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Disli HB, Hizlisoy H, Gungor C, Barel M, Dishan A, Gundog DA, Al S, Onmaz NE, Yildirim Y, Gonulalan Z. Investigation and characterization of Aliarcobacter spp. isolated from cattle slaughterhouse in Türkiye. Int Microbiol 2024; 27:1321-1332. [PMID: 38206523 DOI: 10.1007/s10123-023-00478-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 10/31/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024]
Abstract
Aliarcobacter spp. have been isolated from numerous food products at retail and from animal carcasses and feces at slaughter. The objectives of this study were as follows: (i) to isolate Aliarcobacter species from different slaughterhouses' samples and (ii) to detect genetic diversity, antibiotic resistance, biofilm ability, and putative virulence gene profiles of the isolates. A molecular investigation of antibiotic resistance and virulence factors was also conducted using polymerase chain reaction (PCR). Among 150 samples, a total of 22 (14.6%) Aliarcobacter spp. isolates were obtained, with varying levels of antibiotic resistance observed. The genes tetO, tetW, and gyrA were detected in 0%, 31.8%, and 27.2% of the isolates, respectively. All isolates were resistant to ampicillin, rifampin, and erythromycin, while tetracycline was found to be the most effective antibiotic, with 81.8% of the isolates showing susceptibility to it. All isolates (100%) harbored more than one of the nine putative virulence genes tested, with 18.1% of isolates carrying more than three. Regarding biofilm formation, 7 (31.8%) and 4 (18.1%) isolates were found to form strong and moderate biofilms, respectively, while one (4.5%) isolate was classified as a weak biofilm producer. ERIC-PCR band patterns suggested that the isolated Aliarcobacter spp. from slaughterhouses had different sources of contamination. These findings highlight the potential risk posed by pathogenic and multidrug-resistant Aliarcobacter spp. in food and the need for control measures throughout the food chain to prevent the spread of these strains. The results indicate that foods of animal origin and cattle slaughterhouses are significant sources of antimicrobial resistant Aliarcobacter.
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Affiliation(s)
- Huseyin Burak Disli
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Turkey.
| | - Harun Hizlisoy
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Turkey
| | - Candan Gungor
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Turkey
| | - Mukaddes Barel
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Turkey
| | - Adalet Dishan
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, Yozgat Bozok University, Yozgat, Turkey
| | - Dursun Alp Gundog
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Turkey
| | - Serhat Al
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Turkey
| | - Nurhan Ertas Onmaz
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Turkey
| | - Yeliz Yildirim
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Turkey
| | - Zafer Gonulalan
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Turkey
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Buzzanca D, Chiarini E, Alessandria V. Arcobacteraceae: An Exploration of Antibiotic Resistance Featuring the Latest Research Updates. Antibiotics (Basel) 2024; 13:669. [PMID: 39061351 PMCID: PMC11273800 DOI: 10.3390/antibiotics13070669] [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: 06/14/2024] [Revised: 07/13/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
The Arcobacteraceae bacterial family includes species isolated from animals and related food products. Moreover, these species have been found in other ecological niches, including water. Some species, particularly Arcobacter butzleri and Arcobacter cryaerophilus, have been isolated from human clinical cases and linked to gastrointestinal symptoms. The presence of antibiotic-resistant strains is a concern for public health, considering the possible zoonoses and foodborne infections caused by contaminated food containing bacteria resistant to antibiotic treatments. This review aims to highlight the importance of antibiotic resistance in Arcobacter spp. isolates from several sources, including information about antibiotic classes to which this bacterium has shown resistance. Arcobacter spp. demonstrated a wide spectrum of antibiotic resistance, including several antibiotic resistance genes. Antibiotic resistance genomic traits include efflux pumps and mutations in antibiotic target proteins. The literature shows a high proportion of Arcobacter spp. that are multidrug-resistant. However, studies in the literature have primarily focused on the evaluation of antibiotic resistance in A. butzleri and A. cryaerophilus, as these species are frequently isolated from various sources. These aspects underline the necessity of studies focused on several Arcobacter species that could potentially be isolated from several sources.
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Affiliation(s)
- Davide Buzzanca
- Department of Agricultural, Forest and Food Sciences, University of Turin, Largo Paolo Braccini nr.2, 10095 Grugliasco, Italy; (E.C.); (V.A.)
