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Zepeda-Velazquez AP, Gómez-De-Anda FR, Aguilar-Mendoza LF, Castrejón-Jiménez NS, Hernández-González JC, Varela-Guerrero JA, de-la-Rosa-Arana JL, Vega-Sánchez V, Reyes-Rodríguez NE. Bullfrogs (Lithobates catesbeianus) as a Potential Source of Foodborne Disease. J Food Prot 2023; 86:100067. [PMID: 36948016 DOI: 10.1016/j.jfp.2023.100067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 02/15/2023] [Accepted: 02/18/2023] [Indexed: 03/24/2023]
Abstract
In Mexico, bullfrogs (Lithobates catesbeianus) are produced as gourmet food. However, bullfrogs can be carriers of pathogens because the frogs' preferred living conditions occur in stagnant water. The present study aimed to identify bacteria that cause foodborne diseases or are associated with human diseases. For molecular identification, based on the sequential analysis by 16S rRNA or rpoD was conducted on all isolates obtained from bullfrog. A total of 91 bacterial isolates were obtained from bullfrogs; 14 genera and 23 species were identified, including Acinetobacter johnsonii 16.5%; Aeromonas media 14.3%; Aeromonas veronii 13.2%; Providencia rettgeri 7.7%; Citrobacter freundii 6.6%; Aeromonas caviae 4.4%; Aeromonas hydrophila and Elizabethkingia ursingii 3.3%; Pseudomonas stutzeri, Raoultella ornithinolytica, and Shewanella putrefaciens 2.2%; Acinetobacter guillouiae, Acinetobacter pseudolwoffii, Citrobacter portucalensis, Citrobacter werkmanii, Edwardsiella anguillarum, Klebsiella michiganensis, Kluyvera intermedia, Kocuria rosea, Myroides odoratimimus, Myroides odoratus, Proteus sp., and Proteus hauseri 1.1%. In this study, 49.4% of the isolates obtained cause foodborne disease, 19.8% are bacteria that play an important role in the spoilage of food, 5.5% of isolates have nosocomial significance, 13.2% of bacteria are considered to be pollutants of the ecosystem, and in the case of A. salmonicida and Edwardsiella anguillarum (12.1%) to have a negative impact on aquaculture. Acinetobacter pseudolwoffii and Citrobacter portucalensis have not been reported to cause disease. Lastly of these isolates, 97.8% (89/91) can cause disease by food consumption or by direct contact for immunocompromised persons. The presence of these bacteria in bullfrogs represents a significant problem for human health. There is evidence that these microorganisms are pathogenic and frogs may also be reservoirs.
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Affiliation(s)
- Andrea P Zepeda-Velazquez
- Área Académica de Medicina Veterinaria y Zootecnia, Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Tulancingo, Hidalgo 43600, Mexico.
| | - Fabián-Ricardo Gómez-De-Anda
- Área Académica de Medicina Veterinaria y Zootecnia, Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Tulancingo, Hidalgo 43600, Mexico.
| | - Luis F Aguilar-Mendoza
- Área Académica de Medicina Veterinaria y Zootecnia, Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Tulancingo, Hidalgo 43600, Mexico
| | - Nayeli Shantal Castrejón-Jiménez
- Área Académica de Medicina Veterinaria y Zootecnia, Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Tulancingo, Hidalgo 43600, Mexico.
| | - Juan Carlos Hernández-González
- Área Académica de Medicina Veterinaria y Zootecnia, Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Tulancingo, Hidalgo 43600, Mexico.
| | - Jorge A Varela-Guerrero
- Universidad Autónoma del Estado de México, Centro de Investigación y Estudios Avanzados en Salud Animal (CIESA), Facultad de Medicina Veterinaria y Zootecnia, km 15.5 Carretera Panamericana Toluca-Atlacomulco, Toluca, Estado de México, Mexico.
| | - Jorge-Luis de-la-Rosa-Arana
- Microbiología en Salud Humana, Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Avenida 1 de mayo S/N, Campo Uno, Cuautitlán Izcalli, CP 54743 Estado de México, Mexico.
| | - Vicente Vega-Sánchez
- Área Académica de Medicina Veterinaria y Zootecnia, Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Tulancingo, Hidalgo 43600, Mexico.
| | - Nydia E Reyes-Rodríguez
- Área Académica de Medicina Veterinaria y Zootecnia, Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Tulancingo, Hidalgo 43600, Mexico.
