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Spreckels JE, Fernández-Pato A, Kruk M, Kurilshikov A, Garmaeva S, Sinha T, Ghosh H, Harmsen H, Fu J, Gacesa R, Zhernakova A. Analysis of microbial composition and sharing in low-biomass human milk samples: a comparison of DNA isolation and sequencing techniques. ISME Commun 2023; 3:116. [PMID: 37945978 PMCID: PMC10636111 DOI: 10.1038/s43705-023-00325-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 10/18/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023]
Abstract
Human milk microbiome studies are currently hindered by low milk bacterial/human cell ratios and often rely on 16S rRNA gene sequencing, which limits downstream analyses. Here, we aimed to find a method to study milk bacteria and assess bacterial sharing between maternal and infant microbiota. We tested four DNA isolation methods, two bacterial enrichment methods and three sequencing methods on mock communities, milk samples and negative controls. Of the four DNA isolation kits, the DNeasy PowerSoil Pro (PS) and MagMAX Total Nucleic Acid Isolation (MX) kits provided consistent 16S rRNA gene sequencing results with low contamination. Neither enrichment method substantially decreased the human metagenomic sequencing read-depth. Long-read 16S-ITS-23S rRNA gene sequencing biased the mock community composition but provided consistent results for milk samples, with little contamination. In contrast to 16S rRNA gene sequencing, 16S-ITS-23S rRNA gene sequencing of milk, infant oral, infant faecal and maternal faecal DNA from 14 mother-infant pairs provided sufficient resolution to detect significantly more frequent sharing of bacteria between related pairs compared to unrelated pairs. In conclusion, PS or MX kit-DNA isolation followed by 16S rRNA gene sequencing reliably characterises human milk microbiota, and 16S-ITS-23S rRNA gene sequencing enables studies of bacterial transmission in low-biomass samples.
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Grants
- This study was supported by funds from the Dutch Research Council (NWO-VIDI grant 016.178.056 to A.Z., NWO-VICI grant VI.C.202.022 to J.F., NWO gravitation grant Exposome-NL 024.004.017 to A.K. and A.Z., NWO gravitation grant Netherlands Organ-on-Chip Initiative 024.003.001 to J.F.), the Dutch Heart Foundation (IN-CONTROL CVON2018-27 to J.F.), the European Research Council (ERC starting grant 715772 to A.Z., ERC consolidator grant 101001678 to J.F.), an EASI-Genomics grant (PID7780 to T.S. and A.Z.), the De-Cock Hadders foundation (2021-57 to J.E.S., 2021-08 to S.G.), the International Society for Research in Human Milk and Lactation (ISRHML, personal grant to J.E.S), the Winston Bakker Fonds (WB-08, granted to T.S.), and the European Union’s Horizon 2020 research innovation program (824110). S.G. and T.S. hold scholarships from the Graduate School of Medical Sciences and the Junior Scientific Masterclass of the University of Groningen, the Netherlands, respectively. The Lifelines NEXT cohort study received funds from the University Medical Center Groningen Hereditary Metabolic Diseases Fund, Health~Holland (Top Sector Life Sciences and Health), the Ubbo Emmius Foundation, the European Union, the Northern Netherlands Alliance (SNN), the provinces of Friesland and Groningen, the municipality of Groningen, Philips, and the Société des Produits Nestlé.
- De-Cock Hadders foundation (2021-57) International Society of Research in Human Milk and Lactation (ISRHML personal grant)
- Dutch Research Council (NWO gravitation grant Exposome-NL 024.004.017)
- De-Cock Hadders foundation (2021-08) University of Groningen Graduate School of Medical Sciences (scholarship)
- EASI-Genomics (grant PID7780) Winston Bakker Fonds (WB-08) University of Groningen Junior Scientific Masterclass (scholarship)
- Dutch Research Council (NWO-VICI grant VI.C.202.022) Dutch Research Council (NWO gravitation grant Netherlands Organ-on-Chip Initiative 024.003.001) European Research Council (ERC consolidator grant 101001678)
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Affiliation(s)
- Johanne E Spreckels
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Asier Fernández-Pato
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Marloes Kruk
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Sanzhima Garmaeva
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Trishla Sinha
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Hiren Ghosh
- Medical Center - University of Freiburg, Institute for Infection Prevention and Hospital Epidemiology, Freiburg, Germany
| | - Hermie Harmsen
- Department of Medical Microbiology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
- Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Ranko Gacesa
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands.
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Paul B, Alam J, Hossain MMK, Hoque SF, Bappy MNI, Akter H, Ahmed N, Akter M, Ali Zinnah M, Das S, Mia MM, Parvej MS, Sarkar S, Ghosh H, Hasan M, Ashour HM, Rahman MM. Immunoinformatics for Novel Multi-Epitope Vaccine Development in Canine Parvovirus Infections. Biomedicines 2023; 11:2180. [PMID: 37626677 PMCID: PMC10452229 DOI: 10.3390/biomedicines11082180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/20/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023] Open
Abstract
Canine parvovirus (CPV-2) is one of the most important pathogens of dogs of all ages, causing pandemic infections that are characterized by fatal hemorrhagic enteritis. The CPV-2 vaccine is recommended as a core vaccine for pet animals. Despite the intensive practice of active immunization, CPV-2 remains a global threat. In this study, a multi-epitope vaccine against CPV-2 was designed, targeting the highly conserved capsid protein (VP2) via in silico approaches. Several immunoinformatics methods, such as epitope screening, molecular docking, and simulation were used to design a potential vaccine construct. The partial protein sequences of the VP2 gene of CPV-2 and protein sequences retrieved from the NCBI were screened to predict highly antigenic proteins through antigenicity, trans-membrane-topology screening, an allergenicity assessment, and a toxicity analysis. Homologous VP2 protein sequences typically linked to the disease were identified using NCBI BLAST, in which four conserved regions were preferred. Overall, 10 epitopes, DPIGGKTGI, KEFDTDLKP, GTDPDDVQ, GGTNFGYIG, GTFYFDCKP, NRALGLPP, SGTPTN, LGLPPFLNSL, IGGKTG, and VPPVYPN, were selected from the conserved regions to design the vaccine construct. The molecular docking demonstrated the higher binding affinity of these epitopes with dog leukocyte antigen (DLA) molecules. The selected epitopes were linked with Salmonella enterica flagellin FliC adjuvants, along with the PADRE sequence, by GGS linkers to construct a vaccine candidate with 272 nucleotides. The codon adaptation and in silico cloning showed that the generated vaccine can be expressed by the E. coli strain, K12, and the sequence of the vaccine construct showed no similarities with dog protein. Our results suggest that the vaccine construct might be useful in preventing canine parvoviral enteritis (CPE) in dogs. Further in vitro and in vivo experiments are needed for the validation of the vaccine candidate.