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Rao RSP, Ghate SD, Pinto L, Suravajhala P, Patil P, Shetty P, Ahsan N. Extent of Virulence and Antibiotic Resistance Genes in Helicobacter pylori and Campylobacteria. Curr Microbiol 2024; 81:154. [PMID: 38652129 DOI: 10.1007/s00284-024-03653-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/26/2024] [Indexed: 04/25/2024]
Abstract
Helicobacter pylori, a member of the clade campylobacteria, is the leading cause of chronic gastritis and gastric cancer. Virulence and antibiotic resistance of H. pylori are of great concern to public health. However, the relationship between virulence and antibiotic resistance genes in H. pylori in relation to other campylobacteria remains unclear. Using the virulence and comprehensive antibiotic resistance databases, we explored all available 354 complete genomes of H. pylori and compared it with 90 species of campylobacteria for virulence and antibiotic resistance genes/proteins. On average, H. pylori had 129 virulence genes, highest among Helicobacter spp. and 71 antibiotic resistance genes, one of the lowest among campylobacteria. Just 2.6% of virulence genes were shared by all campylobacterial members, whereas 9.4% were unique to H. pylori. The cytotoxin-associated genes (cags) seemed to be exclusive to H. pylori. Majority of the isolates from Asia and South America were cag2-negative and many antibiotic resistance genes showed isolate-specific patterns of occurrence. Just 15 (8.8%) antibiotic resistance genes, but 103 (66%) virulence genes including 25 cags were proteomically identified in H. pylori. Arcobacterial members showed large variation in the number of antibiotic resistance genes and there was a positive relation with the genome size. Large repository of antibiotic resistance genes in campylobacteria and a unique set of virulence genes might have important implications in shaping the course of virulence and antibiotic resistance in H. pylori.
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Affiliation(s)
- R Shyama Prasad Rao
- Center for Bioinformatics, NITTE Deemed to be University, Mangaluru, 575018, India.
| | - Sudeep D Ghate
- Center for Bioinformatics, NITTE Deemed to be University, Mangaluru, 575018, India.
| | - Larina Pinto
- Center for Bioinformatics, NITTE Deemed to be University, Mangaluru, 575018, India
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Prashanth Suravajhala
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, 690525, India
| | - Prakash Patil
- Central Research Laboratory, KS Hegde Medical Academy (KSHEMA), NITTE Deemed to be University, Mangaluru, 575018, India
| | - Praveenkumar Shetty
- Central Research Laboratory, KS Hegde Medical Academy (KSHEMA), NITTE Deemed to be University, Mangaluru, 575018, India
- Department of Biochemistry, KS Hegde Medical Academy (KSHEMA), NITTE Deemed to be University, Mangaluru, 575018, India
| | - Nagib Ahsan
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
- Mass Spectrometry, Proteomics and Metabolomics Core Facility, Stephenson Life Sciences Research Center, The University of Oklahoma, Norman, OK, USA
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Isokpehi RD, Kim Y, Krejci SE, Trivedi VD. Ecological Trait-Based Digital Categorization of Microbial Genomes for Denitrification Potential. Microorganisms 2024; 12:791. [PMID: 38674735 PMCID: PMC11052009 DOI: 10.3390/microorganisms12040791] [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: 03/25/2024] [Revised: 04/09/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Microorganisms encode proteins that function in the transformations of useful and harmful nitrogenous compounds in the global nitrogen cycle. The major transformations in the nitrogen cycle are nitrogen fixation, nitrification, denitrification, anaerobic ammonium oxidation, and ammonification. The focus of this report is the complex biogeochemical process of denitrification, which, in the complete form, consists of a series of four enzyme-catalyzed reduction reactions that transforms nitrate to nitrogen gas. Denitrification is a microbial strain-level ecological trait (characteristic), and denitrification potential (functional performance) can be inferred from trait rules that rely on the presence or absence of genes for denitrifying enzymes in microbial genomes. Despite the global significance of denitrification and associated large-scale genomic and scholarly data sources, there is lack of datasets and interactive computational tools for investigating microbial genomes according to denitrification trait rules. Therefore, our goal is to categorize archaeal and bacterial genomes by denitrification potential based on denitrification traits defined by rules of enzyme involvement in the denitrification reduction steps. We report the integration of datasets on genome, taxonomic lineage, ecosystem, and denitrifying enzymes to provide data investigations context for the denitrification potential of microbial strains. We constructed an ecosystem and taxonomic annotated denitrification potential dataset of 62,624 microbial genomes (866 archaea and 61,758 bacteria) that encode at least one of the twelve denitrifying enzymes in the four-step canonical denitrification pathway. Our four-digit binary-coding scheme categorized the microbial genomes to one of sixteen denitrification traits including complete denitrification traits assigned to 3280 genomes from 260 bacteria genera. The bacterial strains with complete denitrification potential pattern included Arcobacteraceae strains isolated or detected in diverse ecosystems including aquatic, human, plant, and Mollusca (shellfish). The dataset on microbial denitrification potential and associated interactive data investigations tools can serve as research resources for understanding the biochemical, molecular, and physiological aspects of microbial denitrification, among others. The microbial denitrification data resources produced in our research can also be useful for identifying microbial strains for synthetic denitrifying communities.
