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Pathak D, Lone R, Nazim N, Alaklabi A, Khan S, Koul K. Plant growth promoting rhizobacterial diversity in potato grown soil in the Gwalior region of India. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2022; 33:e00713. [PMID: 35242621 PMCID: PMC8866904 DOI: 10.1016/j.btre.2022.e00713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/06/2022] [Accepted: 02/16/2022] [Indexed: 04/14/2023]
Abstract
There seems to be meager studies with regards to rhizo and non-rhizo microbial association with potato plant from the central India. Present study was undertaken to evaluate the microbial diversity of rhizospheric and non-rhizospheric isolates from three varieties of potato viz Kufri sindhuri, Kufri lauvkar and Kufri chipsona-3 procured from the Central Potato Research Station, Maharajpura, Gwalior. A total of 130 bacterial forms were isolated, and amongst these forty isolates were further characterized on their morphological basis, and those showing some of PGPR characteristics were identified to species level using VITEK-2 method. Various bacterial populations were found in potato rhizosphere and dominant presence was those of Bacillus subtilis, Bacillus Megaterium and Lysinibacillus sphaericus. The non-rhizospheric soil was dominant in the forms like Aeromonas salmonicida, Morxella group and Bacillus coagulans. Highest bacterial diversity was found in the rhizosphere soil of different potato cultivars than in the non-rhizospheric soil of potato.
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Affiliation(s)
- Deepmala Pathak
- School of Studies in Botany, Jiwaji University, Gwalior M.P,474011 India
| | - Rafiq Lone
- Department of Botany, Central University of Kashmir, Ganderbal, Jammu and Kashmir India
- Corresponding author.
| | - Naveena Nazim
- College of Temperate Sericulture, Mirgund, SKUAST-Kashmir, Jammu and Kashmir India
| | - Abdullah Alaklabi
- Department of Biology, College of Science, University of Bisha, P.O. Box 551, Bisha 61922, Saudi Arabia
| | - Salim Khan
- Department of Botany and Microbiology, King Saud University, Riyadh Saudi Arabia
| | - K.K. Koul
- School of Studies in Botany, Jiwaji University, Gwalior M.P,474011 India
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Zhang J, Hu DK, Gao CY, Shen WW, Luo XH, Yu J, Li XY, Jiang XY, Zhu WS, Chen WQ. Homology analysis of 51 penicillin-intermediate Streptococcus pneumoniae isolates from Wenzhou City, China. J Int Med Res 2021; 48:300060520919061. [PMID: 32529912 PMCID: PMC7294386 DOI: 10.1177/0300060520919061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Objective To investigate drug resistance features and homology among penicillin-intermediate Streptococcus pneumoniae isolates from Wenzhou City, China. Methods Fifty-one penicillin-intermediate S. pneumoniae isolates were obtained from respiratory samples of infants and children hospitalized with lung infections. An antimicrobial susceptibility test was used to assess drug resistance. Polymerase chain reaction and agarose gel electrophoresis were used to identify S. pneumoniae isolates and pulsed-field gel electrophoresis (PFGE) was used to analyze molecular subtypes. Hierarchical cluster analysis of PFGE fingerprints was used to compare genetic diversity and relatedness of S. pneumoniae isolates. The Quellung test was used for serotyping. Results Fifty-one penicillin-intermediate S. pneumoniae isolates showed evidence of multi-drug resistance and polyclonal origins. The isolates were classified into 25 subtypes through hierarchical cluster analysis of PFGE fingerprints. Three of these subtypes formed a supertype (15/51, 16/51 and 8/51 isolates), while the remaining subtypes occurred sporadically (12/51 isolates). Conclusions Transmission of penicillin-intermediate S. pneumoniae is mostly vertical and to a lesser extent horizontal. Effective prevention strategies, including respiratory tract management and contact isolation, are essential to control nosocomial S. pneumoniae infection. Once susceptibility is confirmed, vancomycin, high-dose penicillin or third-generation cephalosporins (cefotaxime and ceftriaxone) may be used to treat penicillin-intermediate S. pneumoniae.
