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Cruz-Medrano MG, Manzanares-Leal GL, González-Nava J, Moreno-Pérez PA, Sandoval-Trujillo H, Ramírez-Durán N. Genetic variability of the 16S rRNA gene of Nocardia brasiliensis, the most common causative agent of actinomycetoma in Latin America and the Caribbean. Rev Inst Med Trop Sao Paulo 2023; 65:e31. [PMID: 37075338 PMCID: PMC10109444 DOI: 10.1590/s1678-9946202365031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 02/24/2023] [Indexed: 04/21/2023] Open
Abstract
Mycetoma is a neglected tropical disease (NTD) declared by the World Health Organization (WHO) in 2016. It is characterized by the progressive growth of nodules and granulomatous lesions on the legs, arms, and trunk. It is potentially disfiguring and causes disability or amputations in working-age people from marginalized areas. The causative agents can be fungi (eumycetoma) or actinobacteria (actinomycetoma), the latter being the most common in America and Asia. Nocardia brasiliensis is the most important causal agent of actinomycetoma in the Americas. Taxonomic problems have been reported when identifying this species, so this study aimed to detect the 16S rRNA gene variations in N. brasiliensis strains using an in silico enzymatic restriction technique. The study included strains from clinical cases of actinomycetoma in Mexico, isolated from humans and previously identified as N. brasiliensis by traditional methods. The strains were characterized microscopically and macroscopically, then subjected to DNA extraction and amplification of the 16S rRNA gene by PCR. The amplification products were sequenced, and consensus sequences were constructed and used for genetic identification and in silico restriction enzyme analysis with the New England BioLabs® NEBcutter program. All study strains were molecularly identified as N. brasiliensis; however, in silico restriction analysis detected a diversity in the restriction patterns that were finally grouped and subclassified into 7 ribotypes. This finding confirms the existence of subgroups within N. brasiliensis. The results support the need to consider N. brasiliensis as a complex species.
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Affiliation(s)
- Michele Guadalupe Cruz-Medrano
- Universidad Autónoma del Estado de México, Facultad de Medicina, Laboratorio de Investigación en Microbiología Médica y Ambiental, Toluca, Mexico
| | - Gauddy Lizeth Manzanares-Leal
- Universidad Autónoma del Estado de México, Facultad de Medicina, Laboratorio de Investigación en Microbiología Médica y Ambiental, Toluca, Mexico
| | - Janette González-Nava
- Laboratorio de Ecología Molecular, Departamento de Sistemas Biológicos, Universidad Autónoma Metropolitana-Xochimilco, Ciudad de México, Mexico
| | - Pablo Antonio Moreno-Pérez
- Universidad Autónoma del Estado de México, Facultad de Medicina, Laboratorio de Investigación en Microbiología Médica y Ambiental, Toluca, Mexico
| | - Horacio Sandoval-Trujillo
- Universidad Autónoma Metropolitana-Xochimilco, Departamento de Sistemas Biológicos, Laboratorio de Producción de Biológicos, Ciudad de México, Mexico
| | - Ninfa Ramírez-Durán
- Universidad Autónoma del Estado de México, Facultad de Medicina, Laboratorio de Investigación en Microbiología Médica y Ambiental, Toluca, Mexico
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Kumar S, Anwer R, Azzi A. Molecular typing methods & resistance mechanisms of MDR Klebsiella pneumoniae. AIMS Microbiol 2023; 9:112-130. [PMID: 36891535 PMCID: PMC9988409 DOI: 10.3934/microbiol.2023008] [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: 11/20/2022] [Revised: 02/12/2023] [Accepted: 02/20/2023] [Indexed: 03/02/2023] Open
Abstract
The emergence and transmission of carbapenem-resistant Klebsiella pneumoniae (CRKP) have been recognized as a major public health concern. Here, we investigated the molecular epidemiology and its correlation with the mechanisms of resistance in CRKP isolates by compiling studies on the molecular epidemiology of CRKP strains worldwide. CRKP is increasing worldwide, with poorly characterized epidemiology in many parts of the world. Biofilm formation, high efflux pump gene expression, elevated rates of resistance, and the presence of different virulence factors in various clones of K. pneumoniae strains are important health concerns in clinical settings. A wide range of techniques has been implemented to study the global epidemiology of CRKP, such as conjugation assays, 16S-23S rDNA, string tests, capsular genotyping, multilocus sequence typing, whole-genome sequencing-based surveys, sequence-based PCR, and pulsed-field gel electrophoresis. There is an urgent need to conduct global epidemiological studies on multidrug-resistant infections of K. pneumoniae across all healthcare institutions worldwide to develop infection prevention and control strategies. In this review, we discuss different typing methods and resistance mechanisms to explore the epidemiology of K. pneumoniae pertaining to human infections.
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Affiliation(s)
- Sunil Kumar
- Department of Microbiology, Kampala International University, Western Campus, Ishaka, Uganda
| | - Razique Anwer
- Department of Pathology, College of Medicine, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Arezki Azzi
- Department of Biochemistry, College of Medicine, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
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A Novel Antimicrobial Metabolite Produced by Paenibacillus apiarius Isolated from Brackish Water of Lake Balkhash in Kazakhstan. Microorganisms 2022; 10:microorganisms10081519. [PMID: 36013937 PMCID: PMC9416454 DOI: 10.3390/microorganisms10081519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/13/2022] [Accepted: 07/15/2022] [Indexed: 11/16/2022] Open
Abstract
Four aerobic bacteria with bacteriolytic capabilities were isolated from the brackish water site Strait Uzynaral of Lake Balkhash in Kazakhstan. The morphology and physiology of the bacterial isolates have subsequently been analyzed. Using matrix assisted laser desorption ionization-time of flight mass spectrum and partial 16S rRNA gene sequence analyses, three of the isolates have been identified as Pseudomonas veronii and one as Paenibacillus apiarius. We determined the capability of both species to lyse pre-grown cells of the Gram-negative strains Pseudomonas putida SBUG 24 and Escherichia coli SBUG 13 as well as the Gram-positive strains Micrococcus luteus SBUG 16 and Arthrobacter citreus SBUG 321 on solid media. The bacteriolysis process was analyzed by creating growth curves and electron micrographs of co-cultures with the bacteriolytic isolates and the lysis sensitive strain Arthrobacter citreus SBUG 321 in nutrient-poor liquid media. One metabolite of Paenibacillus apiarius was isolated and structurally characterized by various chemical structure determination methods. It is a novel antibiotic substance.
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Molecular subtyping for source tracking of Escherichia coli using core genome multilocus sequence typing at a food manufacturing plant. PLoS One 2021; 16:e0261352. [PMID: 34941901 PMCID: PMC8699670 DOI: 10.1371/journal.pone.0261352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 11/30/2021] [Indexed: 12/05/2022] Open
Abstract
When harmful bacteria are detected in the final product at a food manufacturing plant, it is necessary to identify and eliminate the source of contamination so that it does not occur again. In the current study, the source of contamination was tracked using core genome multilocus sequence typing (cgMLST) analysis in cases where Escherichia coli was detected in the final product at a food manufacturing plant. cgMLST analysis was performed on 40 strains of E. coli collected from the environment [floor (26 strains), drainage ditch (5 strains), container (4 strains), post-heating production line (1 strain)] and products [final product (3 strains) and intermediate product (1 strain)]. In total, 40 E. coli isolates were classified into 17 genogroups by cgMLST analysis. The 4 E. coli strains isolated from the intermediate and final products were classified into two genogroups (I and II). Certain isolates collected from the environment also belonged to those genogroups, it was possible to estimate the transmission of E. coli in the manufacturing plant. Thus, the dynamics of E. coli in the food manufacturing location were clarified by using cgMLST analysis. In conclusion, our results indicate that cgMLST analysis can be effectively used for hygiene management at food manufacturing locations.
