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Caldeira NGS, de Souza MLS, de Miranda RVDSL, da Costa LV, Forsythe SJ, Zahner V, Brandão MLL. Characterization by MALDI-TOF MS and 16S rRNA Gene Sequencing of Aerobic Endospore-Forming Bacteria Isolated from Pharmaceutical Facility in Rio de Janeiro, Brazil. Microorganisms 2024; 12:724. [PMID: 38674668 PMCID: PMC11051829 DOI: 10.3390/microorganisms12040724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/28/2024] Open
Abstract
Bacillus and related genera are among the most important contaminants in the pharmaceutical production environment, and the identification of these microorganisms at the species level assists in the investigation of sources of contamination and in preventive and corrective decision making. The aim of this study was to evaluate three methodologies for the characterization of endospore-forming aerobic bacterial strains isolated from a pharmaceutical unit in Rio de Janeiro, Brazil. MALDI-TOF MS was performed using MALDI Biotyper® and VITEK® MS RUO systems, and complete 16S rRNA gene sequencing was performed using the Sanger methodology. The results showed the prevalence of the genera Bacillus (n = 9; 36.0%), Priestia (n = 5; 20.0%), and Paenibacillus (n = 4; 16.0%). Three (20.0%) strains showed <98.7% of DNA sequencing similarity on the EzBioCloud Database, indicating possible new species. In addition, the reclassification of Bacillus pseudoflexus to the genus Priestia as Priestia pseudoflexus sp. nov. is proposed. In conclusion, 16S rRNA and MALDI TOF/MS were not sufficient to identify all strains at the species level, and complementary analyses were necessary.
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Affiliation(s)
- Nathalia Gonçalves Santos Caldeira
- National Institute for Quality Control in Health, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, Brazil;
- Integrated Laboratory–Simulids and Onchocerciasis & Medical and Forensic Entomology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, Brazil;
| | - Maria Luiza Soares de Souza
- Integrated Laboratory–Simulids and Onchocerciasis & Medical and Forensic Entomology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, Brazil;
| | | | - Luciana Veloso da Costa
- Institute of Technology in Immunobiologicals, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, Brazil; (R.V.d.S.L.d.M.); (M.L.L.B.)
| | | | - Viviane Zahner
- Integrated Laboratory–Simulids and Onchocerciasis & Medical and Forensic Entomology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, Brazil;
| | - Marcelo Luiz Lima Brandão
- Institute of Technology in Immunobiologicals, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, Brazil; (R.V.d.S.L.d.M.); (M.L.L.B.)
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de Miranda RVDSL, Monteiro GM, da Costa LV, Dos Santos MCS, Dos Reis CMF, Braga LMPDS, Forsythe SJ, Villas Bôas MHS, Brandão MLL. Evaluation of phenotypical and genotypical methods for the identification and typing of Stenotrophomonas maltophilia isolated from a pharmaceutical facility. J Appl Microbiol 2023; 134:lxad236. [PMID: 37838475 DOI: 10.1093/jambio/lxad236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/03/2023] [Accepted: 10/13/2023] [Indexed: 10/16/2023]
Abstract
AIMS Evaluate methods for identification and typing of Stenotrophomonas maltophilia isolated from a pharmaceutical facility. METHODS AND RESULTS From 270 S. maltophilia strains identified by VITEK®2, 40 were selected and submitted to MALDI TOF-MS, 16S and 23S rRNA gene analysis, enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR), and an antimicrobial susceptibility profile. 16S rRNA sequencing was able to identify 39 (97.5%) strains as Stenotrophomonas spp. and one (2.5%) as Luteimonas huabeiensis. MALDI TOF-MS identified 37 (92.5%) strains as S. maltophilia, and three (7.5%) were not identified. PCR targeting 23S rRNA yielded a positive result for 39 (97.5%) strains. However, after sequencing, two strains were identified as Stenotrophomonas rhizophila, showing false-positive results. The confirmed S. maltophilia strains (n = 37) showed 35 distinct ERIC-PCR profiles and exhibited sensitivity to minocycline and levofloxacin, and six (16.3%) showed intermediate resistance to sulfamethoxazole-trimethoprim. CONCLUSION Matrix-assisted laser desorption lonization-time of flight mass spectrometry (MALDI-TOF MS) was a satisfactory methodology for the identification of S. maltophilia, but expansion of the database is necessary for the identification of other species. 16S rDNA sequencing showed low resolution for Stenotrophomonas species differentiation. PCR targeting 23S rRNA could not differentiate S. maltophilia from S. rhizophila. ERIC-PCR was shown to be a useful tool for the microbial source tracking of S. maltophilia.
