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Sheinman M, Arndt PF, Massip F. Modeling the mosaic structure of bacterial genomes to infer their evolutionary history. Proc Natl Acad Sci U S A 2024; 121:e2313367121. [PMID: 38517978 PMCID: PMC10990148 DOI: 10.1073/pnas.2313367121] [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: 08/03/2023] [Accepted: 01/30/2024] [Indexed: 03/24/2024] Open
Abstract
The chronology and phylogeny of bacterial evolution are difficult to reconstruct due to a scarce fossil record. The analysis of bacterial genomes remains challenging because of large sequence divergence, the plasticity of bacterial genomes due to frequent gene loss, horizontal gene transfer, and differences in selective pressure from one locus to another. Therefore, taking advantage of the rich and rapidly accumulating genomic data requires accurate modeling of genome evolution. An important technical consideration is that loci with high effective mutation rates may diverge beyond the detection limit of the alignment algorithms used, biasing the genome-wide divergence estimates toward smaller divergences. In this article, we propose a novel method to gain insight into bacterial evolution based on statistical properties of genome comparisons. We find that the length distribution of sequence matches is shaped by the effective mutation rates of different loci, by the horizontal transfers, and by the aligner sensitivity. Based on these inputs, we build a model and show that it accounts for the empirically observed distributions, taking the Enterobacteriaceae family as an example. Our method allows to distinguish segments of vertical and horizontal origins and to estimate the time divergence and exchange rate between any pair of taxa from genome-wide alignments. Based on the estimated time divergences, we construct a time-calibrated phylogenetic tree to demonstrate the accuracy of the method.
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Affiliation(s)
- Michael Sheinman
- Institute for Advanced Studies, Sevastopol State University, Sevastopol299053, Crimea
| | - Peter F. Arndt
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin12163, Germany
| | - Florian Massip
- Department U900, Centre for Computational Biology, Mines Paris, PSL University, Paris75006, France
- Department U900, Institut Curie, Université Paris Sciences et Lettres, Paris75005, France
- INSERM, U900, Paris75005, France
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2
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Richie TG, Heeren L, Kamke A, Monk K, Pogranichniy S, Summers T, Wiechman H, Ran Q, Sarkar S, Plattner BL, Lee STM. Limitation of amino acid availability by bacterial populations during enhanced colitis in IBD mouse model. mSystems 2023; 8:e0070323. [PMID: 37909786 PMCID: PMC10746178 DOI: 10.1128/msystems.00703-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/27/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Inflammatory bowel disease is associated with an increase in Enterobacteriaceae and Enterococcus species; however, the specific mechanisms are unclear. Previous research has reported the associations between microbiota and inflammation, here we investigate potential pathways that specific bacteria populations use to drive gut inflammation. Richie et al. show that these bacterial populations utilize an alternate sulfur metabolism and are tolerant of host-derived immune-response products. These metabolic pathways drive host gut inflammation and fuel over colonization of these pathobionts in the dysbiotic colon. Cultured isolates from dysbiotic mice indicated faster growth supplemented with L-cysteine, showing these microbes can utilize essential host nutrients.
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Affiliation(s)
- Tanner G. Richie
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Leah Heeren
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Abigail Kamke
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Kourtney Monk
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | | | - Trey Summers
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Hallie Wiechman
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Qinghong Ran
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Soumyadev Sarkar
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Brandon L. Plattner
- Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, Kansas, USA
| | - Sonny T. M. Lee
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
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3
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Yamakawa M, Wada K, Hayashi M, Ezaki T, Nakashima Y, Nagata C, Sumoto Y. Milk and dairy product intakes, intestinal bacteria, and respiratory infections in children of elementary school age and older in Japan. Nutrition 2023; 115:112145. [PMID: 37517304 DOI: 10.1016/j.nut.2023.112145] [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: 04/05/2023] [Revised: 06/11/2023] [Accepted: 06/27/2023] [Indexed: 08/01/2023]
Abstract
OBJECTIVES The aim of this study was to examine the associations between milk and dairy product intakes, intestinal bacteria, and respiratory infections in children of elementary school age and older in Japan. METHODS We conducted cross-sectional surveys each year from 2013 to 2015 for grades 2, 5, and 8 students of an elementary and junior high school (n = 1020). Exclusion owing to ineligibility regarding data on dietary intake, respiratory infections, and intestinal bacteria led to 922 participants for the analyses. Dietary intake was assessed with a self-administered food frequency questionnaire. Respiratory infections occurring ≥ 4 episodes over the past year were determined based on the caregivers' reports. Intestinal bacteria (species and counts) were analyzed with real-time polymerase chain reaction. Logistic regression models were used to estimate the odds ratios (ORs) and 95% CIs. RESULTS The odds of ≥ 4 respiratory infection episodes decreased with higher milk intake after adjusting for potential confounders, and the ORs (95% CIs) for the second and third tertile categories, compared with the first tertile category, were 0.91 (0.58-1.42) and 0.48 (0.29-0.77), respectively (P for trend = 0.001). A decreasing trend in the ORs for lactic acid drink intake was observed only in those with a low count of intestinal Faecalibacterium prausnitzii. CONCLUSIONS We found that higher milk intake was inversely associated with respiratory infections in children older than preschool age. Higher lactic acid drink intake could be inversely associated only in children with a low F. prausnitzii count in the intestine.
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Affiliation(s)
- Michiyo Yamakawa
- Department of Epidemiology and Preventive Medicine, Gifu University Graduate School of Medicine, Gifu, Japan.
| | - Keiko Wada
- Department of Epidemiology and Preventive Medicine, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Masahiro Hayashi
- Division of Anaerobe Research, Life Science Research Center, Gifu University, Gifu, Japan; Center for Conservation of Microbial Genetic Resource, Gifu University, Gifu, Japan
| | - Takayuki Ezaki
- Center for Conservation of Microbial Genetic Resource, Gifu University, Gifu, Japan
| | - Yuma Nakashima
- Department of Epidemiology and Preventive Medicine, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Chisato Nagata
- Department of Epidemiology and Preventive Medicine, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Yoshio Sumoto
- Department of Social Studies Education, Graduate School of Education, Gifu University, Gifu, Japan
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4
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Reis FYT, Rocha VP, Janampa-Sarmiento PC, Costa HL, Egger RC, Passos NC, de Assis CHS, Carneiro SP, Santos ÁF, Silva BA, Dorella FA, Leibowitz MP, Luz RK, Pierezan F, Gallani SU, Tavares GC, Figueiredo HCP. Edwardsiella tarda in Tambaqui ( Colossoma macropomum): A Pathogenicity, Antimicrobial Susceptibility, and Genetic Analysis of Brazilian Isolates. Animals (Basel) 2023; 13:2910. [PMID: 37760310 PMCID: PMC10526069 DOI: 10.3390/ani13182910] [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: 08/17/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Edwardsiella tarda is a crucial pathogenic bacterium in tropical aquaculture. This bacterium was recently isolated from tambaqui (Colossoma macropomum), a commercially important fish species in Brazil. This study assessed the antimicrobial susceptibility, pathogenicity, and genetic diversity of the tambaqui-derived E. tarda isolates. Fourteen bacterial isolates isolated from tambaqui were identified as E. tarda by using matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry and dnaJ gene sequencing. Antimicrobial susceptibility tests were conducted against seven drugs using the disc diffusion assay. The pathogenicity test conducted by intraperitoneal injection of 2.4 × 107 colony-forming units (CFU) fish-1 of E. tarda (ED38-17) into tambaqui juveniles eventually revealed that neither clinical signs nor death were present. However, splenomegaly and whitish areas in the spleen and kidneys were observed. The histological investigation also revealed granulomatous splenitis, nephritis, and hepatitis occurring internally. Repetitive extragenic palindromic-PCR fingerprinting separated the 14 isolates into three genetic groups. The antibiogram revealed that all E. tarda isolates were wild-type (WT) to florfenicol (FLO), norfloxacin (NOR), neomycin (NEO), erythromycin (ERY), and oxytetracycline (OXY); however, some were non-wild-type to sulfamethoxazole/trimethoprim (7.1%) and amoxicillin (21.4%). Therefore, through experimental infection, E. tarda ED38-17 could induce pathogenic effects in C. macropomum. Additionally, three distinct genetic types were found, and the E. tarda isolates were WT to FLO, NOR, NEO, ERY, and OXY. These findings raise awareness of a bacteria causing unseen lesions, a pathogen that will potentially impact tambaqui aquaculture in the future.
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Affiliation(s)
- Francisco Yan Tavares Reis
- Department of Preventive Veterinary Medicine, School of Veterinary Medicine, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (F.Y.T.R.); (V.P.R.)
| | - Victória Pontes Rocha
- Department of Preventive Veterinary Medicine, School of Veterinary Medicine, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (F.Y.T.R.); (V.P.R.)
| | - Peter Charrie Janampa-Sarmiento
- Department of Preventive Veterinary Medicine, School of Veterinary Medicine, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (F.Y.T.R.); (V.P.R.)
| | - Henrique Lopes Costa
- Department of Preventive Veterinary Medicine, School of Veterinary Medicine, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (F.Y.T.R.); (V.P.R.)
| | - Renata Catão Egger
- Department of Preventive Veterinary Medicine, School of Veterinary Medicine, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (F.Y.T.R.); (V.P.R.)
| | - Naísa Cristine Passos
- Department of Preventive Veterinary Medicine, School of Veterinary Medicine, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (F.Y.T.R.); (V.P.R.)
| | - Carlos Henrique Santos de Assis
- Department of Preventive Veterinary Medicine, School of Veterinary Medicine, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (F.Y.T.R.); (V.P.R.)
| | - Sarah Portes Carneiro
- Department of Preventive Veterinary Medicine, School of Veterinary Medicine, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (F.Y.T.R.); (V.P.R.)
| | - Ágna Ferreira Santos
- Department of Veterinary Clinics and Surgery, School of Veterinary Medicine, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
| | - Brendhal Almeida Silva
- Department of Preventive Veterinary Medicine, School of Veterinary Medicine, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (F.Y.T.R.); (V.P.R.)
| | - Fernanda Alves Dorella
- Department of Preventive Veterinary Medicine, School of Veterinary Medicine, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (F.Y.T.R.); (V.P.R.)
| | - Márcia Pimenta Leibowitz
- Department of Preventive Veterinary Medicine, School of Veterinary Medicine, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (F.Y.T.R.); (V.P.R.)
| | - Ronald Kennedy Luz
- Department of Animal Science, School of Veterinary Medicine, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
| | - Felipe Pierezan
- Department of Veterinary Clinics and Surgery, School of Veterinary Medicine, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
| | - Sílvia Umeda Gallani
- Postgraduate Program in Aquaculture, Nilton Lins University, Manaus 69058-030, AM, Brazil
| | - Guilherme Campos Tavares
- Department of Preventive Veterinary Medicine, School of Veterinary Medicine, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (F.Y.T.R.); (V.P.R.)
| | - Henrique César Pereira Figueiredo
- Department of Preventive Veterinary Medicine, School of Veterinary Medicine, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (F.Y.T.R.); (V.P.R.)
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Kong X, Wang H, Guo G, Li P, Tong P, Liu M, Ma X, Dong C, Li Y, Zhang H, Zhang W. Duck sewage source coliphage P762 can lyse STEC and APEC. Virus Genes 2022; 58:436-447. [PMID: 35705841 DOI: 10.1007/s11262-022-01915-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 05/10/2022] [Indexed: 11/27/2022]
Abstract
Multiple pathogenic types or serotypes restrict treatment for colibacillosis. In addition, rising antibiotic resistance has heightened public awareness to prevent and control pathogenic Escherichia coli. The bacteriophage is a viable technique to treat colibacillosis as an alternative to antibiotics. P762, a coliphage isolated from duck farm sewage, was demonstrated to cloud lyse Shiga toxin-producing Escherichia Coli serotypes O157 and non-O157 (17/39), Avian pathogenic E. coli covered serotype O78, O83, and O9 (5/19), and other pathogenic Escherichia coli (5/17). Additional fundamental biological characteristics analysis revealed that P762 is stable at pH 3 ~ 11 and temperature between 4 °C and 60 °C, and its optimum multiplicity of infection (MOI) is 0.1. The one-step curve of P762 exhibited three bursts of growth stage: two rapid and one slow stage. Furthermore, the first rapid burst size is 80 CFU/PFU, the burst size of the slow stage is 10 CFU/PFU, and the second rapid burst size is about 990 CFU/PFU. In addition, P762 can form a "halo" on a double agar plate, implying that the phage secretes depolymerase. With 95.14% identity and 90% query coverage, genome sequence analysis revealed that P762 is most closely related to Escherichia phage DY1, which belongs to the genus Kayfunavirus. After screening using RAST and VFDB, no virulence factors were discovered in P762. In vitro antibacterial tests revealed that P762 has high bactericidal activity in lettuce leaves contaminated with STEC. In conclusion, phage P762 might be employed in the future to prevent and control pathogenic Escherichia coli.