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Affiliation(s)
| | - Yungkul Kim
- Oyster Microbiome Project, College of Science, Engineering and Mathematics, Bethune-Cookman University, Daytona Beach, FL 32114, USA; (S.E.K.); (V.D.T.)
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Arias Echandi ML, Huete Soto A, Castillo Blanco JM, Fernández F, Fernandez Jaramillo H. Occurrence of Aliarcobacter spp. in fresh and pre-cut vegetables of common use in San José, Costa Rica. Ital J Food Saf 2023; 12:10344. [PMID: 38116377 PMCID: PMC10726391 DOI: 10.4081/ijfs.2023.10344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 06/27/2023] [Indexed: 12/21/2023] Open
Abstract
Aliarcobacter is a Gram-negative rod that can cause disease in both animals and humans. Several studies have evidenced its presence in a wide variety of foods. Given that the number of foodborne illness outbreaks linked to the consumption of vegetables has increased worldwide and that there is a lack of information about the occurrence of Aliarcobacter spp. in these, the aim of this study was to evaluate its presence and the occurrence of virulence factors in both fresh and ready-to-eat vegetable samples. 180 vegetable samples from Costa Rica were analyzed for the presence of Aliarcobacter spp., including 90 pre-cut vegetable packages and 90 fresh vegetables. Two (2.2%) of the isolates from pre-cut vegetables and 19 (21.1%) of the isolates obtained from fresh vegetables were confirmed as Aliarcobacter spp. One of the isolates from the pre-cut vegetable samples was identified as A. butzleri. For the fresh vegetables, 11 isolates were identified as A. skirrowii, one as A. butzleri, and the 7 remaining isolates could not be identified at a species level. There is an 87.5% positivity for hecA and 93.8% for pldA, virulence genes in strains isolated from fresh produce, contrasting with an absolute absence from pre-cut vegetable-isolated strains. These results evidence the presence of Aliarcobacter on fresh and pre-cut vegetables from Costa Rica and the potential hazard it might represent for public health.
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Affiliation(s)
- María Laura Arias Echandi
- Tropical Diseases Research Center, Faculty of Microbiology, University of Costa Rica, San José, Costa Rica
| | - Alejandra Huete Soto
- Tropical Diseases Research Center, Faculty of Microbiology, University of Costa Rica, San José, Costa Rica
| | | | - Fernanda Fernández
- Tropical Diseases Research Center, Faculty of Microbiology, University of Costa Rica, San José, Costa Rica
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Zhou G, Gu Y, Wang H, Chen X, Zhang X, Shao Z, Yan X, Zhang J, Zhang M. Genomic diversity and taxonomic marker for Arcobacter species. Front Microbiol 2023; 14:1278268. [PMID: 37881248 PMCID: PMC10594997 DOI: 10.3389/fmicb.2023.1278268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 09/27/2023] [Indexed: 10/27/2023] Open
Abstract
Arcobacter was recognized as an emerging enteropathogen and controversies regarding its classification persisted. This study aimed to reevaluate the taxonomy of Arcobacter utilizing the 16S rRNA gene, 23S rRNA gene, single-copy orthologous genes, as well as genomic indices such as Average Nucleotide Identity (ANI) and in silico DNA-DNA hybridization (isDDH). The taxonomy of this genus was reevaluated in this study using multiple indices with a dataset of 371 genomes comprising 34 known species and 14 potentially new species. Good discrimination could be achieved only in some species but not for the species with higher sequence similarity using the comparisons of the 16S rRNA gene and 23S rRNA gene sequences. A high-accuracy phylogenomic approach for Arcobacter was established using 84 single-copy orthologous genes obtained through various bioinformatics methods. One marker gene (gene711), which was found to possess the same distinguishing ability as ANI, isDDH, and single-copy orthologous methods, was identified as a reliable locus for inferring the phylogeny of the genus. The effective species classification was achieved by employing gene711 with a sequence similarity exceeding 96%, even for species like A. cloacae, A. lanthieri, and A. skirrowii, which exhibited ambiguous classification using ANI and isDDH. Additionally, excellent subspecies categorizing among A. cryaerophilus could be distinguished using gene711. In conclusion, this framework strategy had the potential advantage of developing rapid species identification, particularly for highly variable species, providing a novel insight into the behavior and characteristics of Arcobacter.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Maojun Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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Aoki M, Takemura Y, Kawakami S, Yoochatchaval W, Tran P. T, Tomioka N, Ebie Y, Syutsubo K. Quantitative detection and reduction of potentially pathogenic bacterial groups of Aeromonas, Arcobacter, Klebsiella pneumoniae species complex, and Mycobacterium in wastewater treatment facilities. PLoS One 2023; 18:e0291742. [PMID: 37768925 PMCID: PMC10538766 DOI: 10.1371/journal.pone.0291742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 09/05/2023] [Indexed: 09/30/2023] Open