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Affiliation(s)
- Bashudeb Paul
- Department of Anatomy and Histology, Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Jahangir Alam
- Animal Biotechnology Division, National Institute of Biotechnology, Dhaka 1349, Bangladesh
| | | | - Syeda Farjana Hoque
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Md. Nazmul Islam Bappy
- Department of Animal and Fish Biotechnology, Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Hafsa Akter
- Department of Biochemistry and Chemistry, Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Nadim Ahmed
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Margia Akter
- Department of Pathology, Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Mohammad Ali Zinnah
- Department of Microbiology and Public Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Shobhan Das
- Jiann-Ping Hsu College of Public Health, Georgia Southern University, Statesboro, GA 30458, USA
| | - Md. Mukthar Mia
- Department of Poultry Science, Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | | | - Sonjoy Sarkar
- Department of Anatomy and Histology, Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Hiren Ghosh
- Institute for Infection Prevention and Hospital Epidemiology, Medical Center, University of Freiburg, 79106 Freiburg, Germany
| | - Mahmudul Hasan
- Department of Pharmaceuticals and Industrial Biotechnology, Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Hossam M. Ashour
- Department of Integrative Biology, College of Arts and Sciences, University of South Florida, St. Petersburg, FL 33701, USA
| | - Md. Masudur Rahman
- Department of Pathology, Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh
- ABEx Bio-Research Center, Dhaka 1230, Bangladesh
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3
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Adler A, Ghosh H, Gross A, Rechavi A, Lasnoy M, Assous MV, Geffen Y, Darawsha B, Wiener-Well Y, Alony A, Grundmann H, Reuter S. Clinical and molecular features of NDM-producing Acinetobacter baumannii in a multicenter study in Israel. Ann Clin Microbiol Antimicrob 2023; 22:52. [PMID: 37391819 DOI: 10.1186/s12941-023-00607-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 06/26/2023] [Indexed: 07/02/2023] Open
Abstract
BACKGROUND NDM-producing Acinetobacter baumannii (NDMAb) were reported sporadically worldwide but little is known about the transmission, epidemiology and clinical features of NDMAb-infected patients. The goals of this study were to characterize (1) the epidemiology and clinical features of NDMAb-infected patients; (2) the microbiological and molecular features of NDMAb isolates and (3) the transmission networks of NDMAb within healthcare facilities. METHODS The study was conducted at the Tel-Aviv Sourasky, Rambam and Sha'are-Zedek Medical centers (TASMC, RMC and SZMC, respectively) in Israel. All cases detected between January 2018 and July 2019 were included. Phylogenetic analysis was based on core genome SNP distances. Clonal transmission was defined according to molecular (≤ 5 SNP) and epidemiological criteria (overlapping hospital stay). NDMAb cases were compared at a ratio of 1:2 with non-NDM carbapenem-resistant A. baumannii (CRAb) cases. RESULTS The study included 54 NDMAb-positive out of 857 CRAb patients, including 6/179 (3.3%) in TASMC, 18/441 (4.0%) in SZMC and 30/237 (12.6%) in RMC. Patients infected by NDMAb had similar clinical features and risk factors as patients with non-NDM CRAb. The length-of-stay was higher in NDMAb cases (48.5 days vs. 36 days, respectively, p = 0.097) and the in-hospital mortality was similarly high in both groups. Most isolates (41/54, 76%) were first detected from surveillance culture. The majority of isolates harbored the blaNDM-2 gene allele (n = 33), followed by the blaNDM-1 (n = 20) allele and the blaNDM-4 allele (n = 1). The majority of isolates were related within the ST level to other isolates in SZMC and RMC: 17/18 and 27/30 isolates, respectfully. The common ST's were the blaNDM-1 harboring ST-2 (n = 3) and ST-107 (n = 8) in SZMC and the blaNDM-2 harboring ST-103 in SZMC (n = 6) and in RMC (n = 27). All blaNDM alleles were located within a conserved mobile genetic environment flanked by the ISAb125 and IS91 family transposon. Clonal transmission was identified in most hospital-acquired cases in RMC and SZMC. CONCLUSION NDMAb constitutes a minor part of CRAb cases and are clinically similar to non-NDM CRAb. Transmission of NDMAb occurs mostly by clonal spread.
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Affiliation(s)
- Amos Adler
- Clinical Microbiology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.
- Department of Epidemiology and Preventive Medicine, School of Public Health, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Hiren Ghosh
- Institute for Infection Prevention and Hospital Epidemiology, Medical Center - University of Freiburg, Freiburg, Germany
| | - Andrea Gross
- Institute for Infection Prevention and Hospital Epidemiology, Medical Center - University of Freiburg, Freiburg, Germany
| | | | - Michal Lasnoy
- Clinical Microbiology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Marc V Assous
- Laboratory of Clinical Microbiology, Faculty of Medicine, Shaare Zedek Medical Center, Hebrew University of Jerusalem, Jerusalem, Israel
| | | | | | - Yonit Wiener-Well
- Infectious disease unit, Sha'are Zedek Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Anat Alony
- Department of Epidemiology and Preventive Medicine, School of Public Health, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Hajo Grundmann
- Institute for Infection Prevention and Hospital Epidemiology, Medical Center - University of Freiburg, Freiburg, Germany
| | - Sandra Reuter
- Institute for Infection Prevention and Hospital Epidemiology, Medical Center - University of Freiburg, Freiburg, Germany
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4
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Adler A, Ghosh H, Gross A, Rechavi A, Lasnoy M, Assous MV, Geffen Y, Darawshe B, Wiener-Well Y, Grundmann H, Reuter S. Molecular features and transmission of NDM-producing Enterobacterales in Israeli hospitals. J Antimicrob Chemother 2023; 78:719-723. [PMID: 36640136 DOI: 10.1093/jac/dkad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 01/03/2023] [Indexed: 01/15/2023] Open
Abstract
OBJECTIVES NDM-producing Enterobacterales (NDME) account for 34.9% of new carbapenemase-producing Enterobacterales cases in Israeli hospitals. The goals of this study were to characterize the genomic composition of NDME isolates and mobile genetic elements (MGEs) and to identify NDME transmission events (TEs). METHODS The study was conducted at the Tel-Aviv Sourasky, Rambam and Sha'are-Zedek Medical Centers (TASMC, RMC and SZMC, respectively). All NDME isolates detected between January 2018 and July 2019 were included.Phylogenetic analysis was based on core-genome SNP distances. Core-genome distance of ≤5 SNPs between isolates from patients with overlapping hospitalization periods was suggestive of a potential TE. MGEs were classified by comparison of the blaNDM gene flanking regions. RESULTS The study included 212 NDME isolates from 203 patients, including 104 isolates from TASMC, 30 isolates from RMC and 78 isolates from SZMC. The majority of isolates (n = 157; 74%) harboured the blaNDM-1 gene, followed by the blaNDM-5 (n = 48) and blaNDM-15 genes (n = 7). The most common NDME species were Klebsiella pneumoniae (n = 67), Escherichia coli (n = 65) and Enterobacter cloacae (n = 45), all showing a highly diverse clonal structure. Most blaNDM-1-harbouring isolates (134/157; 85%) were divided into nine different MGE modules, variably distributed across species and hospitals.The numbers of post-admission acquisition cases (n = 118) that could be linked to other cases by both molecular and epidemiological criteria were 13/58 (24.2%), 3/48 (6.3%) and 4/12 (33.3%) in TASMC, SZMC and RMC, respectively. CONCLUSIONS The study depicted a complex and diverse population structure, suggesting that NDME had not spread via clonal expansion.