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Affiliation(s)
- Jin Zhang
- Department of Laboratory Medicine, Taizhou Municipal Hospital, Taizhou, Zhejiang Province, China
| | - Da-Kang Hu
- Department of Laboratory Medicine, Taizhou Municipal Hospital, Taizhou, Zhejiang Province, China
| | - Chun-Yan Gao
- Department of Laboratory Medicine, Tangshan Maternal and Child Health Hospital, Tangshan, Hebei Province, China
| | - Wei-Wei Shen
- Department of Microbiology, Taizhou Center for Disease Control and Prevention, Taizhou, Zhejiang Province, China
| | - Xin-Hua Luo
- Department of Laboratory Medicine, Taizhou Municipal Hospital, Taizhou, Zhejiang Province, China
| | - Jian Yu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Xiang-Yang Li
- Department of Laboratory Medicine, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Xin-Yu Jiang
- Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Wu-Shuang Zhu
- Department of Laboratory Medicine, Taizhou Municipal Hospital, Taizhou, Zhejiang Province, China
| | - Wei-Qing Chen
- Department of Laboratory Medicine, Taizhou Women and Children's Hospital, Taizhou, Zhejiang Province, China
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Moehario LH, Tjoa E, Putranata H, Joon S, Edbert D, Robertus T. Performance of TDR-300B and VITEK®2 for the identification of Pseudomonas aeruginosa in comparison with VITEK®-MS. J Int Med Res 2021; 49:300060521989893. [PMID: 33626939 PMCID: PMC7925945 DOI: 10.1177/0300060521989893] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Objective Automated systems are needed for the rapid and accurate diagnosis of Pseudomonas-associated nosocomial infections among critically ill patients admitted to the intensive care unit. We assessed the performance of TDR-300B and VITEK®2 for the identification of P. aeruginosa using VITEK®-MS as the gold standard. Methods This analytical study employed a cross-sectional approach. First, 44 clinical isolates of P. aeruginosa were collected and refreshed. Next, a single colony of oxidase-positive, gram-negative rods (30 samples) was inoculated into a TDR-300B NF-64 card and VITEK®2 GN cassette for each isolate. Finally, bacterial identification was performed using VITEK®-MS for comparative analysis. Results Compared with the results for VITEK®-MS, the congruence rates for TDR-300B and VITEK®2 were 80.76% (21/26) and 92.30% (24/26), respectively. Further, high sensitivity was observed for TDR-300B and VITEK®2 (95.45% and 100%, respectively). In addition, TDR-300B had a lower positive predictive value and accuracy than VITEK®2, albeit without significance. Conclusions Conclusively, there were no significant differences regarding the diagnostic efficiency of TDR-300B and VITEK®2 for P. aeruginosa.