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Streptomonospora litoralis sp. nov., a halophilic thiopeptides producer isolated from sand collected at Cuxhaven beach. Antonie van Leeuwenhoek 2021; 114:1483-1496. [PMID: 34355285 PMCID: PMC8448680 DOI: 10.1007/s10482-021-01609-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 06/23/2021] [Indexed: 11/04/2022]
Abstract
Strain M2T was isolated from the beach of Cuxhaven, Wadden Sea, Germany, in course of a program to attain new producers of bioactive natural products. Strain M2T produces litoralimycin and sulfomycin-type thiopeptides. Bioinformatic analysis revealed a potential biosynthetic gene cluster encoding for the M2T thiopeptides. The strain is Gram-stain-positive, rod shaped, non-motile, spore forming, showing a yellow colony color and forms extensively branched substrate mycelium and aerial hyphae. Inferred from the 16S rRNA gene phylogeny strain M2T affiliates with the genus Streptomonospora. It shows 96.6% 16S rRNA gene sequence similarity to the type species Streptomonospora salina DSM 44593 T and forms a distinct branch with Streptomonospora sediminis DSM 45723 T with 97.0% 16S rRNA gene sequence similarity. Genome-based phylogenetic analysis revealed that M2T is closely related to Streptomonospora alba YIM 90003 T with a digital DNA-DNA hybridisation (dDDH) value of 26.6%. The predominant menaquinones of M2T are MK-10(H6), MK-10(H8), and MK-11(H6) (> 10%). Major cellular fatty acids are iso-C16:0, anteiso C17:0 and C18:0 10-methyl. The polar lipid profile consisted of diphosphatidylglycerol phosphatidyl glycerol, phosphatidylinositol, phosphatidylcholine, phosphatidylethanolamine, three glycolipids, two unknown phospholipids, and two unknown lipids. The genome size of type strain M2T is 5,878,427 bp with 72.1 mol % G + C content. Based on the results obtained from phylogenetic and chemotaxonomic studies, strain M2T (= DSM 106425 T = NCCB 100650 T) is considered to represent a novel species within the genus Streptomonospora for which the name Streptomonospora litoralis sp. nov. is proposed.
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Regassa H, Bose D, Mukherjee A. Review of Microorganisms and Their Enzymatic Products for Industrial Bioprocesses. Ind Biotechnol (New Rochelle N Y) 2021. [DOI: 10.1089/ind.2021.0002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Hailemeleak Regassa
- Faculty of Applied Sciences & Biotechnology, Shoolini University of Biotechnology & Management Sciences, Solan, Himachal Pradesh, India
| | - Debajyoti Bose
- Faculty of Applied Sciences & Biotechnology, Shoolini University of Biotechnology & Management Sciences, Solan, Himachal Pradesh, India
| | - Alivia Mukherjee
- Department of Chemical and Biological Engineering, University of Saskatchewan, Saskatoon, SK, Canada
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Wongkuna S, Janvilisri T, Phanchana M, Harnvoravongchai P, Aroonnual A, Aimjongjun S, Malaisri N, Chankhamhaengdecha S. Temporal Variations in Patterns of Clostridioides difficile Strain Diversity and Antibiotic Resistance in Thailand. Antibiotics (Basel) 2021; 10:antibiotics10060714. [PMID: 34199301 PMCID: PMC8231780 DOI: 10.3390/antibiotics10060714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/05/2021] [Accepted: 06/08/2021] [Indexed: 01/04/2023] Open
Abstract
Clostridioides difficile has been recognized as a life-threatening pathogen that causes enteric diseases, including antibiotic-associated diarrhea and pseudomembranous colitis. The severity of C. difficile infection (CDI) correlates with toxin production and antibiotic resistance of C. difficile. In Thailand, the data addressing ribotypes, toxigenic, and antimicrobial susceptibility profiles of this pathogen are scarce and some of these data sets are limited. In this study, two groups of C. difficile isolates in Thailand, including 50 isolates collected from 2006 to 2009 (THA group) and 26 isolates collected from 2010 to 2012 (THB group), were compared for toxin genes and ribotyping profiles. The production of toxins A and B were determined on the basis of toxin gene profiles. In addition, minimum inhibitory concentration of eight antibiotics were examined for all 76 C. difficile isolates. The isolates of the THA group were categorized into 27 A−B+CDT− (54%) and 23 A-B-CDT- (46%), while the THB isolates were classified into five toxigenic profiles, including six A+B+CDT+ (23%), two A+B+CDT− (8%), five A−B+CDT+ (19%), seven A−B+CDT− (27%), and six A−B−CDT− (23%). By visually comparing them to the references, only five ribotypes were identified among THA isolates, while 15 ribotypes were identified within THB isolates. Ribotype 017 was the most common in both groups. Interestingly, 18 unknown ribotyping patterns were identified. Among eight tcdA-positive isolates, three isolates showed significantly greater levels of toxin A than the reference strain. The levels of toxin B in 3 of 47 tcdB-positive isolates were significantly higher than that of the reference strain. Based on the antimicrobial susceptibility test, metronidazole showed potent efficiency against most isolates in both groups. However, high MIC values of cefoxitin (MICs 256 μg/mL) and chloramphenicol (MICs ≥ 64 μg/mL) were observed with most of the isolates. The other five antibiotics exhibited diverse MIC values among two groups of isolates. This work provides evidence of temporal changes in both C. difficile strains and patterns of antimicrobial resistance in Thailand.
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Affiliation(s)
- Supapit Wongkuna
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (S.W.); (T.J.)
| | - Tavan Janvilisri
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (S.W.); (T.J.)
| | - Matthew Phanchana
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand;
| | - Phurt Harnvoravongchai
- Department of Biology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (P.H.); (N.M.)
| | - Amornrat Aroonnual
- Department of Tropical Nutrition and Food Science, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand;
| | - Sathid Aimjongjun
- Graduate Program in Molecular Medicine, Faculty of Science, Mahidol University, Bangkok 10400, Thailand;
| | - Natamon Malaisri
- Department of Biology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (P.H.); (N.M.)
| | - Surang Chankhamhaengdecha
- Department of Biology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (P.H.); (N.M.)
- Correspondence:
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Gupta Y, Ghrera AS. Recent advances in gold nanoparticle-based lateral flow immunoassay for the detection of bacterial infection. Arch Microbiol 2021; 203:3767-3784. [PMID: 34086107 DOI: 10.1007/s00203-021-02357-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/24/2021] [Accepted: 05/03/2021] [Indexed: 12/17/2022]
Abstract
Diagnosis of bacterial infections (BI) is becoming an increasingly difficult task in clinical practice due to their high prevalence and frequency, as well as the growth of antibiotic resistance worldwide. World Health Organization (WHO) reported antibiotic resistance is a major public health problem. BI becomes difficult or impossible to treat when the bacteria acquire immunity against antibiotics. Thus, there is a need for a quick and accurate technique to detect infection. Lateral flow immunoassay (LFIA) is an ideal technique for point-of-care testing of a disease or pathological changes inside the human body. In recent years, several LFIA based strips are being used for the detection of BI by targeting specific analytes which may range from the causative bacterium, whole-cell, DNA, or biomarker. Numerous nanoparticles like lipid-based nanoparticles, polymeric nanoparticles, and inorganic nanoparticles such as quantum dots, magnetic, ceramic, and metallic nanoparticles (copper, silver gold, iron) are widely being used in the advanced treatment of BI. Out of these gold nanoparticle (AuNPs), is being used for detection BI more effectively than other nanoparticles due to their surface functionalization, extraordinary chemical stability, biorecognition, and signal amplification properties and help to improve in conjugation with capture antibodies, and act as a color marker with unique optical properties on LFIA strips. Herein, a review that provides an overview of the principle of LFIA, how LFIA based strip is developed, and how it is helpful to detect a specific biomarker for bedside detection of the BI.
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Affiliation(s)
- Yachana Gupta
- Applied Science Department, The NorthCap University, Gurugram, India
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Streptomyces bathyalis sp. nov., an actinobacterium isolated from the sponge in a deep sea. Antonie Van Leeuwenhoek 2021; 114:425-435. [PMID: 33595745 PMCID: PMC7979654 DOI: 10.1007/s10482-021-01528-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 01/23/2021] [Indexed: 11/26/2022]
Abstract
A novel actinobacterium, designated ASO4wetT, was isolated from the unidentified sponge (SO4) in the deep sea collected of the North Atlantic Ocean. Study of 16S rRNA gene sequences indicated that strain ASO4wetT is a member of the genus Streptomyces and showed the closest similarities to Streptomyces karpasiensis K413T (98.87 %), Streptomyces glycovorans YIM M 10366T (98.38 %), and Streptomyces abyssalis YIM M 10400T (97.53 %). Strain ASO4wetT contained MK-9(H8) as the predominant menaquinone and the major fatty acids are iso-C16:0, anteiso-C15:0, and iso-C15:0. Polyphasic taxonomy was carried out between strain ASO4wetT and its phylogenetically closely related Streptomyces strains, which further elucidated their relatedness and revealed that strain ASO4wetT could be distinguished from currently known Streptomyces species. Strain ASO4wetT clearly represents a novel species in genus Streptomyces. We propose the name Streptomyces bathyalis sp. nov., with the type strain ASO4wetT (= DSM 106605T = NCCB 100657T). Analysis of the whole-genome sequence of S. bathyalis revealed that genome size is 7,377,472 bp with 6332 coding sequences.