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Liu YH, Ma YM, Tian HO, Yang B, Han WX, Zhao WH, Chai HL, Zhang ZS, Wang LF, Chen L, Xing Y, Ding YL, Zhao L. First determination of DNA virus and some additional bacteria from Melophagus ovinus (sheep ked) in Tibet, China. Front Microbiol 2022; 13:988136. [PMID: 36147838 PMCID: PMC9486064 DOI: 10.3389/fmicb.2022.988136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/16/2022] [Indexed: 12/03/2022] Open
Abstract
Melophagus ovinus (sheep ked) is one of the common ectoparasites in sheep. In addition to causing direct damage to the host through biting and sucking blood, sheep ked is a potential vector of helminths, protozoa, bacteria, and viruses. Sheep M. ovinus samples from three regions in Tibet were selected for DNA extraction. The 16S rDNA V3-V4 hypervariable region was amplified, after genomic DNA fragmentation, Illumina Hiseq libraries were constructed. The 16S rRNA sequencing and viral metagenomics sequencing were separately conducted on the Illumina Novaseq 6000 platform and molecular biology software and platforms were employed to analyze the sequencing data. Illumina PE250 sequencing results demonstrated that the dominant bacteria phylum in M. ovinus from Tibet, China was Proteobacteria, where 29 bacteria genera were annotated. The dominant bacterial genera were Bartonella, Wolbachia, and Arsenophonus; Bartonella chomelii, Wolbachia spp., and Arsenophonus spp. were the dominant bacterial species in M. ovinus from Tibet, China. We also detected Kluyvera intermedia, Corynebacterium maris DSM 45190, Planomicrobium okeanokoites, and Rhodococcus erythropolis, of which the relative abundance of Kluyvera intermedia was high. Illumina Hiseq sequencing results demonstrated that 4 virus orders were detected in M. ovinus from Tibet, China, and 3 samples were annotated into 29 families, 30 families, and 28 families of viruses, respectively. Virus families related to vertebrates and insects mainly included Mimiviridae, Marseilleviridae, Poxviridae, Ascoviridae, Iridoviridae, Baculoviridae, Hytrosaviridae, Nudiviridae, Polydnaviridae, Adomaviridae, Asfarviridae, Hepeviridae, Herpesviridae, and Retroviridae; at the species level, the relative abundance of Tupanvirus_soda_lake, Klosneuvirus_KNV1, and Indivirus_ILV1 was higher. African swine fever virus and many poxviruses from the family Poxviridae were detected, albeit their relative abundance was low. The dominant bacterial phylum of M. ovinus from Tibet, China was Proteobacteria, and the dominant bacterial genera were Bartonella, Wolbachia, and Arsenophonus, where 23 out of 29 annotated bacteria genera were first reported in M. ovinus. Kluyvera intermedia, Corynebacterium maris DSM 45190, Planomicrobium okeanokoites, and Rhodococcus erythropolis were detected for the first time. All DNA viruses detected in this study have been reported in M. ovinus for the first time.