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Affiliation(s)
- Lucky Hartati Moehario
- Department of Microbiology, School of Medicine and Sciences, Atma Jaya Catholic University of Indonesia, Jakarta, Indonesia
| | - Enty Tjoa
- Department of Microbiology, School of Medicine and Sciences, Atma Jaya Catholic University of Indonesia, Jakarta, Indonesia
| | - Hans Putranata
- Department of Microbiology, School of Medicine and Sciences, Atma Jaya Catholic University of Indonesia, Jakarta, Indonesia
| | - Shikha Joon
- Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China.,iGlobal Research and Publishing Foundation, New Delhi, India
| | - Daniel Edbert
- Department of Microbiology, School of Medicine and Sciences, Atma Jaya Catholic University of Indonesia, Jakarta, Indonesia
| | - Thomas Robertus
- Department of Microbiology, Faculty of Medicine, Trisakti University, Jakarta, Indonesia
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Garza-González E, Bocanegra-Ibarias P, Dinh A, Morfín-Otero R, Camacho-Ortiz A, Rojas-Larios F, Rodríguez-Zulueta P, Arias CA. Species identification of Enterococcus spp: Whole genome sequencing compared to three biochemical test-based systems and two Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) systems. J Clin Lab Anal 2020; 34:e23348. [PMID: 32358872 PMCID: PMC7439347 DOI: 10.1002/jcla.23348] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 04/06/2020] [Accepted: 04/08/2020] [Indexed: 11/09/2022] Open
Abstract
Aim Here, we evaluated the performance of two commercial MALDI‐TOF MS systems and three biochemical‐based systems and compared them to WGS as the gold standard for identifying isolates of vancomycin‐resistant enterococci (VRE). Methods A total of 87 VRE clinical isolates were included. The mass spectrometers were the Microflex system with Biotyper software 3.1 and the Vitek MS system. The biochemical‐based systems included the Vitek 2, Phoenix, and MicroScan WalkAway systems. WGS was performed on an Illumina MiSeq instrument using the MiSeq v3 reagent kit. Vancomycin resistance was determined according to CLSI criteria. Results Among the 87 VRE, 71 and 16 were identified as Enterococcus faecium and Enterococcus faecalis by WGS. All 71 E faecium were correctly identified by both mass spectrometers, as well as the Vitek 2 and Phoenix instruments. However, only 51 E faecium isolates were correctly identified by the MicroScan system. The most frequent misidentification was Enterococcus casseliflavus (n = 20). For vancomycin‐resistant E faecium, the Microflex Biotyper system had the highest sensitivity (85.54%), and all instruments (except for the Microscan) had a 100% specificity and PPV. Up to 87% of E faecalis isolates were misidentified by VITEK MS and VITEK2, 81% by Microscan and Phoenix, and 75% by Bruker biotyper. Conclusion As the coverage of type strain‐genome sequence database continues to grow and the cost of DNA sequencing continues to decrease, genome‐based identification can be a useful tool for diagnostic laboratories, with its superior accuracy even over MALDI‐TOF and database‐driven operations.
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Affiliation(s)
- Elvira Garza-González
- Hospital Universitario "Dr. José Eleuterio González", Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | - Paola Bocanegra-Ibarias
- Hospital Universitario "Dr. José Eleuterio González", Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | - An Dinh
- Division of Infectious Diseases and Center for Antimicrobial Resistance and Microbial Genomics (CARMiG), McGovern Medical School, UTHealth, Houston, TX, USA
| | - Rayo Morfín-Otero
- Centro Universitario de Ciencias de la Salud, Hospital Civil de Guadalajara "Fray Antonio Alcalde" e Instituto de Patología Infecciosa y Experimental, Universidad de Guadalajara, Guadalajara, Mexico
| | - Adrián Camacho-Ortiz
- Hospital Universitario "Dr. José Eleuterio González", Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | | | | | - Cesar A Arias
- Division of Infectious Diseases and Center for Antimicrobial Resistance and Microbial Genomics (CARMiG), McGovern Medical School, UTHealth, Houston, TX, USA.,School of Public Health, Center for Infectious Diseases, UTHealth, Houston, TX, USA.,Molecular Genetics and Antimicrobial Resistance Unit and International Center for Microbial Genomics, Universidad El Bosque, Bogotá, Colombia
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Lemos TC, Cogo LL, Maestri AC, Hadad M, Nogueira KDS. Is it possible to perform bacterial identification and antimicrobial susceptibility testing with a positive blood culture bottle for quick diagnosis of bloodstream infections? Rev Soc Bras Med Trop 2018; 51:215-218. [PMID: 29768557 DOI: 10.1590/0037-8682-0311-2017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/10/2017] [Indexed: 11/22/2022] Open
Abstract
INTRODUCTION Bloodstream infections can be fatal, and timely identification of the etiologic agent is important for treatment. METHODOLOGY An alternative method, consisting of direct identification and susceptibility testing of blood culture bottles using the automated VITEK 2® system, was assessed. RESULTS All 37 of the Gram-negative bacilli (GNB) identifications and 57.1% of the 28 Gram-positive cocci (GPC) identifications matched those obtained with standard methods. In susceptibility testing, the agreement was greater than 90%. CONCLUSIONS This alternative methodology may assist in the early identification and susceptibility testing of GNB. Further research is necessary to develop appropriate methods for GPC.