Abstract
Water quality parameters influence the abundance of pathogenic bacteria. The genera Aeromonas, Arcobacter, Klebsiella, and Mycobacterium are among the representative pathogenic bacteria identified in wastewater. However, information on the correlations between water quality and the abundance of these bacteria, as well as their reduction rate in existing wastewater treatment facilities (WTFs), is lacking. Hence, this study aimed to determine the abundance and reduction rates of these bacterial groups in WTFs. Sixty-eight samples (34 influent and 34 non-disinfected, treated, effluent samples) were collected from nine WTFs in Japan and Thailand. 16S rRNA gene amplicon sequencing analysis revealed the presence of Aeromonas, Arcobacter, and Mycobacterium in all influent wastewater and treated effluent samples. Quantitative real-time polymerase chain reaction (qPCR) was used to quantify the abundance of Aeromonas, Arcobacter, Klebsiella pneumoniae species complex (KpSC), and Mycobacterium. The geometric mean abundances of Aeromonas, Arcobacter, KpSC, and Mycobacterium in the influent wastewater were 1.2 × 104-2.4 × 105, 1.0 × 105-4.5 × 106, 3.6 × 102-4.3 × 104, and 6.9 × 103-5.5 × 104 cells mL-1, respectively, and their average log reduction values were 0.77-2.57, 1.00-3.06, 1.35-3.11, and -0.67-1.57, respectively. Spearman's rank correlation coefficients indicated significant positive or negative correlations between the abundances of the potentially pathogenic bacterial groups and Escherichia coli as well as water quality parameters, namely, chemical/biochemical oxygen demand, total nitrogen, nitrate-nitrogen, nitrite-nitrogen, ammonium-nitrogen, suspended solids, volatile suspended solids, and oxidation-reduction potential. This study provides valuable information on the development and appropriate management of WTFs to produce safe, hygienic water.
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Affiliation(s)
- Masataka Aoki
- Regional Environment Conservation Division, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
| | - Yasuyuki Takemura
- Regional Environment Conservation Division, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
| | - Shuji Kawakami
- Department of Civil Engineering, National Institute of Technology (KOSEN), Nagaoka College, Nagaoka, Niigata, Japan
| | - Wilasinee Yoochatchaval
- Department of Environmental Engineering, Faculty of Engineering, Kasetsart University, Bangkok, Thailand
| | - Thao Tran P.
- Regional Environment Conservation Division, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
| | - Noriko Tomioka
- Regional Environment Conservation Division, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
| | - Yoshitaka Ebie
- Material Cycles Division, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
| | - Kazuaki Syutsubo
- Regional Environment Conservation Division, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
- Research Center of Water Environment Technology, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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Mateus C, Maia CJ, Domingues F, Bücker R, Oleastro M, Ferreira S. Evaluation of Bile Salts on the Survival and Modulation of Virulence of Aliarcobacter butzleri. Antibiotics (Basel) 2023; 12:1387. [PMID: 37760684 PMCID: PMC10525121 DOI: 10.3390/antibiotics12091387] [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: 07/19/2023] [Revised: 08/17/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Aliarcobacter butzleri is a Gram-negative bacterium associated with infections of the gastrointestinal tract and widely distributed in various environments. For successful infection, A. butzleri should be able to tolerate various stresses during gastrointestinal passage, such as bile. Bile represents an antimicrobial host barrier that acts against external noxious agents and consists of a variety of bile salts. The intestinal bile salts act as detergents involved in the antimicrobial host defense; although, on the bacterial side, they could also serve as a signal to activate virulence mechanisms. The aim of this work was to understand the effects of bile salts on the survival and virulence of A. butzleri. In our study, A. butzleri was able to survive in the presence of human physiological concentrations of bile salts. Regarding the virulence features, an increase in cellular hydrophobicity, a decrease in motility and expression of flaA gene, as well as an increase in biofilm formation with a concomitant change in the type of biofilm structure were observed in the presence of sub-inhibitory concentration of bile salts. Concerning adhesion and invasion ability, no significant difference was observed. Overall, the results demonstrated that A. butzleri is able to survive in physiological concentrations of bile salts and that exposure to bile salts could change its virulence mechanisms.