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Affiliation(s)
- Xuewei Kong
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Hui Wang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Genglin Guo
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Pei Li
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Panpan Tong
- College of Veterinary Medicine, Shihezi Agricultural University, Xinjiang, China
| | - Maojun Liu
- Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xun Ma
- College of Animal Science and Technology, Xinjiang Agricultural University, Xinjiang, China
| | - Chen Dong
- Jiangsu Province CDC: Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Yubao Li
- Agricultural Science and Engineering School, Liaocheng University, Liaocheng, China
| | - Haiyan Zhang
- Department of Food and Biology Engineering, Wuhu Institute of Technology, Wuhu, China.
| | - Wei Zhang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China.
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.
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Smits THM, Arend LNVS, Cardew S, Tång-Hallbäck E, Mira MT, Moore ERB, Sampaio JLM, Rezzonico F, Pillonetto M. Resolving taxonomic confusion: establishing the genus Phytobacter on the list of clinically relevant Enterobacteriaceae. Eur J Clin Microbiol Infect Dis 2022; 41:547-558. [PMID: 35169969 PMCID: PMC8934334 DOI: 10.1007/s10096-022-04413-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/25/2022] [Indexed: 11/30/2022]
Abstract
Although many clinically significant strains belonging to the family Enterobacteriaceae fall into a restricted number of genera and species, there is still a substantial number of isolates that elude this classification and for which proper identification remains challenging. With the current improvements in the field of genomics, it is not only possible to generate high-quality data to accurately identify individual nosocomial isolates at the species level and understand their pathogenic potential but also to analyse retrospectively the genome sequence databases to identify past recurrences of a specific organism, particularly those originally published under an incorrect or outdated taxonomy. We propose a general use of this approach to classify further clinically relevant taxa, i.e., Phytobacter spp., that have so far gone unrecognised due to unsatisfactory identification procedures in clinical diagnostics. Here, we present a genomics and literature-based approach to establish the importance of the genus Phytobacter as a clinically relevant member of the Enterobacteriaceae family.
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Affiliation(s)
- Theo H M Smits
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences (IUNR), Zurich University of Applied Sciences ZHAW, Wädenswil, Switzerland.
| | - Lavinia N V S Arend
- Central Public Health Laboratory - State of Paraná - LACEN/PR, Molecular Bacteriology Division, São José Dos Pinhais, PR, Brazil
| | - Sofia Cardew
- Culture Collection University of Gothenburg (CCUG), Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
| | - Erika Tång-Hallbäck
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
| | - Marcelo T Mira
- Core for Advanced Molecular Investigation, Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica Do Paraná, Curitiba, PR, Brazil
| | - Edward R B Moore
- Culture Collection University of Gothenburg (CCUG), Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden.,Department of Infectious Disease, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Jorge L M Sampaio
- Faculdade de Ciências Farmacêuticas - University of São Paulo and Fleury Medicina Diagnóstica, São Paulo, SP, Brazil
| | - Fabio Rezzonico
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences (IUNR), Zurich University of Applied Sciences ZHAW, Wädenswil, Switzerland
| | - Marcelo Pillonetto
- Central Public Health Laboratory - State of Paraná - LACEN/PR, Molecular Bacteriology Division, São José Dos Pinhais, PR, Brazil. .,Core for Advanced Molecular Investigation, Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica Do Paraná, Curitiba, PR, Brazil.
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7
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Valdez C, Costa C, Simões M, de Carvalho CCCR, Baptista T, Campos MJ. Detection of mcr-1 Gene in Undefined Vibrio Species Isolated from Clams. Microorganisms 2022; 10:microorganisms10020394. [PMID: 35208850 PMCID: PMC8876837 DOI: 10.3390/microorganisms10020394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/24/2022] [Accepted: 02/03/2022] [Indexed: 01/27/2023] Open
Abstract
The increase of antimicrobial resistant strains is leading to an emerging threat to public health. Pathogenic Vibrio are responsible for human and animal illness. The Enterobacteriaceae family includes microorganisms that affect humans, causing several infections. One of the main causes of human infection is related to the ingestion of undercooked seafood. Due to their filter-feeding habit, marine invertebrates, such as clams, are known to be a natural reservoir of specific microbial communities. In the present study, Vibrionaceae and coliforms microorganisms were isolated from clams. A microbial susceptibility test was performed using the disk diffusion method. From 43 presumptive Vibrio spp. and 17 coliforms, three Vibrio spp. with MICs to colistin >512 mg L−1 were found. From the 23 antimicrobial resistance genes investigated, only the three isolates that showed phenotypic resistance to colistin contained the mcr-1 gene. Genotypic analysis for virulence genes in EB07V indicated chiA gene presence. The results from the plasmid cure and transformation showed that the resistance is chromosomally mediated. Biochemical analysis and MLSA, on the basis of four protein-coding gene sequences (recA, rpoB, groEL and dnaJ), grouped the isolates into the genus Vibrio but distinguished them as different from any known Vibrio spp.
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Affiliation(s)
- Christian Valdez
- MARE-Marine and Environmental Sciences Centre, ESTM, Polytechnic of Leiria, 2520-630 Peniche, Portugal; (C.V.); (C.C.); (M.S.); (T.B.)
| | - Cátia Costa
- MARE-Marine and Environmental Sciences Centre, ESTM, Polytechnic of Leiria, 2520-630 Peniche, Portugal; (C.V.); (C.C.); (M.S.); (T.B.)
| | - Marco Simões
- MARE-Marine and Environmental Sciences Centre, ESTM, Polytechnic of Leiria, 2520-630 Peniche, Portugal; (C.V.); (C.C.); (M.S.); (T.B.)
| | - Carla C. C. R. de Carvalho
- iBB-Institute for Bioengineering and Biosciences, Department of Bioengineering, Associate Laboratory i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal;
| | - Teresa Baptista
- MARE-Marine and Environmental Sciences Centre, ESTM, Polytechnic of Leiria, 2520-630 Peniche, Portugal; (C.V.); (C.C.); (M.S.); (T.B.)
| | - Maria J. Campos
- MARE-Marine and Environmental Sciences Centre, ESTM, Polytechnic of Leiria, 2520-630 Peniche, Portugal; (C.V.); (C.C.); (M.S.); (T.B.)
- Correspondence:
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8
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Hernandez-Alonso E, Barreault S, Augusto LA, Jatteau P, Villet M, Tissieres P, Doucet-Populaire F, Bourgeois-Nicolaos N. dnaJ: a New Approach to Identify Species within the Genus Enterobacter. Microbiol Spectr 2021; 9:e0124221. [PMID: 34937187 PMCID: PMC8694106 DOI: 10.1128/spectrum.01242-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 11/19/2021] [Indexed: 01/19/2023] Open
Abstract
The taxonomy of the genus Enterobacter can be confusing and has been considerably revised in recent years. We propose a PCR and amplicon sequencing technique based on a partial sequence of the dnaJ gene for species assignment consistent with DNA-DNA digital hybridization (dDDH) and pairwise average nucleotide identity (ANI). We performed a validation of the method by comparing the type strains of each species, sequences obtained from the GenBank database, and clinical specimens. Our results show that the polymorphism of the target sequence of dnaJ allows the identification of species. Using this gene, we assigned the species to 100 strains deposited in the GenBank database that were consistent with the species assignment by dDDH and ANI. The analysis showed that using the partial dnaJ sequence is congruent with WGS as far as correct identification of Enterobacter species is concerned. Finally, we applied our dnaJ method on a national collection of 68 strains identified as Enterobacter isolated from the blood cultures of premature babies using an algorithm based on a type-strain library and the SeqScape software. For the first time, we identified Enterobacter quasihormaechei in blood cultures from four neonatal sepsis cases. We also noticed a higher prevalence of E. bugandensis (36.3%; 32/88) and E. xiangfangensis (46.5%; 41/88). E. bugandensis is a novel species recently described specifically in instances of neonatal sepsis. In conclusion, sequencing a part of the dnaJ gene could be a quick, more economical, and highly discriminating method of identifying Enterobacter species in clinical practice and research. IMPORTANCE We propose a new approach for Enterobacter species identification based on the diversity of the gene encoding the heat shock protein DnaJ. This new tool can be easily implemented in clinical laboratories in addition to identification by MALDI-TOF.
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Affiliation(s)
- Enrique Hernandez-Alonso
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
- Department of Bacteriology-Hygiene, AP-HP Université Paris-Saclay, Antoine Beclere Hospital, Clamart, France
| | - Simon Barreault
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
- Department of Pediatrics Intensive Care and Neonatal Medicine, AP-HP Université Paris-Saclay, Bicêtre Hospital, Paris, France
| | - Luis A. Augusto
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Pierre Jatteau
- Department of Bacteriology-Hygiene, AP-HP Université Paris-Saclay, Antoine Beclere Hospital, Clamart, France
| | - Millie Villet
- Department of Bacteriology-Hygiene, AP-HP Université Paris-Saclay, Antoine Beclere Hospital, Clamart, France
| | - Pierre Tissieres
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
- Department of Pediatrics Intensive Care and Neonatal Medicine, AP-HP Université Paris-Saclay, Bicêtre Hospital, Paris, France
- FHU Sepsis, AP-HP/Université Paris-Saclay/Inserm, Le Kremlin-Bicêtre, France
| | - Florence Doucet-Populaire
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
- Department of Bacteriology-Hygiene, AP-HP Université Paris-Saclay, Antoine Beclere Hospital, Clamart, France
| | - Nadege Bourgeois-Nicolaos
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
- Department of Bacteriology-Hygiene, AP-HP Université Paris-Saclay, Antoine Beclere Hospital, Clamart, France
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9
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The Association of the Phylogenetic Typing of the Klebsiella pneumoniae Isolates with Antibiotic Resistance. Emerg Med Int 2021; 2021:1316992. [PMID: 34777863 PMCID: PMC8589475 DOI: 10.1155/2021/1316992] [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: 06/28/2021] [Revised: 10/09/2021] [Accepted: 10/22/2021] [Indexed: 11/17/2022] Open
Abstract
Klebsiella pneumoniae complex (KPC) accounts for approximately one-third of all Gram-negative infections. Moreover, it is highly resistant and can taxonomically be distributed into KpI, KpII, and KpIII phylogroups. This study aimed to investigate the distribution of phylogenetic groups and the relationship between them and antibiotic resistance patterns. For this purpose, we collected KPC isolates from Tabriz, Iran, between 2018 and 2020. Antimicrobial susceptibility testing was performed by disk diffusion agar, and phylogenetic groups were then examined using gyrA restriction fragment length polymorphism (RFLP) and parC PCR methods. A total of 100 KPC isolates were obtained from the clinical specimens (urine, respiratory secretion, blood, wounds, and trachea). The enrolled patients included 47 men and 53 women aged from 1 to 91 years old. The highest sensitivity was found related to fosfomycin as 85%, followed by amikacin as 66%. The three phylogenetically groups by the RFLP-PCR method were found in KPC, 96% (96 isolates) as KpI, 3% (3 isolates) as KpII, and 1% (1isolate) as KpIII. The highest antibiotic resistance was observed in KpI. It was shown that a valid identification of three phylogenetic groups of KPC can be done by combining both gyrA PCR-RFLP and parC PCR. Of note, the KpI group was also observed as the dominant phylogenetic group with the highest resistance to antibiotics.
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10
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Boufafa M, Kadri S, Redder P, Bensouilah M. Occurrence and distribution of fecal indicators and pathogenic bacteria in seawater and Perna perna mussel in the Gulf of Annaba (Southern Mediterranean). ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:46035-46052. [PMID: 33884549 DOI: 10.1007/s11356-021-13978-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 04/13/2021] [Indexed: 06/12/2023]
Abstract
The identification of fecal contamination in coastal marine ecosystems is one of the main requirements for evaluation of potential risks to human health. The objective of this study was to investigate the occurrence and distribution of fecal indicators and pathogenic bacteria in seawaters and mussels collected monthly during a period of 1 year from four different sites in Northeastern Algeria (sites S1 to S4), through biochemical and molecular analyses. Our research is the first to use molecular analysis to unambiguously identify the potentially pathogenic bacteria present in Algerian Perna perna mussels. The obtained results revealed that the levels of fecal indicator bacteria (FIB) from both P. perna and seawater samples largely exceeded the permissible limits at S2 and S3. This is mainly related to their location close to industrial and coastal activity zones, which contain a mixture of urban, agricultural, and industrial pollutants. Besides, P. perna collected from all sites were severalfold more contaminated by FIB than seawater samples, primarily during the warm season of the study period. Biochemical and molecular analyses showed that isolated bacteria from both seawater and mussels were mainly potentially pathogenic species such as E. coli, Salmonella spp., Staphylococcus spp., Klebsiella spp., Pseudomonas spp., and Proteus spp.