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Affiliation(s)
- Amos Adler
- Clinical Microbiology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Department of Epidemiology and Preventative Medicine, School of Public Health, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Hiren Ghosh
- Institute for Infection Prevention and Hospital Epidemiology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Andrea Gross
- Institute for Infection Prevention and Hospital Epidemiology, Medical Center-University of Freiburg, Freiburg, Germany
| | | | - Michal Lasnoy
- Clinical Microbiology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Marc V Assous
- Microbiology Laboratory, Shaare Zedek Medical Center, and the Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | | | | | - Yonit Wiener-Well
- Infectious Disease Unit, Sha'are Zedek Medical Center, Jerusalem, Israel.,Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hajo Grundmann
- Institute for Infection Prevention and Hospital Epidemiology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Sandra Reuter
- Institute for Infection Prevention and Hospital Epidemiology, Medical Center-University of Freiburg, Freiburg, Germany
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5
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Brand EC, Klaassen MAY, Gacesa R, Vich Vila A, Ghosh H, de Zoete MR, Boomsma DI, Hoentjen F, Horjus Talabur Horje CS, van de Meeberg PC, Willemsen G, Fu J, Wijmenga C, van Wijk F, Zhernakova A, Oldenburg B, Weersma RK. Healthy Cotwins Share Gut Microbiome Signatures With Their Inflammatory Bowel Disease Twins and Unrelated Patients. Gastroenterology 2021; 160:1970-1985. [PMID: 33476671 DOI: 10.1053/j.gastro.2021.01.030] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 01/06/2021] [Accepted: 01/07/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND & AIMS It is currently unclear whether reported changes in the gut microbiome are cause or consequence of inflammatory bowel disease (IBD). Therefore, we studied the gut microbiome of IBD-discordant and -concordant twin pairs, which offers the unique opportunity to assess individuals at increased risk of developing IBD, namely healthy cotwins from IBD-discordant twin pairs. METHODS Fecal samples were obtained from 99 twins (belonging to 51 twin pairs), 495 healthy age-, sex-, and body mass index-matched controls, and 99 unrelated patients with IBD. Whole-genome metagenomic shotgun sequencing was performed. Taxonomic and functional (pathways) composition was compared among healthy cotwins, IBD-twins, unrelated patients with IBD, and healthy controls with multivariable (ie, adjusted for potential confounding) generalized linear models. RESULTS No significant differences were observed in the relative abundance of species and pathways between healthy cotwins and their IBD-twins (false discovery rate <0.10). Compared with healthy controls, 13, 19, and 18 species, and 78, 105, and 153 pathways were found to be differentially abundant in healthy cotwins, IBD-twins, and unrelated patients with IBD, respectively (false discovery rate <0.10). Of these, 8 (42.1%) of 19 and 1 (5.6%) of 18 species, and 37 (35.2%) of 105 and 30 (19.6%) of 153 pathways overlapped between healthy cotwins and IBD-twins, and healthy cotwins and unrelated patients with IBD, respectively. Many of the shared species and pathways have previously been associated with IBD. The shared pathways include potentially inflammation-related pathways, for example, an increase in propionate degradation and L-arginine degradation pathways. CONCLUSIONS The gut microbiome of healthy cotwins from IBD-discordant twin pairs displays IBD-like signatures. These IBD-like microbiome signatures might precede the onset of IBD. However, longitudinal follow-up studies are needed to infer a causal relationship.
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Affiliation(s)
- Eelco C Brand
- Department of Gastroenterology and Hepatology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands; Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Marjolein A Y Klaassen
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ranko Gacesa
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Arnau Vich Vila
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Hiren Ghosh
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Marcel R de Zoete
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Behavioral and Movement Sciences, Vrije Universiteit, Amsterdam, the Netherlands; Amsterdam Public Health Research Institute, Vrije Universiteit Medical Center, Amsterdam, the Netherlands
| | - Frank Hoentjen
- Department of Gastroenterology and Hepatology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Carmen S Horjus Talabur Horje
- Crohn & Colitis Center Rijnstate, Department of Gastroenterology and Hepatology, Rijnstate Hospital, Arnhem, the Netherlands
| | - Paul C van de Meeberg
- Department of Gastroenterology & Hepatology, Slingeland Hospital, Doetinchem, the Netherlands
| | - Gonneke Willemsen
- Department of Biological Psychology, Behavioral and Movement Sciences, Vrije Universiteit, Amsterdam, the Netherlands; Amsterdam Public Health Research Institute, Vrije Universiteit Medical Center, Amsterdam, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Femke van Wijk
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Bas Oldenburg
- Department of Gastroenterology and Hepatology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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6
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Ghosh H, Doijad S, Falgenhauer L, Fritzenwanker M, Imirzalioglu C, Chakraborty T. bla CTX-M-27-Encoding Escherichia coli Sequence Type 131 Lineage C1-M27 Clone in Clinical Isolates, Germany. Emerg Infect Dis 2018; 23:1754-1756. [PMID: 28930021 PMCID: PMC5621564 DOI: 10.3201/eid2310.170938] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We examined extended-spectrum β-lactamase-producing isolates from livestock, humans, companion animals, food, and the environment during 2009-2016 in Germany for the presence of CTX-M-27 allele within Escherichia coli sequence type (ST) 131. E. coli ST131 C1-M27 was exclusively present in humans; its incidence increased from 0% in 2009 to 45% in 2016.
