1
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Schmid PJ, Forstner P, Kittinger C. Sliding motility of Bacillus cereus mediates vancomycin pseudo-resistance during antimicrobial susceptibility testing. J Antimicrob Chemother 2024; 79:1628-1636. [PMID: 38785365 PMCID: PMC11215547 DOI: 10.1093/jac/dkae156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND The glycopeptide vancomycin is the antimicrobial agent-of-choice for the treatment of severe non-gastrointestinal infections with members of Bacillus cereus sensu lato (s.l.). Recently, sporadic detection of vancomycin-resistant phenotypes emerged, mostly for agar diffusion testing such as the disc diffusion method or gradient test (e.g. Etest®) method. RESULTS In this work, we were able to disprove a preliminarily assumed high resistance to vancomycin in an isolate of B. cereus s.l. using broth microdilution and agar dilution. Microscopic imaging during vancomycin susceptibility testing showed spreading towards the inhibition zone, which strongly suggested sliding motility. Furthermore, transcriptomic analysis using RNA-Seq on the nanopore platform revealed several key genes of biofilm formation (e.g. calY, tasA, krsEABC) to be up-regulated in pseudo-resistant cells, substantiating that bacterial sliding is responsible for the observed mobility. Down-regulation of virulence (e.g. hblABCD, nheABC, plcR) and flagellar genes compared with swarming cells also confirmed the non-swarming phenotype of the pseudo-resistant isolate. CONCLUSIONS The results highlight an insufficiency of agar diffusion testing for vancomycin susceptibility in the B. cereus group, and reference methods like broth microdilution are strongly recommended. As currently no guideline mentions interfering phenotypes in antimicrobial susceptibility testing of B. cereus s.l., this knowledge is essential to obtain reliable results on vancomycin susceptibility. In addition, this is the first report of sliding motility undermining accurate antimicrobial susceptibility testing in B. cereus s.l. and may serve as a basis for future studies on bacterial motility in susceptibility testing and its potential impact on treatment efficacy.
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Affiliation(s)
- Paul J Schmid
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, Graz, Austria
| | - Patrick Forstner
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, Graz, Austria
| | - Clemens Kittinger
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, Graz, Austria
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2
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He N, Yang X, Haque A, Chen J, Guo Y, Li J, Yao L, Zhuo C, Wang J, Wang Y, Li M, Lin Y, Xiao S, Zhuo C. Practice of standardization of CLSI M45 A3 antimicrobial susceptibility testing of Infrequently Isolated or Fastidious Bacteria strains isolated from blood specimens in Guangdong Province 2017-2021. Front Microbiol 2024; 15:1335169. [PMID: 38741731 PMCID: PMC11089136 DOI: 10.3389/fmicb.2024.1335169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 04/03/2024] [Indexed: 05/16/2024] Open
Abstract
The concentration of antimicrobial agents in environments like water and food has increased rapidly, which led to a rapid increase in antimicrobial resistance levels in the environment. Monitoring of bacterial resistance levels is considered as a necessary means to control the bacterial resistance. Reference standards are critical for antimicrobial susceptibility testing. CLSI M45 A3 standard defines pathogenic microorganisms that cause infections less frequently than those covered by CLSI M02, M07, and M100 as Infrequently Isolated or Fastidious Bacteria and specifies antimicrobial susceptibility testing methods. Our study investigated the epidemiology and antimicrobial susceptibility testing data of Infrequently Isolated or Fastidious Bacteria strains isolated from blood specimens in 70 hospitals in Guangdong Province between 2017 and 2021. We defined testing methods other than those specified in CLSI M45 A3 as "Non-Standardized." The proportion of standardized antimicrobial susceptibility testing for penicillin increased significantly (Corynebacterium spp. 17.4% vs. 50.0% p < 0.05; Micrococcus spp. 50.0% vs. 77.8% p < 0.05; Abiotrophia spp. and Granulicatella spp. 21.4% vs. 90.9% p < 0.001), while for cefotaxime (Corynebacterium spp. 0.0% vs. 45.2% p < 0.05; Abiotrophia spp. and Granulicatella spp. 0.0% vs. 14.3% p = 0.515) and vancomycin increased finitely. Non-standardized methods were used for all other antimicrobials. Due to limitations in the economic and medical environment, some clinical laboratories are unable to fully comply with CLSI M45 A3 standard. We recommend that CLSI should add breakpoints for disk diffusion method to improve the standardization of antimicrobial susceptibility testing.
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Affiliation(s)
- Nanhao He
- Department of Guangdong Antimicrobial Resistant Bacteria Monitoring and Quality Control Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xu Yang
- Department of Guangdong Antimicrobial Resistant Bacteria Monitoring and Quality Control Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Anwarul Haque
- Department of Infectious Diseases, School of Medicine, International University of Health and Welfare, Narita, Japan
| | - Jiakang Chen
- Department of Guangdong Antimicrobial Resistant Bacteria Monitoring and Quality Control Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yingyi Guo
- Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Jiahui Li
- Department of Guangdong Antimicrobial Resistant Bacteria Monitoring and Quality Control Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Likang Yao
- Department of Guangdong Antimicrobial Resistant Bacteria Monitoring and Quality Control Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Chuyue Zhuo
- Department of Guangdong Antimicrobial Resistant Bacteria Monitoring and Quality Control Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jiong Wang
- Department of Guangdong Antimicrobial Resistant Bacteria Monitoring and Quality Control Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yijing Wang
- Department of Guangdong Antimicrobial Resistant Bacteria Monitoring and Quality Control Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Mingxin Li
- Department of Guangdong Antimicrobial Resistant Bacteria Monitoring and Quality Control Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yexin Lin
- Department of Guangdong Antimicrobial Resistant Bacteria Monitoring and Quality Control Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shunian Xiao
- Department of Guangdong Antimicrobial Resistant Bacteria Monitoring and Quality Control Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Chao Zhuo
- Department of Guangdong Antimicrobial Resistant Bacteria Monitoring and Quality Control Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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3
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Castellana S, De Laurentiis V, Bianco A, Del Sambro L, Grassi M, De Leonardis F, Derobertis AM, De Carlo C, Sparapano E, Mosca A, Stolfa S, Ronga L, Santacroce L, Chironna M, Parisi M, Capozzi L, Parisi A. Pannonibacter anstelovis sp. nov. Isolated from Two Cases of Bloodstream Infections in Paediatric Patients. Microorganisms 2024; 12:799. [PMID: 38674743 PMCID: PMC11051880 DOI: 10.3390/microorganisms12040799] [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: 03/20/2024] [Revised: 04/05/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
This study describes two cases of bacteraemia sustained by a new putative Pannonibacter species isolated at the U.O.C. of Microbiology and Virology of the Policlinico of Bari (Bari, Italy) from the blood cultures of two patients admitted to the Paediatric Oncohaematology Unit. Pannonibacter spp. is an environmental Gram-negative bacterium not commonly associated with nosocomial infections. Species identification was performed using Sanger sequencing of the 16S rRNA gene and Whole-Genome Sequencing (WGS) for both strains. Genomic analyses for the two isolates, BLAST similarity search, and phylogeny for the 16S rDNA sequences lead to an assignment to the species Pannonibacter phragmitetus. However, by performing ANIb, ANIm, tetranucleotide correlation, and DNA-DNA digital hybridization, analyses of the two draft genomes showed that they were very different from those of the species P. phragmitetus. MALDI-TOF analysis, assessment of antimicrobial susceptibility by E-test method, and Analytical Profile Index (API) tests were also performed. This result highlights how environmental bacterial species can easily adapt to the human host and, especially in nosocomial environments, also gain pathogenic potential through antimicrobial resistance.
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Affiliation(s)
- Stefano Castellana
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71121 Foggia, Italy; (S.C.); (A.B.); (L.D.S.); (A.M.D.); (A.P.)
| | - Vittoriana De Laurentiis
- UOC Microbiology and Virology, Azienda Ospedaliera-Universitaria Policlinico of Bari, 70124 Bari, Italy; (V.D.L.); (C.D.C.); (E.S.); (S.S.); (L.R.)
| | - Angelica Bianco
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71121 Foggia, Italy; (S.C.); (A.B.); (L.D.S.); (A.M.D.); (A.P.)
| | - Laura Del Sambro
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71121 Foggia, Italy; (S.C.); (A.B.); (L.D.S.); (A.M.D.); (A.P.)
| | - Massimo Grassi
- Division of Paediatric Haematology and Oncology, Azienda Ospedaliera-Universitaria Policlinico of Bari, 70124 Bari, Italy; (M.G.); (F.D.L.)
| | - Francesco De Leonardis
- Division of Paediatric Haematology and Oncology, Azienda Ospedaliera-Universitaria Policlinico of Bari, 70124 Bari, Italy; (M.G.); (F.D.L.)
| | - Anna Maria Derobertis
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71121 Foggia, Italy; (S.C.); (A.B.); (L.D.S.); (A.M.D.); (A.P.)
| | - Carmen De Carlo
- UOC Microbiology and Virology, Azienda Ospedaliera-Universitaria Policlinico of Bari, 70124 Bari, Italy; (V.D.L.); (C.D.C.); (E.S.); (S.S.); (L.R.)
| | - Eleonora Sparapano
- UOC Microbiology and Virology, Azienda Ospedaliera-Universitaria Policlinico of Bari, 70124 Bari, Italy; (V.D.L.); (C.D.C.); (E.S.); (S.S.); (L.R.)
| | - Adriana Mosca
- Department of Interdisciplinary Medicine, School of Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.M.); (L.S.)
| | - Stefania Stolfa
- UOC Microbiology and Virology, Azienda Ospedaliera-Universitaria Policlinico of Bari, 70124 Bari, Italy; (V.D.L.); (C.D.C.); (E.S.); (S.S.); (L.R.)
| | - Luigi Ronga
- UOC Microbiology and Virology, Azienda Ospedaliera-Universitaria Policlinico of Bari, 70124 Bari, Italy; (V.D.L.); (C.D.C.); (E.S.); (S.S.); (L.R.)
| | - Luigi Santacroce
- Department of Interdisciplinary Medicine, School of Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.M.); (L.S.)
| | - Maria Chironna
- Department of Interdisciplinary Medicine, Hygiene Section, University of Bari “Aldo Moro”, 70124 Bari, Italy;
| | - Michela Parisi
- University-Hospital Pediatric Department, Bambino Gesù Paediatric Hospital, 00165 Rome, Italy;
| | - Loredana Capozzi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71121 Foggia, Italy; (S.C.); (A.B.); (L.D.S.); (A.M.D.); (A.P.)
| | - Antonio Parisi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71121 Foggia, Italy; (S.C.); (A.B.); (L.D.S.); (A.M.D.); (A.P.)
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4
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Manzulli V, Schiavone A, Castellana S, Albenzio M, Cafiero MA, Camarda A, Capozzi L, D'Angelo F, Parisi A, Vasco I, Sciancalepore D, Marino L, Serrecchia L, Rondinone V, Campaniello M, Crescenzo G, Galante D, Pugliese N. Psychrobacter raelei sp. nov., isolated from a dog with peritonitis. Int J Syst Evol Microbiol 2024; 74. [PMID: 38683659 DOI: 10.1099/ijsem.0.006353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024] Open
Abstract
A strain belonging to the genus Psychrobacter, named PraFG1T, was isolated from the peritoneal effusion of a stray dog during necropsy procedures. The strain was characterized by the phylogenetic analyses based on the nucleotide sequences of 16S and 23S rRNA genes and of gyrB, which placed the strain in the genus Psychrobacter. The nucleotide sequence of the chromosome confirmed the placement, showing an average nucleotide identity of 72.1, 77.7, and 77.5 % with the closest related species, namely Psychrobacter sanguinis, Psychrobacter piechaudii, and Psychrobacter phenylpyruvicus, respectively, thus indicating a novel species. The polyphasic characterization by biochemical and fatty acid profiling as well as MALDI-TOF supported those findings. The strain was halotolerant, capable of growing within a temperature range between 4 and 37 °C, it was positive for catalase and oxidase, indole producing, nitrate reducing, and not able to use 5-keto-d-gluconic acid as a carbon source. Taken together, the data suggest that strain PraFG1T could be considered as representing a novel species, with the name Psychrobacter raelei sp. nov. (type strain PraFG1T=CIP 111873T=LMG 32233T).