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Affiliation(s)
- Mouna Boufafa
- Laboratory of Eco-biology for Marine Environment and Coastlines, Faculty of Science, Badji Moukhtar University, BP 12, 23000, Annaba, Algeria.
| | - Skander Kadri
- Laboratory of Eco-biology for Marine Environment and Coastlines, Faculty of Science, Badji Moukhtar University, BP 12, 23000, Annaba, Algeria
| | - Peter Redder
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Intégrative, Université Paul Sabatier, 118 Route de Narbonne, 31062, Toulouse, France.
| | - Mourad Bensouilah
- Laboratory of Eco-biology for Marine Environment and Coastlines, Faculty of Science, Badji Moukhtar University, BP 12, 23000, Annaba, Algeria
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11
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The Role of Enterobacteriaceae in Gut Microbiota Dysbiosis in Inflammatory Bowel Diseases. Microorganisms 2021; 9:microorganisms9040697. [PMID: 33801755 PMCID: PMC8066304 DOI: 10.3390/microorganisms9040697] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/19/2021] [Accepted: 03/23/2021] [Indexed: 12/12/2022] Open
Abstract
Inflammatory bowel diseases (IBDs) are a group of chronic gastrointestinal inflammatory diseases with unknown etiology. There is a combination of well documented factors in their pathogenesis, including intestinal microbiota dysbiosis. The symbiotic microbiota plays important functions in the host, and the loss of beneficial microbes could favor the expansion of microbial pathobionts. In particular, the bloom of potentially harmful Proteobacteria, especially Enterobacteriaceae, has been described as enhancing the inflammatory response, as observed in IBDs. Herein, we seek to investigate the contribution of Enterobacteriaceae to IBD pathogenesis whilst considering the continuous expansion of the literature and data. Despite the mechanism of their expansion still remaining unclear, their expansion could be correlated with the increase in nitrate and oxygen levels in the inflamed gut and with the bile acid dysmetabolism described in IBD patients. Furthermore, in several Enterobacteriaceae studies conducted at a species level, it has been suggested that some adherent-invasive Escherichia coli (AIEC) play an important role in IBD pathogenesis. Overall, this review highlights the pivotal role played by Enterobacteriaceae in gut dysbiosis associated with IBD pathogenesis and progression.
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12
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Nitrogen Fixation in Pozol, a Traditional Fermented Beverage. Appl Environ Microbiol 2020; 86:AEM.00588-20. [PMID: 32503911 DOI: 10.1128/aem.00588-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/03/2020] [Indexed: 11/20/2022] Open
Abstract
Traditional fermentations have been widely studied from the microbiological point of view, but little is known from the functional perspective. In this work, nitrogen fixation by free-living nitrogen-fixing bacteria was conclusively demonstrated in pozol, a traditional Mayan beverage prepared with nixtamalized and fermented maize dough. Three aspects of nitrogen fixation were investigated to ensure that fixation actually happens in the dough: (i) the detection of acetylene reduction activity directly in the substrate, (ii) the presence of potential diazotrophs, and (iii) an in situ increase in acetylene reduction by inoculation with one of the microorganisms isolated from the dough. Three genera were identified by sequencing the 16S rRNA and nifH genes as Kosakonia, Klebsiella, and Enterobacter, and their ability to fix nitrogen was confirmed.IMPORTANCE Nitrogen-fixing bacteria are found in different niches, as symbionts in plants, in the intestinal microbiome of several insects, and as free-living microorganisms. Their use in agriculture for plant growth promotion via biological nitrogen fixation has been extensively reported. This work demonstrates the ecological and functional importance that these bacteria can have in food fermentations, reevaluating the presence of these genera as an element that enriches the nutritional value of the dough.
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13
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Exclusive use of digital PCR allows an absolute assay of heat-killed Lactobacilli in foods targeting multiple copies of 16S rDNA. Sci Rep 2020; 10:12691. [PMID: 32728064 PMCID: PMC7391674 DOI: 10.1038/s41598-020-69206-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 07/09/2020] [Indexed: 11/15/2022] Open
Abstract
The real-time PCR (qPCR) and digital PCR (dPCR) to amplify a single-copy of house-keeping genes (i.e., hsp60, pheS or tuf) are used for the assay of limited microbial species. In general, with a single-copy gene, there are obviously varied DNA sequences for even the same microbial species, which could cause difficulties with design of primers and probes for PCR when targeting various single copy genes. In general, for identification by dPCR (as a representative case: Lactobacillus paracasei), accumulated DNA sequence information of 16S rDNA, which is much more frequently used, should be targeted. In contrast, next-generation sequencing revealed that there are five copies of 16S rDNA in a live L. paracasei MCC1849. Therefore, we aimed to reveal, if heat-killed L. paracasei supplemented in nutritional foods that aid the host immune system have the relevant five copies per chromosomal DNA, and if the relevant copies remain unchanged on the same chromosomal DNA or remain to be different chromosomal DNA fragments. So, we revealed the actual distribution of the potential original five copies of 16S rDNA using our innovative dPCR, in which both 16S rDNA and hsp60 genes were simultaneously elongated. The molecular ratios of 16S rDNA/hsp60 dispersed in the dPCR chip were then estimated. The 16S rDNA/hsp60 molecular ratios of the heat-killed L. paracasei in foods, resultantly ranged from 5.0 to 7.2, being the same or higher than that of the five copies determined by next-generation sequencing. The 16S rDNA copy number/ratio indicated the chromosomal DNA molecular number and the associated cell number. As significance, different nutritional foods could potentially cause the loss of chromosomal DNA of supplemented beneficial microbes to a much greater degree. Our absolute dPCR does not require standard correlative samples for the estimation of final products. The estimation principle of the ratio of 16S rDNA/a house-keeping single-copy gene by our absolute dPCR could lead to a useful and accurate assay for various nutritional foods.
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14
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Lu Z, Pérez-Díaz IM, Hayes JS, Breidt F. Bacteriophages Infecting Gram-Negative Bacteria in a Commercial Cucumber Fermentation. Front Microbiol 2020; 11:1306. [PMID: 32670232 PMCID: PMC7332585 DOI: 10.3389/fmicb.2020.01306] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 05/22/2020] [Indexed: 11/30/2022] Open
Abstract
Cucumber fermentations are one of the most important vegetable fermentations in the United States. The fermentation is usually driven by lactic acid bacteria (LAB) indigenous to fresh cucumbers. But LAB are greatly outnumbered by many Gram-negative bacteria on fresh cucumbers, which may influence the growth of LAB and the incidence of bloater defect (hollow cavities formed inside fermented cucumbers) leading to serious economic loss to the pickle industry. Rapid elimination of Gram-negative bacteria is crucial to the dominance of LAB and the reduction of bloater defect in the fermentation. Various factors can affect the viability of Gram-negative bacteria in cucumber fermentation. Bacteriophages (phages) may be one of such factors. This study explored the abundance, diversity, and functional role of phages infecting Gram-negative bacteria in a commercial cucumber fermentation. Cover brine samples were taken from a commercial fermentation tank over a 30-day period. On day 1 and day 3 of the fermentation, 39 Gram-negative bacteria and 26 independent phages were isolated. Nearly 67% of Gram-negative bacterial isolates were susceptible to phage infection. Phage hosts include Enterobacter, Citrobacter, Escherichia, Pantoea, Serratia, Leclercia, Providencia, and Pseudomonas species. About 88% of the isolated phages infected the members in the family Enterobacteriaceae and 58% of phages infected Enterobacter species. Eight phages with unique host ranges were characterized. These phages belong to the Myoviridae, Siphoviridae, or Podoviridae family and showed distinct protein profiles and DNA fingerprints. The infectivity of a phage against Enterobacter cancerogenus was evaluated in cucumber juice as a model system. The phage infection at the multiplicity of infection 1 or 100 resulted in a 5-log reduction in cell concentration within 3 h and rapidly eliminated its host. This study revealed the abundance and variety of phages infecting Gram-negative bacteria, particularly Enterobacteriaceae, in the commercial cucumber fermentation, suggesting that phages may play an important role in the elimination of Gram-negative bacteria, thereby facilitating the dominance of LAB and minimizing bloater defect. To our knowledge, this is the first report on the ecology of phages infecting Gram-negative bacteria in commercial cucumber fermentations.
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Affiliation(s)
- Zhongjing Lu
- Department of Molecular & Cellular Biology, Kennesaw State University, Kennesaw, GA, United States
| | - Ilenys M Pérez-Díaz
- United States Department of Agriculture, Agricultural Research Service, Washington, DC, United States.,Department of Food, Bioprocessing & Nutrition Sciences, North Carolina State University, Raleigh, NC, United States
| | - Janet S Hayes
- United States Department of Agriculture, Agricultural Research Service, Washington, DC, United States.,Department of Food, Bioprocessing & Nutrition Sciences, North Carolina State University, Raleigh, NC, United States
| | - Fred Breidt
- United States Department of Agriculture, Agricultural Research Service, Washington, DC, United States.,Department of Food, Bioprocessing & Nutrition Sciences, North Carolina State University, Raleigh, NC, United States
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15
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Zhan Y, Tian H, Ji X, Liu Y. Myzus persicae (Hemiptera: Aphididae) infestation increases the risk of bacterial contamination and alters nutritional content in storage Chinese cabbage. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2020; 100:3007-3012. [PMID: 32052457 DOI: 10.1002/jsfa.10331] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 02/02/2020] [Accepted: 02/12/2020] [Indexed: 05/24/2023]
Abstract
BACKGROUND Aphids are common insect pests that feed on and excrete feces/honeydew on storage vegetables, especially in the temperate region of the northern hemisphere. The honeydew of aphids is an excellent growth medium for microorganisms. To explore the effects of aphid infestation on the risk of microbial contamination and food safety: (i) the bacterial diversity and community in aphid honeydew were investigated; (ii) the nutritional components of the cabbage were analyzed; and (iii) safety was evaluated. RESULTS The results showed that the dominant bacteria in storage Chinese cabbage under different exposure times belonged to the phylum Proteobacteria, family Enterobacteriaceae. The richness of Enterobacteriaceae increased from 36.35% (1 day) to 39.70% (5 days) and to 50.74% (10 days) as the exposure time increased. Serratia was the genus with the highest abundance (23.38% for 1 day, 30.56% for 5 days and 37.85% for 10 days). The abundance of pathways associated with Staphylococcus aureus infection and Shigellosis increased significantly after prolonged storage. In addition, when the aphid density increased from 0 to 100 per 250 g of Chinese cabbage leaves, the protein content in Chinese cabbage decreased significantly, whereas the reducing sugar content increased significantly. CONCLUSION These results demonstrate that the honeydew excreted by the green peach aphid Myzus persicae (Sulzer) on storage Chinese cabbage can serve as a medium for some foodborne disease pathogens. The present study may provide both a theoretical and practical basis for vegetable storage to reduce the risk of foodborne pathogen infection and to maintain the balance of nutrients. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Yidi Zhan
- College of Plant Protection, Shandong Agricultural University, Taian, Shandong, China
| | - Haohong Tian
- College of Plant Protection, Shandong Agricultural University, Taian, Shandong, China
| | - Xianglong Ji
- Green Food Development Centre of Shandong, Shandong Provincial Department of Agriculture and Rural Affairs, Jinan, Shandong, China
| | - Yong Liu
- College of Plant Protection, Shandong Agricultural University, Taian, Shandong, China
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16
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Cho GS, Stein M, Brinks E, Rathje J, Lee W, Suh SH, Franz CM. Serratia nevei sp. nov. and Serratia bockelmannii sp. nov., isolated from fresh produce in Germany and reclassification of Serratia marcescens subsp. sakuensis Ajithkumar et al. 2003 as a later heterotypic synonym of Serratia marcescens subsp. marcescens. Syst Appl Microbiol 2020; 43:126055. [DOI: 10.1016/j.syapm.2020.126055] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 01/03/2020] [Accepted: 01/13/2020] [Indexed: 11/30/2022]
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17
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Marathe NP, Salvà-Serra F, Karlsson R, Larsson DGJ, Moore ERB, Svensson-Stadler L, Jakobsson HE. Scandinavium goeteborgense gen. nov., sp. nov., a New Member of the Family Enterobacteriaceae Isolated From a Wound Infection, Carries a Novel Quinolone Resistance Gene Variant. Front Microbiol 2019; 10:2511. [PMID: 31781055 PMCID: PMC6856666 DOI: 10.3389/fmicb.2019.02511] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 10/18/2019] [Indexed: 12/03/2022] Open
Abstract
The family Enterobacteriaceae is a taxonomically diverse and widely distributed family containing many human commensal and pathogenic species that are known to carry transferable antibiotic resistance determinants. Characterization of novel taxa within this family is of great importance in order to understand the associated health risk and provide better treatment options. The aim of the present study was to characterize a Gram-negative bacterial strain (CCUG 66741) belonging to the family Enterobacteriaceae, isolated from a wound infection of an adult patient, in Sweden. Initial phenotypic and genotypic analyses identified the strain as a member of the family Enterobacteriaceae but could not assign it to any previously described species. The complete 16S rRNA gene sequence showed highest similarity (98.8%) to four species. Whole genome sequencing followed by in silico DNA-DNA similarity analysis and average nucleotide identity (ANI) analysis confirmed that strain CCUG 66741 represents a novel taxon. Sequence comparisons of six house-keeping genes (16S rRNA, atpD, dnaJ, gyrB, infB, rpoB) with those of the type strains of the type species of related genera within the family Enterobacteriaceae indicated that the strain embodies a novel species within the family. Phylogenomic analyses (ANI-based and core genome-based phylogeny) showed that strain CCUG 66741 forms a distinct clade, representing a novel species of a distinct, new genus within the family Enterobacteriaceae, for which the name Scandinavium goeteborgense gen. nov., sp. nov. is proposed, with CCUG 66741T as the type strain (= CECT 9823T = NCTC 14286T). S. goeteborgense CCUG 66741T carries a novel variant of a chromosomally-encoded quinolone resistance gene (proposed qnrB96). When expressed in Escherichia coli, the qnrB96 gene conferred five-fold increase in minimum inhibitory concentration against ciprofloxacin. This study highlights the importance and the utility of whole genome sequencing for pathogen identification in clinical settings.