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7
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Irrgang A, Falgenhauer L, Fischer J, Ghosh H, Guiral E, Guerra B, Schmoger S, Imirzalioglu C, Chakraborty T, Hammerl JA, Käsbohrer A. CTX-M-15-Producing E. coli Isolates from Food Products in Germany Are Mainly Associated with an IncF-Type Plasmid and Belong to Two Predominant Clonal E. coli Lineages. Front Microbiol 2017; 8:2318. [PMID: 29209306 PMCID: PMC5702323 DOI: 10.3389/fmicb.2017.02318] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 11/09/2017] [Indexed: 01/06/2023] Open
Abstract
Extended-spectrum beta-lactamases (ESBL) mediating resistance to 3rd generation cephalosporins are a major public health issue. As food may be a vehicle in the spread of ESLB-producing bacteria, a study on the occurrence of cephalosporin-resistantu Escherichia coli in food was initiated. A total of 404 ESBL-producing isolates were obtained from animal-derived food samples (e.g., poultry products, pork, beef and raw milk) between 2011 and 2013. As CTX-M-15 is the most abundant enzyme in ESBL-producing E. coli causing human infections, this study focusses on E. coli isolates from food samples harboring the blaCTX-M-15 gene. The blaCTX-M-15 gene was detected in 5.2% (n = 21) of all isolates. Molecular analyses revealed a phylogenetic group A ST167 clone that was repeatedly isolated from raw milk and beef samples over a period of 6 months. The analyses indicate that spread of CTX-M-15-producing E. coli in German food samples were associated with a multireplicon IncF (FIA FIB FII) plasmid and additional antimicrobial resistance genes such as aac(6)-Ib-cr, blaOXA-1, catB3, different tet-variants as well as a class 1 integron with an aadA5/dfrA17 gene cassette. In addition, four phylogenetic group A ST410 isolates were detected. Three of them carried a chromosomal copy of the blaCTX-M-15 gene and a single isolate with the gene on a 90 kb IncF plasmid. The blaCTX-M-15 gene was always associated with the ISEcp1 element. In conclusion, CTX-M-15-producing E. coli were detected in German food samples. Among isolates of different matrices, two prominent clonal lineages, namely A-ST167 and A-ST410, were identified. These lineages may be important for the foodborne dissemination of CTX-M-15-producing E. coli in Germany. Interestingly, these clonal lineages were reported to be widely distributed and especially prevalent in isolates from humans and livestock. Transmission of CTX-M-15-harboring isolates from food-producing animals to food appears probable, as isolates obtained from livestock and food samples within the same time period exhibit comparable characteristics as compared to isolates detected from human. However, the routes and direction of transmission need further investigation.
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Affiliation(s)
- Alexandra Irrgang
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Linda Falgenhauer
- Institute of Medical Microbiology, German Center for Infection Research, Partner Site Giessen-Marburg-Langen, Justus Liebig University, Giessen, Germany
| | - Jennie Fischer
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Hiren Ghosh
- Institute of Medical Microbiology, German Center for Infection Research, Partner Site Giessen-Marburg-Langen, Justus Liebig University, Giessen, Germany
| | - Elisabet Guiral
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany.,Barcelona Institute for Global Health (ISGlobal), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Beatriz Guerra
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany.,European Food Safety Authority, Parma, Italy
| | - Silvia Schmoger
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Can Imirzalioglu
- Institute of Medical Microbiology, German Center for Infection Research, Partner Site Giessen-Marburg-Langen, Justus Liebig University, Giessen, Germany
| | - Trinad Chakraborty
- Institute of Medical Microbiology, German Center for Infection Research, Partner Site Giessen-Marburg-Langen, Justus Liebig University, Giessen, Germany
| | - Jens A Hammerl
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Annemarie Käsbohrer
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany.,Institute of Veterinary Public Health, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
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Moremi N, Manda EV, Falgenhauer L, Ghosh H, Imirzalioglu C, Matee M, Chakraborty T, Mshana SE. Predominance of CTX-M-15 among ESBL Producers from Environment and Fish Gut from the Shores of Lake Victoria in Mwanza, Tanzania. Front Microbiol 2016; 7:1862. [PMID: 27990135 PMCID: PMC5130978 DOI: 10.3389/fmicb.2016.01862] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 11/04/2016] [Indexed: 11/13/2022] Open
Abstract
Extended-Spectrum Beta-Lactamase (ESBL)-producing bacteria are a common cause of healthcare and community-associated infections worldwide. The distribution of such isolates in the environment and their presence in fish as a result of sewage contamination is not well-studied. Here we examined fish and environmental samples from Mwanza city for the presence of ESBL-producing bacteria. From 196 fish sampled from local markets, 26 (13.3%) contained lactose-fermenting ESBL-producing bacteria, while 39/73 (53.4%) environmental samples from the same area were ESBL producers. Antibiotic resistance genes, multi locus sequence types (MLST) and plasmid replicon types in 24 selected isolates from both populations were identified with whole genome sequencing using Illumina MiSeq. Nine of eleven sequenced fish isolates had the blaCTX-M-15 gene whereas 12/13 from environment carried blaCTX-M-15. Antibiotic resistance genes encoding resistance to sulfonamides (sul1/sul2), tetracyclines [tet(A)/tet(B)] fluoroquinolones [e.g., aac(6′)-Ib-cr, qnrS1], aminoglycosides [e.g., aac(3)-lld, strB, strA,] and trimethoprim (e.g., dfrA14) were detected. E. coli sequence type ST-38 (2) and ST-5173 (2) were detected in isolates both from the environment and fish. IncY plasmids carrying blaCTX-M-15, qnrS1, strA, and strB were detected in five environmental E. coli isolates and in one E. coli isolate from fish. Our data indicate spillage of resistant environmental isolates into Lake Victoria through the sewage system. Persistence of blaCTX-M-15 in the Mwanza city environment is complex, and involves both clonal spread of resistant strains as well as dissemination by commonly occurring IncY plasmids circulating in isolates present in humans, the environment as well as in the food chain.