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Affiliation(s)
- Cristiana Mateus
- CICS-UBI—Health Sciences Research Centre, University of Beira Interior, 6200-506 Covilhã, Portugal; (C.M.); (C.J.M.); (F.D.)
| | - Cláudio J. Maia
- CICS-UBI—Health Sciences Research Centre, University of Beira Interior, 6200-506 Covilhã, Portugal; (C.M.); (C.J.M.); (F.D.)
| | - Fernanda Domingues
- CICS-UBI—Health Sciences Research Centre, University of Beira Interior, 6200-506 Covilhã, Portugal; (C.M.); (C.J.M.); (F.D.)
| | - Roland Bücker
- Clinical Physiology/Nutritional Medicine, Medical Department of Gastroenterology, Infectiology, Rheumatology, Charité—Universitätsmedizin Berlin, 12203 Berlin, Germany;
| | - Mónica Oleastro
- National Reference Laboratory for Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Av. Padre Cruz, 1649-016 Lisbon, Portugal;
| | - Susana Ferreira
- CICS-UBI—Health Sciences Research Centre, University of Beira Interior, 6200-506 Covilhã, Portugal; (C.M.); (C.J.M.); (F.D.)
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Buzzanca D, Kerkhof PJ, Alessandria V, Rantsiou K, Houf K. Arcobacteraceae comparative genome analysis demonstrates genome heterogeneity and reduction in species isolated from animals and associated with human illness. Heliyon 2023; 9:e17652. [PMID: 37449094 PMCID: PMC10336517 DOI: 10.1016/j.heliyon.2023.e17652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 05/30/2023] [Accepted: 06/25/2023] [Indexed: 07/18/2023] Open
Abstract
The Arcobacteraceae family groups Gram-negative bacterial species previously included in the family Campylobacteraceae. These species of which some are considered foodborne pathogens, have been isolated from different environmental niches and hosts. They have been isolated from various types of foods, though predominantly from food of animal origin, as well as from stool of humans with enteritis. Their different abilities to survive in different hosts and environments suggest an evolutionary pressure with consequent variation in their genome content. Moreover, their different physiological and genomic characteristics led to the recent proposal to create new genera within this family, which is however criticized due to the lack of discriminatory features and biological and clinical relevance. Aims of the present study were to assess the Arcobacteraceae pangenome, and to characterize existing similarities and differences in 20 validly described species. For this, analysis has been conducted on the genomes of the corresponding type strains obtained by Illumina sequencing, applying several bioinformatic tools. Results of the present study do not support the proposed division into different genera and revealed the presence of pangenome partitions with numbers comparable to other Gram-negative bacteria genera, such as Campylobacter. Different gene class compositions in animal and human-associated species are present, including a higher percentage of virulence-related gene classes such as cell motility genes. The adaptation to environmental and/or host conditions of some species was identified by the presence of specific genes. Furthermore, a division into pathogenic and non-pathogenic species is suggested, which can support future research on food safety and public health.
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Affiliation(s)
- Davide Buzzanca
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, Merelbeke, Belgium
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Turin, Largo Paolo Braccini 2, 10095 Grugliasco (TO), Italy
| | - Pieter-Jan Kerkhof
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, Merelbeke, Belgium
| | - Valentina Alessandria
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Turin, Largo Paolo Braccini 2, 10095 Grugliasco (TO), Italy
| | - Kalliopi Rantsiou
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Turin, Largo Paolo Braccini 2, 10095 Grugliasco (TO), Italy
| | - Kurt Houf
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, Merelbeke, Belgium
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Karel Lodewijk Ledeganckstraat 35, 9000 Ghent, Belgium
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Uljanovas D, Gölz G, Fleischmann S, Kudirkiene E, Kasetiene N, Grineviciene A, Tamuleviciene E, Aksomaitiene J, Alter T, Malakauskas M. Genomic Characterization of Arcobacter butzleri Strains Isolated from Various Sources in Lithuania. Microorganisms 2023; 11:1425. [PMID: 37374927 DOI: 10.3390/microorganisms11061425] [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: 03/15/2023] [Revised: 05/09/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
Arcobacter (A.) butzleri, the most widespread species within the genus Arcobacter, is considered as an emerging pathogen causing gastroenteritis in humans. Here, we performed a comparative genome-wide analysis of 40 A. butzleri strains from Lithuania to determine the genetic relationship, pangenome structure, putative virulence, and potential antimicrobial- and heavy-metal-resistance genes. Core genome single nucleotide polymorphism (cgSNP) analysis revealed low within-group variability (≤4 SNPs) between three milk strains (RCM42, RCM65, RCM80) and one human strain (H19). Regardless of the type of input (i.e., cgSNPs, accessory genome, virulome, resistome), these strains showed a recurrent phylogenetic and hierarchical grouping pattern. A. butzleri demonstrated a relatively large and highly variable accessory genome (comprising of 6284 genes with around 50% of them identified as singletons) that only partially correlated to the isolation source. Downstream analysis of the genomes resulted in the detection of 115 putative antimicrobial- and heavy-metal-resistance genes and 136 potential virulence factors that are associated with the induction of infection in host (e.g., cadF, degP, iamA), survival and environmental adaptation (e.g., flagellar genes, CheA-CheY chemotaxis system, urease cluster). This study provides additional knowledge for a better A. butzleri-related risk assessment and highlights the need for further genomic epidemiology studies in Lithuania and other countries.