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Affiliation(s)
- Nachiket P Marathe
- Institute of Marine Research, Bergen, Norway.,Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research, University of Gothenburg, Gothenburg, Sweden
| | - Francisco Salvà-Serra
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Microbiology, Culture Collection University of Gothenburg, Sahlgrenska University Hospital and Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
| | - Roger Karlsson
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research, University of Gothenburg, Gothenburg, Sweden.,Nanoxis Consulting AB, Gothenburg, Sweden
| | - D G Joakim Larsson
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research, University of Gothenburg, Gothenburg, Sweden
| | - Edward R B Moore
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Microbiology, Culture Collection University of Gothenburg, Sahlgrenska University Hospital and Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Liselott Svensson-Stadler
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research, University of Gothenburg, Gothenburg, Sweden
| | - Hedvig E Jakobsson
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research, University of Gothenburg, Gothenburg, Sweden
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18
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Al-Kharousi ZS, Guizani N, Al-Sadi AM, Al-Bulushi IM. Antibiotic Resistance of Enterobacteriaceae Isolated from Fresh Fruits and Vegetables and Characterization of their AmpC β-Lactamases. J Food Prot 2019; 82:1857-1863. [PMID: 31609646 DOI: 10.4315/0362-028x.jfp-19-089] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Enterobacteria may gain antibiotic resistance and be potent pathogens wherever they are present, including in fresh fruits and vegetables. This study tested the antibiotic resistance of enterobacteria isolated from 13 types of local and imported fresh fruits and vegetables (n = 105), using the standard Kirby-Bauer disk diffusion method. Phenotypic and genotypic characterizations of AmpC β-lactamases were determined in cefoxitin-resistant isolates. Ten percent of the enterobacteria tested (n = 88) were pansusceptible, 74% were resistant to at least one antibiotic, and 16% were multidrug resistant. Enterobacteria isolates showed the highest antibiotic resistance against ampicillin (66%), cephalothin (57%), amoxicillin-clavulanic acid (33%), cefoxitin (31%), tetracycline (9%), nalidixic acid (7%), trimethoprim (6%), and kanamycin (5%). Three isolates showed intermediate resistance to the clinically important antibiotic imipenem. Escherichia coli isolated from lettuce exhibited multidrug resistance against five antibiotics. Fifteen isolates were confirmed to have AmpC β-lactamase, using the inhibitor-based test and the antagonism test; the latter test confirmed that the enzyme was an inducible type. Four types of ampC β-lactamase genes (CIT, EBC, FOX, and MOX) were detected in eight isolates: four Enterobacter cloacae isolates and one isolate each of Citrobacter freundii, Enterobacter asburiae, Enterobacter hormaechei, and Enterobacter ludwigii. It was concluded that fresh fruits and vegetables might play a role as a source or vehicle for transferring antibiotic-resistant bacteria that might spread to other countries through exportation. The clinically significant AmpC β-lactamase was rarely documented in the literature on bacteria isolated from fruits and vegetables, and to our knowledge, this is the first report on the detection of an inducible type in such commodities.
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Affiliation(s)
- Zahra S Al-Kharousi
- Department of Food Science and Nutrition, Sultan Qaboos University, P.O. Box 34, Al-Khod 123, Sultanate of Oman
| | - Nejib Guizani
- Department of Food Science and Nutrition, Sultan Qaboos University, P.O. Box 34, Al-Khod 123, Sultanate of Oman
| | - Abdullah M Al-Sadi
- Department of Crop Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, P.O. Box 34, Al-Khod 123, Sultanate of Oman (ORCID: https://orcid.org/0000-0003-0702-9298 [N.G.])
| | - Ismail M Al-Bulushi
- Department of Food Science and Nutrition, Sultan Qaboos University, P.O. Box 34, Al-Khod 123, Sultanate of Oman
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19
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Improved Species-Level Clinical Identification of Enterobacteriaceae through Broad-Range dnaJ PCR and Sequencing. J Clin Microbiol 2019; 57:JCM.00986-19. [PMID: 31434720 DOI: 10.1128/jcm.00986-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 08/16/2019] [Indexed: 12/18/2022] Open
Abstract
Enterobacteriaceae represent a diverse and medically important family of bacteria that are difficult to identify to the species level using the standard molecular method of 16S rRNA gene sequencing. Prior work has demonstrated the value of dnaJ gene sequence analysis in resolving different members of the family. However, existing protocols are not optimized for clinical use and exhibit several limitations in practice. Here, we describe an improved assay for dnaJ-based identification of Enterobacteriaceae which boasts increased broad-range specificity across genera, shorter amplicon sizes that are suitable for use with formalin-fixed or direct patient specimens, and enhanced amplification efficiency and assay sensitivity through the incorporation of locked nucleic acid chemistries. Sequence analysis of public databases indicates that the partial dnaJ sequence interrogated by this design retains high discriminatory power among Enterobacteriaceae genera and species, with only particular lineages of Shigella sp. and Escherichia coli proving unresolvable. Limits of detection studies using 8 disparate species indicated that amplification was consistently achievable across organisms and allowed robust dideoxynucleotide chain terminator sequencing from as little as 10 genome equivalents of template, depending on the species interrogated. Retrospective application of the dnaJ assay to patient specimens enabled unambiguous classification of Enterobacteriaceae to the species level in 22 of 27 (81.5%) positive specimens examined, with most remaining cases representing unresolvable calls between closely related Escherichia coli and Shigella species. We expect that this assay will facilitate the accurate molecular identification of species from the Enterobacteriaceae family in a variety of clinical specimens and diagnostic contexts.
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20
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Adesina T, Nwinyi O, De N, Akinnola O, Omonigbehin E. First Detection of Carbapenem-Resistant Escherichia fergusonii Strains Harbouring Beta-Lactamase Genes from Clinical Samples. Pathogens 2019; 8:pathogens8040164. [PMID: 31557915 PMCID: PMC6963453 DOI: 10.3390/pathogens8040164] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 07/26/2019] [Accepted: 07/26/2019] [Indexed: 01/10/2023] Open
Abstract
Recently discovered extraintestinal Escherichia fergusonii obtained from non-clinical samples has exhibited the potential for acquiring multiple beta-lactamase genes, just like many extraintestinal Escherichia coli strains. Albeit, they are often omitted or classified as E. coli. This study aimed to, therefore, identify carbapenem-resistant extended-spectrum beta-lactamase (ESBL) producing E. fergusonii isolates from clinical samples, determine their evolutionary relatedness using 16S rRNA sequencing analysis and screen for beta-lactamase genes. A total of 135 septic wound samples were obtained from patients on referral at a General Hospital in Lagos, Nigeria. For the phenotypic identification of isolates from culture-positive samples, morphological, and physiological tests were carried out. Identities of the isolates harbouring beta-lactamase genes were assigned to their genus strains using the 16S rRNA sequencing. The Kirby Bauer disc diffusion technique and double-disc synergy test were used to screen isolates for multidrug resistance and ESBL production. Carbapenem-resistant ESBL producing isolates were screened for beta-lactamase genes in a polymerase chain reaction. Three E. fergusonii isolates (CR11, CR35 and CR49) were obtained during this study. E. fergusonii strains were motile, non-lactose and non-sorbitol fermenting but positive for cellobiose and adonitol fermentation. The I6S rRNA assigned the phenotypically identified isolates to E. fergusonii species. All three isolates were multidrug-resistant, carbapenem-resistant and ESBL producers. Isolates CR11 and CR35 harboured cefotaximase (CTX-M) and temoniera (TEM) beta-lactamase genes while CR49 harboured sulfhydryl variable (SHV) beta-lactamase gene. We herein report the detection of multiple beta-lactamase genes in carbapenem-resistant ESBL producing E. fergusonii from clinical samples.
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Affiliation(s)
- Tomilola Adesina
- Department of Microbiology, College of Science and Technology, Covenant University, 112103 Ota, Nigeria.
| | - Obinna Nwinyi
- Department of Microbiology, College of Science and Technology, Covenant University, 112103 Ota, Nigeria.
| | - Nandita De
- Department of Microbiology, College of Science and Technology, Covenant University, 112103 Ota, Nigeria.
| | - Olayemi Akinnola
- Department of Microbiology, College of Science and Technology, Covenant University, 112103 Ota, Nigeria.
| | - Emmanuel Omonigbehin
- Department of Microbiology, College of Science and Technology, Covenant University, 112103 Ota, Nigeria.
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21
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Rausch P, Rühlemann M, Hermes BM, Doms S, Dagan T, Dierking K, Domin H, Fraune S, von Frieling J, Hentschel U, Heinsen FA, Höppner M, Jahn MT, Jaspers C, Kissoyan KAB, Langfeldt D, Rehman A, Reusch TBH, Roeder T, Schmitz RA, Schulenburg H, Soluch R, Sommer F, Stukenbrock E, Weiland-Bräuer N, Rosenstiel P, Franke A, Bosch T, Baines JF. Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms. MICROBIOME 2019; 7:133. [PMID: 31521200 PMCID: PMC6744666 DOI: 10.1186/s40168-019-0743-1] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 08/23/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND The interplay between hosts and their associated microbiome is now recognized as a fundamental basis of the ecology, evolution, and development of both players. These interdependencies inspired a new view of multicellular organisms as "metaorganisms." The goal of the Collaborative Research Center "Origin and Function of Metaorganisms" is to understand why and how microbial communities form long-term associations with hosts from diverse taxonomic groups, ranging from sponges to humans in addition to plants. METHODS In order to optimize the choice of analysis procedures, which may differ according to the host organism and question at hand, we systematically compared the two main technical approaches for profiling microbial communities, 16S rRNA gene amplicon and metagenomic shotgun sequencing across our panel of ten host taxa. This includes two commonly used 16S rRNA gene regions and two amplification procedures, thus totaling five different microbial profiles per host sample. CONCLUSION While 16S rRNA gene-based analyses are subject to much skepticism, we demonstrate that many aspects of bacterial community characterization are consistent across methods. The resulting insight facilitates the selection of appropriate methods across a wide range of host taxa. Overall, we recommend single- over multi-step amplification procedures, and although exceptions and trade-offs exist, the V3 V4 over the V1 V2 region of the 16S rRNA gene. Finally, by contrasting taxonomic and functional profiles and performing phylogenetic analysis, we provide important and novel insight into broad evolutionary patterns among metaorganisms, whereby the transition of animals from an aquatic to a terrestrial habitat marks a major event in the evolution of host-associated microbial composition.
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Affiliation(s)
- Philipp Rausch
- Evolutionary Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Institute for Experimental Medicine, Kiel University, Kiel, Germany
- Department of Biology, Laboratory of Genomics and Molecular Biomedicine, University of Copenhagen, Copenhagen Ø, Denmark
| | - Malte Rühlemann
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Britt M. Hermes
- Evolutionary Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Institute for Experimental Medicine, Kiel University, Kiel, Germany
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Shauni Doms
- Evolutionary Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - Tal Dagan
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Katja Dierking
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
| | - Hanna Domin
- Zoological Institute, Kiel University, Kiel, Germany
| | | | - Jakob von Frieling
- Molecular Physiology, Zoological Institute, Kiel University, Kiel, Germany
| | - Ute Hentschel
- Marine Ecology, Research Unit Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
- Kiel University, Kiel, Germany
| | | | - Marc Höppner
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Martin T. Jahn
- Marine Ecology, Research Unit Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Cornelia Jaspers
- Kiel University, Kiel, Germany
- Marine Ecology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Kohar Annie B. Kissoyan
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
| | | | - Ateequr Rehman
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Thorsten B. H. Reusch
- Kiel University, Kiel, Germany
- Marine Ecology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Thomas Roeder
- Molecular Physiology, Zoological Institute, Kiel University, Kiel, Germany
| | - Ruth A. Schmitz
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Hinrich Schulenburg
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
| | - Ryszard Soluch
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Felix Sommer
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Eva Stukenbrock
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Environmental Genomics, Botanical Institute, Kiel University, Kiel, Germany
| | | | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Thomas Bosch
- Zoological Institute, Kiel University, Kiel, Germany
| | - John F. Baines
- Evolutionary Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Institute for Experimental Medicine, Kiel University, Kiel, Germany
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22
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Li X, Lau SKP, Woo PCY. Molecular characterisation of emerging pathogens of unexplained infectious disease syndromes. Expert Rev Mol Diagn 2019; 19:839-848. [PMID: 31385539 DOI: 10.1080/14737159.2019.1651200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Introduction: The discoveries of HIV and Helicobacter pylori in the 1980s were landmarks in identification of novel pathogens causing unexplained infectious syndromes using conventional microbiological technologies. In the last few decades, advancement of molecular technologies has provided us with more robust tools to expand our armamentarium in this microbial hunting process. Areas covered: In this article, we give a brief overview of the most important molecular technologies we use for identification of emerging microbes associated with unexplained infectious syndromes, including 16S rRNA and other conserved targets sequencing for bacteria, internal transcribed spacer (ITS) and other target gene sequencing for fungi, polymerase and other gene sequencing for viruses, as well as deep sequencing. Then, we use several representative examples to illustrate how these techniques have been used for the discoveries of a few notable bacterial, fungal and viral pathogens associated with unexplained infectious syndromes in the last 20-30 years. Expert opinion: In the past and present, characterization of emerging pathogens of unexplained infectious disease syndromes has relied on a combination of conventional culture- and phenotype-based technologies and nucleic acid amplification and sequencing. In the next era, we envisage more widespread adoption of next generation technologies that can detect both known and previously undescribed pathogens.