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Iqbal MZ, Durrani AZ, Khan JA, Ahmad N, Usman M, Jabbar A, Khan A, Usman S, Anjum A, Husnain M. Molecular epidemiology of Coxiella Brunetii in small ruminants in Punjab, Pakistan: a novel reporting analytical cross sectional study. Trop Anim Health Prod 2021; 53:68. [PMID: 33394174 DOI: 10.1007/s11250-020-02496-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 12/03/2020] [Indexed: 11/26/2022]
Abstract
Coxiella burnetii, an intracellular zoonotic bacterium, causes query (Q) fever in ruminants. Its role has never been elucidated in small ruminants from Pakistan. The current study is designed to (a) determine the prevalence of coxiellosis in small ruminants, (b) evaluate the association of various potential risk factors and biomarkers in the occurrence of Coxiella burnetii, (c) and determine phylogeny and genetic variability of its various isolates identified during the study. For this purpose, 320 blood samples from sheep (n = 160) and goats (n = 160) were collected from 9 Union Councils of district Kasur, Punjab, and processed for DNA extraction. C. burnetii was confirmed by amplification of IS1111 transposase gene with an amplicon size of 294 bp. The results showed that the overall positive percentage of C. burnetii is 36.87% (sheep: 46.9% and goats: 30%). The phylogenetic tree was also constructed which described the possible origin of this pathogen from environment. Besides, after translation into amino acid, the resultant alignment showed several unique changes at position numbers 18 and 27 in the isolates from goats and at 27 and 66 from those of sheep. These mutations can have major impact on the infectious characteristics of this pathogen. Furthermore, different potential risk factors and clinical biomarkers like age, tick infestation, abortion, mastitis, and infertility were also studied and found that these are significantly (p < 0.05) associated with the occurrence of coxiellosis. It is concluded from the study that C. burnetii is endemic in small ruminants in Punjab, Pakistan. The outcomes of this study are alarming for scientific community as well as for policy makers because coxiellosis is an emerging threat to both humans and animals in this region due to its interspecies transmission ability.
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Affiliation(s)
- Muhammad Zahid Iqbal
- Department of Veterinary Medicine, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Aneela Zameer Durrani
- Department of Veterinary Medicine, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Jawaria Ali Khan
- Department of Veterinary Medicine, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Nisar Ahmad
- Department of Parasitology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Muhammad Usman
- Department of Veterinary Medicine, University of Veterinary and Animal Sciences, Lahore, Pakistan.
| | - Abdul Jabbar
- Department of Veterinary Medicine, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Amjad Khan
- Department of Public Health/Nutrition, The University of Haripur, Haripur, Pakistan
| | - Saba Usman
- Department of Pathology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Ahsan Anjum
- Department of Pathology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Muhammad Husnain
- Department of Veterinary Medicine, University of Veterinary and Animal Sciences, Lahore, Pakistan
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Martínez-Meléndez A, Morfin-Otero R, Villarreal-Treviño L, Baines SD, Camacho-Ortíz A, Garza-González E. Molecular epidemiology of predominant and emerging Clostridioides difficile ribotypes. J Microbiol Methods 2020; 175:105974. [PMID: 32531232 DOI: 10.1016/j.mimet.2020.105974] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/05/2020] [Accepted: 06/05/2020] [Indexed: 12/18/2022]
Abstract
There has been an increase in the incidence and severity of Clostridioides difficile infection (CDI) worldwide, and strategies to control, monitor, and diminish the associated morbidity and mortality have been developed. Several typing methods have been used for typing of isolates and studying the epidemiology of CDI; serotyping was the first typing method, but then was replaced by pulsed-field gel electrophoresis (PFGE). PCR ribotyping is now the gold standard method; however, multi locus sequence typing (MLST) schemes have been developed. New sequencing technologies have allowed comparing whole bacterial genomes to address genetic relatedness with a high level of resolution and discriminatory power to distinguish between closely related strains. Here, we review the most frequent C. difficile ribotypes reported worldwide, with a focus on their epidemiology and genetic characteristics.
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Affiliation(s)
- Adrián Martínez-Meléndez
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Químicas, Pedro de Alba S/N, Ciudad Universitaria, CP 66450 San Nicolás de los Garza, Nuevo Leon, Mexico
| | - Rayo Morfin-Otero
- Hospital Civil de Guadalajara "Fray Antonio Alcalde" e Instituto de Patología Infecciosa y Experimental, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara. Sierra Mojada 950, Col. Independencia, CP 44350 Guadalajara, Jalisco, Mexico
| | - Licet Villarreal-Treviño
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, Departamento de Microbiología e Inmunología, Pedro de Alba S/N, Ciudad Universitaria, CP 66450 San Nicolás de los Garza, Nuevo Leon, Mexico
| | - Simon D Baines
- University of Hertfordshire, School of Life and Medical Sciences, Department of Biological and Environmental Sciences, Hatfield AL10 9AB, UK
| | - Adrián Camacho-Ortíz
- Universidad Autónoma de Nuevo León, Hospital Universitario "Dr. José Eleuterio González", Servicio de Infectología. Av. Francisco I. Madero Pte. S/N y Av. José E. González. Col. Mitras Centro, CP 64460 Monterrey, Nuevo Leon, Mexico
| | - Elvira Garza-González
- Universidad Autónoma de Nuevo León, Hospital Universitario "Dr. José Eleuterio González", Servicio de Infectología. Av. Francisco I. Madero Pte. S/N y Av. José E. González. Col. Mitras Centro, CP 64460 Monterrey, Nuevo Leon, Mexico.
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Puopolo R, Gallo G, Mormone A, Limauro D, Contursi P, Piochi M, Bartolucci S, Fiorentino G. Identification of a New Heavy-Metal-Resistant Strain of Geobacillus stearothermophilus Isolated from a Hydrothermally Active Volcanic Area in Southern Italy. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:E2678. [PMID: 32295125 PMCID: PMC7215868 DOI: 10.3390/ijerph17082678] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/09/2020] [Accepted: 04/13/2020] [Indexed: 01/08/2023]
Abstract
Microorganisms thriving in hot springs and hydrothermally active volcanic areas are dynamically involved in heavy-metal biogeochemical cycles; they have developed peculiar resistance systems to cope with such metals which nowadays can be considered among the most permanent and toxic pollutants for humans and the environment. For this reason, their exploitation is functional to unravel mechanisms of toxic-metal detoxification and to address bioremediation of heavy-metal pollution with eco-sustainable approaches. In this work, we isolated a novel strain of the thermophilic bacterium Geobacillus stearothermophilus from the solfataric mud pool in Pisciarelli, a well-known hydrothermally active zone of the Campi Flegrei volcano located near Naples in Italy, and characterized it by ribotyping, 16S rRNA sequencing and mass spectrometry analyses. The minimal inhibitory concentration (MIC) toward several heavy-metal ions indicated that the novel G. stearothermophilus isolate is particularly resistant to some of them. Functional and morphological analyses suggest that it is endowed with metal resistance systems for arsenic and cadmium detoxification.
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Affiliation(s)
- Rosanna Puopolo
- Dipartimento di Biologia, Università Degli Studi di Napoli Federico II, 80139 Napoli, Italy; (R.P.); (G.G.); (D.L.); (P.C.); (S.B.)
| | - Giovanni Gallo
- Dipartimento di Biologia, Università Degli Studi di Napoli Federico II, 80139 Napoli, Italy; (R.P.); (G.G.); (D.L.); (P.C.); (S.B.)
| | - Angela Mormone
- Istituto Nazionale di Geofisica e Vulcanologia, Sezione Osservatorio Vesuviano, 80125 Napoli, Italy; (A.M.); (M.P.)
| | - Danila Limauro
- Dipartimento di Biologia, Università Degli Studi di Napoli Federico II, 80139 Napoli, Italy; (R.P.); (G.G.); (D.L.); (P.C.); (S.B.)
| | - Patrizia Contursi
- Dipartimento di Biologia, Università Degli Studi di Napoli Federico II, 80139 Napoli, Italy; (R.P.); (G.G.); (D.L.); (P.C.); (S.B.)
| | - Monica Piochi
- Istituto Nazionale di Geofisica e Vulcanologia, Sezione Osservatorio Vesuviano, 80125 Napoli, Italy; (A.M.); (M.P.)
| | - Simonetta Bartolucci
- Dipartimento di Biologia, Università Degli Studi di Napoli Federico II, 80139 Napoli, Italy; (R.P.); (G.G.); (D.L.); (P.C.); (S.B.)
| | - Gabriella Fiorentino
- Dipartimento di Biologia, Università Degli Studi di Napoli Federico II, 80139 Napoli, Italy; (R.P.); (G.G.); (D.L.); (P.C.); (S.B.)