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Affiliation(s)
- Dainius Uljanovas
- Department of Food Safety and Quality, Faculty of Veterinary Medicine, Veterinary Academy, Lithuanian University of Health Sciences, Tilzes St. 18, LT-47181 Kaunas, Lithuania
| | - Greta Gölz
- Institute of Food Safety and Food Hygiene, Freie Universität Berlin, Königsweg 69, 14163 Berlin, Germany
| | - Susanne Fleischmann
- Institute of Food Safety and Food Hygiene, Freie Universität Berlin, Königsweg 69, 14163 Berlin, Germany
| | - Egle Kudirkiene
- Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen, Denmark
| | - Neringa Kasetiene
- Department of Food Safety and Quality, Faculty of Veterinary Medicine, Veterinary Academy, Lithuanian University of Health Sciences, Tilzes St. 18, LT-47181 Kaunas, Lithuania
| | - Audrone Grineviciene
- Kaunas Clinical Hospital Microbiology Laboratory, Medical Academy, Lithuanian University of Health Sciences, Josvainiu St. 2, LT-47144 Kaunas, Lithuania
| | - Egle Tamuleviciene
- Department of Pediatrics, Medical Academy, Lithuanian University of Health Sciences, Eiveniu St. 2, LT-50161 Kaunas, Lithuania
| | - Jurgita Aksomaitiene
- Department of Food Safety and Quality, Faculty of Veterinary Medicine, Veterinary Academy, Lithuanian University of Health Sciences, Tilzes St. 18, LT-47181 Kaunas, Lithuania
| | - Thomas Alter
- Institute of Food Safety and Food Hygiene, Freie Universität Berlin, Königsweg 69, 14163 Berlin, Germany
| | - Mindaugas Malakauskas
- Department of Food Safety and Quality, Faculty of Veterinary Medicine, Veterinary Academy, Lithuanian University of Health Sciences, Tilzes St. 18, LT-47181 Kaunas, Lithuania
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Binder R, Hahn A, Eberhardt KA, Hagen RM, Rohde H, Loderstädt U, Feldt T, Sarfo FS, Di Cristanziano V, Kahlfuss S, Frickmann H, Zautner AE. Comparison of the Diagnostic Accuracy of Three Real-Time PCR Assays for the Detection of Arcobacter butzleri in Human Stool Samples Targeting Different Genes in a Test Comparison without a Reference Standard. Microorganisms 2023; 11:1313. [PMID: 37317286 DOI: 10.3390/microorganisms11051313] [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: 04/03/2023] [Revised: 05/13/2023] [Accepted: 05/15/2023] [Indexed: 06/16/2023] Open
Abstract
Potential etiological relevance for gastroenteric disorders including diarrhea has been assigned to Arcobacter butzleri. However, standard routine diagnostic algorithms for stool samples of patients with diarrhea are rarely adapted to the detection of this pathogen and so, A. butzleri is likely to go undetected unless it is specifically addressed, e.g., by applying pathogen-specific molecular diagnostic approaches. In the study presented here, we compared three real-time PCR assays targeting the genes hsp60, rpoB/C (both hybridization probe assays) and gyrA (fluorescence resonance energy transfer assay) of A. butzleri in a test comparison without a reference standard using a stool sample collection with a high pretest probability from the Ghanaian endemicity setting. Latent class analysis was applied with the PCR results obtained with a collection of 1495 stool samples showing no signs of PCR inhibition to assess the real-time PCR assays' diagnostic accuracy. Calculated sensitivity and specificity were 93.0% and 96.9% for the hsp60-PCR, 100% and 98.2% for the rpoB/C-PCR, as well as 12.7% and 99.8% for the gyrA-PCR, respectively. The calculated A. butzleri prevalence within the assessed Ghanaian population was 14.7%. As indicated by test results obtained with high-titer spiked samples, cross-reactions of the hsp60-assay and rpoB/C-assay with phylogenetically related species such as A. cryaerophilus can occur but are less likely with phylogenetically more distant species like, e.g., A. lanthieri. In conclusion, the rpoB/C-assay showed the most promising performance characteristics as the only assay with sensitivity >95%, albeit associated with a broad 95%-confidence interval. In addition, this assay showed still-acceptable specificity of >98% in spite of the known cross-reactivity with phylogenetically closely related species such as A. cryaerophilus. If higher certainty is desired, the gyrA-assay with specificity close to 100% can be applied for confirmation testing with samples showing positive rpoB/C-PCR results. However, in case of a negative result in the gyrA-assay, this cannot reliably exclude the detection of A. butzleri in the rpoB/C-assay due to the gyrA-assay's very low sensitivity.