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Affiliation(s)
- Viviana Manzulli
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Antonella Schiavone
- Dipartimento di Medicina Veterinaria, Università degli Studi di Bari, Valenzano, Italy
- Moredun Research Institute, Edinburgh, UK
| | - Stefano Castellana
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Putignano, Italy
| | - Marzia Albenzio
- Dipartimento di Scienze Agrarie, Alimenti, Risorse naturali e Ingegneria, Università di Foggia, Foggia, Italy
| | - Maria Assunta Cafiero
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Antonio Camarda
- Dipartimento di Medicina Veterinaria, Università degli Studi di Bari, Valenzano, Italy
| | - Loredana Capozzi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Putignano, Italy
| | - Francesca D'Angelo
- Dipartimento di Scienze Agrarie, Alimenti, Risorse naturali e Ingegneria, Università di Foggia, Foggia, Italy
| | - Antonio Parisi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Putignano, Italy
| | - Ilaria Vasco
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Dario Sciancalepore
- Dipartimento di Medicina Veterinaria, Università degli Studi di Bari, Valenzano, Italy
| | - Leonardo Marino
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Luigina Serrecchia
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Valeria Rondinone
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Maria Campaniello
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Giuseppe Crescenzo
- Dipartimento di Medicina Veterinaria, Università degli Studi di Bari, Valenzano, Italy
| | - Domenico Galante
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Nicola Pugliese
- Dipartimento di Medicina Veterinaria, Università degli Studi di Bari, Valenzano, Italy
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5
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Cooper AL, Wong A, Tamber S, Blais BW, Carrillo CD. Analysis of Antimicrobial Resistance in Bacterial Pathogens Recovered from Food and Human Sources: Insights from 639,087 Bacterial Whole-Genome Sequences in the NCBI Pathogen Detection Database. Microorganisms 2024; 12:709. [PMID: 38674654 PMCID: PMC11051753 DOI: 10.3390/microorganisms12040709] [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: 03/05/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
Understanding the role of foods in the emergence and spread of antimicrobial resistance necessitates the initial documentation of antibiotic resistance genes within bacterial species found in foods. Here, the NCBI Pathogen Detection database was used to query antimicrobial resistance gene prevalence in foodborne and human clinical bacterial isolates. Of the 1,843,630 sequence entries, 639,087 (34.7%) were assigned to foodborne or human clinical sources with 147,788 (23.14%) from food and 427,614 (76.88%) from humans. The majority of foodborne isolates were either Salmonella (47.88%), Campylobacter (23.03%), Escherichia (11.79%), or Listeria (11.3%), and the remaining 6% belonged to 20 other genera. Most foodborne isolates were from meat/poultry (95,251 or 64.45%), followed by multi-product mixed food sources (29,892 or 20.23%) and fish/seafood (6503 or 4.4%); however, the most prominent isolation source varied depending on the genus/species. Resistance gene carriage also varied depending on isolation source and genus/species. Of note, Klebsiella pneumoniae and Enterobacter spp. carried larger proportions of the quinolone resistance gene qnrS and some clinically relevant beta-lactam resistance genes in comparison to Salmonella and Escherichia coli. The prevalence of mec in S. aureus did not significantly differ between meat/poultry and multi-product sources relative to clinical sources, whereas this resistance was rare in isolates from dairy sources. The proportion of biocide resistance in Bacillus and Escherichia was significantly higher in clinical isolates compared to many foodborne sources but significantly lower in clinical Listeria compared to foodborne Listeria. This work exposes the gaps in current publicly available sequence data repositories, which are largely composed of clinical isolates and are biased towards specific highly abundant pathogenic species. We also highlight the importance of requiring and curating metadata on sequence submission to not only ensure correct information and data interpretation but also foster efficient analysis, sharing, and collaboration. To effectively monitor resistance carriage in food production, additional work on sequencing and characterizing AMR carriage in common commensal foodborne bacteria is critical.
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Affiliation(s)
- Ashley L. Cooper
- Research and Development, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON K1A 0C6, Canada;
| | - Alex Wong
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada;
| | - Sandeep Tamber
- Microbiology Research Division, Bureau of Microbial Hazards, Health Canada, Ottawa, ON K1A0K9, Canada;
| | - Burton W. Blais
- Research and Development, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON K1A 0C6, Canada;
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada;
| | - Catherine D. Carrillo
- Research and Development, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON K1A 0C6, Canada;
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada;
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6
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Baev V, Iliev I, Stefanov Y, Tsankova M, Marhova M, Apostolova E, Gozmanova M, Yahubyan G, Kostadinova S. Exploring the Genomic Landscape of Bacillus paranthracis PUMB_17 as a Proficient Phosphatidylcholine-Specific Phospholipase C Producer. Curr Issues Mol Biol 2024; 46:2497-2513. [PMID: 38534774 DOI: 10.3390/cimb46030158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/08/2024] [Accepted: 03/12/2024] [Indexed: 03/28/2024] Open
Abstract
Phospholipases find versatile applications across industries, including detergent production, food modification, pharmaceuticals (especially in drug delivery systems), and cell signaling research. In this study, we present a strain of Bacillus paranthracis for the first time, demonstrating significant potential in the production of phosphatidylcholine-specific phospholipase C (PC-PLC). The investigation thoroughly examines the B. paranthracis PUMB_17 strain, focusing on the activity of PC-PLC and its purification process. Notably, the PUMB_17 strain displays extracellular PC-PLC production with high specific activity during the late exponential growth phase. To unravel the genetic makeup of PUMB_17, we employed nanopore-based whole-genome sequencing and subsequently conducted a detailed genome annotation. The genome comprises a solitary circular chromosome spanning 5,250,970 bp, featuring a guanine-cytosine ratio of 35.49. Additionally, two plasmids of sizes 64,250 bp and 5845 bp were identified. The annotation analysis reveals the presence of 5328 genes, encompassing 5186 protein-coding sequences, and 142 RNA genes, including 39 rRNAs, 103 tRNAs, and 5 ncRNAs. The aim of this study was to make a comprehensive genomic exploration that promises to enhance our understanding of the previously understudied and recently documented capabilities of Bacillus paranthracis and to shed light on a potential use of the strain in the industrial production of PC-PLC.
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Affiliation(s)
- Vesselin Baev
- Department of Molecular Biology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
| | - Ivan Iliev
- Department of Biochemistry and Microbiology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
| | | | - Marinela Tsankova
- Department of Biochemistry and Microbiology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
| | - Mariana Marhova
- Department of Biochemistry and Microbiology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
| | - Elena Apostolova
- Department of Molecular Biology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
| | - Mariyana Gozmanova
- Department of Molecular Biology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
| | - Galina Yahubyan
- Department of Molecular Biology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
| | - Sonya Kostadinova
- Department of Biochemistry and Microbiology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
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7
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Sornchuer P, Saninjuk K, Amonyingcharoen S, Ruangtong J, Thongsepee N, Martviset P, Chantree P, Sangpairoj K. Whole Genome Sequencing Reveals Antimicrobial Resistance and Virulence Genes of Both Pathogenic and Non-Pathogenic B. cereus Group Isolates from Foodstuffs in Thailand. Antibiotics (Basel) 2024; 13:245. [PMID: 38534680 DOI: 10.3390/antibiotics13030245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 03/01/2024] [Accepted: 03/05/2024] [Indexed: 03/28/2024] Open
Abstract
Members of the Bacillus cereus group are spore-forming Gram-positive bacilli that are commonly associated with diarrheal or emetic food poisoning. They are widespread in nature and frequently present in both raw and processed food products. Here, we genetically characterized 24 B. cereus group isolates from foodstuffs. Whole-genome sequencing (WGS) revealed that most of the isolates were closely related to B. cereus sensu stricto (12 isolates), followed by B. pacificus (5 isolates), B. paranthracis (5 isolates), B. tropicus (1 isolate), and "B. bingmayongensis" (1 isolate). The most detected virulence genes were BAS_RS06430, followed by bacillibactin biosynthesis genes (dhbA, dhbB, dhbC, dhbE, and dhbF), genes encoding the three-component non-hemolytic enterotoxin (nheA, nheB, and nheC), a gene encoding an iron-regulated leucine-rich surface protein (ilsA), and a gene encoding a metalloprotease (inhA). Various biofilm-associated genes were found, with high prevalences of tasA and sipW genes (matrix protein-encoding genes); purA, purC, and purL genes (eDNA synthesis genes); lytR and ugd genes (matrix polysaccharide synthesis genes); and abrB, codY, nprR, plcR, sinR, and spo0A genes (biofilm transcription regulator genes). Genes related to fosfomycin and beta-lactam resistance were identified in most of the isolates. We therefore demonstrated that WGS analysis represents a useful tool for rapidly identifying and characterizing B. cereus group strains. Determining the genetic epidemiology, the presence of virulence and antimicrobial resistance genes, and the pathogenic potential of each strain is crucial for improving the risk assessment of foodborne B. cereus group strains.
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Affiliation(s)
- Phornphan Sornchuer
- Department of Preclinical Science, Faculty of Medicine, Thammasat University, Pathum Thani 12120, Thailand
- Thammasat University Research Unit in Nutraceuticals and Food Safety, Faculty of Medicine, Thammasat University, Pathum Thani 12120, Thailand
| | | | - Sumet Amonyingcharoen
- Medical Life Sciences Institute, Department of Medical Sciences, Ministry of Public Health, Nonthaburi 11000, Thailand
| | - Jittiporn Ruangtong
- Thammasat University Research Unit in Nutraceuticals and Food Safety, Faculty of Medicine, Thammasat University, Pathum Thani 12120, Thailand
| | - Nattaya Thongsepee
- Department of Preclinical Science, Faculty of Medicine, Thammasat University, Pathum Thani 12120, Thailand
- Thammasat University Research Unit in Nutraceuticals and Food Safety, Faculty of Medicine, Thammasat University, Pathum Thani 12120, Thailand
| | - Pongsakorn Martviset
- Department of Preclinical Science, Faculty of Medicine, Thammasat University, Pathum Thani 12120, Thailand
- Thammasat University Research Unit in Nutraceuticals and Food Safety, Faculty of Medicine, Thammasat University, Pathum Thani 12120, Thailand
| | - Pathanin Chantree
- Department of Preclinical Science, Faculty of Medicine, Thammasat University, Pathum Thani 12120, Thailand
- Thammasat University Research Unit in Nutraceuticals and Food Safety, Faculty of Medicine, Thammasat University, Pathum Thani 12120, Thailand
| | - Kant Sangpairoj
- Department of Preclinical Science, Faculty of Medicine, Thammasat University, Pathum Thani 12120, Thailand
- Thammasat University Research Unit in Nutraceuticals and Food Safety, Faculty of Medicine, Thammasat University, Pathum Thani 12120, Thailand
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8
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Li Y, Chen S, Yu Z, Yao J, Jia Y, Liao C, Chen J, Wei Y, Guo R, He L, Ding K. A Novel Bacillus Velezensis for Efficient Degradation of Zearalenone. Foods 2024; 13:530. [PMID: 38397507 PMCID: PMC10888444 DOI: 10.3390/foods13040530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/03/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Zearalenone (ZEN) is considered one of the most serious mycotoxins contaminating grains and their by-products, causing significant economic losses in the feed and food industries. Biodegradation pathways are currently considered the most efficient solution to remove ZEN contamination from foods. However, low degradation rates and vulnerability to environmental impacts limit the application of biodegradation pathways. Therefore, the main research objective of this article was to screen strains that can efficiently degrade ZEN and survive under harsh conditions. This study successfully isolated a new strain L9 which can efficiently degrade ZEN from 108 food ingredients. The results of sequence alignment showed that L9 is Bacillus velezensis. Meanwhile, we found that the L9 degradation rate reached 91.14% at 24 h and confirmed that the primary degradation mechanism of this strain is biodegradation. The strain exhibits resistance to high temperature, acid, and 0.3% bile salts. The results of whole-genome sequencing analysis showed that, it is possible that the strain encodes the key enzyme, such as chitinase, carboxylesterases, and lactone hydrolase, that work together to degrade ZEN. In addition, 227 unique genes in this strain are primarily involved in its replication, recombination, repair, and protective mechanisms. In summary, we successfully excavated a ZEN-degrading, genetically distinct strain of Bacillus velezensis that provides a solid foundation for the detoxification of feed and food contamination in the natural environment.