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Affiliation(s)
- Nyambura Moremi
- Department of Microbiology and Immunology, Weill Bugando School of Medicine Mwanza, Tanzania
| | - Elizabeth V Manda
- Department of Microbiology and Immunology, Weill Bugando School of Medicine Mwanza, Tanzania
| | - Linda Falgenhauer
- Institute of Medical Microbiology, Justus Liebig UniversityGiessen, Germany; German Center for Infection Research, Partner site Giessen-Marburg-Langen, Campus GiessenGiessen, Germany
| | - Hiren Ghosh
- Institute of Medical Microbiology, Justus Liebig UniversityGiessen, Germany; German Center for Infection Research, Partner site Giessen-Marburg-Langen, Campus GiessenGiessen, Germany
| | - Can Imirzalioglu
- Institute of Medical Microbiology, Justus Liebig UniversityGiessen, Germany; German Center for Infection Research, Partner site Giessen-Marburg-Langen, Campus GiessenGiessen, Germany
| | - Mecky Matee
- Department of Microbiology/Immunology, Muhimbili University of Health and Allied Sciences Dar es Salaam, Tanzania
| | - Trinad Chakraborty
- Institute of Medical Microbiology, Justus Liebig UniversityGiessen, Germany; German Center for Infection Research, Partner site Giessen-Marburg-Langen, Campus GiessenGiessen, Germany
| | - Stephen E Mshana
- Department of Microbiology and Immunology, Weill Bugando School of Medicine Mwanza, Tanzania
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Doijad S, Ghosh H, Glaeser S, Kämpfer P, Chakraborty T. Taxonomic reassessment of the genus Elizabethkingia using whole-genome sequencing: Elizabethkingia endophytica Kämpfer et al. 2015 is a later subjective synonym of Elizabethkingia anophelis Kämpfer et al. 2011. Int J Syst Evol Microbiol 2016; 66:4555-4559. [DOI: 10.1099/ijsem.0.001390] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Swapnil Doijad
- Institute for Medical Microbiology, Justus-Liebig University of Giessen, Hesse, 35392 Germany and German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Campus Giessen, Justus-Liebig University, Germany
| | - Hiren Ghosh
- Institute for Medical Microbiology, Justus-Liebig University of Giessen, Hesse, 35392 Germany and German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Campus Giessen, Justus-Liebig University, Germany
| | - Stefanie Glaeser
- Institut für Angewandte Mikrobiologie, Universität Giessen, Giessen, Germany
| | - Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Universität Giessen, Giessen, Germany
| | - Trinad Chakraborty
- Institute for Medical Microbiology, Justus-Liebig University of Giessen, Hesse, 35392 Germany and German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Campus Giessen, Justus-Liebig University, Germany
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Falgenhauer L, Waezsada SE, Gwozdzinski K, Ghosh H, Doijad S, Bunk B, Spröer C, Imirzalioglu C, Seifert H, Irrgang A, Fischer J, Guerra B, Käsbohrer A, Overmann J, Goesmann A, Chakraborty T. Chromosomal Locations of mcr-1 and bla CTX-M-15 in Fluoroquinolone-Resistant Escherichia coli ST410. Emerg Infect Dis 2016; 22:1689-91. [PMID: 27322919 PMCID: PMC4994348 DOI: 10.3201/eid2209.160692] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
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Falgenhauer L, Imirzalioglu C, Ghosh H, Gwozdzinski K, Schmiedel J, Gentil K, Bauerfeind R, Kämpfer P, Seifert H, Michael GB, Schwarz S, Pfeifer Y, Werner G, Pietsch M, Roesler U, Guerra B, Fischer J, Sharp H, Käsbohrer A, Goesmann A, Hille K, Kreienbrock L, Chakraborty T. Circulation of clonal populations of fluoroquinolone-resistant CTX-M-15-producing Escherichia coli ST410 in humans and animals in Germany. Int J Antimicrob Agents 2016; 47:457-65. [PMID: 27208899 DOI: 10.1016/j.ijantimicag.2016.03.019] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 03/23/2016] [Accepted: 03/28/2016] [Indexed: 12/14/2022]
Abstract
Multidrug-resistant Escherichia coli encoding CTX-M-type extended-spectrum β-lactamases (ESBLs) are isolated in increasing numbers from humans, companion animals and livestock, raising concern regarding the exchange and spread of isolates in these populations. In this study, whole-genome sequencing of CTX-M-15-producing E. coli isolates recently sampled from humans, companion animals, livestock and farm environments was performed. In total, 26 different sequence types (STs) were detected, of which ST410 was the most frequent and was the only ST present in all populations studied. Five clades (designated A-E) were detected within the ST410 isolates. In particular, isolates of clade B were present in all four populations and had core genomes that differed by less than 70 single nucleotide polymorphisms (SNPs). Isolates of clades B and C were also clonally marked, exhibiting identical chromosomal insertions of blaCTX-M-15 at distinct loci. These data provide strong evidence for the clonal dissemination of specific clades of CTX-M-15-producing E. coli ST410 in human and animal populations.
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Affiliation(s)
- Linda Falgenhauer
- Institute of Medical Microbiology, Justus Liebig University Giessen and German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Giessen, Germany; German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Can Imirzalioglu
- Institute of Medical Microbiology, Justus Liebig University Giessen and German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Giessen, Germany; German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Hiren Ghosh
- Institute of Medical Microbiology, Justus Liebig University Giessen and German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Giessen, Germany; German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Konrad Gwozdzinski
- Institute of Medical Microbiology, Justus Liebig University Giessen and German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Giessen, Germany; German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Judith Schmiedel
- Institute of Medical Microbiology, Justus Liebig University Giessen and German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Giessen, Germany; German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Katrin Gentil
- Institute of Medical Microbiology, Justus Liebig University Giessen and German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Giessen, Germany; German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Rolf Bauerfeind
- Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Giessen, Germany
| | - Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus Liebig University Giessen, Giessen, Germany
| | - Harald Seifert
- German Center for Infection Research (DZIF), Braunschweig, Germany; Institute for Medical Microbiology, Immunology, and Hygiene, University of Cologne, Cologne, Germany
| | - Geovana Brenner Michael
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt-Mariensee, Germany
| | - Stefan Schwarz
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt-Mariensee, Germany
| | - Yvonne Pfeifer
- Division of Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode Branch, Wernigerode, Germany
| | - Guido Werner
- Division of Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode Branch, Wernigerode, Germany
| | - Michael Pietsch
- Division of Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode Branch, Wernigerode, Germany
| | - Uwe Roesler
- Institute for Animal Hygiene and Environmental Health, Free University Berlin, Berlin, Germany
| | - Beatriz Guerra
- Department of Biological Safety, Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Jennie Fischer
- Department of Biological Safety, Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Hannah Sharp
- Department of Biological Safety, Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Annemarie Käsbohrer
- Department of Biological Safety, Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Alexander Goesmann
- Institute of Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Katja Hille
- Institute for Biometry, Epidemiology, and Information Processing, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Lothar Kreienbrock
- Institute for Biometry, Epidemiology, and Information Processing, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Trinad Chakraborty
- Institute of Medical Microbiology, Justus Liebig University Giessen and German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Giessen, Germany; German Center for Infection Research (DZIF), Braunschweig, Germany.