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Affiliation(s)
- Xin Li
- Department of Microbiology, The University of Hong Kong , Hong Kong , China
| | - Susanna K P Lau
- Department of Microbiology, The University of Hong Kong , Hong Kong , China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong , Hong Kong , China.,Carol Yu Centre for Infection, The University of Hong Kong , Hong Kong , China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University , Hangzhou , China
| | - Patrick C Y Woo
- Department of Microbiology, The University of Hong Kong , Hong Kong , China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong , Hong Kong , China.,Carol Yu Centre for Infection, The University of Hong Kong , Hong Kong , China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University , Hangzhou , China
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23
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Enterobacter spp.: Update on Taxonomy, Clinical Aspects, and Emerging Antimicrobial Resistance. Clin Microbiol Rev 2019; 32:32/4/e00002-19. [PMID: 31315895 DOI: 10.1128/cmr.00002-19] [Citation(s) in RCA: 239] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The genus Enterobacter is a member of the ESKAPE group, which contains the major resistant bacterial pathogens. First described in 1960, this group member has proven to be more complex as a result of the exponential evolution of phenotypic and genotypic methods. Today, 22 species belong to the Enterobacter genus. These species are described in the environment and have been reported as opportunistic pathogens in plants, animals, and humans. The pathogenicity/virulence of this bacterium remains rather unclear due to the limited amount of work performed to date in this field. In contrast, its resistance against antibacterial agents has been extensively studied. In the face of antibiotic treatment, it is able to manage different mechanisms of resistance via various local and global regulator genes and the modulation of the expression of different proteins, including enzymes (β-lactamases, etc.) or membrane transporters, such as porins and efflux pumps. During various hospital outbreaks, the Enterobacter aerogenes and E. cloacae complex exhibited a multidrug-resistant phenotype, which has stimulated questions about the role of cascade regulation in the emergence of these well-adapted clones.
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24
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Nepal S, Bonn F, Grasso S, Stobernack T, de Jong A, Zhou K, Wedema R, Rosema S, Becher D, Otto A, Rossen JW, van Dijl JM, Bathoorn E. An ancient family of mobile genomic islands introducing cephalosporinase and carbapenemase genes in Enterobacteriaceae. Virulence 2019; 9:1377-1389. [PMID: 30101693 PMCID: PMC6177240 DOI: 10.1080/21505594.2018.1509666] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The exchange of mobile genomic islands (MGIs) between microorganisms is often mediated by phages, which may provide benefits to the phage’s host. The present study started with the identification of Enterobacter cloacae, Klebsiella pneumoniae and Escherichia coli isolates with exceptional cephalosporin and carbapenem resistance phenotypes from patients in a neonatal ward. To identify possible molecular connections between these isolates and their β-lactam resistance phenotypes, the respective bacterial genome sequences were compared. This unveiled the existence of a family of ancient MGIs that were probably exchanged before the species E. cloacae, K. pneumoniae and E. coli emerged from their common ancestry. A representative MGI from E. cloacae was named MIR17-GI, because it harbors the novel β-lactamase gene variant blaMIR17. Importantly, our observations show that the MIR17-GI-like MGIs harbor genes associated with high-level resistance to cephalosporins. Among them, MIR17-GI stands out because MIR17 also displays carbapenemase activity. As shown by mass spectrometry, the MIR17 carbapenemase is among the most abundantly expressed proteins of the respective E. cloacae isolate. Further, we show that MIR17-GI-like islands are associated with integrated P4-like prophages. This implicates phages in the spread of cephalosporin and carbapenem resistance amongst Enterobacteriaceae. The discovery of an ancient family of MGIs, mediating the spread of cephalosporinase and carbapenemase genes, is of high clinical relevance, because high-level cephalosporin and carbapenem resistance have serious implications for the treatment of patients with enterobacteriaceal infections.
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Affiliation(s)
- Suruchi Nepal
- a Department of Medical Microbiology , University of Groningen, University Medical Center Groningen , Groningen , the Netherlands
| | - Florian Bonn
- b Institute for Microbiology , Ernst-Moritz-Arndt-University Greifswald , Greifswald , Germany
| | - Stefano Grasso
- a Department of Medical Microbiology , University of Groningen, University Medical Center Groningen , Groningen , the Netherlands
| | - Tim Stobernack
- a Department of Medical Microbiology , University of Groningen, University Medical Center Groningen , Groningen , the Netherlands
| | - Anne de Jong
- c Department of Molecular Genetics , University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute , Groningen , The Netherlands
| | - Kai Zhou
- a Department of Medical Microbiology , University of Groningen, University Medical Center Groningen , Groningen , the Netherlands.,d State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital , Zhejiang University , Hangzhou , China
| | - Ronald Wedema
- a Department of Medical Microbiology , University of Groningen, University Medical Center Groningen , Groningen , the Netherlands
| | - Sigrid Rosema
- a Department of Medical Microbiology , University of Groningen, University Medical Center Groningen , Groningen , the Netherlands
| | - Dörte Becher
- b Institute for Microbiology , Ernst-Moritz-Arndt-University Greifswald , Greifswald , Germany
| | - Andreas Otto
- b Institute for Microbiology , Ernst-Moritz-Arndt-University Greifswald , Greifswald , Germany
| | - John W Rossen
- a Department of Medical Microbiology , University of Groningen, University Medical Center Groningen , Groningen , the Netherlands
| | - Jan Maarten van Dijl
- a Department of Medical Microbiology , University of Groningen, University Medical Center Groningen , Groningen , the Netherlands
| | - Erik Bathoorn
- a Department of Medical Microbiology , University of Groningen, University Medical Center Groningen , Groningen , the Netherlands
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25
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Assessment of the non-lactic acid bacteria microbiota in fresh cucumbers and commercially fermented cucumber pickles brined with 6% NaCl. Food Microbiol 2019; 77:10-20. [DOI: 10.1016/j.fm.2018.08.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 07/31/2018] [Accepted: 08/02/2018] [Indexed: 11/18/2022]
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26
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Zhang J, Zhu X, Xu R, Gao Q, Wang D, Zhang Y. Isolation and identification of histamine-producing Enterobacteriaceae from Qu fermentation starter for Chinese rice wine brewing. Int J Food Microbiol 2018; 281:1-9. [PMID: 29800825 DOI: 10.1016/j.ijfoodmicro.2018.05.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 04/21/2018] [Accepted: 05/16/2018] [Indexed: 02/05/2023]
Abstract
Histamine (HIS) producers in fermented wines are generally believed to be lactic acid bacteria (LAB), and other microorganisms have received little or no attention. In this work, HIS-producing bacteria were isolated from Qu fermentation starter for Chinese rice wine brewing by decarboxylase medium, and their identity was confirmed by RP-HPLC and PCR. Surprisingly, the histidine decarboxylase gene (hdc) was present in only 2 out of 26 isolates. All 26 isolates were genotyped using the randomly amplified polymorphic DNA (RAPD)-PCR assay, which revealed the presence of 21 biotypes. Single type isolates were identified via 16S rRNA sequence analysis, in some cases coupled with partial sequencing of the rpoB or dnaJ gene. All isolates belonged to the Enterobacteriaceae, and included Enterobacter asburiae, Enterobacter cloacae, Enterobacter hormaechei, Citrobacter amalonaticus and Cronobacter sakazakii. All these strains were capable of producing >3.5 mg/L of HIS in TS medium without ethanol, but did not grow in TS medium with 8% ethanol. Small-scale Chinese rice wine fermentation revealed that HIS contents exhibited the same trend as the LAB and ethanol no matter what kinds of Qu were used. However, in the early stages of fermentation (from day 2 to day 4), the HIS contents had a stronger correlation with Enterobacteriaceae (0.943) than with LAB (0.369) when the Qu fermented samples are analyzed as a whole. Moreover, the lowest HIS content was measured in Xiao Qu (Q) fermented sample at the end of fermentation, which suggests that the formation of HIS in the early stages of fermentation has a decisive effect on HIS content in the final product. Our results demonstrate that Enterobacteriaceae from Qu are an important cause for HIS formation in Chinese rice wine. Consequently, selecting Qu with a low content of Enterobacteriaceae contaminants and inhibiting the growth of Enterobacteriaceae in the early stages of fermentation are useful approaches for preventing excessive amounts of HIS formation in Chinese rice wine brewing.
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Affiliation(s)
- Jian Zhang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China; State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Xiaojuan Zhu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Ruitao Xu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Qiang Gao
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Depei Wang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Ying Zhang
- Key Laboratory of Food Nutrition and Safety, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China.
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27
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Buján N, Balboa S, L Romalde J, E Toranzo A, Magariños B. Population genetic and evolution analysis of controversial genus Edwardsiella by multilocus sequence typing. Mol Phylogenet Evol 2018; 127:513-521. [PMID: 29751087 DOI: 10.1016/j.ympev.2018.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 04/19/2018] [Accepted: 05/07/2018] [Indexed: 10/17/2022]
Abstract
At present, the genus Edwardsiella compiles five species: E. tarda, E. hoshinae, E. ictaluri, E. piscicida and E. anguillarum. Some species of this genus such us E. ictaluri and E. piscicida are important pathogens of numerous fish species. With the description of the two latter species, the phylogeny of Edwardsiella became more complicated. With the aim to clarify the relationships among all species in the genus, a multilocus sequence typing (MLST) approach was developed and applied to characterize 56 isolates and 6 reference strains belonging to the five Edwardsiella species. Moreover, several analyses based on the MLST scheme were performed to investigate the evolution within the genus, as well as the influence of recombination and mutation in the speciation. Edwardsiella isolates presented a high genetic variability reflected in the fourteen sequence types (ST) represented by a single isolates out of eighteen total ST. Mutation events were considerably more frequent than recombination, although both approximately equal influenced the genetic diversification. However, the speciation among species occurred mostly by recombination. Edwardsiella genus displays a non-clonal population structure with some degree of geographical isolation followed by a population expansion of E. piscicida. A database from this study was created and hosted on pubmlst.org (http://pubmlst.org/edwardsiella/).
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Affiliation(s)
- Noemí Buján
- Departamento de Microbioloxía e Parasitoloxía, CIBUS-Facultade de Bioloxía and Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.
| | - Sabela Balboa
- Departamento de Microbioloxía e Parasitoloxía, CIBUS-Facultade de Bioloxía and Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Jesús L Romalde
- Departamento de Microbioloxía e Parasitoloxía, CIBUS-Facultade de Bioloxía and Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Alicia E Toranzo
- Departamento de Microbioloxía e Parasitoloxía, CIBUS-Facultade de Bioloxía and Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Beatriz Magariños
- Departamento de Microbioloxía e Parasitoloxía, CIBUS-Facultade de Bioloxía and Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
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28
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Amos GCA, Ploumakis S, Zhang L, Hawkey PM, Gaze WH, Wellington EMH. The widespread dissemination of integrons throughout bacterial communities in a riverine system. ISME JOURNAL 2018; 12:681-691. [PMID: 29374269 PMCID: PMC5864220 DOI: 10.1038/s41396-017-0030-8] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 08/01/2017] [Accepted: 09/14/2017] [Indexed: 12/31/2022]
Abstract
Anthropogenic inputs increase levels of antimicrobial resistance (AMR) in the environment, however, it is unknown how these inputs create this observed increase, and if anthropogenic sources impact AMR in environmental bacteria. The aim of this study was to characterise the role of waste water treatment plants (WWTPs) in the dissemination of class 1 integrons (CL1s) in the riverine environment. Using sample sites from upstream and downstream of a WWTP, we demonstrate through isolation and culture-independent analysis that WWTP effluent significantly increases both CL1 abundance and antibiotic resistance in the riverine environment. Characterisation of CL1-bearing isolates revealed that CL1s were distributed across a diverse range of bacteria, with identical complex genetic resistance determinants isolated from both human-associated and common environmental bacteria across connected sites. Over half of sequenced CL1s lacked the 3′-conserved sequence ('atypical’ CL1s); surprisingly, bacteria carrying atypical CL1s were on average resistant to more antibiotics than bacteria carrying 3′-CS CL1s. Quaternary ammonium compound (QAC) resistance genes were observed across 75% of sequenced CL1 gene cassette arrays. Chemical data analysis indicated high levels of boron (a detergent marker) downstream of the WWTP. Subsequent phenotypic screening of CL1-bearing isolates demonstrated that ~90% were resistant to QAC detergents, with in vitro experiments demonstrating that QACs could solely select for the transfer of clinical antibiotic resistance genes to a naive Escherichia coli recipient. In conclusion, this study highlights the significant impact of WWTPs on environmental AMR, and demonstrates the widespread carriage of clinically important resistance determinants by environmentally associated bacteria.