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Affiliation(s)
- Yijia Li
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China; (Y.L.); (S.C.); (Z.Y.); (J.Y.); (Y.J.); (C.L.); (J.C.); (Y.W.); (R.G.); (L.H.)
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
| | - Songbiao Chen
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China; (Y.L.); (S.C.); (Z.Y.); (J.Y.); (Y.J.); (C.L.); (J.C.); (Y.W.); (R.G.); (L.H.)
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou 450000, China
| | - Zuhua Yu
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China; (Y.L.); (S.C.); (Z.Y.); (J.Y.); (Y.J.); (C.L.); (J.C.); (Y.W.); (R.G.); (L.H.)
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
| | - Jie Yao
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China; (Y.L.); (S.C.); (Z.Y.); (J.Y.); (Y.J.); (C.L.); (J.C.); (Y.W.); (R.G.); (L.H.)
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
| | - Yanyan Jia
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China; (Y.L.); (S.C.); (Z.Y.); (J.Y.); (Y.J.); (C.L.); (J.C.); (Y.W.); (R.G.); (L.H.)
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou 450000, China
| | - Chengshui Liao
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China; (Y.L.); (S.C.); (Z.Y.); (J.Y.); (Y.J.); (C.L.); (J.C.); (Y.W.); (R.G.); (L.H.)
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
| | - Jian Chen
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China; (Y.L.); (S.C.); (Z.Y.); (J.Y.); (Y.J.); (C.L.); (J.C.); (Y.W.); (R.G.); (L.H.)
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
| | - Ying Wei
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China; (Y.L.); (S.C.); (Z.Y.); (J.Y.); (Y.J.); (C.L.); (J.C.); (Y.W.); (R.G.); (L.H.)
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
| | - Rongxian Guo
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China; (Y.L.); (S.C.); (Z.Y.); (J.Y.); (Y.J.); (C.L.); (J.C.); (Y.W.); (R.G.); (L.H.)
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
| | - Lei He
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China; (Y.L.); (S.C.); (Z.Y.); (J.Y.); (Y.J.); (C.L.); (J.C.); (Y.W.); (R.G.); (L.H.)
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
| | - Ke Ding
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China; (Y.L.); (S.C.); (Z.Y.); (J.Y.); (Y.J.); (C.L.); (J.C.); (Y.W.); (R.G.); (L.H.)
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou 450000, China
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9
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Nocera FP, Capozzi L, Simone D, Pizzano F, Iovane V, Bianco A, Parisi A, De Martino L. Multi-locus sequence typing and in vitro antimicrobial resistance of equine Streptococcus equi subspecies zooepidemicus strains. Vet Res Commun 2024; 48:215-224. [PMID: 37626228 DOI: 10.1007/s11259-023-10165-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 06/30/2023] [Indexed: 08/27/2023]
Abstract
Streptococcus equi subsp. zooepidemicus (S. zooepidemicus) is one of the most important pathogens frequently associated with the main causes of equine infertility. In this study, we surveyed 22 strains of S. zooepidemicus collected during 2021 from cervico-uterine swabs of mares with endometritis. The genetic variability of the isolated strains was studied by multi-locus sequence typing (MLST) from whole-genome sequencing (WGS) data. The average length of reconstructed genomes was 2,088,286 bp (95% CI: 2,061,569 bp-2,114,967 bp), which was expected for S. zooepidemicus genomes. The assembled genomes were assigned to sequence types (STs) using the S. zooepidemicus scheme targeting seven loci (arcC, nrdE, proS, spi, tdk, tpi, yqiL) available in PubMLST database. MLST revealed a wide variability of STs with two (9.1%) novel STs identified in this study, precisely ST521 with two isolates and ST522 with one isolate. Furthermore, 4/22 (18.2%) isolates were assigned to ST92, 3/22 (13.6%) to ST205, 2/22 (9.1%) to ST475, and one strain (4.5%) for each of the following STs: ST10, ST30, ST39, ST49, ST101, ST132, ST147, ST314, ST369, ST467. Isolates were also tested for antimicrobial resistance using Kirby-Bauer disk diffusion method. Resistance to amoxicillin-clavulanate, ampicillin, amikacin, gentamicin, streptomycin, enrofloxacin, sulfamethoxazole-trimethoprim, tetracycline, oxytetracycline represented the most common resistance profile (13/22, 59.1%). No correlation between specific ST and antimicrobial resistance profile was found. Our study provides a comprehensive insight into the epidemiology, ST diversity and antimicrobial resistance profile of S. zooepidemicus strains, isolated in Italy, causing subfertility problems in mares.
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Affiliation(s)
- Francesca Paola Nocera
- Department of Veterinary Medicine and Animal Production, University of Naples "Federico II", Naples, 80137, Italy.
| | - Loredana Capozzi
- Istituto Zooprofilattico Sperimentale di Puglia e Basilicata, Contrada San Pietro Piturno, Putignano-Bari, 70017, Italy
| | - Domenico Simone
- Istituto Zooprofilattico Sperimentale di Puglia e Basilicata, Contrada San Pietro Piturno, Putignano-Bari, 70017, Italy
| | - Francesca Pizzano
- Department of Veterinary Medicine and Animal Production, University of Naples "Federico II", Naples, 80137, Italy
| | - Valentina Iovane
- Department of Agricultural Sciences, University of Naples "Federico II", Naples, 80055, Italy
| | - Angelica Bianco
- Istituto Zooprofilattico Sperimentale di Puglia e Basilicata, Contrada San Pietro Piturno, Putignano-Bari, 70017, Italy
| | - Antonio Parisi
- Istituto Zooprofilattico Sperimentale di Puglia e Basilicata, Contrada San Pietro Piturno, Putignano-Bari, 70017, Italy
| | - Luisa De Martino
- Department of Veterinary Medicine and Animal Production, University of Naples "Federico II", Naples, 80137, Italy
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10
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Vanhee C, Jacobs B, Kamugisha A, Canfyn M, Van Der Meersch H, Ceyssens B, Deconinck E, Van Hoorde K, Willocx M. Substandard and falsified ivermectin tablets obtained for self-medication during the COVID-19 pandemic as a source of potential harm. Drug Test Anal 2023. [PMID: 38043940 DOI: 10.1002/dta.3618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/07/2023] [Accepted: 11/10/2023] [Indexed: 12/05/2023]
Abstract
In 2019, a global viral pandemic, due to the SARS-CoV-2 virus, broke out. Soon after, the search for a vaccine and/or antiviral medicine began. One of the candidate antiviral medicines tested was ivermectin. Although several health authorities warned the public against the use of this medicine outside clinical trials, the drug was widely used at the end of 2020 and in 2021. Simultaneously, several reports started to emerge demonstrating serious adverse effects after self-medicating with ivermectin. It stands to reason that the self-administration of substandard or falsified (SF) medicines bearing harmful quality deficiencies have contributed to this phenomenon. In order to have a better view on the nature of these harmful quality deficiencies, SF ivermectin samples, intercepted in large quantities by the Belgian regulatory agencies during the period 2021-2022, were analyzed in our official medicines control laboratory. None of the samples (n = 19) were compliant to the quality criteria applicable to medicinal products. These SF products either suffered from a systematic underdosing of the active pharmaceutical ingredient or were severely contaminated with bacteria, two of which were contaminated with known pathogens that cause gastrointestinal illness upon oral intake. In addition to the direct risks of self-medicating with such a product, the improper usage and dosage of ivermectin medication might also facilitate ivermectin tolerance or resistance in parasites. This may have detrimental consequences on a global scale, certainly as the number of newly developed active pharmaceutical ingredients that can safely be used to combat parasites is rather scarce.
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Affiliation(s)
- Celine Vanhee
- Service Medicines and Health Products, Scientific Direction of Chemical and Physical Health Risks, Sciensano, Brussels, Belgium
| | - Bram Jacobs
- Service of Foodborne Pathogen, Scientific Direction of Infectious Diseases in Humans, Sciensano, Brussels, Belgium
| | - Angélique Kamugisha
- Service Medicines and Health Products, Scientific Direction of Chemical and Physical Health Risks, Sciensano, Brussels, Belgium
| | - Michael Canfyn
- Service Medicines and Health Products, Scientific Direction of Chemical and Physical Health Risks, Sciensano, Brussels, Belgium
| | | | - Bart Ceyssens
- Federal Agency for Medicine and Health Care Products, Brussels, Belgium
| | - Eric Deconinck
- Service Medicines and Health Products, Scientific Direction of Chemical and Physical Health Risks, Sciensano, Brussels, Belgium
| | - Koenraad Van Hoorde
- Service of Foodborne Pathogen, Scientific Direction of Infectious Diseases in Humans, Sciensano, Brussels, Belgium
| | - Marie Willocx
- Service Medicines and Health Products, Scientific Direction of Chemical and Physical Health Risks, Sciensano, Brussels, Belgium
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11
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Abdelli M, Falaise C, Morineaux-Hilaire V, Cumont A, Taysse L, Raynaud F, Ramisse V. Get to Know Your Neighbors: Characterization of Close Bacillus anthracis Isolates and Toxin Profile Diversity in the Bacillus cereus Group. Microorganisms 2023; 11:2721. [PMID: 38004733 PMCID: PMC10673079 DOI: 10.3390/microorganisms11112721] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 10/27/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
Unexpected atypical isolates of Bacillus cereus s.l. occasionally challenge conventional microbiology and even the most advanced techniques for anthrax detection. For anticipating and gaining trust, 65 isolates of Bacillus cereus s.l. of diverse origin were sequenced and characterized. The BTyper3 tool was used for assignation to genomospecies B. mosaicus (34), B. cereus s.s (29) and B. toyonensis (2), as well as virulence factors and toxin profiling. None of them carried any capsule or anthrax-toxin genes. All harbored the non-hemolytic toxin nheABC and sphygomyelinase spH genes, whereas 41 (63%), 30 (46%), 11 (17%) and 6 (9%) isolates harbored cytK-2, hblABCD, cesABCD and at least one insecticidal toxin gene, respectively. Matrix-assisted laser desorption ionization-time of flight mass spectrometry confirmed the production of cereulide (ces genes). Phylogeny inferred from single-nucleotide polymorphisms positioned isolates relative to the B. anthracis lineage. One isolate (BC38B) was of particular interest as it appeared to be the closest B. anthracis neighbor described so far. It harbored a large plasmid similar to other previously described B. cereus s.l. megaplasmids and at a lower extent to pXO1. Whereas bacterial collection is enriched, these high-quality public genetic data offer additional knowledge for better risk assessment using future NGS-based technologies of detection.
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Affiliation(s)
- Mehdi Abdelli
- DGA CBRN Defence Center, Biology Division, French Ministry of the Armed Forces, 91710 Vert-le-Petit, France; (M.A.); (V.M.-H.); (A.C.); (L.T.); (F.R.)