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Affiliation(s)
- Yong-Hong Liu
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Clinical Diagnosis and Treatment Technology in Animal Disease, Ministry of Agriculture and Rural Affairs, Hohhot, China
| | - Yi-Min Ma
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China
| | - Hong-Ou Tian
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China
| | - Bo Yang
- Animal Disease Control Center of Ordos, Ordos City, China
| | - Wen-Xiong Han
- Inner Mongolia Saikexing Reproductive Biotechnology (Group) Co., Ltd., Hohhot, China
| | - Wei-Hong Zhao
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China
| | - Hai-Liang Chai
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhan-Sheng Zhang
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China
| | - Li-Feng Wang
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China
| | - Lei Chen
- Shanghai Origingene Bio-pharm Technology Co., Ltd., Shanghai, China
| | - Yu Xing
- Shanghai Origingene Bio-pharm Technology Co., Ltd., Shanghai, China
| | - Yu-Lin Ding
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Clinical Diagnosis and Treatment Technology in Animal Disease, Ministry of Agriculture and Rural Affairs, Hohhot, China
| | - Li Zhao
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Clinical Diagnosis and Treatment Technology in Animal Disease, Ministry of Agriculture and Rural Affairs, Hohhot, China
- *Correspondence: Li Zhao,
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Annotation-free delineation of prokaryotic homology groups. PLoS Comput Biol 2022; 18:e1010216. [PMID: 35675326 PMCID: PMC9212150 DOI: 10.1371/journal.pcbi.1010216] [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: 12/10/2021] [Revised: 06/21/2022] [Accepted: 05/16/2022] [Indexed: 11/19/2022] Open
Abstract
Phylogenomic studies of prokaryotic taxa often assume conserved marker genes are homologous across their length. However, processes such as horizontal gene transfer or gene duplication and loss may disrupt this homology by recombining only parts of genes, causing gene fission or fusion. We show using simulation that it is necessary to delineate homology groups in a set of bacterial genomes without relying on gene annotations to define the boundaries of homologous regions. To solve this problem, we have developed a graph-based algorithm to partition a set of bacterial genomes into Maximal Homologous Groups of sequences (MHGs) where each MHG is a maximal set of maximum-length sequences which are homologous across the entire sequence alignment. We applied our algorithm to a dataset of 19 Enterobacteriaceae species and found that MHGs cover much greater proportions of genomes than markers and, relatedly, are less biased in terms of the functions of the genes they cover. We zoomed in on the correlation between each individual marker and their overlapping MHGs, and show that few phylogenetic splits supported by the markers are supported by the MHGs while many marker-supported splits are contradicted by the MHGs. A comparison of the species tree inferred from marker genes with the species tree inferred from MHGs suggests that the increased bias and lack of genome coverage by markers causes incorrect inferences as to the overall relationship between bacterial taxa. Assuming genes to be the basic evolutionary unit has been commonplace in bacterial genomics. For example, when quantifying the extent of horizontal gene transfer it is common to infer gene trees and reconcile them against a species tree to account for recombination-based processes. We have developed a new method which challenges this assumption by identifying contiguous regions of true homology without regards to gene boundaries and applied it to Enterobacteriaceae, a family of bacteria containing several important human pathogens. Our results show that genes are composed of distinct homologous regions with conflicting phylogenetic histories. We further demonstrate that failing to take account of this conflict, together with the functional biases we show exist among single-copy marker genes, significantly changes the consensus evolutionary tree of Enterobacteriaceae.
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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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ENTEROBACTERIACEAE IN SOILS AND ATMOSPHERIC DUST AEROSOL ACCUMULATIONS OF MOSCOW CITY. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100124. [PMID: 35909602 PMCID: PMC9325881 DOI: 10.1016/j.crmicr.2022.100124] [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: 09/29/2021] [Revised: 02/23/2022] [Accepted: 03/01/2022] [Indexed: 11/23/2022] Open
Abstract
The topsoils and atmospheric dust aerosols of the various areas of the city of Moscow were studied. Most of the dust samples contained a considerable number of particles enriched in phosphorus - a sign of contamination by feces. A variety of Enterobacteriaceae species, including opportunistic and pathogenic species, were isolated from the topsoil and dust samples and identified using 16S rDNA nucleotide sequences: Enterobacter aerogenes, E. agglomerans, E. cloacae, E. kobei, E. nimipressuralis, Escherichia coli, Citrobacter europaeus, Klebsiella granulomatis, K. grimontii, K. oxytoca, K. quasipneumoniae, K. variicola, Kluyvera ascorbate, Kluyvera intermedia, Leclercia adecarboxylata, Salmonella enterica and Trabulsiella guamensis. The greatest diversity of pathogens was isolated from spring soil and dust samples immediately after spring snowmelt. Antibiotic resistance of the isolated E. coli strains was tested using disks with a wide range of antimicrobial drugs: Amoxicillin, Ampicillin, Meropenem, Pefloxacin, Streptomycin, Ticarcillin+clavulanic acid, Fosfomycin, Ceftibuten, Ciprofloxacin. Resistance was observed in more than 22% of E. coli strains. The traffic area had a significant number of antibiotic-resistant E. coli strains, clearly indicating a high health risk from soil and dust exposure.