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De Vero L, Boniotti MB, Budroni M, Buzzini P, Cassanelli S, Comunian R, Gullo M, Logrieco AF, Mannazzu I, Musumeci R, Perugini I, Perrone G, Pulvirenti A, Romano P, Turchetti B, Varese GC. Preservation, Characterization and Exploitation of Microbial Biodiversity: The Perspective of the Italian Network of Culture Collections. Microorganisms 2019; 7:microorganisms7120685. [PMID: 31842279 PMCID: PMC6956255 DOI: 10.3390/microorganisms7120685] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 02/06/2023] Open
Abstract
Microorganisms represent most of the biodiversity of living organisms in every ecological habitat. They have profound effects on the functioning of any ecosystem, and therefore on the health of our planet and of human beings. Moreover, microorganisms are the main protagonists in food, medical and biotech industries, and have several environmental applications. Accordingly, the characterization and preservation of microbial biodiversity are essential not only for the maintenance of natural ecosystems but also for research purposes and biotechnological exploitation. In this context, culture collections (CCs) and microbial biological resource centres (mBRCs) are crucial for the safeguarding and circulation of biological resources, as well as for the progress of life sciences. This review deals with the expertise and services of CCs, in particular concerning preservation and characterization of microbial resources, by pointing to the advanced approaches applied to investigate a huge reservoir of microorganisms. Data sharing and web services as well as the tight interconnection between CCs and the biotechnological industry are highlighted. In addition, guidelines and regulations related to quality management systems (QMSs), biosafety and biosecurity issues are discussed according to the perspectives of CCs and mBRCs.
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Affiliation(s)
- Luciana De Vero
- Unimore Microbial Culture Collection, Department of Life Sciences, University of Modena and Reggio Emilia, via Amendola 2, 42122 Reggio Emilia, Italy; (S.C.); (M.G.); (A.P.)
- Correspondence: ; Tel.: +39-0522-522-057
| | - Maria Beatrice Boniotti
- Biobank of Veterinary Resources, Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna, via Bianchi 9, 25124 Brescia, Italy;
| | - Marilena Budroni
- Department of Agricultural Science, University of Sassari, viale Italia 39, 07100 Sassari, Italy; (M.B.); (I.M.)
| | - Pietro Buzzini
- Department of Agriculture, Food and Environmental Science, University of Perugia, borgo XX Giugno, 74, I-06121 Perugia, Italy; (P.B.); (B.T.)
| | - Stefano Cassanelli
- Unimore Microbial Culture Collection, Department of Life Sciences, University of Modena and Reggio Emilia, via Amendola 2, 42122 Reggio Emilia, Italy; (S.C.); (M.G.); (A.P.)
| | - Roberta Comunian
- Agris Sardegna, Agenzia regionale per la ricerca in agricoltura, Loc. Bonassai, km 18.600 SS291, 07100 Sassari, Italy;
| | - Maria Gullo
- Unimore Microbial Culture Collection, Department of Life Sciences, University of Modena and Reggio Emilia, via Amendola 2, 42122 Reggio Emilia, Italy; (S.C.); (M.G.); (A.P.)
| | - Antonio F. Logrieco
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via G. Amendola 122/O, 70126 Bari, Italy; (A.F.L.); (G.P.)
| | - Ilaria Mannazzu
- Department of Agricultural Science, University of Sassari, viale Italia 39, 07100 Sassari, Italy; (M.B.); (I.M.)
| | - Rosario Musumeci
- MicroMiB Culture Collection, Department of Medicine and Surgery, University of Milano-Bicocca, via Cadore 48, 20900 Monza, Italy;
| | - Iolanda Perugini
- Department of Life Sciences and Systems Biology, University of Turin, viale Mattioli, 25, 10125 Torino, Italy; (I.P.); (G.C.V.)
| | - Giancarlo Perrone
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via G. Amendola 122/O, 70126 Bari, Italy; (A.F.L.); (G.P.)
| | - Andrea Pulvirenti
- Unimore Microbial Culture Collection, Department of Life Sciences, University of Modena and Reggio Emilia, via Amendola 2, 42122 Reggio Emilia, Italy; (S.C.); (M.G.); (A.P.)
| | - Paolo Romano
- Mass Spectrometry and Proteomics, Scientific Direction, IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132 Genova, Italy;
| | - Benedetta Turchetti
- Department of Agriculture, Food and Environmental Science, University of Perugia, borgo XX Giugno, 74, I-06121 Perugia, Italy; (P.B.); (B.T.)
| | - Giovanna Cristina Varese
- Department of Life Sciences and Systems Biology, University of Turin, viale Mattioli, 25, 10125 Torino, Italy; (I.P.); (G.C.V.)
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Mamishi S, Mohammadian M, Pourakbari B, Hosseinpour Sadeghi R, Haghi Ashtiani MT, Abdosalehi MR, Rahmani M, Mahmoudi S. Antibiotic Resistance And Genotyping Of Gram-Positive Bacteria Causing Hospital-Acquired Infection In Patients Referring To Children's Medical Center. Infect Drug Resist 2019; 12:3719-3726. [PMID: 31819554 PMCID: PMC6885556 DOI: 10.2147/idr.s220522] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 10/09/2019] [Indexed: 12/20/2022] Open
Abstract
Introduction A serious problem affecting human society is the development of bacterial resistance. The purpose of the current study was to evaluate the antibiotic resistance of Gram-positive bacteria (GPB) and genotyping of common GPB causing hospital-acquired infections (HAIs) in patients who were referred to Children’s Medical Center during a 6-month period by random amplified polymorphic DNA (RAPD) and enterobacterial repetitive intergenic consensus sequence polymerase chain reaction (ERIC-PCR). Methods During the 6-month period, antimicrobial resistance profiles of GPB isolates recovered from patients in Children’s Medical Center were determined using the Kirby–Bauer disk diffusion and MIC. Typing of common GPB was performed and the results were analyzed by gel compare software. Results In this cross-sectional study, 6524 cultures were performed and 138 Ggram-positive bacteria were isolated (2%). Staphylococcus aureus strains showed the highest antibiotic penicillin resistance (96.3%). Twenty-six per cent of the strains were methicillin-resistant S. aureus (MRSA) and no resistance was found against vancomycin. All isolates of Enterococcus faecium were resistant to ciprofloxacin (100%). The resistance to vancomycin was very high (67%) and no resistance was observed to linezolid. The results of genotyping analysis of S. epidermidis strains showed the presence of two clones with a genetic relationship of over 80%. All of the S. aureus strains were in one cluster and half of the E. faecium strains were in a cluster with a genetic predilection of over 80%. Conclusion This study indicated frequent occurrence of antimicrobial resistance, especially in Enterococcus spp. isolates. Rapid spreads of MRSA and VREF from a clonal origin require implementing careful isolation and infection control measures.