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Affiliation(s)
- Ramona Binder
- Laboratory Department, Bundeswehr Hospital Hamburg, 20359 Hamburg, Germany
| | - Andreas Hahn
- Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, 18057 Rostock, Germany
| | - Kirsten Alexandra Eberhardt
- Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine & I. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20359 Hamburg, Germany
- Division of Hygiene and Infectious Diseases, Institute of Hygiene and Environment, 20539 Hamburg, Germany
| | - Ralf Matthias Hagen
- Department of Microbiology and Hospital Hygiene, Bundeswehr Central Hospital Koblenz, 56070 Koblenz, Germany
| | - Holger Rohde
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20251 Hamburg, Germany
| | - Ulrike Loderstädt
- Department of Hospital Hygiene & Infectious Diseases, University Medicine Göttingen, 37075 Göttingen, Germany
| | - Torsten Feldt
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Medical Center Düsseldorf, 40225 Düsseldorf, Germany
| | - Fred Stephen Sarfo
- Kwame Nkrumah University of Science and Technology, Kumasi 00233, Ghana
- Department of Medicine, Komfo Anokye Teaching Hospital, Kumasi 00233, Ghana
| | - Veronica Di Cristanziano
- Institute of Virology, Faculty of Medicine, University Hospital of Cologne, University of Cologne, 50935 Cologne, Germany
| | - Sascha Kahlfuss
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty, Otto-von-Guericke-University Magdeburg, 39120 Magdeburg, Germany
- CHaMP-Center for Health and Medical Prevention, Otto-von-Guericke-University Magdeburg, 39120 Magdeburg, Germany
- Institute of Molecular and Clinical Immunology, Medical Faculty, Otto-von-Guericke University Magdeburg, 39104 Magdeburg, Germany
- Health Campus Immunology, Infectiology and Inflammation (GCI), Medical Faculty, Otto-von-Guericke University Magdeburg, 39104 Magdeburg, Germany
| | - Hagen Frickmann
- Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, 18057 Rostock, Germany
- Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg, 20359 Hamburg, Germany
| | - Andreas Erich Zautner
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty, Otto-von-Guericke-University Magdeburg, 39120 Magdeburg, Germany
- CHaMP-Center for Health and Medical Prevention, Otto-von-Guericke-University Magdeburg, 39120 Magdeburg, Germany
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12
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Grudlewska-Buda K, Bauza-Kaszewska J, Wiktorczyk-Kapischke N, Budzyńska A, Gospodarek-Komkowska E, Skowron K. Antibiotic Resistance in Selected Emerging Bacterial Foodborne Pathogens-An Issue of Concern? Antibiotics (Basel) 2023; 12:antibiotics12050880. [PMID: 37237783 DOI: 10.3390/antibiotics12050880] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/30/2023] [Accepted: 05/07/2023] [Indexed: 05/28/2023] Open
Abstract
Antibiotic resistance (AR) and multidrug resistance (MDR) have been confirmed for all major foodborne pathogens: Campylobacter spp., Salmonella spp., Escherichia coli and Listeria monocytogenes. Of great concern to scientists and physicians are also reports of antibiotic-resistant emerging food pathogens-microorganisms that have not previously been linked to food contamination or were considered epidemiologically insignificant. Since the properties of foodborne pathogens are not always sufficiently recognized, the consequences of the infections are often not easily predictable, and the control of their activity is difficult. The bacteria most commonly identified as emerging foodborne pathogens include Aliarcobacter spp., Aeromonas spp., Cronobacter spp., Vibrio spp., Clostridioides difficile, Escherichia coli, Mycobacterium paratuberculosis, Salmonella enterica, Streptocccus suis, Campylobacter jejuni, Helicobacter pylori, Listeria monocytogenes and Yersinia enterocolitica. The results of our analysis confirm antibiotic resistance and multidrug resistance among the mentioned species. Among the antibiotics whose effectiveness is steadily declining due to expanding resistance among bacteria isolated from food are β-lactams, sulfonamides, tetracyclines and fluoroquinolones. Continuous and thorough monitoring of strains isolated from food is necessary to characterize the existing mechanisms of resistance. In our opinion, this review shows the scale of the problem of microbes related to health, which should not be underestimated.