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Affiliation(s)
| | | | - Lihong Zhang
- School of Life Sciences, University of Warwick, Coventry, UK.,European Centre for Environment and Human Health, University of Exeter Medical School, Knowledge Spa, Royal Cornwall Hospital, UK
| | | | - William H Gaze
- School of Life Sciences, University of Warwick, Coventry, UK.,European Centre for Environment and Human Health, University of Exeter Medical School, Knowledge Spa, Royal Cornwall Hospital, UK
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29
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Metagenomic Analysis of Therapeutic PYO Phage Cocktails from 1997 to 2014. Viruses 2017; 9:v9110328. [PMID: 29099783 PMCID: PMC5707535 DOI: 10.3390/v9110328] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 10/31/2017] [Accepted: 11/02/2017] [Indexed: 11/17/2022] Open
Abstract
Phage therapy has regained interest in recent years due to the alarming spread of antibiotic resistance. Whilst phage cocktails are commonly sold in pharmacies in countries such as Georgia and Russia, this is not the case in western countries due to western regulatory agencies requiring a thorough characterization of the drug. Here, DNA sequencing of constituent biological entities constitutes a first step. The pyophage (PYO) cocktail is one of the main commercial products of the Georgian Eliava Institute of Bacteriophage, Microbiology and Virology and is used to cure skin infections. Since its first production in the 1930s, the composition of the cocktail has been periodically modified to add phages effective against emerging pathogenic strains. In this paper, we compared the composition of three PYO cocktails from 1997 (PYO97), 2000 (PYO2000) and 2014 (PYO2014). Based on next generation sequencing, de novo assembly and binning of contigs into draft genomes based on tetranucleotide distance, thirty and twenty-nine phage draft genomes were predicted in PYO97 and PYO2014, respectively. Of these, thirteen and fifteen shared high similarity to known phages. Eleven draft genomes were found to be common in the two cocktails. One of these showed no similarity to publicly available phage genomes. Representatives of phages targeting E. faecalis, E. faecium, E. coli, Proteus, P. aeruginosa and S. aureus were found in both cocktails. Finally, we estimated larger overlap of the PYO2000 cocktail to PYO97 compared to PYO2014. Using next generation sequencing and metagenomics analysis, we were able to characterize and compare the content of PYO cocktails separated by 17 years in time. Even though the cocktail composition is upgraded every six months, we found it to remain relatively stable over the years.
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30
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Buján N, Mohammed H, Balboa S, Romalde JL, Toranzo AE, Arias CR, Magariños B. Genetic studies to re-affiliate Edwardsiella tarda fish isolates to Edwardsiella piscicida and Edwardsiella anguillarum species. Syst Appl Microbiol 2017; 41:30-37. [PMID: 29150173 DOI: 10.1016/j.syapm.2017.09.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 08/30/2017] [Accepted: 09/01/2017] [Indexed: 10/18/2022]
Abstract
Until 2012, the genus Edwardsiella was composed by three species Edwardsiella tarda, Edwardsiella hoshinae and Edwardsiella ictaluri. In 2013, Edwardsiella piscicida, compiling fish pathogenic strains previously identified as E. tarda was described, and more recently a new species isolated from diseased eel was reported, namely Edwardsiella anguillarum. The incorporation of these species into the genus makes necessary a revision of the taxonomic position of the isolates previously identified as E. tarda. Using AFLP technique, MLSA studies and in silico DNA-DNA hybridization, 46 of 49 E. tarda isolates were re-assigned as E. piscicida and 2 as E. anguillarum, whereas it was confirmed previous classification of the Edwardsiella types and reference strains used. The study of the taxonomic resolution of the genes 16S rRNA, adk, atpD, dnaJ, glnA, hsp60, tuf as well as the possible combinations among housekeeping genes, showed that the gene dnaJ was the more resolutive. In conclusion, the use of molecular techniques is necessary to accurately identify Edwardsiella isolates, especially when differentiating new species from E. tarda.
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Affiliation(s)
- Noemí Buján
- Departamento de Microbioloxía y Parasitoloxía, CIBUS-Facultade de Bioloxía and Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain.
| | - Haitham Mohammed
- Aquatic Microbiology Laboratory, SFAAS, Center for Advanced Science, Innovation, and Commerce, Auburn University, Auburn, AL 36849, USA; Department of Animal Medicine, Faculty of Veterinary Medicine, Assiut University, Assiut 71526, Egypt
| | - Sabela Balboa
- Departamento de Microbioloxía y Parasitoloxía, CIBUS-Facultade de Bioloxía and Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Jesús L Romalde
- Departamento de Microbioloxía y Parasitoloxía, CIBUS-Facultade de Bioloxía and Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Alicia E Toranzo
- Departamento de Microbioloxía y Parasitoloxía, CIBUS-Facultade de Bioloxía and Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Cova R Arias
- Aquatic Microbiology Laboratory, SFAAS, Center for Advanced Science, Innovation, and Commerce, Auburn University, Auburn, AL 36849, USA
| | - Beatriz Magariños
- Departamento de Microbioloxía y Parasitoloxía, CIBUS-Facultade de Bioloxía and Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
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31
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Brady C, Allainguillaume J, Denman S, Arnold D. Rapid identification of bacteria associated with Acute Oak Decline by high-resolution melt analysis. Lett Appl Microbiol 2017; 63:89-95. [PMID: 27227694 DOI: 10.1111/lam.12593] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 05/06/2016] [Accepted: 05/23/2016] [Indexed: 11/28/2022]
Abstract
UNLABELLED Two Gram-negative Enterobacteriaceae, Gibbsiella quercinecans and Brenneria goodwinii, are frequently isolated from oak suffering from Acute Oak Decline. These two species are difficult to identify based on colony morphology, carbohydrate utilization or 16S rRNA gene sequence, and identification using gyrB gene sequencing is time-consuming and laborious. A rapid identification technique, based on high-resolution melt analysis of the atpD gene, was designed to efficiently process numerous isolates from an increasing number of affected woodlands and parks. Principal component analysis of the resulting melt curves from strains of G. quercinecans, B. goodwinii and their close phylogenetic relatives allowed differentiation into distinct clusters based on species or subspecies identity. SIGNIFICANCE AND IMPACT OF THE STUDY Acute Oak Decline is an increasing threat to Britain's native oak population. Two novel bacterial species both belonging to the family Enterobacteriaceae, Gibbsiella quercinecans and Brenneria goodwinii, are thought to play an important role in symptom development. Here, we describe a rapid identification technique using high-resolution melt analysis of the atpD gene able to assign isolates to either G. quercinecans or B. goodwinii in a single assay, greatly reducing the time taken to identify if either or both of these species are present in symptomatic oak.
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Affiliation(s)
- C Brady
- Faculty of Health and Applied Sciences, Centre for Research in Bioscience, University of the West of England, Bristol, UK
| | - J Allainguillaume
- Faculty of Health and Applied Sciences, Centre for Research in Bioscience, University of the West of England, Bristol, UK
| | - S Denman
- Forest Research, Centre for Ecosystems Society and Biosecurity, Farnham, UK
| | - D Arnold
- Faculty of Health and Applied Sciences, Centre for Research in Bioscience, University of the West of England, Bristol, UK
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32
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Hata H, Natori T, Mizuno T, Kanazawa I, Eldesouky I, Hayashi M, Miyata M, Fukunaga H, Ohji S, Hosoyama A, Aono E, Yamazoe A, Tsuchikane K, Fujita N, Ezaki T. Phylogenetics of family Enterobacteriaceae and proposal to reclassify Escherichia hermannii and Salmonella subterranea as Atlantibacter hermannii and Atlantibacter subterranea gen. nov., comb. nov. Microbiol Immunol 2017; 60:303-11. [PMID: 26970508 DOI: 10.1111/1348-0421.12374] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 02/25/2016] [Accepted: 03/07/2016] [Indexed: 11/27/2022]
Abstract
Multilocus sequence analysis based on hypervariable housekeeping proteins was utilized to differentiate closely related species in the family Enterobacteriaceae. Of 150 housekeeping proteins, the top 10 hypervariable proteins were selected and concatenated to obtain distance data. Distances between concatenated proteins within the family were 0.9-41.2%, whereas the 16S rRNA and atpD-gyrB-infB-rpoB concatenated sequence (4MLSA) distances were 0.8-6.0% and 0.9-22.1%, respectively. These data indicate that phylogenetic analysis by concatenation of hypervariable proteins is a powerful tool for discriminating species in the family Enterobacteriaceae. To confirm the discriminatory power of the 10 chosen concatenated hypervariable proteins (C10HKP), phylogenetic trees based on C10HKP, 4MLSA, and the 16S rRNA gene were constructed. Comparison of average bootstrap values among C10HKP, 4MLSA and 16S rRNA genes indicated that the C10HKP tree was the most reliable. Location via the C10HKP tree was consistent with existing assignments for almost all species in the family Enterobacteriaceae. However, the C10HKP tree suggested that several species (including Enterobacter massiliensis, Escherichia vulneris, Escherichia hermannii, and Salmonella subterranea) should be reassigned to different clusters than those defined in previous analyses. Furthermore, E. hermannii and S. subterranea appeared to fall onto a branch independent from those occupied by the other Enterobacteriaceae. Therefore, we propose Atlantibacter gen. nov., such that E. hermannii and S. subterranea would be transferred to genus Atlantibacter as Atlantibacter hermannii, comb. nov. and Atlantibacter subterranea. comb. nov., respectively.
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Affiliation(s)
- Hiroyuki Hata
- Department of Microbiology, Gifu University Graduate School of Medicine
| | - Tatsuya Natori
- Department of Microbiology, Gifu University Graduate School of Medicine
| | - Takuya Mizuno
- Department of Microbiology, Gifu University Graduate School of Medicine
| | - Izumi Kanazawa
- Department of Microbiology, Gifu University Graduate School of Medicine
| | - Ibrahim Eldesouky
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Kafrelsheikh University, 33516, Egypt
| | - Masahiro Hayashi
- Division of Anaerobe Research, Life Science Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1194
| | - Machiko Miyata
- Department of Microbiology, Gifu University Graduate School of Medicine
| | - Hajime Fukunaga
- Department of Microbiology, Gifu University Graduate School of Medicine
| | - Shoko Ohji
- Biological Resource Center, National Institute of Technology and Evaluation, 2-5-8, Kazusakamatari, Kisarazu-shi, Chiba 292-0818, Japan
| | - Akira Hosoyama
- Biological Resource Center, National Institute of Technology and Evaluation, 2-5-8, Kazusakamatari, Kisarazu-shi, Chiba 292-0818, Japan
| | - Eiji Aono
- Biological Resource Center, National Institute of Technology and Evaluation, 2-5-8, Kazusakamatari, Kisarazu-shi, Chiba 292-0818, Japan
| | - Atsushi Yamazoe
- Biological Resource Center, National Institute of Technology and Evaluation, 2-5-8, Kazusakamatari, Kisarazu-shi, Chiba 292-0818, Japan
| | - Keiko Tsuchikane
- Biological Resource Center, National Institute of Technology and Evaluation, 2-5-8, Kazusakamatari, Kisarazu-shi, Chiba 292-0818, Japan
| | - Nobuyuki Fujita
- Biological Resource Center, National Institute of Technology and Evaluation, 2-5-8, Kazusakamatari, Kisarazu-shi, Chiba 292-0818, Japan
| | - Takayuki Ezaki
- Department of Microbiology, Gifu University Graduate School of Medicine
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Hamdi S, Rousseau GM, Labrie SJ, Tremblay DM, Kourda RS, Ben Slama K, Moineau S. Characterization of two polyvalent phages infecting Enterobacteriaceae. Sci Rep 2017; 7:40349. [PMID: 28091598 PMCID: PMC5238451 DOI: 10.1038/srep40349] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 12/05/2016] [Indexed: 01/30/2023] Open
Abstract
Bacteriophages display remarkable genetic diversity and host specificity. In this study, we explore phages infecting bacterial strains of the Enterobacteriaceae family because of their ability to infect related but distinct hosts. We isolated and characterized two novel virulent phages, SH6 and SH7, using a strain of Shigella flexneri as host bacterium. Morphological and genomic analyses revealed that phage SH6 belongs to the T1virus genus of the Siphoviridae family. Conversely, phage SH7 was classified in the T4virus genus of the Myoviridae family. Phage SH6 had a short latent period of 16 min and a burst size of 103 ± 16 PFU/infected cell while the phage SH7 latent period was 23 min with a much lower burst size of 26 ± 5 PFU/infected cell. Moreover, phage SH6 was sensitive to acidic conditions (pH < 5) while phage SH7 was stable from pH 3 to 11 for 1 hour. Of the 35 bacterial strains tested, SH6 infected its S. flexneri host strain and 8 strains of E. coli. Phage SH7 lysed additionally strains of E. coli O157:H7, Salmonella Paratyphi, and Shigella dysenteriae. The broader host ranges of these two phages as well as their microbiological properties suggest that they may be useful for controlling bacterial populations.