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Affiliation(s)
- Setareh Mamishi
- Department of Infectious Diseases, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.,Pediatric Infectious Disease Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Mohammadian
- Department of Infectious Diseases, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Babak Pourakbari
- Pediatric Infectious Disease Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Mohammad Taghi Haghi Ashtiani
- Department of Pathology, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Abdosalehi
- Department of Infectious Diseases, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Rahmani
- Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Shima Mahmoudi
- Pediatric Infectious Disease Research Center, Tehran University of Medical Sciences, Tehran, Iran
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Verma A, Pal Y, Ojha AK, Kumari M, Khatri I, Rameshkumar N, Schumann P, Dastager SG, Mayilraj S, Subramanian S, Krishnamurthi S. Taxonomic insights into the phylogeny of Bacillus badius and proposal for its reclassification to the genus Pseudobacillus as Pseudobacillus badius comb. nov. and reclassification of Bacillus wudalianchiensis Liu et al., 2017 as Pseudobacillus wudalianchiensis comb. nov. Syst Appl Microbiol 2019; 42:360-372. [DOI: 10.1016/j.syapm.2019.03.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 03/04/2019] [Accepted: 03/08/2019] [Indexed: 11/26/2022]
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On-line quantification of thickness and strength of single and mixed species biofilm grown under controlled laminar flow conditions. FOOD AND BIOPRODUCTS PROCESSING 2019. [DOI: 10.1016/j.fbp.2018.08.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Borsodi AK, Korponai K, Schumann P, Spröer C, Felföldi T, Márialigeti K, Szili-Kovács T, Tóth E. Nitrincola alkalilacustris sp. nov. and Nitrincola schmidtii sp. nov., alkaliphilic bacteria isolated from soda pans, and emended description of the genus Nitrincola. Int J Syst Evol Microbiol 2017; 67:5159-5164. [DOI: 10.1099/ijsem.0.002437] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Andrea K. Borsodi
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
| | - Kristóf Korponai
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
| | - Peter Schumann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7 B, 38124 Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7 B, 38124 Braunschweig, Germany
| | - Tamás Felföldi
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
| | - Károly Márialigeti
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
| | - Tibor Szili-Kovács
- Institute for Soil Sciences and Agricultural Chemistry, Agricultural Research Center, Hungarian Academy of Sciences, Herman Ottó út 15, H-1022 Budapest, Hungary
| | - Erika Tóth
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
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Schumann P, Pukall R. Leucobacter weissii sp. nov., an isolate from activated sludge once described as first representative of the peptidoglycan variation B2δ, and emended description of the genus Leucobacter. Int J Syst Evol Microbiol 2017; 67:5244-5251. [PMID: 29087268 DOI: 10.1099/ijsem.0.002454] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain S27T is a Gram-stain-positive, regular rod-shaped, non-motile, non-spore-forming, yellow pigmented actinobacterium which was isolated from an aerated laboratory scale fermenter fed with wastes of a yeast factory. The strain was classified as Microbacterium sp. after the analysis of its peptidoglycan revealed a novel B-type structure established as variation B2δ by Hensel in 1984. As the combination of the peptidoglycan amino acids 2,4-diaminobutyric acid (Dab), threonine (Thr), glycine (Gly), alanine (Ala) and glutamic acid (Glu) is in disagreement with the current genus definition of Microbacterium but is typical of several Leucobacter species, the taxonomic status of strain S27T was re-examined by a polyphasic study. Comparative analyses of 16S rRNA gene sequences and the occurrence of l-Dab, d-Ala, l-Ala, Gly, l-Thr, d-Glu and lower amounts of l-Glu in the peptidoglycan in combination with the predominating menaquinones MK-11, MK-10 and MK-9, phosphatidylglycerol, and one unknown glycolipid as the major polar lipids (and trace amounts of diphosphatidylglycerol and an unknown phospholipid), a profile with anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0, anteiso-C17 : 0 and iso-C17 : 0 as major fatty acids and the G+C value of 70.1 mol% confirmed the affiliation to the genus Leucobacter and revealed that S27T (=DSM 20621T =CCM 8762T) is the type strain of a new species for which the name Leucobacter weissii sp. nov. is proposed. The availability of new data allows for an emended description of the genus Leucobacter.
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Affiliation(s)
- Peter Schumann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Rüdiger Pukall
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
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Atasayar E, Zimmermann O, Spröer C, Schumann P, Groß U. Corynebacterium gottingense sp. nov., isolated from a clinical patient. Int J Syst Evol Microbiol 2017; 67:4494-4499. [PMID: 28950931 DOI: 10.1099/ijsem.0.002322] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive bacterial strain, 99221/2016T, was isolated from blood of a patient with bacteraemia at the Institute of Medical Microbiology, Göttingen, Germany. The strain was rod-shaped with a palisade arrangement of cells, non-spore-forming, non-lipophilic, catalase-positive and oxidase-negative. It grew well at 37 °C on Columbia blood agar and showed good growth under aerobic, microaerophilic and anaerobic conditions. The colonies were white-cream, circular and convex with a shiny, smooth surface. The predominant respiratory quinones were MK-8(H2) and MK-9(H2). The polar lipids profile contained phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. Two unidentified phospholipids and several unidentified lipids were also detected. The prevalent cellular fatty acids comprised cis-9-octadecenoic acid (C18 : 1 ω9c), hexadecanoic acid (C16 : 0) and pentadecanoic acid (C15 : 0). Corynemycolates with 28-36 carbons in length were present. The whole-cell hydrolysate contained meso-diaminopimelic acid and arabinose, glucose, galactose and ribose as major sugars. Analysis of the 16S rRNA gene sequence identities revealed that the strain is most closely related to Corynebacterium imitans DSM 44264T (98.0 %), Corynebacterium lipophiloflavum DSM 44291T (96.9 %), Corynebacterium afermentans subsp. afermentans DSM 44280T (96.9 %) and Corynebacterium afermentans subsp. lipophilum DSM 44282T (96.8 %). The identity with Corynebacterium diphtheriae DSM 44123T, the type species of the genus, was 94 %. The DNA G+C content was 69.2 mol%. DNA-DNA hybridization with Corynebacterium imitans DSM 44264T revealed a value of 34 %, confirming that the strain represents a novel species. The type strain 99221/2016T (DSM 103494T=JCM 31931T) is proposed to represent a novel species of the genus Corynebacterium with the name Corynebacterium gottingense.
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Affiliation(s)
- Ewelina Atasayar
- Leibniz-Institut DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7b, 38124 Braunschweig, Germany
| | - Ortrud Zimmermann
- Institut für Medizinische Mikrobiologie, Universitätsmedizin Göttingen, Kreuzbergring 57, 37075 Göttingen, Germany
| | - Cathrin Spröer
- Leibniz-Institut DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7b, 38124 Braunschweig, Germany
| | - Peter Schumann
- Leibniz-Institut DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7b, 38124 Braunschweig, Germany
| | - Uwe Groß
- Institut für Medizinische Mikrobiologie, Universitätsmedizin Göttingen, Kreuzbergring 57, 37075 Göttingen, Germany
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Verma A, Pal Y, Khatri I, Ojha AK, Gruber-Vodicka H, Schumann P, Dastager S, Subramanian S, Mayilraj S, Krishnamurthi S. Examination into the taxonomic position of Bacillus thermotolerans Yang et al., 2013, proposal for its reclassification into a new genus and species Quasibacillus thermotolerans gen. nov., comb. nov. and reclassification of B. encimensis Dastager et al., 2015 as a later heterotypic synonym of B. badius. Syst Appl Microbiol 2017; 40:411-422. [PMID: 28947104 DOI: 10.1016/j.syapm.2017.07.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 07/26/2017] [Indexed: 11/28/2022]
Abstract
Two novel Gram-staining positive, rod-shaped, moderately halotolerant, endospore forming bacterial strains 5.5LF 38TD and 5.5LF 48TD were isolated and taxonomically characterized from a landfill in Chandigarh, India. The analysis of 16S rRNA gene sequences of the strains confirmed their closest identity to Bacillus thermotolerans SgZ-8T with 99.9% sequence similarity. A comparative phylogenetic analysis of strains 5.5LF 38TD, 5.5LF 48TD and B. thermotolerans SgZ-8T confirmed their separation into a novel genus with B. badius and genus Domibacillus as the closest phylogenetic relatives. The major fatty acids of the strains are iso-C15:0 and iso-C16:0 and MK-7 is the only quinone. The major polar lipids are diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The digital DNA-DNA hybridization (DDH) and ortho average nucleotide identity (ANI) values calculated through whole genome sequences indicated that the three strains showed low relatedness with their phylogenetic neighbours. Based on evidences from phylogenomic analyses and polyphasic taxonomic characterization we propose reclassification of the species B. thermotolerans into a novel genus named Quasibacillus thermotolerans gen. nov., comb. nov with the type strain SgZ-8T (=CCTCC AB2012108T=KACC 16706T). Further our analyses also revealed that B. encimensis SGD-V-25T is a later heterotypic synonym of Bacillus badius DSM 23T.