- Institute for Integrative Biology of the Cell (I2BC), CNRS, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Charlotte Falaise
- DGA CBRN Defence Center, Biology Division, French Ministry of the Armed Forces, 91710 Vert-le-Petit, France; (M.A.); (V.M.-H.); (A.C.); (L.T.); (F.R.)
| | - Valérie Morineaux-Hilaire
- DGA CBRN Defence Center, Biology Division, French Ministry of the Armed Forces, 91710 Vert-le-Petit, France; (M.A.); (V.M.-H.); (A.C.); (L.T.); (F.R.)
| | - Amélie Cumont
- DGA CBRN Defence Center, Biology Division, French Ministry of the Armed Forces, 91710 Vert-le-Petit, France; (M.A.); (V.M.-H.); (A.C.); (L.T.); (F.R.)
| | - Laurent Taysse
- DGA CBRN Defence Center, Biology Division, French Ministry of the Armed Forces, 91710 Vert-le-Petit, France; (M.A.); (V.M.-H.); (A.C.); (L.T.); (F.R.)
| | - Françoise Raynaud
- DGA CBRN Defence Center, Biology Division, French Ministry of the Armed Forces, 91710 Vert-le-Petit, France; (M.A.); (V.M.-H.); (A.C.); (L.T.); (F.R.)
| | - Vincent Ramisse
- DGA CBRN Defence Center, Biology Division, French Ministry of the Armed Forces, 91710 Vert-le-Petit, France; (M.A.); (V.M.-H.); (A.C.); (L.T.); (F.R.)
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12
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Wallace VJ, Sakowski EG, Preheim SP, Prasse C. Bacteria exposed to antiviral drugs develop antibiotic cross-resistance and unique resistance profiles. Commun Biol 2023; 6:837. [PMID: 37573457 PMCID: PMC10423222 DOI: 10.1038/s42003-023-05177-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 07/25/2023] [Indexed: 08/14/2023] Open
Abstract
Antiviral drugs are used globally as treatment and prophylaxis for long-term and acute viral infections. Even though antivirals also have been shown to have off-target effects on bacterial growth, the potential contributions of antivirals to antimicrobial resistance remains unknown. Herein we explored the ability of different classes of antiviral drugs to induce antimicrobial resistance. Our results establish the previously unrecognized capacity of antivirals to broadly alter the phenotypic antimicrobial resistance profiles of both gram-negative and gram-positive bacteria Escherichia coli and Bacillus cereus. Bacteria exposed to antivirals including zidovudine, dolutegravir and raltegravir developed cross-resistance to commonly used antibiotics including trimethoprim, tetracycline, clarithromycin, erythromycin, and amoxicillin. Whole genome sequencing of antiviral-resistant E. coli isolates revealed numerous unique single base pair mutations, as well as multi-base pair insertions and deletions, in genes with known and suspected roles in antimicrobial resistance including those coding for multidrug efflux pumps, carbohydrate transport, and cellular metabolism. The observed phenotypic changes coupled with genotypic results indicate that bacteria exposed to antiviral drugs with antibacterial properties in vitro can develop multiple resistance mutations that confer cross-resistance to antibiotics. Our findings underscore the potential contribution of wide scale usage of antiviral drugs to the development and spread of antimicrobial resistance in humans and the environment.
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Affiliation(s)
- Veronica J Wallace
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Eric G Sakowski
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD, USA
- Department of Science, Mount St. Mary's University, Emmitsburg, MD, USA
| | - Sarah P Preheim
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Carsten Prasse
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD, USA.
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13
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Romanò A, Ivanovic I, Segessemann T, Vazquez Rojo L, Widmer J, Egger L, Dreier M, Sesso L, Vaccani M, Schuler M, Frei D, Frey J, Ahrens CH, Steiner A, Graber HU. Elucidation of the Bovine Intramammary Bacteriome and Resistome from healthy cows of Swiss dairy farms in the Canton Tessin. Front Microbiol 2023; 14:1183018. [PMID: 37583512 PMCID: PMC10425240 DOI: 10.3389/fmicb.2023.1183018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 06/26/2023] [Indexed: 08/17/2023] Open
Abstract
Healthy, untreated cows of nine dairy herds from the Swiss Canton Tessin were analyzed three times within one year to identify the most abundant species of the intramammary bacteriome. Aseptically collected milk samples were cultured and bacteria identified using MALDI-TOF. Of 256 cows analyzed, 96% were bacteriologically positive and 80% of the 1,024 quarters were positive for at least one bacterial species. 84.5% of the quarters were healthy with somatic cell counts (SCC) < 200,000 cells/mL, whereas 15.5% of the quarters showed a subclinical mastitis (SCC ≥ 200,000 cells/mL). We could assign 1,288 isolates to 104 different bacterial species including 23 predominant species. Non-aureus staphylococci and mammaliicocci (NASM) were most prevalent (14 different species; 73.5% quarters). Staphylococcus xylosus and Mammaliicoccus sciuri accounted for 74.7% of all NASM isolates. To describe the intramammary resistome, 350 isolates of the predominant species were selected and subjected to short-read whole genome sequencing (WGS) and phenotypic antibiotic resistance profiling. While complete genomes of eight type strains were available, the remaining 15 were de novo assembled with long reads as a resource for the community. The 23 complete genomes served for reference-based assembly of the Illumina WGS data. Both chromosomes and mobile genetic elements were examined for antibiotic resistance genes (ARGs) using in-house and online software tools. ARGs were then correlated with phenotypic antibiotic resistance data from minimum inhibitory concentration (MIC). Phenotypic and genomic antimicrobial resistance was isolate-specific. Resistance to clindamycin and oxacillin was most frequently observed (65 and 30%) in Staphylococcus xylosus but could not be linked to chromosomal or plasmid-borne ARGs. However, in several cases, the observed antimicrobial resistance could be explained by the presence of mobile genetic elements like tetK carried on small plasmids. This represents a possible mechanism of transfer between non-pathogenic bacteria and pathogens of the mammary gland within and between herds. The-to our knowledge-most extensive bacteriome reported and the first attempt to link it with the resistome promise to profoundly affect veterinary bacteriology in the future and are highly relevant in a One Health context, in particular for mastitis, the treatment of which still heavily relies on antibiotics.
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Affiliation(s)
- Alicia Romanò
- Food Microbial Systems, Group Microbiological Safety of Foods of Animal Origin, Agroscope, Bern, Switzerland
- Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Ivana Ivanovic
- Food Microbial Systems, Group Microbiological Safety of Foods of Animal Origin, Agroscope, Bern, Switzerland
| | - Tina Segessemann
- SIB, Swiss Institute of Bioinformatics, Zürich, Switzerland
- Method Development and Analytics, Group Molecular Ecology, Agroscope, Zürich, Switzerland
| | - Laura Vazquez Rojo
- Food Microbial Systems, Group Microbiological Safety of Foods of Animal Origin, Agroscope, Bern, Switzerland
| | - Jérôme Widmer
- Method Development and Analytics, Group Biochemistry of Milk, Agroscope, Bern, Switzerland
| | - Lotti Egger
- Method Development and Analytics, Group Biochemistry of Milk, Agroscope, Bern, Switzerland
| | - Matthias Dreier
- Food Microbial Systems, Group Cultures, Biodiversity, and Terroir, Agroscope, Bern, Switzerland
| | - Lorenzo Sesso
- Clinic of Ruminants, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Michael Vaccani
- Clinic of Ruminants, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Martin Schuler
- SIB, Swiss Institute of Bioinformatics, Zürich, Switzerland
- Method Development and Analytics, Group Molecular Ecology, Agroscope, Zürich, Switzerland
| | - Daniel Frei
- Method Development and Analytics, Group Molecular Diagnostics, Genomics, and Bioinformatics, Agroscope, Wädenswil, Switzerland
| | - Juerg Frey
- Method Development and Analytics, Group Molecular Diagnostics, Genomics, and Bioinformatics, Agroscope, Wädenswil, Switzerland
| | - Christian H. Ahrens
- SIB, Swiss Institute of Bioinformatics, Zürich, Switzerland
- Method Development and Analytics, Group Molecular Ecology, Agroscope, Zürich, Switzerland
| | - Adrian Steiner
- Clinic of Ruminants, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Hans Ulrich Graber
- Food Microbial Systems, Group Microbiological Safety of Foods of Animal Origin, Agroscope, Bern, Switzerland
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14
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Bogaerts B, Fraiture MA, Huwaert A, Van Nieuwenhuysen T, Jacobs B, Van Hoorde K, De Keersmaecker SCJ, Roosens NHC, Vanneste K. Retrospective surveillance of viable Bacillus cereus group contaminations in commercial food and feed vitamin B 2 products sold on the Belgian market using whole-genome sequencing. Front Microbiol 2023; 14:1173594. [PMID: 37415815 PMCID: PMC10321352 DOI: 10.3389/fmicb.2023.1173594] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 06/01/2023] [Indexed: 07/08/2023] Open
Abstract
Bacillus cereus is a spore-forming bacterium that occurs as a contaminant in food and feed, occasionally resulting in food poisoning through the production of various toxins. In this study, we retrospectively characterized viable B. cereus sensu lato (s.l.) isolates originating from commercial vitamin B2 feed and food additives collected between 2016 and 2022 by the Belgian Federal Agency for the Safety of the Food Chain from products sold on the Belgian market. In total, 75 collected product samples were cultured on a general medium and, in case of bacterial growth, two isolates per product sample were collected and characterized using whole-genome sequencing (WGS) and subsequently characterized in terms of sequence type (ST), virulence gene profile, antimicrobial resistance (AMR) gene profile, plasmid content, and phylogenomic relationships. Viable B. cereus was identified in 18 of the 75 (24%) tested products, resulting in 36 WGS datasets, which were classified into eleven different STs, with ST165 (n = 10) and ST32 (n = 8) being the most common. All isolates carried multiple genes encoding virulence factors, including cytotoxin K-2 (52.78%) and cereulide (22.22%). Most isolates were predicted to be resistant to beta-lactam antibiotics (100%) and fosfomycin (88.89%), and a subset was predicted to be resistant to streptothricin (30.56%). Phylogenomic analysis revealed that some isolates obtained from different products were closely related or even identical indicating a likely common origin, whereas for some products the two isolates obtained did not show any close relationship to each other or other isolates found in other products. This study reveals that potentially pathogenic and drug-resistant B. cereus s.l. can be present in food and feed vitamin B2 additives that are commercially available, and that more research is warranted to assess whether their presence in these types of products poses a threat to consumers.