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Affiliation(s)
- Sana Hamdi
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis El Manar, 2092 Tunis, Tunisie
- Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université de Tunis El Manar, 2092 Tunis, Tunisie
| | - Geneviève M. Rousseau
- Département de Biochimie, de Microbiologie, et de Bio-informatique and PROTEO, Faculté des Sciences et de Génie, Félix d’Hérelle Reference Center for Bacterial Viruses, and GREB, Faculté de Médecine Dentaire, Université Laval, Québec City, Québec, Canada
| | - Simon J. Labrie
- Département de Biochimie, de Microbiologie, et de Bio-informatique and PROTEO, Faculté des Sciences et de Génie, Félix d’Hérelle Reference Center for Bacterial Viruses, and GREB, Faculté de Médecine Dentaire, Université Laval, Québec City, Québec, Canada
| | - Denise M. Tremblay
- Département de Biochimie, de Microbiologie, et de Bio-informatique and PROTEO, Faculté des Sciences et de Génie, Félix d’Hérelle Reference Center for Bacterial Viruses, and GREB, Faculté de Médecine Dentaire, Université Laval, Québec City, Québec, Canada
| | - Rim Saïed Kourda
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis El Manar, 2092 Tunis, Tunisie
- Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université de Tunis El Manar, 2092 Tunis, Tunisie
| | - Karim Ben Slama
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis El Manar, 2092 Tunis, Tunisie
- Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université de Tunis El Manar, 2092 Tunis, Tunisie
| | - Sylvain Moineau
- Département de Biochimie, de Microbiologie, et de Bio-informatique and PROTEO, Faculté des Sciences et de Génie, Félix d’Hérelle Reference Center for Bacterial Viruses, and GREB, Faculté de Médecine Dentaire, Université Laval, Québec City, Québec, Canada
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Genome-based phylogeny and taxonomy of the ‘Enterobacteriales’: proposal for Enterobacterales ord. nov. divided into the families Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam. nov., Hafniaceae fam. nov., Morganellaceae fam. nov., and Budviciaceae fam. nov. Int J Syst Evol Microbiol 2016; 66:5575-5599. [DOI: 10.1099/ijsem.0.001485] [Citation(s) in RCA: 556] [Impact Index Per Article: 69.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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Shaffer JP, Sarmiento C, Zalamea PC, Gallery RE, Davis AS, Baltrus DA, Arnold AE. Diversity, Specificity, and Phylogenetic Relationships of Endohyphal Bacteria in Fungi That Inhabit Tropical Seeds and Leaves. Front Ecol Evol 2016. [DOI: 10.3389/fevo.2016.00116] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Gene content dissimilarity for subclassification of highly similar microbial strains. BMC Genomics 2016; 17:647. [PMID: 27530250 PMCID: PMC4988056 DOI: 10.1186/s12864-016-2991-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 08/03/2016] [Indexed: 11/23/2022] Open
Abstract
Background Identification and classification of highly similar microbial strains is a challenging issue in microbiology, ecology and evolutionary biology. Among various available approaches, gene content analysis is also at the core of microbial taxonomy. However, no threshold has been determined for grouping microorgnisms to different taxonomic levels, and it is still not clear that to what extent genomic fluidity should occur to form a microbial taxonomic group. Results By taking advantage of the eggNOG database for orthologous groups, we calculated gene content dissimilarity among different microbial strains based on the orthologous gene profiles and tested the possibility of applying gene content dissimilarity as a quantitative index in classifying microbial taxonomic groups, as well as its potential application in subclassification of highly similar microbial strains. Evaluation of gene content dissimilarity to completed microbial genomes at different taxonomic levels suggested that cutoffs of 0.2 and 0.4 can be respectively used for species and family delineation, and that 0.2 gene content dissimilarity cutoff approximately corresponded to 98 % 16S rRNA gene identity and 94 % ANI for microbial species delineation. Furthermore, application of gene content dissimilarity to highly similar microbial strains suggested it as an effective approach in classifying closely related microorganisms into subgroups. Conclusions This approach is especially useful in identifying pathogens from commensals in clinical microbiology. It also provides novel insights into how genomic fluidity is linked with microbial taxonomy. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2991-9) contains supplementary material, which is available to authorized users.
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Tian Y, Zhao Y, Yuan X, Yi J, Fan J, Xu Z, Hu B, De Boer SH, Li X. Dickeya
fangzhongdai sp. nov., a plant-pathogenic bacterium isolated from pear trees (Pyrus pyrifolia). Int J Syst Evol Microbiol 2016; 66:2831-2835. [DOI: 10.1099/ijsem.0.001060] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yanli Tian
- College of Plant Protection and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Yuqiang Zhao
- Shanghai Agricultural Technology Extension and Service Center, Shanghai 201103, PR China
| | - Xiaoli Yuan
- Charlottetown Laboratory, Canadian Food Inspection Agency, Charlottetown, Canada
| | - Jianping Yi
- Shanghai Entry-Exit Inspection and Quarantine Bureau, Shanghai 200135, PR China
| | - Jiaqin Fan
- College of Plant Protection and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Zhigang Xu
- College of Plant Protection and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Baishi Hu
- College of Plant Protection and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Solke H. De Boer
- Charlottetown Laboratory, Canadian Food Inspection Agency, Charlottetown, Canada
| | - Xiang Li
- Charlottetown Laboratory, Canadian Food Inspection Agency, Charlottetown, Canada
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Rees CA, Smolinska A, Hill JE. The volatile metabolome of
Klebsiella pneumoniae
in human blood. J Breath Res 2016; 10:027101. [DOI: 10.1088/1752-7155/10/2/027101] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Benslama O, Boulahrouf A. High-quality draft genome sequence of Enterobacter sp. Bisph2, a glyphosate-degrading bacterium isolated from a sandy soil of Biskra, Algeria. GENOMICS DATA 2016; 8:61-6. [PMID: 27222800 PMCID: PMC4856816 DOI: 10.1016/j.gdata.2016.03.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Revised: 03/16/2016] [Accepted: 03/21/2016] [Indexed: 11/18/2022]
Abstract
Enterobacter sp. strain Bisph2 was isolated from a sandy soil from Biskra, Algeria and exhibits glyphosate-degrading activity. Multilocus sequence analysis of the 16S rRNA, rpoB, hsp60, gyrB and dnaJ genes demonstrated that Bisph2 might be a member of a new species of the genus Enterobacter. Genomic sequencing of Bisph2 was used to better clarify the relationships among Enterobacter species. Annotation and analysis of the genome sequence showed that the 5.535.656 bp genome of Enterobacter sp. Bisph2 consists in one chromosome and no detectable plasmid, has a 53.19% GC content and 78% of genes were assigned a putative function. The genome contains four prophages of which 3 regions are intact and no CRISPER was detected. The nucleotide sequence of this genome was deposited into DDBJ/EMBL/GenBank under the accession JXAF00000000.
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40
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Hiding in Fresh Fruits and Vegetables: Opportunistic Pathogens May Cross Geographical Barriers. Int J Microbiol 2016; 2016:4292417. [PMID: 26989419 PMCID: PMC4772400 DOI: 10.1155/2016/4292417] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 01/24/2016] [Indexed: 01/11/2023] Open
Abstract
Different microbial groups of the microbiome of fresh produce can have diverse effects on human health. This study was aimed at identifying some microbial communities of fresh produce by analyzing 105 samples of imported fresh fruits and vegetables originated from different countries in the world including local samples (Oman) for aerobic plate count and the counts of Enterobacteriaceae, Enterococcus, and Staphylococcus aureus. The isolated bacteria were identified by molecular (PCR) and biochemical methods (VITEK 2). Enterobacteriaceae occurred in 60% of fruits and 91% of vegetables. Enterococcus was isolated from 20% of fruits and 42% of vegetables. E. coli and S. aureus were isolated from 22% and 7% of vegetables, respectively. Ninety-seven bacteria comprising 21 species were similarly identified by VITEK 2 and PCR to species level. E. coli, Klebsiella pneumoniae, Enterococcus casseliflavus, and Enterobacter cloacae were the most abundant species; many are known as opportunistic pathogens which may raise concern to improve the microbial quality of fresh produce. Phylogenetic trees showed no relationship between clustering of the isolates based on the 16S rRNA gene and the original countries of fresh produce. Intercountry passage of opportunistic pathogens in fresh produce cannot be ruled out, which requires better management.
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41
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Saputra D, Rasmussen S, Larsen MV, Haddad N, Sperotto MM, Aarestrup FM, Lund O, Sicheritz-Pontén T. Reads2Type: a web application for rapid microbial taxonomy identification. BMC Bioinformatics 2015; 16:398. [PMID: 26608174 PMCID: PMC4659212 DOI: 10.1186/s12859-015-0829-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 11/17/2015] [Indexed: 12/03/2022] Open
Abstract
Background Identification of bacteria may be based on sequencing and molecular analysis of a specific locus such as 16S rRNA, or a set of loci such as in multilocus sequence typing. In the near future, healthcare institutions and routine diagnostic microbiology laboratories may need to sequence the entire genome of microbial isolates. Therefore we have developed Reads2Type, a web-based tool for taxonomy identification based on whole bacterial genome sequence data. Results Raw sequencing data provided by the user are mapped against a set of marker probes that are derived from currently available bacteria complete genomes. Using a dataset of 1003 whole genome sequenced bacteria from various sequencing platforms, Reads2Type was able to identify the species with 99.5 % accuracy and on the minutes time scale. Conclusions In comparison with other tools, Reads2Type offers the advantage of not needing to transfer sequencing files, as the entire computational analysis is done on the computer of whom utilizes the web application. This also prevents data privacy issues to arise. The Reads2Type tool is available at http://www.cbs.dtu.dk/~dhany/reads2type.html.
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Affiliation(s)
- Dhany Saputra
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Kgs. Lyngby, DK-2800, Denmark.
| | - Simon Rasmussen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Kgs. Lyngby, DK-2800, Denmark.
| | - Mette V Larsen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Kgs. Lyngby, DK-2800, Denmark.
| | - Nizar Haddad
- Bee Research Department, National Centre for Agricultural Research and Extension, P.O. Box 639, Baqa', 19381, Jordan.
| | - Maria Maddalena Sperotto
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Kgs. Lyngby, DK-2800, Denmark.
| | - Frank M Aarestrup
- National Food Institute, Division for Epidemiology and Microbial Genomics, Technical University of Denmark, Kemitorvet, Kgs. Lyngby, DK-2800, Denmark.
| | - Ole Lund
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Kgs. Lyngby, DK-2800, Denmark.
| | - Thomas Sicheritz-Pontén
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Kgs. Lyngby, DK-2800, Denmark.
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42
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Guérin F. Infections à Enterobacter cloacae complex : résistance aux antibiotiques et traitement. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.antinf.2015.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Shah MM, Odoyo E, Larson PS, Apondi E, Kathiiko C, Miringu G, Nakashima M, Ichinose Y. First Report of a Foodborne Providencia alcalifaciens Outbreak in Kenya. Am J Trop Med Hyg 2015; 93:497-500. [PMID: 26123962 DOI: 10.4269/ajtmh.15-0126] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 05/12/2015] [Indexed: 11/07/2022] Open
Abstract
Providencia alcalifaciens is an emerging bacterial pathogen known to cause acute gastroenteritis in children and travelers. In July 2013, P. alcalifaciens was isolated from four children appearing for diarrhea at Kiambu District Hospital (KDH) in Kenya. This study describes the outbreak investigation, which aimed to identify the source and mechanisms of infection. We identified seven primary and four secondary cases. Among primary cases were four mothers who had children and experienced mild diarrhea after eating mashed potatoes. The mothers reported feeding children after visiting the toilet and washing their hands without soap. P. alcalifaciens was detected from all secondary cases, and the isolates were found to be clonal by random amplified polymorphic DNA (RAPD) fingerprinting. Our study suggests that the outbreak was caused by P. alcalifaciens, although no fluid accumulation was observed in rabbit ileal loops. The vehicle of the outbreak was believed to be the mashed potato dish, but the source of P. alcalifaciens could not be confirmed. We found that lack of hygiene, inadequate food storage, and improper hand washing before food preparation was the likely cause of the current outbreak. This is the first report of a foodborne infection caused by P. alcalifaciens in Kenya.