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The Leaf Microbiome of Tobacco Plants across Eight Chinese Provinces. Microorganisms 2022; 10:microorganisms10020450. [PMID: 35208904 PMCID: PMC8878116 DOI: 10.3390/microorganisms10020450] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/10/2022] [Accepted: 02/12/2022] [Indexed: 02/05/2023] Open
Abstract
Leaf microorganism communities play significant roles in the process of plant growth, but the microbiome profiling of crop leaves is still a relatively new research area. Here, we used 16S rDNA sequencing to profile the microbiomes of 78 primary dried tobacco leaf samples from 26 locations in eight Chinese provinces. Our analyses revealed that the national leaf microbial communities contain 4473 operational taxonomic units (OTU) representing 1234 species, but there is a small, national core microbiome with only 14 OTU representing nine species. The function of this core microbiome is related to processes including nitrogen fixation, detoxification of diverse pollutants, and heavy-metal reduction. The leaf microorganism communities are obviously affected by local environments but did not exhibit obvious relationships to single ecological factors (e.g., temperature, precipitation). Our findings enhance the understanding of microbial diversity of tobacco leaves, which could be utilized for a variety of bioprocess, agricultural, and environmental detoxification applications.
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Zheng R, Wu M, Wang H, Chai L, Peng J. Copper-induced sublethal effects in Bufo gargarizans tadpoles: growth, intestinal histology and microbial alternations. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:502-513. [PMID: 33587250 DOI: 10.1007/s10646-021-02356-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/20/2021] [Indexed: 06/12/2023]
Abstract
Copper (Cu) is one of the environmental contaminations which can pose significant risks for organisms. The current study explores the effects of Cu exposure on the growth, intestinal histology and microbial ecology in Bufo gargarizans. The results revealed that 0.5-1 μM Cu exposure induced growth retardation (including reduction of total body length and wet weight) and intestinal histological injury (including disordered enterocyte, changes in the villi and vacuoles) of tadpoles. Also, high-throughput sequencing analysis showed that Cu exposure caused changes in richness, diversity and structure of intestinal microbiota. Moreover, the composition of intestinal microbiota was altered in tadpoles exposed to different concentrations of Cu. At the phylum level, we observed the abundance of proteobacteria was increased, while the abundance of fusobacteria was decreased in the intestinal microbiota of tadpoles exposed to 1 μM Cu. At the genus level, a reduced abundance of kluyvera and aeromonas was observed in the intestinal microbiota of tadpoles under the exposure of 0-0.5 μM Cu. Finally, functional predictions revealed that tadpoles exposed to copper may be at a higher risk of developing metabolic disorders or diseases. Above all, our results will develop a comprehensive view of the Cu exposure in amphibians and will yield a new consideration for sublethal effects of Cu on aquatic organisms.