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Affiliation(s)
- Rebeca Vitória da Silva Lage de Miranda
- Laboratory of Microbiological Control, Bio-Manguinhos/Fiocruz, CEP 21040-900, Rio de Janeiro, Brazil
- Laboratory of Microbiology of Food and Sanitizes, INCQS/Fiocruz, CEP 21040-900, Rio de Janeiro, Brazil
| | | | - Luciana Veloso da Costa
- Laboratory of Microbiological Control, Bio-Manguinhos/Fiocruz, CEP 21040-900, Rio de Janeiro, Brazil
| | | | | | | | | | | | - Marcelo Luiz Lima Brandão
- Laboratory of Microbiological Control, Bio-Manguinhos/Fiocruz, CEP 21040-900, Rio de Janeiro, Brazil
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Moreira FM, Pereira PDA, Miranda RVDSLD, Reis CMFD, Braga LMPDS, de Andrade JM, do Nascimento LG, Mattoso JMV, Forsythe SJ, da Costa LV, Brandão MLL. Evaluation of MALDI-TOF MS, sequencing of D2 LSU rRNA and internal transcribed spacer regions (ITS) for the identification of filamentous fungi isolated from a pharmaceutical facility. J Pharm Biomed Anal 2023; 234:115531. [PMID: 37354630 DOI: 10.1016/j.jpba.2023.115531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/12/2023] [Accepted: 06/12/2023] [Indexed: 06/26/2023]
Abstract
The identification of filamentous fungi through culture characterization may be hampered by phenotypic variability. Information obtained from the identification of microorganisms are important for investigation of sources of contamination of a product or process. The aim of this study was to identify filamentous fungal strains (n = 50) isolated from a pharmaceutical facility by using Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS), as well as D2 domain of the large-subunit (LSU) ribosomal RNA gene and internal transcribed spacer regions (ITS) sequencing. MALDI-TOF MS system only identified five strains at the species level, while 45 were not identified. The analysis through GenBank allowed the identification of up to 19 strains at the species level, while MycoBank allowed the identification of up to nine strains at the species level. The databases identified up to 11 genera: Penicillium, Aspergillus, Cladosporium, Chaetomium, Coniochaeta, Curvularia, Diaporthe, Fusarium, Trichoderma, Rhizopus and Microdochium. MALDI-TOF MS showed an insufficient database to identify the species of fungi. DNA sequencing was the best methodology to identify to the genus level but was unable to differentiate between closely related species. Therefore further methods for the identification of filamentous fungi from pharmaceutical areas at species level need to be developed.
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Vasconcellos L, Silva SV, da Costa LV, de Miranda RVDSL, Dos Reis CMF, Braga LMPDS, Silva C, Conceição G, Mattoso J, Silva IB, Forsythe SJ, Midlej V, Boas MHSV, Brandão MLL. Phenotypical and molecular characterization of Acinetobacter spp. isolated from a pharmaceutical facility. Lett Appl Microbiol 2023; 76:ovad101. [PMID: 37660241 DOI: 10.1093/lambio/ovad101] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/14/2023] [Accepted: 08/31/2023] [Indexed: 09/04/2023]
Abstract
Characterizing microorganisms according to different criteria is useful when investigating sources of microbiological contamination in the pharmaceutical industry. The aim of this study was to characterize 38 Acinetobacter baumannii complex strains isolated from a biopharmaceutical industry by 16S rRNA sequencing, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF/MS), multilocus sequence typing (MLST), antimicrobial susceptibility profile, biofilm formation, and sensibility to disinfectants. Thirty-three (86.9%) strains were identified by 16S rRNA gene sequencing as A. seifertii/pitti/nosocomialis/lactucae, four (10.5%) as A. baumannii, and one (2.6%) as A. vivianii/courvalini. MALDI-TOF/MS did not identify one strain, and incorrectly identified 30/37 (81.1%) strains as A. baumannii. Strains were assigned to 12 different STs, of which nine were newly defined in this study (STs 2091-2099). Twenty-six (68.4%) strains showed resistance to amikacin and gentamicin. Thirty-three (86.8%) strains were classified as moderately or strongly adherent on polystyrene. Alcohol 70%/15 min and quaternary ammonium 0.08%/20 min were not able to eliminate the biofilm formed, but sodium hypochlorite 0.1%/15 min was efficient. In conclusion, improved methods are needed to improve the identification of Acinetobacter strains in pharmaceutical industries. This organism is of particular concern as it forms recalcitrant biofilms, leading to persistence in the manufacturing environment and increased risk of product contamination.