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Affiliation(s)
- Bert Bogaerts
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | | | | | | | - Bram Jacobs
- Foodborne Pathogens, Sciensano, Brussels, Belgium
- Laboratory of Food Microbiology and Food Preservation, Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | | | | | | | - Kevin Vanneste
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
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15
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Yossa N, Huang S, Canida T, Binet R, Macarisin D, Bell R, Tallent S, Brown E, Hammack T. qPCR detection of viable Bacillus cereus group cells in cosmetic products. Sci Rep 2023; 13:4477. [PMID: 36934171 PMCID: PMC10024758 DOI: 10.1038/s41598-023-31128-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 03/07/2023] [Indexed: 03/20/2023] Open
Abstract
Reference methods for microbiological safety assessments of cosmetics rely on culture methods that reveal colonies of live microorganisms on growth media. Rapid molecular technologies, such as qPCR, detects the presence of target DNA in samples from dead and viable cells. DNA intercalating dyes, such as propidium monoazide (PMAxx), are capable of restricting PCR amplification to viable microbial cells. Here we developed singleplex and multiplex real time (qPCR) assays for the detection of Bacillus cereus (B. cereus) using 16S rRNA and phosphatidylcholine-specific phospholipase C (PLC) gene specific sequences coupled with PMAxx. The limit of detection was determined to be ~ 1 log CFU/ml for 16S rRNA and 3 log CFU/ml for PLC detection in pure culture using an eye shadow isolate, B. cereus 3A. We assessed the inclusivity and exclusivity of our qPCR assays using 212 strains, including 143 members of B. cereus, 38 non- B. cereus. and 31 non-Bacillus species; inclusivity was 100% for the 16S rRNA and 97.9% for the PLC targets; the exclusivity was 100% for 16S rRNA and 98.6% for PLC targets. These qPCR assays were then used to assess samples of commercial cosmetics: one set of liquid face toners (N = 3), artificially contaminated with B. cereus 3A, and one set of powdered cosmetics (N = 8), previously determined to be contaminated with B. cereus. For some samples, test portions were analyzed by qPCR in parallel, with and without PMAxx treatment. All test portions were simultaneously streaked on BACARA plates to confirm viable cells of B. cereus, according to the culture method. We found no difference in sensitivity between the singleplex and the multiplex qPCR assays (P > 0.05). Inoculated samples that did not recover B. cereus on plates still showed amplification of the DNA targets. However, that amplification was significantly delayed in PMAxx -treated samples (P < 0.0001) with CT value differences of 7.82 for 16S rRNA and 7.22 for PLC. Likewise, amplification delay was significant (P < 0.0001) with inoculated samples that recovered B. cereus on plates with CT value differences of 2.96 and 2.36 for 16S rRNA and PLC, respectively, demonstrating the presence of dead cells in the samples. All our qPCR results correlated with detection on BACARA plates (kappa, k = 0.99), independently of the presence of PMAxx in the PCR assays. Nevertheless, the amplification threshold with PMAxx dyes was significantly higher than the non-PMAxx dyes. Our findings confirm qPCR can be used for more rapid detection of microorganisms in cosmetics, including B. cereus, and selective detection of viable cells can be improved using PMAxx dyes.
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Affiliation(s)
- Nadine Yossa
- FDA, Office of Regulatory Science, College Park, MD, USA.
| | - Sonny Huang
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, 37831, USA
| | - Travis Canida
- FDA, Office of Analytics and Outreach, College Park, MD, 20740, USA
| | - Rachel Binet
- FDA, Office of Regulatory Science, College Park, MD, USA
| | | | - Rebecca Bell
- FDA, Office of Regulatory Science, College Park, MD, USA
| | - Sandra Tallent
- FDA, Office of Regulatory Science, College Park, MD, USA
| | - Eric Brown
- FDA, Office of Regulatory Science, College Park, MD, USA
| | - Thomas Hammack
- FDA, Office of Regulatory Science, College Park, MD, USA.
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Bonilla Moncada J, Ríos CA, Castro CM, Leal AL, Arturo JA, Diaz K, Duarte C, Puerto G, Moreno N, Velasco A, Moreno J. Infections in patients with adverse reactions to the use of unknown modeling substances for soft tissue enhancement in Cali, Colombia. PLoS One 2023; 18:e0277958. [PMID: 36757960 PMCID: PMC9910686 DOI: 10.1371/journal.pone.0277958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 11/07/2022] [Indexed: 02/10/2023] Open
Abstract
The infiltration of foreign materials not approved for medical purposes or of modeling substances used in soft tissue to modify the anatomical appearance for aesthetic purposes represents a serious health problem. These procedures lead to the development of delayed complications, including infections. The objective of this study was to characterize infections in patients with adverse reactions to the use of modeling substances in Cali, Colombia. A cross-sectional and descriptive study was used to determine the frequency of bacterial and fungal infections associated with complications from and adverse reactions to the use of modeling substances in 113 patients. We identified microorganisms in 22 patients and a frequency of 68.1% monomicrobial infections and 31.8% polymicrobial infections. The microorganisms identified in our study included Bacillus cereus, Mycobacterium fortuitum, and Pseudomonas stutzeri, among other microorganisms. The presence of adverse effects derived from the use of illegal modeling substances has been demonstrated; among these effects, infections occur with high frequency and place the health of the patient at risk and increase problems in health care.
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Affiliation(s)
- Jennifer Bonilla Moncada
- Department of Microbiology, National Health Institute, Bogotá, Colombia
- Biotechnology Institute, National University of Colombia, Bogotá, Colombia
| | | | | | - Aura Lucia Leal
- Department of Microbiology, National Health Institute, Bogotá, Colombia
| | | | | | - Carolina Duarte
- Department of Microbiology, National Health Institute, Bogotá, Colombia
| | - Gloria Puerto
- Department of Microbiology, National Health Institute, Bogotá, Colombia
- Department of Mycobacteria, National Health Institute, Bogotá, Colombia
| | | | - Amelia Velasco
- Department of Mycobacteria, National Health Institute, Bogotá, Colombia
| | - Jaime Moreno
- Department of Microbiology, National Health Institute, Bogotá, Colombia
- * E-mail:
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Moshe M, Gupta CL, Sela N, Minz D, Banin E, Frenkel O, Cytryn E. Comparative genomics of Bacillus cereus sensu lato spp. biocontrol strains in correlation to in-vitro phenotypes and plant pathogen antagonistic capacity. Front Microbiol 2023; 14:996287. [PMID: 36846749 PMCID: PMC9947482 DOI: 10.3389/fmicb.2023.996287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 01/12/2023] [Indexed: 02/11/2023] Open
Abstract
Bacillus cereus sensu lato (Bcsl) strains are widely explored due to their capacity to antagonize a broad range of plant pathogens. These include B. cereus sp. UW85, whose antagonistic capacity is attributed to the secondary metabolite Zwittermicin A (ZwA). We recently isolated four soil and root-associated Bcsl strains (MO2, S-10, S-25, LSTW-24) that displayed different growth profiles and in-vitro antagonistic effects against three soilborne plant pathogens models: Pythium aphanidermatum (oomycete) Rhizoctonia solani (basidiomycete), and Fusarium oxysporum (ascomycete). To identify genetic mechanisms potentially responsible for the differences in growth and antagonistic phenotypes of these Bcsl strains, we sequenced and compared their genomes, and that of strain UW85 using a hybrid sequencing pipeline. Despite similarities, specific Bcsl strains had unique secondary metabolite and chitinase-encoding genes that could potentially explain observed differences in in-vitro chitinolytic potential and anti-fungal activity. Strains UW85, S-10 and S-25 contained a (~500 Kbp) mega-plasmid that harbored the ZwA biosynthetic gene cluster. The UW85 mega-plasmid contained more ABC transporters than the other two strains, whereas the S-25 mega-plasmid carried a unique cluster containing cellulose and chitin degrading genes. Collectively, comparative genomics revealed several mechanisms that can potentially explain differences in in-vitro antagonism of Bcsl strains toward fungal plant pathogens.
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Affiliation(s)
- Maya Moshe
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Rishon-Lezion, Israel
- Institute of Plant Pathology and Weed Research, Agricultural Research Organization, Rishon-Lezion, Israel
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Chhedi Lal Gupta
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Rishon-Lezion, Israel
| | - Noa Sela
- Institute of Plant Pathology and Weed Research, Agricultural Research Organization, Rishon-Lezion, Israel
| | - Dror Minz
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Rishon-Lezion, Israel
| | - Ehud Banin
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Omer Frenkel
- Institute of Plant Pathology and Weed Research, Agricultural Research Organization, Rishon-Lezion, Israel
| | - Eddie Cytryn
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Rishon-Lezion, Israel
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Schäfer L, Volk F, Kleespies RG, Jehle JA, Wennmann JT. Elucidating the genomic history of commercially used Bacillus thuringiensis subsp. tenebrionis strain NB176. Front Cell Infect Microbiol 2023; 13:1129177. [PMID: 37021121 PMCID: PMC10067926 DOI: 10.3389/fcimb.2023.1129177] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/17/2023] [Indexed: 04/07/2023] Open
Abstract
Bacillus thuringiensis subsp. tenebrionis (Btt) produces a coleopteran-specific crystal protoxin protein (Cry3Aa δ-endotoxin). After its discovery in 1982, the strain NB125 (DSM 5526) was eventually registered in 1990 to control the Colorado potato beetle (Leptinotarsa decemlineata). Gamma-irradiation of NB125 resulted in strain NB176-1 (DSM 5480) that exhibited higher cry3Aa production and became the active ingredient of the plant protection product Novodor® FC. Here, we report a comparative genome analysis of the parental strain NB125, its derivative NB176-1 and the current commercial production strain NB176. The entire genome sequences of the parental and derivative strains were deciphered by a hybrid de novo approach using short (Illumina) and long (Nanopore) read sequencing techniques. Genome assembly revealed a chromosome of 5.4 to 5.6 Mbp and six plasmids with a size range from 14.9 to 250.5 kbp for each strain. The major differences among the original NB125 and the derivative strains NB176-1 and NB176 were an additional copy of the cry3Aa gene, which translocated to another plasmid as well as a chromosomal deletion (~ 178 kbp) in NB176. The assembled genome sequences were further analyzed in silico for the presence of virulence and antimicrobial resistance (AMR) genes.
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Affiliation(s)
- Lea Schäfer
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Dossenheim, Germany
| | | | - Regina G. Kleespies
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Dossenheim, Germany
| | - Johannes A. Jehle
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Dossenheim, Germany
| | - Jörg T. Wennmann
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Dossenheim, Germany
- *Correspondence: Jörg T. Wennmann,
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Yossa N, Bell R, Tallent S, Brown E, Binet R, Hammack T. Genomic characterization of Bacillus cereus sensu stricto 3A ES isolated from eye shadow cosmetic products. BMC Microbiol 2022; 22:240. [PMID: 36199032 PMCID: PMC9533521 DOI: 10.1186/s12866-022-02652-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/20/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Bacillus cereus group, also known as B. cereus sensu lato (s.l.) contains ubiquitous spore-forming bacteria found in the environment including strains from the B. cereus sensu stricto (s.s.) species. They occur naturally in a wide range of raw materials and in consumer products. Characterizing isolates that have survived in consumer products allows us to better understand the mechanisms that permit spores to persist and potentially cause illness. Here we characterize the draft genome sequence of B. cereus s. s. 3A-ES, originally isolated from eye shadow and since investigated in several cosmetic studies and compared it to other top ten published complete genome sequences of B. cereus s.l. members. RESULTS The draft genome sequence of B. cereus s.s. 3A ES consisted of an average of 90 contigs comprising approximately 5,335,727 bp and a GC content of 34,988%, and with 5509 predicted coding sequences. Based on the annotation statistics and comparison to other genomes within the same species archived in the Pathosystems Resource Integration Center (PATRIC), this genome "was of good quality. Annotation of B. cereus s.s. 3A ES revealed a variety of subsystem features, virulence factors and antibiotic resistant genes. The phylogenetic analysis of ten B. cereus group members showed B. cereus s.s. 3A-ES to be a closely related homolog of B. cereus s.s. ATCC 14,579, an established reference strain that is not adapted for cosmetic microbiological studies. Survival of 3A-ES in eye shadow could be linked to predicted stress-response genes and strengthened by additional stress-response genes such as VanB-type, VanRB, CAT15/16, BcrA, BcrB, Lsa(B), and recA that are lacking in B. cereus s.s. ATCC 14,579. CONCLUSION Our genomic analysis of B. cereus s.s. 3A-ES revealed genes, which may allow this bacterium to withstand the action of preservatives and inhibitors in cosmetics, as well as virulence factors that could contribute to its pathogenicity. Having a well-characterized strain obtained from eye-shadow may be useful for establishing a reference strain for cosmetics testing.
