); (X.Z.); (P.C.); (Y.D.); (T.S.); (Z.W.); (H.X.)
| | - Mingding Chang
- Zhengzhou University Industrial Technology Institute Co. Ltd., Zhengzhou 450000, China;
| | - Xiaochen Zhang
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China; (H.Z.); (X.Z.); (P.C.); (Y.D.); (T.S.); (Z.W.); (H.X.)
| | - Peiyan Cai
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China; (H.Z.); (X.Z.); (P.C.); (Y.D.); (T.S.); (Z.W.); (H.X.)
| | - Yixin Dai
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China; (H.Z.); (X.Z.); (P.C.); (Y.D.); (T.S.); (Z.W.); (H.X.)
| | - Tongzhen Song
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China; (H.Z.); (X.Z.); (P.C.); (Y.D.); (T.S.); (Z.W.); (H.X.)
| | - Zhenzhou Wu
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China; (H.Z.); (X.Z.); (P.C.); (Y.D.); (T.S.); (Z.W.); (H.X.)
| | - Haijin Xu
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China; (H.Z.); (X.Z.); (P.C.); (Y.D.); (T.S.); (Z.W.); (H.X.)
| | - Mingqiang Qiao
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China; (H.Z.); (X.Z.); (P.C.); (Y.D.); (T.S.); (Z.W.); (H.X.)
- Correspondence:
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Abstract
While the description of resistance to quinolones is almost as old as these antimicrobial agents themselves, transferable mechanisms of quinolone resistance (TMQR) remained absent from the scenario for more than 36 years, appearing first as sporadic events and afterward as epidemics. In 1998, the first TMQR was soundly described, that is, QnrA. The presence of QnrA was almost anecdotal for years, but in the middle of the first decade of the 21st century, there was an explosion of TMQR descriptions, which definitively changed the epidemiology of quinolone resistance. Currently, 3 different clinically relevant mechanisms of quinolone resistance are encoded within mobile elements: (i) target protection, which is mediated by 7 different families of Qnr (QnrA, QnrB, QnrC, QnrD, QnrE, QnrS, and QnrVC), which overall account for more than 100 recognized alleles; (ii) antibiotic efflux, which is mediated by 2 main transferable efflux pumps (QepA and OqxAB), which together account for more than 30 alleles, and a series of other efflux pumps (e.g., QacBIII), which at present have been sporadically described; and (iii) antibiotic modification, which is mediated by the enzymes AAC(6')Ib-cr, from which different alleles have been claimed, as well as CrpP, a newly described phosphorylase.
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Sanches MS, Baptista AAS, de Souza M, Menck-Costa MF, Koga VL, Kobayashi RKT, Rocha SPD. Genotypic and phenotypic profiles of virulence factors and antimicrobial resistance of Proteus mirabilis isolated from chicken carcasses: potential zoonotic risk. Braz J Microbiol 2019; 50:685-694. [PMID: 31049879 PMCID: PMC6863274 DOI: 10.1007/s42770-019-00086-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/25/2019] [Indexed: 10/26/2022] Open
Abstract
Proteus mirabilis is an opportunistic pathogen often associated with a variety of human infections acquired both in the community and in hospitals. In this context, the present work aimed to evaluate the genotypic and phenotypic characteristics of the virulence factors and antimicrobial resistance determinants of 32 P. mirabilis strains isolated from chicken carcasses in a poultry slaughterhouse in the north of the state of Paraná, Brazil, in order to assess a potential zoonotic risk. The isolates presented a variety of virulence genes that contribute to the development of infection in humans. The mrpA, pmfA, atfA (fimbriae), ireA (siderophores receptor), zapA, ptA (Proteases), and hpmA (hemolysin) genes were found in 32 (100%) isolates and ucaA (fimbriae) in 16 (50%). All isolates showed aggregative adherence in HEp-2 cells and formed biofilms. Of all strains, 27 (84.38%) showed cytotoxic effects in Vero cells. Antimicrobial susceptibility was tested using 20 antimicrobials, in which 25 (78.13%) strains were considered multidrug-resistant. The presence of blaESBL and blaampC genes conferring resistance to β-lactams and qnr to quinolones were also detected in the isolates after presumption in the phenotypic test, in which 7 (21.88%) isolates contained the CTX-M-2 group, 11 (34.38%) contained CIT group and 19 (59.38%) contained qnrD. Therefore, chicken carcasses contaminated with P. mirabilis may pose a health risk to the consumer, as these isolates have a variety of virulence and antimicrobial resistance characteristics that can be found in P. mirabilis strains isolated from human infections.
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Affiliation(s)
- Matheus Silva Sanches
- Laboratory of Bacteriology, Department of Microbiology, Center of Biological Sciences, Universidade Estadual de Londrina, Londrina, Brazil
| | - Ana Angelita Sampaio Baptista
- Laboratory of Avian Medicine, Department of Preventive Veterinary Medicine, Agricultural Sciences Center, Universidade Estadual de Londrina, Londrina, Brazil
| | - Marielen de Souza
- Laboratory of Avian Medicine, Department of Preventive Veterinary Medicine, Agricultural Sciences Center, Universidade Estadual de Londrina, Londrina, Brazil
| | - Maísa Fabiana Menck-Costa
- Laboratory of Avian Medicine, Department of Preventive Veterinary Medicine, Agricultural Sciences Center, Universidade Estadual de Londrina, Londrina, Brazil
| | - Vanessa Lumi Koga
- Laboratory of Basic and Applied Bacteriology, Department of Microbiology, Center of Biological Sciences, Universidade Estadual de Londrina, Londrina, Brazil
| | - Renata Katsuko Takayama Kobayashi
- Laboratory of Basic and Applied Bacteriology, Department of Microbiology, Center of Biological Sciences, Universidade Estadual de Londrina, Londrina, Brazil
| | - Sergio Paulo Dejato Rocha
- Laboratory of Bacteriology, Department of Microbiology, Center of Biological Sciences, Universidade Estadual de Londrina, Londrina, Brazil.
- Department of Microbiology, Center of Biological Science, State University of Londrina, Rodovia Celso Garcia Cid, PO-BOX 6001, Londrina, Paraná, 86051-980, Brazil.
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