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Affiliation(s)
- Luiza Vasconcellos
- Microbiological Control Laboratory, Bio-Manguinhos, Fiocruz, Rio de Janeiro, CEP:21040-360, Brazil
- Laboratory of Microbiology of Food and Sanitizes, INCQS/Fiocruz, Rio de Janeiro, CEP:21040-360, Brazil
| | - Samara Verly Silva
- Microbiological Control Laboratory, Bio-Manguinhos, Fiocruz, Rio de Janeiro, CEP:21040-360, Brazil
| | - Luciana Veloso da Costa
- Microbiological Control Laboratory, Bio-Manguinhos, Fiocruz, Rio de Janeiro, CEP:21040-360, Brazil
| | - Rebeca Vitoria da Silva Lage de Miranda
- Microbiological Control Laboratory, Bio-Manguinhos, Fiocruz, Rio de Janeiro, CEP:21040-360, Brazil
- Laboratory of Microbiology of Food and Sanitizes, INCQS/Fiocruz, Rio de Janeiro, CEP:21040-360, Brazil
| | | | | | - Claudiane Silva
- Laboratory of Cellular Ultrastructure, IOC/Fiocruz, Rio de Janeiro, CEP:21040-360, Brazil
| | - Greice Conceição
- Department of Quality Control, Bio-Manguinhos, Fiocruz, Rio de Janeiro, CEP:21040-360, Brazil
| | - Josiane Mattoso
- Microbiological Control Laboratory, Bio-Manguinhos, Fiocruz, Rio de Janeiro, CEP:21040-360, Brazil
| | - Igor Barbosa Silva
- Microbiological Control Laboratory, Bio-Manguinhos, Fiocruz, Rio de Janeiro, CEP:21040-360, Brazil
| | | | - Victor Midlej
- Laboratory of Cellular Ultrastructure, IOC/Fiocruz, Rio de Janeiro, CEP:21040-360, Brazil
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Costa LVD, Miranda RVDSLD, Reis CMFD, Andrade JMD, Cruz FV, Frazão AM, Fonseca ELD, Ramos JN, Brandão MLL, Vieira VV. MALDI-TOF MS database expansion for identification of Bacillus and related genera isolated from a pharmaceutical facility. J Microbiol Methods 2022; 203:106625. [PMID: 36403787 DOI: 10.1016/j.mimet.2022.106625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/14/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022]
Abstract
Bacillus and related genera are among the main bacterial groups isolated from pharmaceutical production areas. The identification of Bacillus species and related genera by classical methods is particularly difficult, due to similarities between closely related species. The Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) is one of the most promising techniques for chemotaxonomic characterization of microorganisms, being an alternative to genotypic methods. This study aimed to identify Bacillus strains and related genera isolated from immunobiological production areas by phylogenetic analysis of housekeeping genes and expand the database associated with MALDI-TOF MS to improve their identification. In a previous study, 97 aerobic endospore-forming bacteria isolated from a pharmaceutical facility were analyzed by MALDI-TOF MS and 16S rRNA gene full-length sequencing. All strains were identified as Bacillus and related genera by the latest methodology. Among the 97 strains, 22 were unidentified and 2 strains were misidentified by MALDI-TOF MS. In the present study, these 24 strains were subjected to 16S rRNA gene phylogenetic analysis. Strains not identified at species level by this methodology were submitted to rpoB gene phylogenetic analysis. After identifying the strains, 19 of the 24 strains were incubated for 24, 48, and 72 h on Tryptic Soy Agar and Sheep Blood Agar and subjected to analysis by MALDI-TOF MS. A SuperSpectrum for each strain was created and entered into the equipment database. Finally, the 24 strains were again submitted to proteomic analysis by MALDI-TOF MS, and, at this time, all were correctly identified. The genotypic identification of in-house isolated strains and the introduction of these spectra in MALDI-TOF MS, in order to obtain a customized database, proved to be an extremely effective tool in the identification of Bacillus and related genera from pharmaceutical industry origin.
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Affiliation(s)
- Luciana Veloso da Costa
- Fundação Oswaldo Cruz, Instituto de Tecnologia em Imunobiológicos (Bio-Manguinhos), Microbiological Control Laboratory, Brazil.