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Affiliation(s)
- Nadine Yossa
- Office of Regulatory Science, FDA, College Park, MD, 20740, USA.
| | - Rebecca Bell
- Office of Regulatory Science, FDA, College Park, MD, 20740, USA
| | - Sandra Tallent
- Office of Regulatory Science, FDA, College Park, MD, 20740, USA
| | - Eric Brown
- Office of Regulatory Science, FDA, College Park, MD, 20740, USA
| | - Rachel Binet
- Office of Regulatory Science, FDA, College Park, MD, 20740, USA
| | - Thomas Hammack
- Office of Regulatory Science, FDA, College Park, MD, 20740, USA
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Morozova MV, Kalmykova GV, Akulova NI, Ites YV, Korkina VI, Litvinova EA. Autoclaved Diet with Inactivated Spores of Bacillus spp. Decreased Reproductive Performance of Muc2−/− and Muc2+/− Mice. Animals (Basel) 2022; 12:ani12182399. [PMID: 36139259 PMCID: PMC9495189 DOI: 10.3390/ani12182399] [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: 07/24/2022] [Revised: 09/05/2022] [Accepted: 09/12/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Within barrier facilities for the housing of laboratory animals, the sterilization of feed, bedding, and cages is used to reduce contact with bacteria. However, in nature, animals come into contact with a lot of bacteria. We investigated the effect of an autoclaved diet on the reproductive performance of Muc2−/− mice. Muc2−/− mice develop intestinal barrier defects and are sensitive to changes of the gut microbiota. We have shown that the autoclaved diet negatively affects the reproductive performance of Muc2−/− females and their healthy Muc2+/− siblings. Thus, the autoclaved diet led to earlier rectal prolapse of Muc2−/− females combined with intestinal inflammation, compared to mice fed with the non-autoclaved diet. We hypothesize that this effect is due to the reduction of the diet nutritional value and inactivation of Bacillus spp. spores in the autoclaved diet. Abstract Within barrier facilities, autoclaved diet and bedding are used for husbandry of laboratory rodents. Bacillus spp. are ubiquitous in nature and some of them are known as probiotics. Inactivation of the Bacillus spores and reduction of the diet nutritional value due to autoclavation could be especially critical for immunodeficient mice. We studied the effect of the autoclaved and non-autoclaved diets on the reproductive performance and the age of prolapse manifestation in Muc2−/− mice with impaired gut barrier function and, therefore, sensitive to change of microbiota. We found that the non-autoclaved diet led to enhancement of the fertility index of Muc2−/− and Muc2+/− female mice. The non-autoclaved diet affected the prolapse of Muc2−/− mice that occurred later in comparison with females eating the autoclaved diet. We showed that Bacillus spp. was present in the non-autoclaved diet and feces of mice on the non-autoclaved diet. Bacterial strains of the non-autoclaved diet and feces belonged to B. amyloliquefaciens, B. thuringiensis, B. subtilis, Lysinibacillus macrolides, B. cereus, and other representatives of Bacillus spp. Moreover, autoclavation of the diet affected on the percent of the blood and spleen immune cells, the bacterial composition of the intestine, and increased the level of methionine in the thigh muscle of mice. Enhanced reproductive performance and delayed prolapse manifestation in Muc2−/− mice could be due to improved digestion, as Bacillus spp. from diet and feces had enzymatic activity.
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Affiliation(s)
- Maryana V. Morozova
- Scientific-Research Institute of Neurosciences and Medicine, St. Timakova, 4, 630117 Novosibirsk, Russia
| | - Galina V. Kalmykova
- Physical Engineering Faculty, Novosibirsk State Technical University, 630073 Novosibirsk, Russia
| | - Nadezhda I. Akulova
- Physical Engineering Faculty, Novosibirsk State Technical University, 630073 Novosibirsk, Russia
| | - Yuriy V. Ites
- Siberian Federal Scientific Center of Agrobiotechnology RAS, St. Central, 1, 630501 Krasnoobsk, Russia
| | - Valentina I. Korkina
- Siberian Federal Scientific Center of Agrobiotechnology RAS, St. Central, 1, 630501 Krasnoobsk, Russia
| | - Ekaterina A. Litvinova
- Scientific-Research Institute of Neurosciences and Medicine, St. Timakova, 4, 630117 Novosibirsk, Russia
- Physical Engineering Faculty, Novosibirsk State Technical University, 630073 Novosibirsk, Russia
- Correspondence: ; Tel.: +7-923-147-94-64
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Kowalska J, Maćkiw E, Korsak D, Postupolski J. Characteristic and Antimicrobial Resistance of <i>Bacillus cereus</i> Group Isolated from Food in Poland. POL J FOOD NUTR SCI 2022. [DOI: 10.31883/pjfns/152677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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22
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Fraccalvieri R, Bianco A, Difato LM, Capozzi L, Del Sambro L, Simone D, Catanzariti R, Caruso M, Galante D, Normanno G, Palazzo L, Tempesta M, Parisi A. Toxigenic Genes, Pathogenic Potential and Antimicrobial Resistance of Bacillus cereus Group Isolated from Ice Cream and Characterized by Whole Genome Sequencing. Foods 2022; 11:foods11162480. [PMID: 36010481 PMCID: PMC9407285 DOI: 10.3390/foods11162480] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/12/2022] [Accepted: 08/15/2022] [Indexed: 11/22/2022] Open
Abstract
Bacillus cereus is isolated from a variety of foods where it may cause food spoilage and/or food poisoning due to its toxigenic and pathogenic nature. In this study, we identified members of B. cereus groups in 65% of the ice cream samples analyzed, which were characterized based on multi locus variable number tandem repeats analysis (MLVA) and whole genome sequencing (WGS). The MLVA revealed that 36 strains showed different allelic profiles. Analyses of WGS data enabled the identification of three members of the B. cereus group: B. cereus sensu stricto, B. mosaicus and B. thuringiensis. Based on the multi locus sequence typing (MLST) scheme, the strains were classified in 27 sequence types (STs), including ST26 that causes food poisoning. Toxin genes’ detection revealed the presence of the genes encoding nonhemolytic enterotoxin (NHE), hemolysin BL (HBL), cytotoxin K (cytK) and cereulide (ces) in 100%, 44%, 42% and 8% of the strains, respectively. The identification of eleven antimicrobial resistance (AMR) genes predicted the resistance to five different antimicrobials, and the resistance to beta-lactam antibiotics was confirmed with a phenotypic antimicrobial test. Taken together, the results showed that the B. cereus strains isolated from ice cream were a potential hazard for consumer safety.
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Affiliation(s)
- Rosa Fraccalvieri
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB), Via Manfredonia 20, 71121 Foggia, Italy
| | - Angelica Bianco
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB), Via Manfredonia 20, 71121 Foggia, Italy
- Experimental Zooprophylactic Institute of Apulia and Basilicata, 71121 Foggia, Italy
- Correspondence: ; Tel.: +39-080-4057858; Fax: +39-080-4057753
| | - Laura Maria Difato
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB), Via Manfredonia 20, 71121 Foggia, Italy
| | - Loredana Capozzi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB), Via Manfredonia 20, 71121 Foggia, Italy
| | - Laura Del Sambro
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB), Via Manfredonia 20, 71121 Foggia, Italy
| | - Domenico Simone
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB), Via Manfredonia 20, 71121 Foggia, Italy
| | - Roberta Catanzariti
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB), Via Manfredonia 20, 71121 Foggia, Italy
| | - Marta Caruso
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB), Via Manfredonia 20, 71121 Foggia, Italy
| | - Domenico Galante
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB), Via Manfredonia 20, 71121 Foggia, Italy
| | - Giovanni Normanno
- Department of Science of Agriculture, Food and the Environment (SAFE), University of Foggia, 71121 Foggia, Italy
| | - Lucia Palazzo
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB), Via Manfredonia 20, 71121 Foggia, Italy
| | - Maria Tempesta
- Department of Veterinary Medicine, University Aldo Moro of Bari, Strada per Casamassima Km 3, 70010 Valenzano, Italy
| | - Antonio Parisi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB), Via Manfredonia 20, 71121 Foggia, Italy
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Mancini ME, Beverelli M, Donatiello A, Didonna A, Dattoli L, Faleo S, Occhiochiuso G, Galante D, Rondinone V, Del Sambro L, Bianco A, Miccolupo A, Goffredo E. Isolation and characterization of Yersinia enterocolitica from foods in Apulia and Basilicata regions (Italy) by conventional and modern methods. PLoS One 2022; 17:e0268706. [PMID: 35830422 PMCID: PMC9278756 DOI: 10.1371/journal.pone.0268706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 05/05/2022] [Indexed: 12/03/2022] Open
Abstract
Yersiniosis is the third most reported food-borne zoonosis in Europe. The aim of the present study was to perform the search for Yersinia enterocolitica in food samples collected from Apulia and Basilicata regions (Southern Italy) and to characterize any isolates by classical and modern analytical methods. A total of 130 samples were analyzed between July 2018 and July 2019: most of them were raw milk and dairy products made from it. Furthermore, 8 out of 130 samples were individual milk samples collected from bovines reared in a Brucella-free farm which showed false positive serological reaction for brucellosis due to the presence of pathogenic Y. enterocolitica O:9 biotype 2 in faeces. The Real Time PCR targeting the ail gene and the culture method were performed to detect pathogenic Y. enterocolitica. Isolates were subjected to API 20E (Biomerieux) and MALDI-TOF MS (Matrix Assisted Laser Desorption Ionization Time-of-Flight) for species identification. All samples were negative for the ail gene. The culture method allowed to isolate suspicious colonies from 28 samples. The API 20E system and the MALDI-TOF MS technique identified 20 Y. enterocolitica and 1 Y. intermedia in a concordant way. The remaining 7 strains were all identified as Y. enterocolitica by the API 20E system, while the MALDI-TOF MS recognized 4 Y. intermedia, 1 Y. bercovieri and 2 Y. massiliensis. Genotypic characterization of the discordant strains was performed by rMLST and it confirmed the MALDI-TOF MS’ results. Only non-pathogenic Y. enterocolitica biotype 1A strains were found, although with a non-negligible prevalence (P = 0.15 with CI 95% = ± 0.06). This study indicates a poor circulation of pathogenic Y. enterocolitica in food products made and marketed in the investigated areas. However, the small number of samples, insufficient for some food categories such as meat and vegetable, does not allow to exclude the presence of pathogenic strains at all.
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Affiliation(s)
- Maria Emanuela Mancini
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
- * E-mail:
| | - Matteo Beverelli
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Adelia Donatiello
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Antonella Didonna
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Luigi Dattoli
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Simona Faleo
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Gilda Occhiochiuso
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Domenico Galante
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Valeria Rondinone
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Laura Del Sambro
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Angelica Bianco
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Angela Miccolupo
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Elisa Goffredo
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
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Detection of emetic Bacillus cereus and the emetic toxin cereulide in food matrices: Progress and perspectives. Trends Food Sci Technol 2022. [DOI: 10.1016/j.tifs.2022.03.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Algammal AM, Alfifi KJ, Mabrok M, Alatawy M, Abdel-moneam DA, Alghamdi S, Azab MM, Ibrahim RA, Hetta HF, El-Tarabili RM. Newly Emerging MDR B. cereus in Mugil seheli as the First Report Commonly Harbor nhe, hbl, cytK, and pc-plc Virulence Genes and bla1, bla2, tetA, and ermA Resistance Genes. Infect Drug Resist 2022; 15:2167-2185. [PMID: 35498633 PMCID: PMC9052338 DOI: 10.2147/idr.s365254] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 04/15/2022] [Indexed: 01/23/2023] Open
Abstract
Background Bacillus cereus is a common food poisoning pathogen in humans. This study aimed to investigate the prevalence, molecular typing, antibiogram profile, pathogenicity, dissemination of virulence and antibiotic resistance genes associated with natural B. cereus infection among Mugil seheli. Methods Consequently, 120 M. seheli (40 healthy and 80 diseased) were obtained from private fish farms in Port-said Governorate, Egypt. Afterward, samples were processed for clinical, post-mortem, and bacteriological examinations. The recovered isolates were tested for antimicrobial susceptibility, phenotypic assessment of virulence factors, pathogeneicity, and PCR-based detection of virulence and antibiotic resistance genes. Results B. cereus was isolated from 30 (25%) examined fish; the highest prevalence was noticed in the liver (50%). The phylogenetic and sequence analyses of the gyrB gene revealed that the tested B. cereus isolate displayed a high genetic similarity with other B. cereus strains from different origins. All the recovered B. cereus isolates (n =60, 100%) exhibited β-hemolytic and lecithinase activities, while 90% (54/60) of the tested isolates were biofilm producers. Using PCR, the tested B. cereus isolates harbor nhe, hbl, cytK, pc-plc, and ces virulence genes with prevalence rates of 91.6%, 86.6%, 83.4%, 50%, and 33.4%, respectively. Moreover, 40% (24/60) of the tested B. cereus isolates were multidrug-resistant (MDR) to six antimicrobial classes and carried the bla1, bla2, tetA, and ermA genes. The experimentally infected fish with B. cereus showed variable mortality in direct proportion to the inoculated doses. Conclusion As far as we know, this is the first report that emphasized the existence of MDR B. cereus in M. seheli that reflects a threat to the public health and the aquaculture sector. Newly emerging MDR B. cereus in M. seheli commonly carried virulence genes nhe, hbl, cytK, and pc-plc, as well as resistance genes bla1, bla2, tetA, and ermA.