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Affiliation(s)
- Ashish Verma
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Yash Pal
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Indu Khatri
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Anup Kumar Ojha
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Harald Gruber-Vodicka
- Max-Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
| | - Peter Schumann
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, GmBH, Inhoffenstrasse 7b, D-38124 Braunschweig, Germany
| | - Syed Dastager
- NCIM Resource Center, CSIR-National Chemical Laboratory, Pune 411 008, Maharashtra, India
| | | | - Shanmugam Mayilraj
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Srinivasan Krishnamurthi
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India.
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Röttig A, Atasayar E, Meier-Kolthoff JP, Spröer C, Schumann P, Schauer J, Steinbüchel A. Streptomyces jeddahensis sp. nov., an oleaginous bacterium isolated from desert soil. Int J Syst Evol Microbiol 2017; 67:1676-1682. [PMID: 28141499 DOI: 10.1099/ijsem.0.001839] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel strain, G25T, was isolated from desert soil collected near Jeddah in Saudi Arabia. The strain could accumulate nearly 65 % of its cell dry weight as fatty acids, grow on a broad range of carbon sources and tolerate temperatures of up to 50 °C. With respect to to its 16S rRNA gene sequence, G25T is most closely related to Streptomyces massasporeus DSM 40035T, Streptomyces hawaiiensis DSM 40042T, Streptomyces indiaensis DSM 43803T, Streptomyces luteogriseus DSM 40483T and Streptomyces purpurascens DSM 40310T. Conventional DNA-DNA hybridization (DDH) values ranged from 18.7 to 46.9 % when G25T was compared with these reference strains. Furthermore, digital DDH values between the draft genome sequence of G25T and the genome sequences of other species of the genus Streptomyces were also significantly below the threshold of 70 %. The DNA G+C content of the draft genome sequence, consisting of 8.46 Mbp, was 70.3 %. The prevalent cellular fatty acids of G25T comprised anteiso-C15 : 0, iso-C15 : 0, C16 : 0 and iso-C16 : 0. The predominant menaquinones were MK-9(H6), MK-9(H8) and MK-9(H4). The polar lipids profile contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylglycerol and phosphatidylinositol mannosides as well as unidentified phospholipids and phosphoaminolipids. The cell wall contained ll-diaminopimelic acid. Whole-cell sugars were predominantly glucose with small traces of ribose and mannose. The results of the polyphasic approach confirmed that this isolate represents a novel species of the genus Streptomyces, for which the name Streptomyces jeddahensis sp. nov. is proposed. The type strain of this species is G25T (=DSM 101878T =LMG 29545T =NCCB 100603T).
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Affiliation(s)
- Annika Röttig
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstraße 3, 48149 Münster, Germany
| | - Ewelina Atasayar
- Leibniz-Institut DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7b, 38124 Braunschweig, Germany
| | - Jan Philipp Meier-Kolthoff
- Leibniz-Institut DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7b, 38124 Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz-Institut DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7b, 38124 Braunschweig, Germany
| | - Peter Schumann
- Leibniz-Institut DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7b, 38124 Braunschweig, Germany
| | - Jennifer Schauer
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstraße 3, 48149 Münster, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstraße 3, 48149 Münster, Germany.,Environmental Sciences Department, Faculty of Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
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Guo X, Zhang J, Wu F, Zhang M, Yi M, Peng Y. Different subtype strains of Akkermansia muciniphila abundantly colonize in southern China. J Appl Microbiol 2016; 120:452-9. [PMID: 26666632 PMCID: PMC4736461 DOI: 10.1111/jam.13022] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 11/23/2015] [Accepted: 12/05/2015] [Indexed: 01/04/2023]
Abstract
Aim This study investigates the colonization rate of Akkermansia muciniphila in the gastrointestinal tracts of people living in southern China and applies a modified method for the isolation and subtyping of A. muciniphila strains from faecal samples. Methods and Results Fresh faecal samples were collected and bacterial DNA was extracted from these samples for real‐time PCR analysis. Strains were separated using a culture‐dependent sPCR‐directed method and classified using an enterobacterial repetitive intergenic consensus (ERIC‐PCR) DNA fingerprinting method. The colonization rate for the sample population from southern China was 51·74%. We isolated 22 strains from human faeces. The results revealed that all strains were identifiable as A. muciniphila with 99–100% identity to the type‐strain ATCC BAA‐835. ERIC‐PCR resulted in grouping of the DNA fingerprints showed that 12 distinct clusters were distinguished with a delineation level of 100%. Conclusions Southern China has a high rate of A. muciniphila colonization and over 12 different subtype strains reside in faecal samples. Significance and Impact of the Study Akkermansia muciniphila has a beneficial role in human gastrointestinal tract. These studies provide a better understanding of A. muciniphila and details of its colonization in the human gastrointestinal tract.
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Affiliation(s)
- X Guo
- Department of Laboratory Medicine, Zhu Jiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - J Zhang
- Department of Laboratory Medicine, Zhu Jiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - F Wu
- Department of Laboratory Medicine, Zhu Jiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - M Zhang
- Department of Laboratory Medicine, Zhu Jiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - M Yi
- Department of Endocrinology, Zhu Jiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Y Peng
- Department of Laboratory Medicine, Zhu Jiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
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Abou Chakra CN, McGeer A, Labbé AC, Simor AE, Gold WL, Muller MP, Powis J, Katz K, Garneau JR, Fortier LC, Pépin J, Cadarette SM, Valiquette L. Factors Associated With Complications of Clostridium difficile Infection in a Multicenter Prospective Cohort. Clin Infect Dis 2015; 61:1781-8. [PMID: 26338788 DOI: 10.1093/cid/civ749] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Accepted: 07/29/2015] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Clostridium difficile infection (CDI) is the most common cause of nosocomial infectious diarrhea and may result in severe complications including death. We conducted a prospective study to identify risk factors for complications of CDI (cCDI). METHODS Adult inpatients with confirmed CDI in 10 Canadian hospitals were enrolled and followed for 90 days. Potential risk factors were measured within 24 hours of diagnosis. Isolates were typed by polymerase chain reaction ribotyping. cCDI was defined as 1 or more of the following: colonic perforation, toxic megacolon, colectomy, admission to an intensive care unit for cCDI, or if CDI contributed to death within 30 days of enrollment. Risk factors for cCDI were investigated by logistic regression. RESULTS A total of 1380 patients were enrolled. cCDI was observed in 8% of patients. The ribotype was identified in 922 patients, of whom 52% were infected with R027. Age ≥ 80 years, heart rate >90/minute, respiratory rate >20/minute, white cell count <4 × 10(9)/L or ≥ 20 × 10(9)/L, albumin <25 g/L, blood urea nitrogen >7 mmol/L, and C-reactive protein ≥ 150 mg/L were independently associated with cCDI. A higher frequency of cCDI was observed among R027-infected patients (10.9% vs 7.2%), but the association was not significant in adjusted analysis. CONCLUSIONS CDI complications were associated with older age, abnormal blood tests, and abnormal vital signs. These factors, which are readily available to clinicians at the time of diagnosis, could be used for outcome prediction and risk stratification to select patients who may need closer monitoring or more aggressive therapy.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Julian R Garneau
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Quebec
| | - Louis-Charles Fortier
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Quebec
| | - Jacques Pépin
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Quebec
| | | | - Louis Valiquette
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Quebec
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24
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Anderson KM, Abbott J, Zhao S, Liu E, Himathongkham S. Molecular Subtyping of Shiga Toxin-Producing Escherichia coli Using a Commercial Repetitive Sequence-Based PCR Assay. J Food Prot 2015; 78:902-11. [PMID: 25951383 DOI: 10.4315/0362-028x.jfp-14-430] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
PCR-based typing methods, such as repetitive sequence-based PCR (rep-PCR), may facilitate the identification of Shiga toxin-producing Escherichia coli (STEC) by serving as screening methods to reduce the number of isolates to be processed for further confirmation. In this study, we used a commercial rep-PCR typing system to generate DNA fingerprint profiles for STEC O157 (n = 60) and non-O157 (n = 91) isolates from human, food, and animal samples and then compared the results with those obtained from pulsed-field gel electrophoresis (PFGE). Fifteen serogroups were analyzed using the Kullback Leibler or extended Jaccard statistical method, and the unweighted pair group method of averages algorithm was used to create dendrograms. Among the 151 STEC isolates tested, all were typeable by rep-PCR. Among the non-O157 isolates, rep-PCR clustered 79 (88.8%) of 89 isolates according to serogroup status, with peak differences ranging from 1 (96.4% similarity) to 12 (58.7% similarity). The genetic relatedness of the non-O157 serogroups mirrored the branching of distinct clonal groups elucidated by other investigators. Although the discriminatory power of rep-PCR (Simpson's index of diversity [SID] = 0.954) for the O157 isolates was less than that of PFGE (SID = 0.993), rep-PCR was able to identify 29 pattern types, suggesting that this method can be used for strain typing, although not to the same level as PFGE. Similar results were obtained from analysis of the non-O157 isolates. With rep-PCR, we assigned non-O157 isolates to 46 pattern types with a SID of 0.977. By PFGE, non-O157 STEC strains were divided into 77 pattern types with a SID of 0.996. Together, these results indicate the ability of the rep-PCR typing system to distinguish between and within O157 and non-O157 STEC groups. Rapid PCR-based typing methods could be invaluable tools for use in outbreak investigations by excluding unrelated STEC isolates within 24 h.