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Affiliation(s)
- Rui Zheng
- College of Life Science, Shaanxi Normal University, Xi'an, 710119, People's Republic of China
| | - Minyao Wu
- College of Life Science, Shaanxi Normal University, Xi'an, 710119, People's Republic of China
| | - Hongyuan Wang
- College of Life Science, Shaanxi Normal University, Xi'an, 710119, People's Republic of China
| | - Lihong Chai
- School of Water and Environment, Chang'an University, Xi'an, 710054, People's Republic of China
- Key Laboratory of Subsurface Hydrology and Ecological Effect in Arid Region of Ministry of Education, Xi'an, 710062, People's Republic of China
| | - Jufang Peng
- College of Life Science, Shaanxi Normal University, Xi'an, 710119, People's Republic of China.
- Basic Experimental Teaching Center, Shaanxi Normal University, Xi'an, 710119, People's Republic of China.
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Proposal for Unification of the Genus Metakosakonia and the Genus Phytobacter to a Single Genus Phytobacter and Reclassification of Metakosakonia massiliensis as Phytobacter massiliensis comb. nov. Curr Microbiol 2020; 77:1945-1954. [PMID: 32350604 DOI: 10.1007/s00284-020-02004-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 04/24/2020] [Indexed: 12/15/2022]
Abstract
The genus Metakosakonia, as the closest phylogenetic neighbor of the genus Kosakonia within the family Enterobacteriaceae, when proposed in 2017, consisted of M. massiliensis JC163T and Metakosakonia spp. strains CAV1151 and GT-16. The strain CAV1151 was later classified into a novel species Phytobacter ursingii. Here, we show that the strain GT-16 shares a digital DNA-DNA hybridization (DDH) similarity of 91.0% with P. diazotrophicus DSM 17806 T and thus also belongs to P. diazotrophicus. M. massiliensis and the strains within the genus Phytobacter formed a monophyletic cluster on a phylogenomic tree based on the core proteins of the family Enterobacteriaceae and on a phylogenetic tree based on the 16S rRNA genes. M. massiliensis and the genus Phytobacter share average amino acid identities of 86.80‒87.41% above the threshold (86%) for genus delimitation within the family Enterobacteriaceae. Moreover, they share conserved signature indels in the intracellular growth protein IgaA and the outer membrane assembly protein AsmA. Therefore, we propose to unite the genus Metakosakonia and the genus Phytobacter to a single genus. Because the genus Phytobacter was validly published earlier in 2017 than the genus Metakosakonia in 2017, the genus name Phytobacter has priority over Metakosakonia. We propose to unite the two genera under the name Phytobacter with the type species P. diazotrophicus and reclassify M. massiliensis as P. massiliensis comb. nov. In addition, the analyses of genome relatedness and phylogenomic relationship identified one potential novel species within the genus Phytobacter and three potential novel species within the genus Kosakonia.
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Philippon A, Jacquier H, Ruppé E, Labia R. Structure-based classification of class A beta-lactamases, an update. Curr Res Transl Med 2019; 67:115-122. [PMID: 31155436 DOI: 10.1016/j.retram.2019.05.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 05/21/2019] [Accepted: 05/21/2019] [Indexed: 02/06/2023]
Abstract
Beta-lactamase (EC 3.5.2.6) synthesis, particularly in Gram-negative bacilli, is a major mechanism of natural and acquired resistance to beta-lactams, sometimes accompanied by impermeability and/or active efflux. These enzymes have been classified into four molecular classes (A-D). The serine enzymes of class A, which may be encoded by the bacterial chromosome or transferable elements and are susceptible to clinically available inhibitors (clavulanic acid, sulbactam, tazobactam, avibactam), are prevalent considering other molecular classes (B,C,D). The continual rapid development of genomic approaches and tremendous progress in automatic sequencer technology have resulted in the accumulation of massive amounts of data. A structure-based classification of class A beta-lactamases based on specific conserved motifs involved in catalytic mechanisms and/or substrate binding (S70XXK, S130DN, K234TG), together with E166 (Ambler numbering) and at least 24 other amino-acid residues or analogs such as G45, F66, V80, L81, L91, L101, P107, A134, L138, G143, G144, G156, L169, T181, T182, P183, was validated on 700 amino-acid sequences, including 132 representative types, but mostly probable enzyme sequences, many produced by environmental bacteria. Two subclasses (A1, A2), six major clusters or groups (e.g. natural limited-spectrum beta-lactamases (LSBL), wider spectrum beta-lactamases (WSBL), and various other clusters were identified on the basis of conserved (> 90%) and specific motifs, and residues such as S70TFKAL, S130DNTAANL, R164XEXXLN, V231GDKTG for subclass A1, S70VFKFH, S130DNNACDI,E166XXM, and V231AHKTG for subclass A2, a probable disulfide bridge C77-C123 and G236, A237, G238, and R244 for the LSBL group. This great diversity of primary structures was used as the basis for a structure-based and phylogenetic classification.