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Affiliation(s)
- Abdelazeem M Algammal
- Department of Bacteriology, Immunology, and Mycology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, 41522, Egypt
| | - Khyreyah J Alfifi
- Biology Department, Faculty of Science, Tabuk University, Tabuk, 71421, Saudi Arabia
| | - Mahmoud Mabrok
- Department of Fish Diseases and Management, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, 41522, Egypt
| | - Marfat Alatawy
- Biology Department, Faculty of Science, Tabuk University, Tabuk, 71421, Saudi Arabia
| | - Dalia A Abdel-moneam
- Department of Aquatic Animal Medicine and Management, Faculty of Veterinary Medicine, Cairo University, Cairo, 12613, Egypt
| | - Saad Alghamdi
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Marwa M Azab
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Ismailia, 41522, Egypt
| | - Reham A Ibrahim
- Marine Environmental Division- National Institute of Oceanography and Fisheries (NIOF), Suez, 43511, Egypt
| | - Helal F Hetta
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut, 71515, Egypt
| | - Reham M El-Tarabili
- Department of Bacteriology, Immunology, and Mycology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, 41522, Egypt
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Comparative analysis of Bacillus cereus group isolates' resistance using disk diffusion and broth microdilution and the correlation between antimicrobial resistance phenotypes and genotypes. Appl Environ Microbiol 2022; 88:e0230221. [PMID: 35225691 PMCID: PMC8939351 DOI: 10.1128/aem.02302-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacillus cereus group isolates (n = 85) were screened for phenotypic resistance to 18 antibiotics using broth microdilution and CLSI M45 Bacillus spp. breakpoints. The susceptibility to 9 out of 18 antibiotics was tested also using disk diffusion method and M100 Staphylococcus spp. breakpoints. Overall, a high prevalence of susceptibility to clinically relevant antibiotics was identified using broth microdilution. For most tested antibiotics, a poor correlation was found between zones of inhibition and minimum inhibitory concentrations. Using the broth microdilution results as a reference for comparison, we identified high error rates and low categorical agreement between results produced using disk diffusion and broth microdilution for the seven tested antibiotics with defined breakpoints. This suggests that disk diffusion should be avoided for AST of B. cereus group isolates. Further, we detected antimicrobial resistance genes with ARIBA and ABRIcate to calculate the sensitivity and specificity for predicting phenotypic resistance determined using broth microdilution based on the presence of detected antimicrobial resistance genes (ARGs). ARGs with poor sensitivity and high specificity included rph (rifampicin, 0%, 93%), mph (erythromycin, 0%, 99%), bla1 (penicillin, 29%, 100), and blaZ (penicillin, 56%, 100%). Compared to penicillin, bla1 and blaZ had lower specificity for the prediction of ampicillin resistance. Overall, none of the ARGs had both high sensitivity and specificity, suggesting the need for further study of the mechanisms underlying phenotypic antimicrobial resistance in the B. cereus group. IMPORTANCE Bacillus cereus group includes human pathogens that can cause severe infections requiring antibiotic treatment. Screening of environmental and food isolates for antimicrobial resistance can provide insight into what antibiotics may be more effective therapeutic options based on the lower prevalence of resistance. Currently, the comparison of antimicrobial susceptibility testing results using the disk diffusion method is complicated by the fact that many previous studies have used Staphylococcus spp. breakpoints to interpret their results. In this study, we compared the results of disk diffusion interpreted using the Staphylococcus spp. breakpoints against the results of broth microdilution interpreted using Bacillus spp. breakpoints. We demonstrated that the disk diffusion method does not produce reliable results for B. cereus group isolates and should therefore be avoided. This study also provides new insight into poor associations between the presence of antimicrobial resistance genes and resistance phenotypes for the B. cereus group.
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Antimicrobial Susceptibility Profile and Whole-Genome Analysis of a Strong Biofilm-Forming Bacillus Sp. B87 Strain Isolated from Food. Microorganisms 2022; 10:microorganisms10020252. [PMID: 35208707 PMCID: PMC8876208 DOI: 10.3390/microorganisms10020252] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/12/2022] [Accepted: 01/20/2022] [Indexed: 02/04/2023] Open
Abstract
Members of the Bacillus cereus group are considered to be foodborne pathogens commonly associated with diarrheal and emetic gastrointestinal syndromes. Biofilm formation is a major virulence determinant of various pathogenic bacteria, including the B. cereus strains, since it can protect the bacteria against antimicrobial agents and the host immune response. Moreover, a biofilm allows the exchange of genetic material, such as antimicrobial resistance genes, among the different bacterial strains inside the matrix. The aim of the current study was to genotypically and phenotypically characterize Bacillus sp. B87, a strain that was isolated from food and which exhibited strong biofilm-forming capacity. Based on the analysis of the phylogenetic relationship, the isolate was phylogenetically mapped close to Bacillus pacificus. Antimicrobial susceptibility testing revealed that the isolate was resistant to tetracycline and β-lactam antimicrobial agents, which corresponded with the genotypic characterization using the whole-genome analysis. The genome of Bacillus sp. B87 carried the three-component non-hemolytic enterotoxin (NHE), which is a type of enterotoxin that causes diarrheal symptoms. In addition, the genome also contained several genes that participate in biofilm formation, including the pelDEADAFG operon. These findings expand our understanding of antimicrobial resistance and virulence in Bacillus species based on the link between genotypic and phenotypic characterization.
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Sturmer FDCR, Moreira PR, Cargnelutti JF, Lopes LQS, Lorenzett E, Burgo TADL, Santos RCV. Detection and characterization of Bacillus cereus isolated from the dialysis fluid. Rev Inst Med Trop Sao Paulo 2022; 64:e67. [DOI: 10.1590/s1678-9946202264067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 09/23/2022] [Indexed: 11/17/2022] Open
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Capozzi L, Simone D, Bianco A, Del Sambro L, Rondinone V, Pace L, Manzulli V, Iacobellis M, Parisi A. Emerging Mutations Potentially Related to SARS-CoV-2 Immune Escape: The Case of a Long-Term Patient. Life (Basel) 2021; 11:1259. [PMID: 34833135 PMCID: PMC8625042 DOI: 10.3390/life11111259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 11/16/2022] Open
Abstract
SARS-CoV-2 isolates from long-term COVID-19 patients play a significant role in understanding the mechanisms of infection and virus persistence. This study describes a SARS-CoV-2 isolate from a 53-year-old woman from Apulia (Italy), who was COVID-19 positive for approximately four months. In this paper we aimed to investigate any potential correlation between genetic mutations and clinical features of this case of infection. The viral isolate was assigned to lineage B.1.177.51 through whole-genome sequencing (WGS) and harbored a novel set of mutations on the Spike protein (V143D, del144/145 and E484K); furthermore, seroneutralization assays showed impaired response of the surveyed strain to BNT162b2 (Comirnaty) Pfizer/BioNTech vaccine-induced (average reduction of 70%) and convalescent sera (average reduction of 19.04%), when compared to VOC P.1. This study highlights the importance of genomic surveillance for the management of the COVID-19 pandemic, the relevance of monitoring of emerging SARS-CoV-2 mutations in all lineages, and the necessity of testing the response of emerging variants to available therapies and vaccines.
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Affiliation(s)
- Loredana Capozzi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (L.C.); (D.S.); (A.B.); (L.D.S.); (V.R.); (L.P.); (V.M.)
| | - Domenico Simone
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (L.C.); (D.S.); (A.B.); (L.D.S.); (V.R.); (L.P.); (V.M.)
| | - Angelica Bianco
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (L.C.); (D.S.); (A.B.); (L.D.S.); (V.R.); (L.P.); (V.M.)
| | - Laura Del Sambro
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (L.C.); (D.S.); (A.B.); (L.D.S.); (V.R.); (L.P.); (V.M.)
| | - Valeria Rondinone
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (L.C.); (D.S.); (A.B.); (L.D.S.); (V.R.); (L.P.); (V.M.)
| | - Lorenzo Pace
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (L.C.); (D.S.); (A.B.); (L.D.S.); (V.R.); (L.P.); (V.M.)
| | - Viviana Manzulli
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (L.C.); (D.S.); (A.B.); (L.D.S.); (V.R.); (L.P.); (V.M.)
| | - Michela Iacobellis
- Cytopathology Department of the Hospital Di Venere, Via Ospedale di Venere 1, 70131 Bari, Italy;
| | - Antonio Parisi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (L.C.); (D.S.); (A.B.); (L.D.S.); (V.R.); (L.P.); (V.M.)
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Tangaro MA, Mandreoli P, Chiara M, Donvito G, Antonacci M, Parisi A, Bianco A, Romano A, Bianchi DM, Cangelosi D, Uva P, Molineris I, Nosi V, Calogero RA, Alessandri L, Pedrini E, Mordenti M, Bonetti E, Sangiorgi L, Pesole G, Zambelli F. Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service. BMC Bioinformatics 2021; 22:544. [PMID: 34749633 PMCID: PMC8574934 DOI: 10.1186/s12859-021-04401-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 09/24/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Improving the availability and usability of data and analytical tools is a critical precondition for further advancing modern biological and biomedical research. For instance, one of the many ramifications of the COVID-19 global pandemic has been to make even more evident the importance of having bioinformatics tools and data readily actionable by researchers through convenient access points and supported by adequate IT infrastructures. One of the most successful efforts in improving the availability and usability of bioinformatics tools and data is represented by the Galaxy workflow manager and its thriving community. In 2020 we introduced Laniakea, a software platform conceived to streamline the configuration and deployment of "on-demand" Galaxy instances over the cloud. By facilitating the set-up and configuration of Galaxy web servers, Laniakea provides researchers with a powerful and highly customisable platform for executing complex bioinformatics analyses. The system can be accessed through a dedicated and user-friendly web interface that allows the Galaxy web server's initial configuration and deployment. RESULTS "Laniakea@ReCaS", the first instance of a Laniakea-based service, is managed by ELIXIR-IT and was officially launched in February 2020, after about one year of development and testing that involved several users. Researchers can request access to Laniakea@ReCaS through an open-ended call for use-cases. Ten project proposals have been accepted since then, totalling 18 Galaxy on-demand virtual servers that employ ~ 100 CPUs, ~ 250 GB of RAM and ~ 5 TB of storage and serve several different communities and purposes. Herein, we present eight use cases demonstrating the versatility of the platform. CONCLUSIONS During this first year of activity, the Laniakea-based service emerged as a flexible platform that facilitated the rapid development of bioinformatics tools, the efficient delivery of training activities, and the provision of public bioinformatics services in different settings, including food safety and clinical research. Laniakea@ReCaS provides a proof of concept of how enabling access to appropriate, reliable IT resources and ready-to-use bioinformatics tools can considerably streamline researchers' work.