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Affiliation(s)
- Kimberly M Anderson
- U.S. Food and Drug Administration, Office of Regulatory Affairs, San Francisco District Laboratory, Alameda, California 94502, USA.
| | - Jason Abbott
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, Laurel, Maryland 20708, USA
| | - Shaohua Zhao
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, Laurel, Maryland 20708, USA
| | - Eileen Liu
- U.S. Food and Drug Administration, Office of Regulatory Affairs, San Francisco District Laboratory, Alameda, California 94502, USA
| | - Sunee Himathongkham
- U.S. Food and Drug Administration, Office of Regulatory Affairs, Office of Regulatory Science, Rockville, Maryland 20857, USA
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25
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Hashemi A, Baghbani-Arani F. The effective differentiation of Salmonella isolates using four PCR-based typing methods. J Appl Microbiol 2015; 118:1530-40. [PMID: 25809397 DOI: 10.1111/jam.12805] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 03/07/2015] [Accepted: 03/12/2015] [Indexed: 11/30/2022]
Abstract
AIMS Discrimination of Salmonella strains below the species level is very important to trace the source of outbreaks. To this end molecular typing methods can be successfully applied to routine analysis in nonspecialized laboratories due to their simplicity and speed. Here, the discriminatory ability of four molecular typing methods was investigated in 74 Salmonella enterica isolates. METHODS AND RESULTS Salmonella strains isolated from human stool, blood, bone marrow, synovial fluid, ascites and urine sources in Iran during the years 2012 and 2013 were differentiated by random amplification of polymorphic DNA (RAPD), enterobacterial repetitive intergenic consensus (ERIC), repetitive extragenic palindromic (REP) and BOX repeat-based (BOXAIR) PCR methods. A total of 74 isolates were obtained, with 67 isolates belonging to eight serotypes/serogroups, while seven were nontypeable. The 74 strains produced 32 fingerprints with OPS-11 primers, 44 RAPD fingerprints using OPP-16 primers and 54 fingerprints with P1254 primers; their discriminatory index (DI) was 0·942, 0·978, and 0·984 respectively. BOXAIR fingerprinting produced 49 patterns (DI 0·985), while REP resulted in 55 patterns (DI 0·991) and ERIC in 48 fingerprints (DI 0·983). The discrimination of Salmonella isolates was improved when methods were combined. The combination of ERIC, REP and BOXAIR as well as the combination of BOXAIR with ERIC or REP could differentiate all 74 investigated Salmonella strains. CONCLUSIONS The combined use of RAPD and ERIC fingerprinting offers an excellent means of differentiating Salmonella strains. SIGNIFICANCE AND IMPACT OF THE STUDY The discrimination power of Salmonella molecular typing by combination of ERIC, REP and BOXAIR methods, or by combination of BOXAIR with ERIC or REP, is sufficient to determine genetic relationships for epidemiological purposes.
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Affiliation(s)
- A Hashemi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - F Baghbani-Arani
- Department of Genetics & Biotechnology, School of Biological Science, Varamin-Pishva Branch, Islamic Azad University, Varamin, Iran
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26
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Makk J, Homonnay ZG, Kéki Z, Nemes-Barnás K, Márialigeti K, Schumann P, Tóth EM. Arenimonas subflava sp. nov., isolated from a drinking water network, and emended description of the genus Arenimonas. Int J Syst Evol Microbiol 2015; 65:1915-1921. [PMID: 25795065 DOI: 10.1099/ijs.0.000201] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A strain designated PYM3-14T was isolated from the drinking water network of Budapest (Hungary) and was studied by polyphasic taxonomic methods. The straight-rod-shaped cells stained Gram-negative, were aerobic and non-motile. Phylogenetic analysis of the 16S rRNA gene sequence of strain PYM3-14T revealed a clear affiliation with members of the family Xanthomonadaceae within the class Gammaproteobacteria. The 16S rRNA gene sequence of strain PYM3-14T showed the closest sequence similarities to Arenimonas daechungensis CH15-1T (96.2 %), Arenimonas oryziterrae YC6267T (95.2 %) and Lysobacter brunescens UASM DT (94.4 %). The DNA G+C content of strain PYM3-14T, measured by two different methods (52.0 mol% and 55.9 mol%, respectively), was much lower than that of any member of the genus Arenimonas. The predominant fatty acids (>8 %) were iso-C16:0, iso-C15:0, iso-C14:0, iso-C17:1ω9c and C16:1ω7c alcohol. Strain PYM3-14T contained Q-8 as the major ubiquinone and phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidylmonomethylethanolamine as the major polar lipids. According to phenotypic and genotypic data strain PYM3-14T represents a novel species of the genus Arenimonas, for which the name Arenimonas subflava sp. nov. is proposed. The type strain is PYM3-14T ( = NCAIM B 02508T = DSM 25526T). On the basis of new data obtained in this study, an emended description of the genus Arenimonas is also proposed.
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Affiliation(s)
- Judit Makk
- Department of Microbiology, Eötvös Loránd University, Pázmány P. sétány 1/C, H-1117 Budapest, Hungary
| | - Zalán G Homonnay
- Department of Microbiology, Eötvös Loránd University, Pázmány P. sétány 1/C, H-1117 Budapest, Hungary
| | - Zsuzsa Kéki
- Department of Microbiology, Eötvös Loránd University, Pázmány P. sétány 1/C, H-1117 Budapest, Hungary
| | - Katalin Nemes-Barnás
- Department of Microbiology, Eötvös Loránd University, Pázmány P. sétány 1/C, H-1117 Budapest, Hungary
| | - Károly Márialigeti
- Department of Microbiology, Eötvös Loránd University, Pázmány P. sétány 1/C, H-1117 Budapest, Hungary
| | - Peter Schumann
- DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany
| | - Erika M Tóth
- Department of Microbiology, Eötvös Loránd University, Pázmány P. sétány 1/C, H-1117 Budapest, Hungary
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27
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Meier-Kolthoff JP, Hahnke RL, Petersen J, Scheuner C, Michael V, Fiebig A, Rohde C, Rohde M, Fartmann B, Goodwin LA, Chertkov O, Reddy TBK, Pati A, Ivanova NN, Markowitz V, Kyrpides NC, Woyke T, Göker M, Klenk HP. Complete genome sequence of DSM 30083(T), the type strain (U5/41(T)) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy. Stand Genomic Sci 2014; 9:2. [PMID: 25780495 PMCID: PMC4334874 DOI: 10.1186/1944-3277-9-2] [Citation(s) in RCA: 353] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 06/16/2014] [Indexed: 12/02/2022] Open
Abstract
Although Escherichia coli is the most widely studied bacterial model organism and often considered to be the model bacterium per se, its type strain was until now forgotten from microbial genomics. As a part of the G enomic E ncyclopedia of B acteria and A rchaea project, we here describe the features of E. coli DSM 30083(T) together with its genome sequence and annotation as well as novel aspects of its phenotype. The 5,038,133 bp containing genome sequence includes 4,762 protein-coding genes and 175 RNA genes as well as a single plasmid. Affiliation of a set of 250 genome-sequenced E. coli strains, Shigella and outgroup strains to the type strain of E. coli was investigated using digital DNA:DNA-hybridization (dDDH) similarities and differences in genomic G+C content. As in the majority of previous studies, results show Shigella spp. embedded within E. coli and in most cases forming a single subgroup of it. Phylogenomic trees also recover the proposed E. coli phylotypes as monophyla with minor exceptions and place DSM 30083(T) in phylotype B2 with E. coli S88 as its closest neighbor. The widely used lab strain K-12 is not only genomically but also physiologically strongly different from the type strain. The phylotypes do not express a uniform level of character divergence as measured using dDDH, however, thus an alternative arrangement is proposed and discussed in the context of bacterial subspecies. Analyses of the genome sequences of a large number of E. coli strains and of strains from > 100 other bacterial genera indicate a value of 79-80% dDDH as the most promising threshold for delineating subspecies, which in turn suggests the presence of five subspecies within E. coli.