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Ghosh H, Doijad S, Bunk B, Falgenhauer L, Yao Y, Spröer C, Gentil K, Schmiedel J, Imirzalioglu C, Overmann J, Chakraborty T. Detection of translocatable units in a blaCTX-M-15 extended-spectrum β-lactamase-producing ST131 Escherichia coli isolate using a hybrid sequencing approach. Int J Antimicrob Agents 2016; 47:245-7. [DOI: 10.1016/j.ijantimicag.2016.01.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 01/05/2016] [Accepted: 01/07/2016] [Indexed: 11/29/2022]
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Falgenhauer L, Ghosh H, Guerra B, Yao Y, Fritzenwanker M, Fischer J, Helmuth R, Imirzalioglu C, Chakraborty T. Comparative genome analysis of IncHI2 VIM-1 carbapenemase-encoding plasmids of Escherichia coli and Salmonella enterica isolated from a livestock farm in Germany. Vet Microbiol 2015; 200:114-117. [PMID: 26411323 DOI: 10.1016/j.vetmic.2015.09.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 09/02/2015] [Accepted: 09/03/2015] [Indexed: 11/16/2022]
Abstract
Carbapenem-resistant Enterobacteriaceae are not any more isolated only from human settings, but also from livestock. We reported for the first time the presence of VIM-1 carbapenemases in a livestock farm in Germany. The VIM-1 resistance gene found in these farms was located on IncHI2 plasmids. In order to be able to analyse these plasmids in more detail, two different plasmids from a single farm (pRH-R27 from Salmonella enterica and pRH-R178 from Escherichia coli) were completely sequenced and analysed for the presence of antibiotic and heavy metal resistances. The plasmids showed to harbour blaVIM-1, aacA4, aadA1, sul1, qacEΔ (encoded in an In110 class 1 integron), as well as blaACC-1, strA/strB, and catA1 genes together with resistance to heavy metals (ter-, mer-, sil-, ars-, rcn-, and pco). Comparison with other IncHI2 plasmid revealed that while pRH-R27 is a mosaic IncHI2 plasmid with both high homology to the plasmid pSTm-A54650 and R478, both isolated from humans, pRH-R178 is a deletion derivative of pRH-R27, presumably caused by several IS-mediated deletions indicating genetic evolution of plasmids in this environment.
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Affiliation(s)
- Linda Falgenhauer
- Institute of Medical Microbiology, Justus-Liebig-University, Giessen, Germany; German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Campus Giessen, Giessen, Germany
| | - Hiren Ghosh
- Institute of Medical Microbiology, Justus-Liebig-University, Giessen, Germany; German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Campus Giessen, Giessen, Germany
| | - Beatriz Guerra
- Federal Institute for Risk Assessment, National Reference Laboratory for Antimicrobial Resistance, Department Biological Safety, Berlin, Germany
| | - Yancheng Yao
- Institute of Medical Microbiology, Justus-Liebig-University, Giessen, Germany; German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Campus Giessen, Giessen, Germany
| | - Moritz Fritzenwanker
- Institute of Medical Microbiology, Justus-Liebig-University, Giessen, Germany; German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Campus Giessen, Giessen, Germany
| | - Jennie Fischer
- Federal Institute for Risk Assessment, National Reference Laboratory for Antimicrobial Resistance, Department Biological Safety, Berlin, Germany
| | - Reiner Helmuth
- Federal Institute for Risk Assessment, National Reference Laboratory for Antimicrobial Resistance, Department Biological Safety, Berlin, Germany
| | - Can Imirzalioglu
- Institute of Medical Microbiology, Justus-Liebig-University, Giessen, Germany; German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Campus Giessen, Giessen, Germany
| | - Trinad Chakraborty
- Institute of Medical Microbiology, Justus-Liebig-University, Giessen, Germany; German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Campus Giessen, Giessen, Germany.
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Falgenhauer L, Schmiedel J, Ghosh H, Fritzenwanker M, Yao Y, Bauerfeind R, Imirzalioglu C, Chakraborty T. Resistance plasmids in ESBL-encoding Escherichia coli isolates from humans, dogs and cats. Berl Munch Tierarztl Wochenschr 2014; 127:458-463. [PMID: 25872255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We characterized ESBL-producing Escherichia coli isolates from diseased dog, cat and human sources for their plasmid content. Plasmids with different Inc groups and combinations of resistance genes were detected in these isolates. The pan-genome of the plasmid-associated genes was found to be large, indicating diversity of the gene pool among the plasmids. No commonly occurring plasmids with similar gene content in isolates from dog, cats and humans were detected.
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Ghosh H, RoyChaudhuri C. Noise spectroscopy as an efficient tool for impedance based sub-femtomolar toxin detection in complex mixture using nanoporous silicon oxide. Biosens Bioelectron 2014; 67:757-62. [PMID: 25442424 DOI: 10.1016/j.bios.2014.09.035] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 08/29/2014] [Accepted: 09/04/2014] [Indexed: 01/07/2023]
Abstract
In this paper we demonstrate an efficient and non-interfering computational method for sub-femtomolar food toxin detection in complex mixture based on nanoporous silicon oxide impedance immunosensor by employing noise spectroscopy analysis at the peak frequency. It has been observed that the peak frequency (fp) values obtained from steady state impedance measurements cannot distinguish between solution with only the specific toxin, which is aflatoxin B1 (AfB1) and mixture of AfB1 with other non-specific toxins (NSTs), thus leading to erroneous quantification of AfB1 in complex mixture. On the other hand, the first cut-off frequency (fc) ranges obtained from noise spectroscopy analysis can qualitatively differentiate between solution containing only AfB1, AfB1 and NSTs and no AfB1. However fc values being very close for different concentration of AfB1 in pure solution and being overlapping for different mixtures cannot quantify AfB1 either in pure solution or in complex mixture. To address this problem, the proposed computational method first clusters the fp and fc values in 11 categories each using k-means clustering algorithm and then applies a simple combinational digital logic on the clusters of fps and fcs to obtain the final output, realizable with standard NAND-NOR gates. The output digital word differs only with AfB1 concentration and not with concentration of NSTs and is found to be capable of detecting sub-femtomolar AfB1 range down to 0.1 fg/ml not only in pure solution but also in complex mixture with as high as 1000 ng/ml NSTs. This is the most sensitive and selective report so far on electrochemical food toxin immunosensors.
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Affiliation(s)
- H Ghosh
- Department of Electronics and Telecommunication Engineering, Indian Institute of Engineering, Science and Technology, Shibpur, Howrah 711103, West Bengal, India.
| | - C RoyChaudhuri
- Department of Electronics and Telecommunication Engineering, Indian Institute of Engineering, Science and Technology, Shibpur, Howrah 711103, West Bengal, India.