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Affiliation(s)
- Marco Antonio Tangaro
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR), Via Giovanni Amendola 122/O, 70126, Bari, Italy
- National Institute for Nuclear Physics (INFN), Section of Bari, Via Orabona 4, 70126, Bari, Italy
| | - Pietro Mandreoli
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR), Via Giovanni Amendola 122/O, 70126, Bari, Italy
- Department of Biosciences, University of Milan, Via Celoria 26, 20133, Milano, Italy
| | - Matteo Chiara
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR), Via Giovanni Amendola 122/O, 70126, Bari, Italy
- Department of Biosciences, University of Milan, Via Celoria 26, 20133, Milano, Italy
| | - Giacinto Donvito
- National Institute for Nuclear Physics (INFN), Section of Bari, Via Orabona 4, 70126, Bari, Italy
| | - Marica Antonacci
- National Institute for Nuclear Physics (INFN), Section of Bari, Via Orabona 4, 70126, Bari, Italy
| | - Antonio Parisi
- Istituto Zooprofilattico Sperimentale Della Puglia e Della Basilicata, Via Manfredonia 20, 71121, Foggia, Italy
| | - Angelica Bianco
- Istituto Zooprofilattico Sperimentale Della Puglia e Della Basilicata, Via Manfredonia 20, 71121, Foggia, Italy
| | - Angelo Romano
- National Reference Laboratory for Coagulase-Positive Staphylococci Including Staphylococcus Aureus, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Via Bologna 148, 10154, Turin, Italy
| | - Daniela Manila Bianchi
- National Reference Laboratory for Coagulase-Positive Staphylococci Including Staphylococcus Aureus, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Via Bologna 148, 10154, Turin, Italy
| | - Davide Cangelosi
- Clinical Bioinformatics Unit, Scientific Direction, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147, Genova, Italy
| | - Paolo Uva
- Clinical Bioinformatics Unit, Scientific Direction, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147, Genova, Italy
- Italian Institute of Technology, Via Morego 30, 16163, Genova, Italy
| | - Ivan Molineris
- Department of Life Science and System Biology, University of Turin, Via Accademia Albertina, 13-1023, Turin, Italy
| | - Vladimir Nosi
- Department of Computer Science, University of Turin, Via Pessinetto 12, 10049, Turin, Italy
| | - Raffaele A Calogero
- Department of Molecular Biotechnology and Health Sciences, Via Nizza 52, 10126, Turin, Italy
| | - Luca Alessandri
- Department of Molecular Biotechnology and Health Sciences, Via Nizza 52, 10126, Turin, Italy
| | - Elena Pedrini
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136, Bologna, Italy
| | - Marina Mordenti
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136, Bologna, Italy
| | - Emanuele Bonetti
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136, Bologna, Italy
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Luca Sangiorgi
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136, Bologna, Italy
| | - Graziano Pesole
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR), Via Giovanni Amendola 122/O, 70126, Bari, Italy.
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona 4, 70126, Bari, Italy.
| | - Federico Zambelli
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR), Via Giovanni Amendola 122/O, 70126, Bari, Italy.
- Department of Biosciences, University of Milan, Via Celoria 26, 20133, Milano, Italy.
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Antimicrobial Effects of Potential Probiotics of Bacillus spp. Isolated from Human Microbiota: In Vitro and In Silico Methods. Microorganisms 2021; 9:microorganisms9081615. [PMID: 34442694 PMCID: PMC8399655 DOI: 10.3390/microorganisms9081615] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 12/14/2022] Open
Abstract
The variable taxa components of human gut microbiota seem to have an enormous biotechnological potential that is not yet well explored. To investigate the usefulness and applications of its biocompounds and/or bioactive substances would have a dual impact, allowing us to better understand the ecology of these microbiota consortia and to obtain resources for extended uses. Our research team has obtained a catalogue of isolated and typified strains from microbiota showing resistance to dietary contaminants and obesogens. Special attention was paid to cultivable Bacillus species as potential next-generation probiotics (NGP) together with their antimicrobial production and ecological impacts. The objective of the present work focused on bioinformatic genome data mining and phenotypic analyses for antimicrobial production. In silico methods were applied over the phylogenetically closest type strain genomes of the microbiota Bacillus spp. isolates and standardized antimicrobial production procedures were used. The main results showed partial and complete gene identification and presence of polyketide (PK) clusters on the whole genome sequences (WGS) analysed. Moreover, specific antimicrobial effects against B. cereus, B. circulans, Staphylococcus aureus, Streptococcus pyogenes, Escherichia coli, Serratia marcescens, Klebsiella spp., Pseudomonas spp., and Salmonella spp. confirmed their capacity of antimicrobial production. In conclusion, Bacillus strains isolated from human gut microbiota and taxonomic group, resistant to Bisphenols as xenobiotics type endocrine disruptors, showed parallel PKS biosynthesis and a phenotypic antimicrobial effect. This could modulate the composition of human gut microbiota and therefore its functionalities, becoming a predominant group when high contaminant exposure conditions are present.
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Trotta A, Del Sambro L, Galgano M, Ciccarelli S, Ottone E, Simone D, Parisi A, Buonavoglia D, Corrente M. Salmonella enterica Subsp. houtenae Associated with an Abscess in Young Roe Deer ( Capreolus capreolus). Pathogens 2021; 10:pathogens10060654. [PMID: 34070532 PMCID: PMC8227071 DOI: 10.3390/pathogens10060654] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 05/16/2021] [Accepted: 05/20/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND S. enterica subsp. houtenae has been rarely documented, and very limited genomic information is available. This report describes a rare case of primary extraintestinal salmonellosis in a young roe deer, associated with Salmonella enterica subsp. houtenae. Methods: A traditional cultural-based analysis was carried out from the contents of a neck abscess; biochemical identification and PCR assay were performed to isolate and identify the pathogen. Through whole-genome sequencing (WGS), multilocus sequence typing (MLST), core genome MLST (cgMLST), and the Salmonella pathogenicity islands (SPIs) survey, resistome and virulome genes were investigated to gain insight into the virulence and antimicrobial resistance of S. houtenae. RESULTS Biochemical identification and PCR confirmed the presence of Salmonella spp. in the swelling. The WGS analysis identified Salmonella enterica subspecies houtenae serovar 43:z4,z23:- and ST 958. The virulence study predicted a multidrug resistance pattern with resistance shown against aminoglycosides, tetracycline, beta-lactamase, fluoroquinolones, fosfomycin, nitroimidazole, aminocoumarin, and peptide. Fifty-three antibiotic-resistant genes were identified. No plasmids were detected. CONCLUSION This study demonstrates the importance of continuous surveillance of pathogenic salmonellae. Biomolecular analyses combined with epidemiological data can provide important information about poorly described Salmonella strains and can help to improve animal welfare.
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Affiliation(s)
- Adriana Trotta
- Department of Veterinary Medicine, University of Bari “Aldo Moro”, Str. Prov. per Casamassima Km 3, 70010 Valenzano, BA, Italy; (A.T.); (M.G.); (S.C.); (D.B.)
| | - Laura Del Sambro
- Istituto Zooprofilattico Sperimentale della Puglia e Basilicata, Sezione di Putignano, Contrada San Pietro Piturno, 70017 Putignano, BA, Italy; (L.D.S.); (D.S.); (A.P.)
| | - Michela Galgano
- Department of Veterinary Medicine, University of Bari “Aldo Moro”, Str. Prov. per Casamassima Km 3, 70010 Valenzano, BA, Italy; (A.T.); (M.G.); (S.C.); (D.B.)
| | - Stefano Ciccarelli
- Department of Veterinary Medicine, University of Bari “Aldo Moro”, Str. Prov. per Casamassima Km 3, 70010 Valenzano, BA, Italy; (A.T.); (M.G.); (S.C.); (D.B.)
| | - Erika Ottone
- Parco Nazionale Pollino, Complesso Monumentale Santa Maria della Consolazione, 85048 Rotonda, PZ, Italy;
| | - Domenico Simone
- Istituto Zooprofilattico Sperimentale della Puglia e Basilicata, Sezione di Putignano, Contrada San Pietro Piturno, 70017 Putignano, BA, Italy; (L.D.S.); (D.S.); (A.P.)
| | - Antonio Parisi
- Istituto Zooprofilattico Sperimentale della Puglia e Basilicata, Sezione di Putignano, Contrada San Pietro Piturno, 70017 Putignano, BA, Italy; (L.D.S.); (D.S.); (A.P.)
| | - Domenico Buonavoglia
- Department of Veterinary Medicine, University of Bari “Aldo Moro”, Str. Prov. per Casamassima Km 3, 70010 Valenzano, BA, Italy; (A.T.); (M.G.); (S.C.); (D.B.)
| | - Marialaura Corrente
- Department of Veterinary Medicine, University of Bari “Aldo Moro”, Str. Prov. per Casamassima Km 3, 70010 Valenzano, BA, Italy; (A.T.); (M.G.); (S.C.); (D.B.)
- Correspondence:
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Capozzi L, Bianco A, Del Sambro L, Simone D, Lippolis A, Notarnicola M, Pesole G, Pace L, Galante D, Parisi A. Genomic Surveillance of Circulating SARS-CoV-2 in South East Italy: A One-Year Retrospective Genetic Study. Viruses 2021; 13:731. [PMID: 33922257 PMCID: PMC8147059 DOI: 10.3390/v13050731] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/16/2021] [Accepted: 04/19/2021] [Indexed: 02/06/2023] Open
Abstract
In order to provide insights into the evolutionary and epidemiological viral dynamics during the current COVID-19 pandemic in South Eastern Italy, a total of 298 genomes of SARS-CoV-2 strains collected in the Apulia and Basilicata regions, between March 2020 and January 2021, were sequenced. The genomic analysis performed on the draft genomes allowed us to assign the genetic clades and lineages of belonging to each sample and provide an overview of the main circulating viral variants. Our data showed the spread in Apulia and Basilicata of SARS-CoV-2 variants which have emerged during the second wave of infections and are being currently monitored worldwide for their increased transmission rate and their possible impact on vaccines and therapies. These results emphasize the importance of genome sequencing for the epidemiological surveillance of the new SARS-CoV-2 variants' spread.
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Affiliation(s)
- Loredana Capozzi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia, 20, 71121 Foggia, Italy; (L.C.); (A.B.); (L.D.S.); (D.S.); (L.P.); (D.G.)
| | - Angelica Bianco
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia, 20, 71121 Foggia, Italy; (L.C.); (A.B.); (L.D.S.); (D.S.); (L.P.); (D.G.)
| | - Laura Del Sambro
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia, 20, 71121 Foggia, Italy; (L.C.); (A.B.); (L.D.S.); (D.S.); (L.P.); (D.G.)
| | - Domenico Simone
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia, 20, 71121 Foggia, Italy; (L.C.); (A.B.); (L.D.S.); (D.S.); (L.P.); (D.G.)
| | - Antonio Lippolis
- National Institute of Gastroenterology “S. de Bellis”, Institute of Research, Via Turi, 27, 70013 Castellana Grotte, Italy; (A.L.); (M.N.)
| | - Maria Notarnicola
- National Institute of Gastroenterology “S. de Bellis”, Institute of Research, Via Turi, 27, 70013 Castellana Grotte, Italy; (A.L.); (M.N.)
| | - Graziano Pesole
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, CNR, Via Amendola 122/O, 70126 Bari, Italy;
| | - Lorenzo Pace
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia, 20, 71121 Foggia, Italy; (L.C.); (A.B.); (L.D.S.); (D.S.); (L.P.); (D.G.)
| | - Domenico Galante
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia, 20, 71121 Foggia, Italy; (L.C.); (A.B.); (L.D.S.); (D.S.); (L.P.); (D.G.)
| | - Antonio Parisi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia, 20, 71121 Foggia, Italy; (L.C.); (A.B.); (L.D.S.); (D.S.); (L.P.); (D.G.)
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