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Affiliation(s)
- Tamily Cristina Lemos
- Residência Multiprofissional em Atenção Hospitalar, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - Laura Lúcia Cogo
- Hospital de Clínicas da Universidade Federal do Paraná, Curitiba, PR, Brasil
| | | | - Milena Hadad
- BioMérieux SA, Jacarepaguá, Rio de Janeiro, RJ, Brasil
| | - Keite da Silva Nogueira
- Hospital de Clínicas da Universidade Federal do Paraná, Curitiba, PR, Brasil.,Departamento de Patologia Básica, Universidade Federal do Paraná, Curitiba, PR, Brasil
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Martini R, Hörner R, Graichen DÂS. Antimicrobial susceptibility profile and research of mec A and erm genes in coagulase-negative staphylococci isolated from platelet concentrates bags. BRAZ J PHARM SCI 2017. [DOI: 10.1590/s2175-97902017000115195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Monteiro ACM, Fortaleza CMCB, Ferreira AM, Cavalcante RDS, Mondelli AL, Bagagli E, da Cunha MDLRDS. Comparison of methods for the identification of microorganisms isolated from blood cultures. Ann Clin Microbiol Antimicrob 2016; 15:45. [PMID: 27496125 PMCID: PMC4974807 DOI: 10.1186/s12941-016-0158-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 07/14/2016] [Indexed: 11/12/2022] Open
Abstract
Background Bloodstream infections are responsible for thousands of deaths each year. The rapid identification of the microorganisms causing these infections permits correct therapeutic management that will improve the prognosis of the patient. In an attempt to reduce the time spent on this step, microorganism identification devices have been developed, including the VITEK® 2 system, which is currently used in routine clinical microbiology laboratories. Methods This study evaluated the accuracy of the VITEK® 2 system in the identification of 400 microorganisms isolated from blood cultures and compared the results to those obtained with conventional phenotypic and genotypic methods. In parallel to the phenotypic identification methods, the DNA of these microorganisms was extracted directly from the blood culture bottles for genotypic identification by the polymerase chain reaction (PCR) and DNA sequencing. Results The automated VITEK® 2 system correctly identified 94.7 % (379/400) of the isolates. The YST and GN cards resulted in 100 % correct identifications of yeasts (15/15) and Gram-negative bacilli (165/165), respectively. The GP card correctly identified 92.6 % (199/215) of Gram-positive cocci, while the ANC card was unable to correctly identify any Gram-positive bacilli (0/5). Conclusions The performance of the VITEK® 2 system was considered acceptable and statistical analysis showed that the system is a suitable option for routine clinical microbiology laboratories to identify different microorganisms.