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Maulik A, Ghosh H, Basu S. Comparative study of protein-protein interaction observed in PolyGalacturonase-Inhibiting Proteins from Phaseolus vulgaris and Glycine max and PolyGalacturonase from Fusarium moniliforme. BMC Genomics 2009; 10 Suppl 3:S19. [PMID: 19958482 PMCID: PMC2788371 DOI: 10.1186/1471-2164-10-s3-s19] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The PolyGalacturonase-Inhibiting Proteins (PGIP) of plant cell wall limit the invasion of phytopathogenic organisms by interacting with the enzyme PolyGalacturonase (PG) they secrete to degrade pectin present in the cell walls. PGIPs from different or same plant differ in their inhibitory activity towards the same PG. PGIP2 from Phaseolus vulgaris (Pv) inhibits the PG from Fusarium moniliforme (Fm) although PGIP1, another member of the multigene family from the same plant sharing 99% sequence similarity, cannot. Interestingly, PGIP3 from Glycine max (Gm) which is a homologue of PGIP2 is capable of inhibiting the same PG although the extent of similarity is lower and is 88%. It therefore appears that subtle changes in the sequence of plant PGIPs give rise to different specificity for inhibiting pathogenic PGs and there exists no direct dependence of function on the extent of sequence similarity. RESULTS Structural information for any PGIP-PG complex being absent, we resorted to molecular modelling to gain insight into the mechanism of recognition and discrimination of PGs by PGIPs. We have built homology models of PvPGIP1 and GmPGIP3 using the crystal structure of PvPGIP2 (1OGQ) as template. These PGIPs were then docked individually to FmPG to elucidate the characteristics of their interactions. The mode of binding for PvPGIP1 to FmPG considerably differs from the mode observed for PvPGIP2-FmPG complex, regardless of the high sequence similarity the two PGIPs share. Both PvPGIP2 and GmPGIP3 despite being relatively less similar, interact with residues of FmPG that are known from mutational studies to constitute the active site of the enzyme. PvPGIP1 tends to interact with residues not located at the active site of FmPG. Looking into the electrostatic potential surface for individual PGIPs, it was evident that a portion of the interacting surface for PvPGIP1 differs from the corresponding region of PvPGIP2 or GmPGIP3. CONCLUSION van der Waals and electrostatic interactions play an active role in PGIPs for proper recognition and discrimination of PGs. Docking studies reveal that PvPGIP2 and GmPGIP3 interact with the residues constituting the active site of FmPG with implications that the proteins bind/block FmPG at its active site and thereby inhibit the enzyme.
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Affiliation(s)
- Aditi Maulik
- Department of Bioinformatics, School of Biotechnology, West Bengal University of Technology BF-142, Salt Lake, Kolkata 700064, India
| | - Hiren Ghosh
- Department of Bioinformatics, School of Biotechnology, West Bengal University of Technology BF-142, Salt Lake, Kolkata 700064, India
| | - Soumalee Basu
- Department of Bioinformatics, School of Biotechnology, West Bengal University of Technology BF-142, Salt Lake, Kolkata 700064, India
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Karthikeyan NS, Sathiyanarayanan K, Aravindan PG, Ghosh H, Rathore RS. (3E,5E)-3,5-Bis(4-allyl-oxybenzyl-idene)-1-benzyl-piperidin-4-one. Acta Crystallogr Sect E Struct Rep Online 2009; 65:o3062. [PMID: 21578792 PMCID: PMC2971870 DOI: 10.1107/s1600536809046716] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Accepted: 11/05/2009] [Indexed: 11/17/2022]
Abstract
In the title compound C32H31NO3, the allyloxy groups on either side of the piperidin-4-one ring are conformationally disordered. The contribution of major and minor components of the allyloxy group at the 3rd position of the ring are 0.576 (4) and 0.424 (4), respectively, and those at the 5th position are 0.885 (3) and 0.115 (3), respectively. The six-membered piperidin-4-one ring adopts a sofa conformation with the benzyl group occupying an equatorial position and the olefinic double bonds possessing an E configuration. Flanking phenyl substituents are stretched out on either side of the six-membered ring. π–π interactions with a centroid–centroid distance of 3.885 (1) Å give rise to molecular dimers and short C—H⋯π contacts lead to chains along the c axis.
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Kaushalya SK, Desai R, Arumugam S, Ghosh H, Balaji J, Maiti S. Three-photon microscopy shows that somatic release can be a quantitatively significant component of serotonergic neurotransmission in the mammalian brain. J Neurosci Res 2009; 86:3469-80. [PMID: 18709651 DOI: 10.1002/jnr.21794] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Recent experiments on monoaminergic neurons have shown that neurotransmission can originate from somatic release. However, little is known about the quantity of monoamine available to be released through this extrasynaptic pathway or about the intracellular dynamics that mediate such release. Using three-photon microscopy, we directly imaged serotonin autofluorescence and investigated the total serotonin content, release competence, and release kinetics of somatic serotonergic vesicles in the dorsal raphe neurons of the rat. We found that the somata of primary cultured neurons contain a large number of serotonin-filled vesicles arranged in a perinuclear fashion. A similar distribution is also observed in fresh tissue slice preparations obtained from the rat dorsal raphe. We estimate that the soma of a cultured neuron on an average contains about 9 fmoles of serotonin in about 450 vesicles (or vesicle clusters) of < or =370 nm average diameter. A substantial fraction (>30%) of this serotonin is released with a time scale of several minutes by K(+)-induced depolarization or by para-chloroamphetamine treatment. The amount of releasable serotonin stored in the somatic vesicles is comparable to the total serotonin content of all the synaptic vesicles in a raphe neuron, indicating that somatic release can potentially play a major role in serotonergic neurotransmission in the mammalian brain.
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Affiliation(s)
- S K Kaushalya
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
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Chaudhury J, Mandal UK, Sharma KL, Ghosh H, Mandal B. Assessing Soil Quality Under Long‐Term Rice‐Based Cropping System. Communications in Soil Science and Plant Analysis 2005; 36:1141-1161. [DOI: 10.1081/css-200056885] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
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Ghosh H, Chaudhury S. Distributed and reactive query planning in R-MAGIC: an agent-based multimedia retrieval system. IEEE Trans Knowl Data Eng 2004; 16:1082-1095. [DOI: 10.1109/tkde.2004.40] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
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Harit G, Chaudhury S, Ghosh H. Managing document images in a digital library:an ontology guided approach. First International Workshop on Document Image Analysis for Libraries, 2004. Proceedings. 2004. [DOI: 10.1109/dial.2004.1263238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
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Arora C, Nirankari P, Ghosh H, Chaudhury S. Content based image retrieval using mobile agents. Proceedings Third International Conference on Computational Intelligence and Multimedia Applications. ICCIMA'99 (Cat. No.PR00300) 2003. [DOI: 10.1109/iccima.1999.798537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
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Ghosh H, Rajarathnam N, Chaudhury S. Knowledge representation for Web based services in a multi-cultural environment. Proceedings 3rd International Workshop on Web Site Evolution. WSE 2001 2001. [DOI: 10.1109/wse.2001.988779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
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Ogasawara T, Ashida M, Motoyama N, Eisaki H, Uchida S, Tokura Y, Ghosh H, Shukla A, Mazumdar S, Kuwata-Gonokami M. Ultrafast optical nonlinearity in the quasi-one-dimensional mott insulator Sr2CuO3. Phys Rev Lett 2000; 85:2204-2207. [PMID: 10970498 DOI: 10.1103/physrevlett.85.2204] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2000] [Indexed: 05/23/2023]
Abstract
We report strong instantaneous photoinduced absorption in the quasi-one-dimensional Mott insulator Sr2CuO3 in the IR spectral region. The observed photoinduced absorption is to an even-parity two-photon state that occurs immediately above the absorption edge. Theoretical calculation based on a two-band extended Hubbard model explains the experimental features and indicates that the strong two-photon absorption is due to a very large dipole coupling between nearly degenerate one- and two-photon states. Room temperature picosecond recovery of the optical transparency suggests the strong potential of Sr2CuO3 for all-optical switching.