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Affiliation(s)
- Alain Philippon
- Faculté de Médecine Paris Descartes, Service de Bactériologie, Paris, France.
| | - Hervé Jacquier
- AP-HP, Hôpital Lariboisière, Laboratoire de Bactériologie, Paris, France; INSERM, IAME, UMR 1137, Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, France
| | - Etienne Ruppé
- INSERM, IAME, UMR 1137, Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, France; AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, F-75018 Paris, France
| | - Roger Labia
- Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne, 6 Rue de l'Université, Quimper, France
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Putative horizontal transfer of carbapenem resistance betweenKlebsiella pneumoniaeandKluyvera ascorbataduring abdominal infection: A case report. Infect Control Hosp Epidemiol 2019; 40:494-496. [DOI: 10.1017/ice.2019.26] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Higuera-Llantén S, Vásquez-Ponce F, Barrientos-Espinoza B, Mardones FO, Marshall SH, Olivares-Pacheco J. Extended antibiotic treatment in salmon farms select multiresistant gut bacteria with a high prevalence of antibiotic resistance genes. PLoS One 2018; 13:e0203641. [PMID: 30204782 PMCID: PMC6133359 DOI: 10.1371/journal.pone.0203641] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 08/26/2018] [Indexed: 01/31/2023] Open
Abstract
The high use of antibiotics for the treatment of bacterial diseases is one of the main problems in the mass production of animal protein. Salmon farming in Chile is a clear example of the above statement, where more than 5,500 tonnes of antibiotics have been used over the last 10 years. This has caused a great impact both at the production level and on the environment; however, there are still few works in relation to it. In order to demonstrate the impact of the high use of antibiotics on fish gut microbiota, we have selected four salmon farms presenting a similar amount of fish of the Atlantic salmon species (Salmo salar), ranging from 4,500 to 6,000 tonnes. All of these farms used treatments with high doses of antibiotics. Thus, 15 healthy fish were selected and euthanised in order to isolate the bacteria resistant to the antibiotics oxytetracycline and florfenicol from the gut microbiota. In total, 47 bacterial isolates resistant to florfenicol and 44 resistant to oxytetracycline were isolated, among which isolates with Minimum Inhibitory Concentrations (MIC) exceeding 2048 μg/mL for florfenicol and 1024 μg/mL for oxytetracycline were found. In addition, another six different antibiotics were tested in order to demonstrate the multiresistance phenomenon. In this regard, six isolates of 91 showed elevated resistance values for the eight tested antibiotics, including florfenicol and oxytetracycline, were found. These bacteria were called “super-resistant” bacteria. This phenotypic resistance was verified at a genotypic level since most isolates showed antibiotic resistance genes (ARGs) to florfenicol and oxytetracycline. Specifically, 77% of antibiotic resistant bacteria showed at least one gene resistant to florfenicol and 89% showed at least one gene resistant to oxytetracycline. In the present study, it was demonstrated that the high use of the antibiotics florfenicol and oxytetracycline has, as a consequence, the selection of multiresistant bacteria in the gut microbiota of farmed fish of the Salmo salar species at the seawater stage. Also, the phenotypic resistance of these bacteria can be correlated with the presence of antibiotic resistance genes.