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Affiliation(s)
- Jan P Meier-Kolthoff
- />Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Richard L Hahnke
- />Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Jörn Petersen
- />Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Carmen Scheuner
- />Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Victoria Michael
- />Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Anne Fiebig
- />Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Christine Rohde
- />Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Manfred Rohde
- />Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | | | | | | | - TBK Reddy
- />DOE Joint Genome Institute, Walnut Creek, Ca USA
| | - Amrita Pati
- />DOE Joint Genome Institute, Walnut Creek, Ca USA
| | | | | | - Nikos C Kyrpides
- />DOE Joint Genome Institute, Walnut Creek, Ca USA
- />Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Tanja Woyke
- />DOE Joint Genome Institute, Walnut Creek, Ca USA
| | - Markus Göker
- />Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Hans-Peter Klenk
- />Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
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28
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Yassin AF, Spröer C, Pukall R, Sylvester M, Siering C, Schumann P. Dissection of the genus Actinobaculum: Reclassification of Actinobaculum schaalii Lawson et al. 1997 and Actinobaculum urinale Hall et al. 2003 as Actinotignum schaalii gen. nov., comb. nov. and Actinotignum urinale comb. nov., description of Actinotignum sanguinis sp. nov. and emended descriptions of the genus Actinobaculum and Actinobaculum suis; and re-examination of the culture deposited as Actinobaculum massiliense CCUG 47753T ( = DSM 19118T), revealing that it does not represent a strain of this species. Int J Syst Evol Microbiol 2014; 65:615-624. [PMID: 25406238 DOI: 10.1099/ijs.0.069294-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The remarkable host specificity of the species of the genus Actinobaculum led us to recharacterize these species by a polyphasic approach. A comparative chemotaxonomic study including analysis of whole-cell sugars, amino acid composition of the peptidoglycan, fatty acid methyl esters, respiratory quinones and polar lipids revealed significant differences that, in combination with molecular data, support a dissection of the genus Actinobaculum. The proposals of this study include the reclassification of Actinobaculum schaalii and Actinobaculum urinale as Actinotignum schaalii gen. nov., comb. nov. (type strain DSM 15541(T) = CCUG 27420(T)) and Actinotignum urinale comb. nov. (type strain DSM 15805(T) = CCUG 46093(T)), respectively. Emended descriptions of the genus Actinobaculum and Actinomyces suis are also provided. The results of 16S rRNA gene sequence analysis and DNA-DNA hybridization also indicated that the type strain of Actinobaculum massiliense deposited as CCUG 47753(T) ( = DSM 19118(T)) should in fact be considered a member of the species Actinobaculum schaalii. In addition, comparative 16S rRNA gene sequencing and DNA-DNA relatedness studies of four strains recovered from clinical materials demonstrated that three of the isolates belonged to Actinotignum schaalii; the remaining strain represents a novel species, for which the name Actinotignum sanguinis sp. nov. is proposed. The type strain is IMMIB L-2199(T) ( = DSM 26039(T) = CCUG 64068(T)).
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Affiliation(s)
- A F Yassin
- Institut für Medizinische Mikrobiologie und Immunologie der Universität Bonn, Sigmund-Freud-Straße 25, D-53127 Bonn, Germany
| | - C Spröer
- Leibniz Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstrasse 7b, D-38124 Braunschweig, Germany
| | - R Pukall
- Leibniz Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstrasse 7b, D-38124 Braunschweig, Germany
| | - M Sylvester
- Institut für Biochemie und Molekularbiologie Universitätsklinikum Bonn, Nussallee 11, D-53115 Bonn, Germany
| | - C Siering
- Institut für Organische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany
| | - P Schumann
- Leibniz Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstrasse 7b, D-38124 Braunschweig, Germany
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29
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Soro-Yao AA, Schumann P, Thonart P, Djè KM, Pukall R. The Use of MALDI-TOF Mass Spectrometry, Ribotyping and Phenotypic Tests to Identify Lactic Acid Bacteria from Fermented Cereal Foods in Abidjan (Côte d'Ivoire). Open Microbiol J 2014; 8:78-86. [PMID: 25279017 PMCID: PMC4181171 DOI: 10.2174/1874285801408010078] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 07/18/2014] [Accepted: 07/23/2014] [Indexed: 11/22/2022] Open
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) protein analysis, automated ribotyping, and phenotypic tests (e.g., cell morphology, gas production from glucose, growth and acid production on homofermemtative-heterofermentative differential (HHD) agar medium, sugar fermentation patterns) were used to identify 23 lactic acid bacteria (LAB) isolated from fermented cereal foods available in Abidjan, Côte d'Ivoire. Pediococcus acidilactici (56.5%), Lactobacillus fermentum (30.4%), L. salivarius (4.3%), P. pentosaceus (4.3%) and L. plantarum subsp. plantarum (4.3%) were the species and subspecies identified. Protein based identification was confirmed by automated ribotyping for selected isolates and was similar to that provided by the phenotypic characterization. MALDI-TOF MS protein analysis provided a high level of discrimination among the isolates and could be used for the rapid screening of LAB starter cultures.
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Affiliation(s)
- Amenan A Soro-Yao
- Food Science and Technology Unit, Nangui Abrogoua University, 02 BP 801 Abidjan 02, Côte d’Ivoire
| | - Peter Schumann
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
| | - Philippe Thonart
- Wallon Center for Industrial Microbiology (CWBI), University of Liège, Bld du Rectorat 29-B40, B 4000 Liège, Belgium
- Wallon Center of Industrial Biology, Bio-industry Unit, Gembloux Agro-BioTech, 5030 Gembloux, Belgium
| | - Koffi M Djè
- Food Science and Technology Unit, Nangui Abrogoua University, 02 BP 801 Abidjan 02, Côte d’Ivoire
| | - Rüdiger Pukall
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
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30
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Felföldi T, Vengring A, Kéki Z, Márialigeti K, Schumann P, Tóth EM. Eoetvoesia caeni gen. nov., sp. nov., isolated from an activated sludge system treating coke plant effluent. Int J Syst Evol Microbiol 2014; 64:1920-1925. [PMID: 24585374 DOI: 10.1099/ijs.0.058875-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterium, PB3-7B(T), was isolated on phenol-supplemented inorganic growth medium from a laboratory-scale wastewater purification system that treated coke plant effluent. 16S rRNA gene sequence analysis revealed that strain PB3-7B(T) belonged to the family Alcaligenaceae and showed the highest pairwise sequence similarity to Parapusillimonas granuli Ch07(T) (97.5%), Candidimonas bauzanensis BZ59(T) (97.3%) and Pusillimonas noertemannii BN9(T) (97.2%). Strain PB3-7B(T) was rod-shaped, motile and oxidase- and catalase-positive. The predominant fatty acids were C(16 : 0), C(17 : 0) cyclo, C(19 : 0) cyclo ω8c and C(14 : 0) 3-OH, and the major respiratory quinone was Q-8. The G+C content of the genomic DNA of strain PB3-7B(T) was 59.7 mol%. The novel bacterium can be distinguished from closely related type strains based on its urease activity and the capacity for assimilation of glycerol and amygdalin. On the basis of the phenotypic, chemotaxonomic and molecular data, strain PB3-7B(T) is considered to represent a new genus and species, for which the name Eoetvoesia caeni gen. nov., sp. nov. is proposed. The type strain of Eoetvoesia caeni is PB3-7B(T) ( = DSM 25520(T) = NCAIM B 02512(T)).
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Affiliation(s)
- Tamás Felföldi
- Department of Microbiology, Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| | - Anita Vengring
- Department of Microbiology, Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| | - Zsuzsa Kéki
- Department of Microbiology, Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| | - Károly Márialigeti
- Department of Microbiology, Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| | - Peter Schumann
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Erika M Tóth
- Department of Microbiology, Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
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31
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Schumann P, Maier T. MALDI-TOF Mass Spectrometry Applied to Classification and Identification of Bacteria. METHODS IN MICROBIOLOGY 2014. [DOI: 10.1016/bs.mim.2014.06.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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