| | | | | | - Joyce Modesto de Andrade
- Fundação Oswaldo Cruz, Instituto de Tecnologia em Imunobiológicos (Bio-Manguinhos), Microbiological Control Laboratory, Brazil
| | - Fernanda Ventura Cruz
- Fundação Oswaldo Cruz, Instituto de Tecnologia em Imunobiológicos (Bio-Manguinhos), Microbiological Control Laboratory, Brazil
| | - Adriana Marques Frazão
- Fundação Oswaldo Cruz, Instituto de Tecnologia em Imunobiológicos (Bio-Manguinhos), Microbiological Control Laboratory, Brazil
| | - Erica Louro da Fonseca
- Fundação Oswaldo Cruz, Instituto de Tecnologia em Imunobiológicos (Bio-Manguinhos), Microbiological Control Laboratory, Brazil
| | - Juliana Nunes Ramos
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz (IOC), Interdisciplinary Medical Research Laboratory, Brazil
| | - Marcelo Luiz Lima Brandão
- Fundação Oswaldo Cruz, Instituto de Tecnologia em Imunobiológicos (Bio-Manguinhos), Microbiological Control Laboratory, Brazil
| | - Verônica Viana Vieira
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz (IOC), Interdisciplinary Medical Research Laboratory, Brazil
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Braga LMPDS, Saad BAA, de Oliveira CTF, Volpe‐Chaves CE, Lacerda MLGG, Forsythe SJ, Venturini J, de Oliveira SMDVL, Paniago AMM, da Costa LV, Lage RVDS, dos Reis CMF, Brandão MLL. Case report of
Curtobacterium
isolated from a catheter tip sample misidentified as
Cronobacter. Lett Appl Microbiol 2022; 75:396-400. [DOI: 10.1111/lam.13741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/13/2022] [Accepted: 05/16/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Lygia Maria Paulo da Silva Braga
- Institute of Technology in Immunobiologicals Oswaldo Cruz Foundation Rio de Janeiro, Rio de Janeiro Brazil
- Federal University of Rio de Janeiro Rio de Janeiro, Rio de Janeiro Brazil
| | - Bruna Abdul Ahad Saad
- Federal University of Mato Grosso do Sul
- Regional Hospital of Mato Grosso do Sul Mato Grosso do Sul Campo Grande Brazil
| | | | | | | | | | | | | | | | - Luciana Veloso da Costa
- Institute of Technology in Immunobiologicals Oswaldo Cruz Foundation Rio de Janeiro, Rio de Janeiro Brazil
| | - Rebeca Vitória da Silva Lage
- Institute of Technology in Immunobiologicals Oswaldo Cruz Foundation Rio de Janeiro, Rio de Janeiro Brazil
- National Institute of Quality Control in Health Oswaldo Cruz Foundation Rio de Janeiro, Rio de Janeiro Brazil
| | | | - Marcelo Luiz Lima Brandão
- Institute of Technology in Immunobiologicals Oswaldo Cruz Foundation Rio de Janeiro, Rio de Janeiro Brazil
- National Institute of Quality Control in Health Oswaldo Cruz Foundation Rio de Janeiro, Rio de Janeiro Brazil
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Dos Reis CMF, Ramos GLDPA, Pereira RDCL, Vallim DC, Costa LEDO. Evaluation of VITEK® 2 and MALDI-TOF/MS automated methodologies in the identification of atypical Listeria spp. isolated from food in different regions of Brazil. METHODS IN MICROBIOLOGY 2022; 194:106434. [PMID: 35176354 DOI: 10.1016/j.mimet.2022.106434] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 10/19/2022]
Abstract
Listeria monocytogenes is a pathogen responsible for listeriosis, a foodborne disease with high mortality rates (20-30%). It mainly affects the elderly, pregnant women, and immunocompromised people. Although not pathogenic, the isolation and identification of Listeria innocua are critical since they can indicate L. monocytogenes' presence as they are closely related and widely distributed in the environment and food processing plants. The objective of this study was to evaluate the effectiveness of the automated methods VITEK® 2 and MALDI-TOF/MS in identifying 94 strains of the genus Listeria with atypical identification profile. The resulting identification by Polymerase Chain Reaction (PCR), using specific primers for the most common species of Listeria, was considered the correct identification and presented a total of 31 strains identified as Listeria innocua (LI), 54 as L. monocytogenes (LM), 8 as Listeria welshimeri (LW) and 1 as Listeria grayi (LG). The VITEK® 2 automated system correctly identified, on average, 79% of the LI strains, 16% of the LM strains, and 88.0% of the LW strains. In the analysis by MALDI-TOF/MS, on average, 73% of LM strains were correctly identified, few LW strains were correctly identified, and all LI strains were incorrectly identified. Both VITEK® 2 and MALDI-TOF/MS correctly identified the LG strain in both analyzes. The results demonstrate that automated methodologies could not discriminate atypical strains of the Listeria genus and point to the need for the use of complementary tests, such as PCR and chromogenic media, for the correct identification of these strains.
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Affiliation(s)
- Cristhiane M F Dos Reis
- Federal Institute of Education, Science, and Technology of Rio de Janeiro (IFRJ), Food Department, 20270-021 Rio de Janeiro, Brazil; Laboratory of Bacterial Zoonoses, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), 21040-360 Rio de Janeiro, Brazil
| | - Gustavo Luis de P A Ramos
- Federal Institute of Education, Science, and Technology of Rio de Janeiro (IFRJ), Food Department, 20270-021 Rio de Janeiro, Brazil; Fluminense Federal University (UFF), Faculty of Veterinary Medicine, 24230-340, Niterói, Rio de Janeiro, Brazil.
| | | | - Deyse Christina Vallim
- Laboratory of Bacterial Zoonoses, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), 21040-360 Rio de Janeiro, Brazil
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