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MESH Headings
- Animals
- Anti-Bacterial Agents/pharmacology
- Aquaculture
- Bacteria/drug effects
- Bacteria/genetics
- Bacteria/isolation & purification
- Drug Resistance, Multiple, Bacterial/drug effects
- Drug Resistance, Multiple, Bacterial/genetics
- Gastrointestinal Microbiome/drug effects
- Intestines/microbiology
- Microbial Sensitivity Tests
- Oxytetracycline/pharmacology
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- Salmo salar
- Thiamphenicol/analogs & derivatives
- Thiamphenicol/pharmacology
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Affiliation(s)
- Sebastián Higuera-Llantén
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Campus Curauma, Valparaíso, CP, Chile
| | - Felipe Vásquez-Ponce
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Campus Curauma, Valparaíso, CP, Chile
| | - Beatriz Barrientos-Espinoza
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Campus Curauma, Valparaíso, CP, Chile
| | - Fernando O. Mardones
- Escuela de Medicina Veterinaria, Facultad de Ecología y Recursos Naturales, Universidad Andrés Bello, Republica 252, CP, Santiago, Chile
| | - Sergio H. Marshall
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Campus Curauma, Valparaíso, CP, Chile
| | - Jorge Olivares-Pacheco
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Campus Curauma, Valparaíso, CP, Chile
- Millenium Nucleus on Interdisciplinary approach to Antimicrobial Resistance, Lo Barnechea, Santiago, CP, Chile
- * E-mail:
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12
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Han Y, Wang Y, Li L, Xu G, Liu J, Yang K. Bacterial population and chemicals in bioaerosols from indoor environment: Sludge dewatering houses in nine municipal wastewater treatment plants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 618:469-478. [PMID: 29136598 DOI: 10.1016/j.scitotenv.2017.11.071] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 11/06/2017] [Accepted: 11/07/2017] [Indexed: 05/04/2023]
Abstract
Municipal wastewater treatment plants (MWTPs) are regarded as sources of airborne microorganisms. Sludge dewatering house (SDH) is one of the most serious indoor bioaerosol pollution treatment sectors in MWTPs. In this study, properties of bioaerosols from SDHs of nine MWTPs were investigated in China. Results suggested that bioaerosols were generated mainly from the mixed liquor and will be promoted by the mechanical motion of belts of dewatering devices. They will accumulate in the SDHs due to the treatment devices placed inside. Levels of airborne bacteria and chemicals showed regional variations. In Hefei and Yixing, the emissions of total suspended particles (TSP) and airborne bacteria were higher than those in Beijing and Guangzhou. Results of bacterial population showed that bacterial species in bioaerosols from SDHs also presented significant regional disparity; these regional disparities were closely related with the source of bioaerosols in SDHs. Among these identified bacterial species, some common potential pathogens were detected in all SDHs, such as Aeromonas caviae, Flavobacterium sp., and Staphylococcus lentus. Relative humidity (RH) and temperature were the major parameters on bioaerosols to survive. As shown in this study, SDHs in wastewater treatment plants should be provided considerable attention for being an emission source of indoor bioaerosols.
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Affiliation(s)
- Yunping Han
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; National Engineering Laboratory for VOCs Pollution Control Material & Technology, University of Chinese Academy of Sciences, Beijing 101408, China.
| | - Yanjie Wang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; National Engineering Laboratory for VOCs Pollution Control Material & Technology, University of Chinese Academy of Sciences, Beijing 101408, China.
| | - Lin Li
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; National Engineering Laboratory for VOCs Pollution Control Material & Technology, University of Chinese Academy of Sciences, Beijing 101408, China.
| | - Guangsu Xu
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; National Engineering Laboratory for VOCs Pollution Control Material & Technology, University of Chinese Academy of Sciences, Beijing 101408, China.
| | - Junxin Liu
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Kaixiong Yang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; National Engineering Laboratory for VOCs Pollution Control Material & Technology, University of Chinese Academy of Sciences, Beijing 101408, China.
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