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Affiliation(s)
- T Ogasawara
- Department of Applied Physics, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
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Abstract
Hospital-acquired septicaemia is common and an important cause of morbidity and expense. Few studies have explored its cause by comparing features of people who do and do not develop septicaemia--the aim of this study. All blood cultures were monitored over one year in a 400-bed tertiary care hospital where special care is taken with intravenous cannulae to prevent septicaemia. Cases had at least one positive blood culture taken at least 48 h after admission. The nearest two patients in the same ward were controls, and information was abstracted on all three from the hospital records by a research nurse. There were 84 cases during the 12 months (3.8 per 1000 admissions) and 167 controls. Univariate odds ratios (95% CI) were 5.57 (2.06-15.95) with the presence of a central venous line, 3.40 (1.16-16.40) with total parenteral nutrition, 2.41 (1.30-4.32) with blood transfusion, 2.10 (1.16-4.56) with immunosuppressive disease, 2.06 (1.02-4.44) with the presence of a urinary catheter and 0.32 (0.17-0.69) with recent surgery. Conditional logistic regression identified a central venous line and blood transfusion to be independent risk factors for septicaemia, odds ratios (and 95% CI) being 5.14 (1.74-15.23) and 2.74 (1.28-5.88), respectively, while recent surgery and antibiotic prophylaxis were independently 'protective' at 0.31 (0.12-0.79) and 0.38 (0.16-0.90), respectively. Thus, in a hospital where great care has been taken to avoid septicaemia, especially by attention to intravenous cannulae, there were only two independent risk factors for the development of hospital-acquired septicaemia--a central venous line and blood transfusion.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- J Duggan
- Department of Gastroenterology, Royal Newcastle Hospital, NSW, Australia
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Hutchinson L, Goldsmith K, Snoddy D, Ghosh H, Graham FL, Johnson DC. Identification and characterization of a novel herpes simplex virus glycoprotein, gK, involved in cell fusion. J Virol 1992; 66:5603-9. [PMID: 1323714 PMCID: PMC289123 DOI: 10.1128/jvi.66.9.5603-5609.1992] [Citation(s) in RCA: 109] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Antipeptide sera were used to identify a novel glycoprotein encoded by the UL53 gene of herpes simplex virus type 1 (HSV-1). The UL53 gene product is thought to play a central role in regulating membrane fusion because mutations giving rise to the syncytial phenotype, wherein cells are extensively fused, frequently map to this gene. A single 40-kDa protein, designated gK (the ninth HSV-1 glycoprotein to be described), was detected with antipeptide sera in cells infected with both wild-type and syncytial strains of HSV-1 which were labelled with [35S]methionine and [35S]cysteine or with [3H]glucosamine, and this protein was sensitive to treatment of cells with tunicamycin. With all other HSV glycoproteins studied to date, at least two glycosylated species, often differing substantially in electrophoretic mobility, have been observed in infected cells; thus, gK is unusual in this respect. The 40-kDa gK protein was also immunoprecipitated from cells infected with a recombinant adenovirus vector carrying the UL53 gene. Two glycosylated species of 39 and 41 kDa were produced when UL53 mRNA was translated in vitro in the presence of microsomes, and these proteins differed from gK produced in infected cells not only because they possessed different electrophoretic mobilities but also because they were unable to enter gels after being heated. In addition, a 36-kDa protein was detected in extracts from cells infected with HSV-2 with use of these sera.
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Affiliation(s)
- L Hutchinson
- Department of Pathology, McMaster University, Hamilton, Ontario, Canada
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Basu AK, Ganguli S, Ghosh H. Spontaneous neonatal gastric perforation causing hemo-pneumo-peritoneum. Indian Pediatr 1988; 25:690-2. [PMID: 3220550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Abstract
The efficiency of a gelatin capsule containing a nylon string for collection of duodenal specimens was investigated in carriers of Salmonella typhosa (typhi). Cultures of duodenal specimens obtained by means of the string capsule were compared with cultures of duodenal specimens obtained by a conventional duodenal tube and with stool cultures Duodenal contents obtained with either the string or tube were more often positive for S. typhosa than were stool cultures. The string, which is as efficient as tube collection but simpler and more comfortable, may be useful in identifying carriers of S. typhosa.
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Mukherjee D, Ghosh H, Mukherjee S. Studies on the effect of administration of tetracycline on free fatty acid metabolism in adrenalectomised and control rats. J Antibiot (Tokyo) 1969; 22:480-3. [PMID: 5350504 DOI: 10.7164/antibiotics.22.480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Khorana HG, Büchi H, Ghosh H, Gupta N, Jacob TM, Kössel H, Morgan R, Narang SA, Ohtsuka E, Wells RD. Polynucleotide synthesis and the genetic code. Cold Spring Harb Symp Quant Biol 1966; 31:39-49. [PMID: 5237635 DOI: 10.1101/sqb.1966.031.01.010] [Citation(s) in RCA: 130] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Ghosh H. A Probable Cause of the Difficulty of Treating Chronic Amœbic Infection in This Country. Ind Med Gaz 1939; 74:27-28. [PMID: 29011709 PMCID: PMC5151196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- H. Ghosh
- Director, Department of Bacteriology, Indian Institute for Medical Research, Calcutta
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Ghosh H. Action of Disinfectants on Microbes: An Interesting Phenomenon. Ind Med Gaz 1925; 60:423-425. [PMID: 29010398 PMCID: PMC5189013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- H. Ghosh
- Bengal Immunity Research Laboratory, Calcutta
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