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Affiliation(s)
- Aydir Cecília Marinho Monteiro
- Departamento de Microbiologia e Imunologia, Instituto de Biociências de Botucatu, UNESP-Univ. Estadual Paulista, Distrito de Rubião Junior, s/n, Botucatu, SP, CEP: 18618-970, Brazil
| | - Carlos Magno Castelo Branco Fortaleza
- Departamento de Doenças Tropicais, Faculdade de Medicina de Botucatu, UNESP-Univ. Estadual Paulista, Distrito de Rubião Junior, s/n, Botucatu, SP, CEP: 18618-970, Brazil
| | - Adriano Martison Ferreira
- Laboratório de Análises Clínicas do Hospital das Clínicas de Botucatu, Faculdade de Medicina de Botucatu, UNESP-Univ. Estadual Paulista, Distrito de Rubião Junior, s/n, Botucatu, SP, CEP: 18618-970, Brazil
| | - Ricardo de Souza Cavalcante
- Comissão de Controle de Infecção Relacionada à Assistência à Saúde, Hospital das Clínicas, Faculdade de Medicina de Botucatu, UNESP-Univ. Estadual Paulista, Distrito de Rubião Junior, s/n, Botucatu, SP, CEP: 18618-970, Brazil
| | - Alessandro Lia Mondelli
- Departamento de Clínica Médica, Faculdade de Medicina de Botucatu, UNESP-Univ. Estadual Paulista, Distrito de Rubião Junior, s/n, Botucatu, SP, CEP: 18618-970, Brazil
| | - Eduardo Bagagli
- Departamento de Microbiologia e Imunologia, Instituto de Biociências de Botucatu, UNESP-Univ. Estadual Paulista, Distrito de Rubião Junior, s/n, Botucatu, SP, CEP: 18618-970, Brazil
| | - Maria de Lourdes Ribeiro de Souza da Cunha
- Departamento de Microbiologia e Imunologia, Instituto de Biociências de Botucatu, UNESP-Univ. Estadual Paulista, Distrito de Rubião Junior, s/n, Botucatu, SP, CEP: 18618-970, Brazil. .,Departamento de Doenças Tropicais, Faculdade de Medicina de Botucatu, UNESP-Univ. Estadual Paulista, Distrito de Rubião Junior, s/n, Botucatu, SP, CEP: 18618-970, Brazil.
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Elbehiry A, Al-Dubaib M, Marzouk E, Osman S, Edrees H. Performance of MALDI biotyper compared with Vitek ™ 2 compact system for fast identification and discrimination of Staphylococcus species isolated from bovine mastitis. Microbiologyopen 2016; 5:1061-1070. [PMID: 27364641 PMCID: PMC5221440 DOI: 10.1002/mbo3.389] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 05/23/2016] [Accepted: 05/28/2016] [Indexed: 12/19/2022] Open
Abstract
This study was designed to evaluate the ability of MALDI Biotyper (MBT) compared with Vitek™ 2 compact system for accurate identification of Staphylococcus aureus (S. aureus) and coagulase‐negative staphylococci (CNS) strains and discriminate methicillin‐sensitive S. aureus (MSSA) from methicillin‐resistant S. aureus (MRSA). Throughout Al‐Qassim region, Saudi Arabia, a total of 198 isolates of S. aureus (132 MSSA and 66 MRSA) and 44 CNS were collected from five dairy farms where the prevalence of staphylococcal mastitis was reported. The results produced by Vitek™ 2 compact system demonstrated that 123/132 MSSA isolates (93.18%), 61/66 MRSA (92.42%), and 37/44 CNS species (84.09%) were correctly identified. However; 130/132 MSSA (98.48%), 64/66 MRSA (96.96%), and 44/44 CNS (100%) were correctly identified by MBT with score ≥2. 00. The principal component analysis (PCA) dendrogram generated by MBT illustrated that the tested isolates were classified into two groups of Staphylococcus species at the distance level of 600. S. aureus isolates were found to be closely related with higher peak intensities in the mass of 3,993 Da, 4,121 Da and 5,845 Da were detected in MRSA, whereas, that were lost in MSSA. Conclusion: This study verified that MBT is an alternative powerful tool for precise identification and discrimination of Staphylococcus species.
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Affiliation(s)
- Ayman Elbehiry
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Sadat City University, Sadat, Egypt.,Department of Public Health, Microbiology Unit, College of Public Health and Health Informatics, Qassim University, Buraidah, Saudi Arabia
| | - Musaad Al-Dubaib
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraidah, Saudi Arabia
| | - Eman Marzouk
- Department of Medical laboratories, College of Applied Medical Science, Qassim University, Buraidah, Saudi Arabia
| | - Salama Osman
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraidah, Saudi Arabia.,Department of Animal Medicine, Faculty of Veterinary Medicine, Kafrelsheikh University, Buraidah, Egypt
| | - Husam Edrees
- Department of Physiology, Faculty of Medicine, Zagazig University, Zagazig, Egypt
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