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Affiliation(s)
- Mohammad Monir Shah
- Centre for Infectious Disease Research in Asia and Africa, Institute of Tropical Medicine Nagasaki University, Nagasaki, Japan; Nagasaki University Institute of Tropical Medicine-Kenya Medical Research Institute Project, Nairobi, Kenya; Department of Tumor and Diagnostic Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Erick Odoyo
- Centre for Infectious Disease Research in Asia and Africa, Institute of Tropical Medicine Nagasaki University, Nagasaki, Japan; Nagasaki University Institute of Tropical Medicine-Kenya Medical Research Institute Project, Nairobi, Kenya; Department of Tumor and Diagnostic Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Peter S Larson
- Centre for Infectious Disease Research in Asia and Africa, Institute of Tropical Medicine Nagasaki University, Nagasaki, Japan; Nagasaki University Institute of Tropical Medicine-Kenya Medical Research Institute Project, Nairobi, Kenya; Department of Tumor and Diagnostic Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Ernest Apondi
- Centre for Infectious Disease Research in Asia and Africa, Institute of Tropical Medicine Nagasaki University, Nagasaki, Japan; Nagasaki University Institute of Tropical Medicine-Kenya Medical Research Institute Project, Nairobi, Kenya; Department of Tumor and Diagnostic Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Cyrus Kathiiko
- Centre for Infectious Disease Research in Asia and Africa, Institute of Tropical Medicine Nagasaki University, Nagasaki, Japan; Nagasaki University Institute of Tropical Medicine-Kenya Medical Research Institute Project, Nairobi, Kenya; Department of Tumor and Diagnostic Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Gabriel Miringu
- Centre for Infectious Disease Research in Asia and Africa, Institute of Tropical Medicine Nagasaki University, Nagasaki, Japan; Nagasaki University Institute of Tropical Medicine-Kenya Medical Research Institute Project, Nairobi, Kenya; Department of Tumor and Diagnostic Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Masahiro Nakashima
- Centre for Infectious Disease Research in Asia and Africa, Institute of Tropical Medicine Nagasaki University, Nagasaki, Japan; Nagasaki University Institute of Tropical Medicine-Kenya Medical Research Institute Project, Nairobi, Kenya; Department of Tumor and Diagnostic Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Yoshio Ichinose
- Centre for Infectious Disease Research in Asia and Africa, Institute of Tropical Medicine Nagasaki University, Nagasaki, Japan; Nagasaki University Institute of Tropical Medicine-Kenya Medical Research Institute Project, Nairobi, Kenya; Department of Tumor and Diagnostic Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
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Geider K, Gernold M, Jock S, Wensing A, Völksch B, Gross J, Spiteller D. Unifying bacteria from decaying wood with various ubiquitous Gibbsiella species as G. acetica sp. nov. based on nucleotide sequence similarities and their acetic acid secretion. Microbiol Res 2015; 181:93-104. [PMID: 26071988 DOI: 10.1016/j.micres.2015.05.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 05/07/2015] [Accepted: 05/09/2015] [Indexed: 11/28/2022]
Abstract
Bacteria were isolated from necrotic apple and pear tree tissue and from dead wood in Germany and Austria as well as from pear tree exudate in China. They were selected for growth at 37 °C, screened for levan production and then characterized as Gram-negative, facultatively anaerobic rods. Nucleotide sequences from 16S rRNA genes, the housekeeping genes dnaJ, gyrB, recA and rpoB alignments, BLAST searches and phenotypic data confirmed by MALDI-TOF analysis showed that these bacteria belong to the genus Gibbsiella and resembled strains isolated from diseased oaks in Britain and Spain. Gibbsiella-specific PCR primers were designed from the proline isomerase and the levansucrase genes. Acid secretion was investigated by screening for halo formation on calcium carbonate agar and the compound identified by NMR as acetic acid. Its production by Gibbsiella spp. strains was also determined in culture supernatants by GC/MS analysis after derivatization with pentafluorobenzyl bromide. Some strains were differentiated by the PFGE patterns of SpeI digests and by sequence analyses of the lsc and the ppiD genes, and the Chinese Gibbsiella strain was most divergent. The newly investigated bacteria as well as Gibbsiella querinecans, Gibbsiella dentisursi and Gibbsiella papilionis, isolated in Britain, Spain, Korea and Japan, are taxonomically related Enterobacteriaceae, tolerate and secrete acetic acid. We therefore propose to unify them in the species Gibbsiella acetica sp. nov.
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Affiliation(s)
- Klaus Geider
- Julius Kuehn Institute, Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Schwabenheimer Str. 101, 69221 Dossenheim, Germany.
| | - Marina Gernold
- Julius Kuehn Institute, Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Schwabenheimer Str. 101, 69221 Dossenheim, Germany.
| | - Susanne Jock
- Julius Kuehn Institute, Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Schwabenheimer Str. 101, 69221 Dossenheim, Germany.
| | - Annette Wensing
- Julius Kuehn Institute, Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Schwabenheimer Str. 101, 69221 Dossenheim, Germany.
| | - Beate Völksch
- FSU Jena, Institute of Microbiology, Microbial Phytopathology, Neugasse 25, Jena, Germany.
| | - Jürgen Gross
- Julius Kuehn Institute, Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Schwabenheimer Str. 101, 69221 Dossenheim, Germany.
| | - Dieter Spiteller
- Max-Planck-Institute for Chemical Ecology, Bioorganic Chemistry, Jena and Chemical Ecology/Biological Chemistry, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany.
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Hong SK, Lee JS, Kim EC. First Korean case of Cedecea lapagei pneumonia in a patient with chronic obstructive pulmonary disease. Ann Lab Med 2015; 35:266-8. [PMID: 25729735 PMCID: PMC4330183 DOI: 10.3343/alm.2015.35.2.266] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 09/11/2014] [Accepted: 12/16/2014] [Indexed: 11/19/2022] Open
Affiliation(s)
- Sung Kuk Hong
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea. ; Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Jee-Soo Lee
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Eui-Chong Kim
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
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Detection of QnrB54 and its novel genetic context in Citrobacter freundii isolated from a clinical case. Antimicrob Agents Chemother 2014; 59:1375-6. [PMID: 25512409 DOI: 10.1128/aac.03895-14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Gaastra W, Kusters JG, van Duijkeren E, Lipman LJA. Escherichia fergusonii. Vet Microbiol 2014; 172:7-12. [PMID: 24861842 DOI: 10.1016/j.vetmic.2014.04.016] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 04/17/2014] [Accepted: 04/18/2014] [Indexed: 10/25/2022]
Abstract
Escherichia fergusonii was introduced in the genus Escherichia almost 65 years later than Escherichia coli after which the genus was named. From then (1985) onwards mainly case reports on E. fergusonii associated with disease in individuals of veterinary or human origin have been reported and only very few more extensive studies became available. This has resulted in very fragmented knowledge on this organism. The aim of this manuscript is to give an overview of what is known on E. fergusonii today and to stimulate more research on this organism so that better insight can be obtained in the role that E. fergusonii plays in human and animal infections.
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Affiliation(s)
- W Gaastra
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, The Netherlands
| | - J G Kusters
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - E van Duijkeren
- Centre for Infectious Disease Control Netherlands (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - L J A Lipman
- Division of Veterinary Public Health, Institute for Risk Assessment Sciences, Utrecht University, The Netherlands.
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Amos GCA, Hawkey PM, Gaze WH, Wellington EM. Waste water effluent contributes to the dissemination of CTX-M-15 in the natural environment. J Antimicrob Chemother 2014; 69:1785-91. [PMID: 24797064 PMCID: PMC4054988 DOI: 10.1093/jac/dku079] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Objectives Multidrug-resistant Enterobacteriaceae pose a significant threat to public health. We aimed to study the impact of sewage treatment effluent on antibiotic resistance reservoirs in a river. Methods River sediment samples were taken from downstream and upstream of a waste water treatment plant (WWTP) in 2009 and 2011. Third-generation cephalosporin (3GC)-resistant Enterobacteriaceae were enumerated. PCR-based techniques were used to elucidate mechanisms of resistance, with a new two-step PCR-based assay developed to investigate blaCTX-M-15 mobilization. Conjugation experiments and incompatibility replicon typing were used to investigate plasmid ecology. Results We report the first examples of blaCTX-M-15 in UK river sediment; the prevalence of blaCTX-M-15 was dramatically increased downstream of the WWTP. Ten novel genetic contexts for this gene were identified, carried in pathogens such as Escherichia coli ST131 as well as indigenous aquatic bacteria such as Aeromonas media. The blaCTX-M-15 gene was readily transferable to other Gram-negative bacteria. We also report the first finding of an imipenem-resistant E. coli in a UK river. Conclusions The high diversity and host range of novel genetic contexts proves that evolution of novel combinations of resistance genes is occurring at high frequency and has to date been significantly underestimated. We have identified a worrying reservoir of highly resistant enteric bacteria in the environment that poses a threat to human and animal health.
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Affiliation(s)
- G C A Amos
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - P M Hawkey
- Health Protection Agency, West Midlands Public Health Laboratory, Heart of England NHS Foundation Trust, Bordesley Green East, Birmingham, UK Institute of Microbiology and Infection, Biosciences, University of Birmingham, Birmingham, UK
| | - W H Gaze
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - E M Wellington
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
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Spitaels F, Wieme AD, Janssens M, Aerts M, Daniel HM, Van Landschoot A, De Vuyst L, Vandamme P. The microbial diversity of traditional spontaneously fermented lambic beer. PLoS One 2014; 9:e95384. [PMID: 24748344 PMCID: PMC3991685 DOI: 10.1371/journal.pone.0095384] [Citation(s) in RCA: 150] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 03/25/2014] [Indexed: 12/14/2022] Open
Abstract
Lambic sour beers are the products of a spontaneous fermentation that lasts for one to three years before bottling. The present study determined the microbiota involved in the fermentation of lambic beers by sampling two fermentation batches during two years in the most traditional lambic brewery of Belgium, using culture-dependent and culture-independent methods. From 14 samples per fermentation, over 2000 bacterial and yeast isolates were obtained and identified. Although minor variations in the microbiota between casks and batches and a considerable species diversity were found, a characteristic microbial succession was identified. This succession started with a dominance of Enterobacteriaceae in the first month, which were replaced at 2 months by Pediococcus damnosus and Saccharomyces spp., the latter being replaced by Dekkera bruxellensis at 6 months fermentation duration.
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Affiliation(s)
- Freek Spitaels
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Anneleen D. Wieme
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
- Laboratory of Biochemistry and Brewing, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Maarten Janssens
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Maarten Aerts
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Heide-Marie Daniel
- Mycothèque de l'Université catholique de Louvain (MUCL), Belgian Coordinated Collection of Microorganisms (BCCM), Earth and Life Institute, Applied Microbiology, Mycology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Anita Van Landschoot
- Laboratory of Biochemistry and Brewing, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
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Parkinson N, DeVos P, Pirhonen M, Elphinstone J. Dickeya aquatica sp. nov., isolated from waterways. Int J Syst Evol Microbiol 2014; 64:2264-2266. [PMID: 24719023 DOI: 10.1099/ijs.0.058693-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pectinolytic Gram-negative bacteria were isolated from different waterways in the UK and Finland. Three strains (174/2(T), 181/2 and Dw054) had the same 16S rRNA gene sequences which shared 99% sequence similarity to species of the genus Dickeya, and a phylogeny of related genera confirmed attribution to this genus. Fatty acid profile analysis of all three strains found a high proportion of C16 : 1ω7c/C16 : 1ω7c and C16 : 0 fatty acids, and library profile searches found closest matches to Dickeya chrysanthemi. Production of a concatenated phylogeny using six loci, recA, gapA, atpD, gyrB, infB and rpoB, provided a high-resolution phylogeny which placed strains 174/2(T) and 181/2 as a distinct clade, separated from the other species of the genus Dickeya by a relatively long branch-length. DNA-DNA hybridization analysis with a limited number of reference species also supported the distinctiveness of strains 174/2(T) and 181/2 within the genus Dickeya. All three strains could be phenotypically distinguished from other species of the genus by fermentation of melibiose and raffinose but not D-arabinose or mannitol. The name Dickeya aquatica sp. nov. is proposed for the new taxon; the type strain is 174/2(T) ( = NCPPB 4580(T) = LMG 27354(T)).
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Affiliation(s)
- Neil Parkinson
- Food and Environment Research Agency (Fera), Sand Hutton, York, YO41 1LZ, UK
| | - Paul DeVos
- BCCM/LMG Bacteria Collection Ghent University Laboratory of Microbiology, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Minna Pirhonen
- Department of Agricultural Sciences, PO Box 27, 00014 University of Helsinki, Finland
| | - John Elphinstone
- Food and Environment Research Agency (Fera), Sand Hutton, York, YO41 1LZ, UK
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