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Affiliation(s)
- Katarzyna Grudlewska-Buda
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-094 Bydgoszcz, Poland
| | - Justyna Bauza-Kaszewska
- Department of Microbiology and Food Technology, Bydgoszcz University of Science and Technology, 85-029 Bydgoszcz, Poland
| | - Natalia Wiktorczyk-Kapischke
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-094 Bydgoszcz, Poland
| | - Anna Budzyńska
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-094 Bydgoszcz, Poland
| | - Eugenia Gospodarek-Komkowska
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-094 Bydgoszcz, Poland
| | - Krzysztof Skowron
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-094 Bydgoszcz, Poland
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13
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Candeliere F, Musmeci E, Amaretti A, Sola L, Raimondi S, Rossi M. Profiling of the intestinal community of Clostridia: taxonomy and evolutionary analysis. MICROBIOME RESEARCH REPORTS 2023; 2:13. [PMID: 38047279 PMCID: PMC10688793 DOI: 10.20517/mrr.2022.19] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/24/2023] [Accepted: 04/06/2023] [Indexed: 12/05/2023]
Abstract
Aim: Clostridia are relevant commensals of the human gut due to their major presence and correlations to the host. In this study, we investigated intestinal Clostridia of 51 healthy subjects and reconstructed their taxonomy and phylogeny. The relatively small number of intestinal Clostridia allowed a systematic whole genome approach based on average amino acid identity (AAI) and core genome with the aim of revising the current classification into genera and determining evolutionary relationships. Methods: 51 healthy subjects' metagenomes were retrieved from public databases. After the dataset's validation through comparison with Human Microbiome Project (HMP) samples, the metagenomes were profiled using MetaPhlAn3 to identify the population ascribed to the class Clostridia. Intestinal Clostridia genomes were retrieved and subjected to AAI analysis and core genome identification. Phylogeny investigation was conducted with RAxML and Unweighted Pair Group Method with Arithmetic Mean (UPGMA) algorithms, and SplitsTree for split decomposition. Results: 225 out of 406 bacterial taxonomic units were ascribed to Bacillota [Firmicutes], among which 124 were assigned to the class Clostridia. 77 out of the 124 taxonomic units were referred to a species, altogether covering 87.7% of Clostridia abundance. According to the lowest AAI genus boundary set at 55%, 15 putative genera encompassing more than one species (G1 to G15) were identified, while 19 species did not cluster with any other one and each appeared to belong to a diverse genus. Phylogenetic investigations highlighted that most of the species clustered into three main evolutive clades. Conclusion: This study shed light on the species of Clostridia colonizing the gut of healthy adults and pinpointed several gaps in knowledge regarding the taxonomy and the phylogeny of Clostridia.
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Affiliation(s)
- Francesco Candeliere
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena 41125, Italy
| | - Eliana Musmeci
- Department of Civil, Chemical, Environmental and Material Engineering (DICAM), Alma Mater Studiorum University of Bologna, Bologna 40136, Italy
| | - Alberto Amaretti
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena 41125, Italy
- Biogest Siteia, University of Modena and Reggio Emilia, Reggio Emilia 42124, Italy
| | - Laura Sola
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena 41125, Italy
| | - Stefano Raimondi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena 41125, Italy
- Biogest Siteia, University of Modena and Reggio Emilia, Reggio Emilia 42124, Italy
| | - Maddalena Rossi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena 41125, Italy
- Biogest Siteia, University of Modena and Reggio Emilia, Reggio Emilia 42124, Italy
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14
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Wada N, Iguchi A, Urabe Y, Yoshioka Y, Abe N, Takase K, Hayashi S, Kawanabe S, Sato Y, Tang SL, Mano N. Microbial mat compositions and localization patterns explain the virulence of black band disease in corals. NPJ Biofilms Microbiomes 2023; 9:15. [PMID: 37015942 PMCID: PMC10073141 DOI: 10.1038/s41522-023-00381-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 03/13/2023] [Indexed: 04/06/2023] Open
Abstract
Black band disease (BBD) in corals is characterized by a distinctive, band-like microbial mat, which spreads across the tissues and often kills infected colonies. The microbial mat is dominated by cyanobacteria but also commonly contains sulfide-oxidizing bacteria (SOB), sulfate-reducing bacteria (SRB), and other microbes. The migration rate in BBD varies across different environmental conditions, including temperature, light, and pH. However, whether variations in the migration rates reflect differences in the microbial consortium within the BBD mat remains unknown. Here, we show that the micro-scale surface structure, bacterial composition, and spatial distribution differed across BBD lesions with different migration rates. The migration rate was positively correlated with the relative abundance of potential SOBs belonging to Arcobacteraceae localized in the middle layer within the mat and negatively correlated with the relative abundance of other potential SOBs belonging to Rhodobacteraceae. Our study highlights the microbial composition in BBD as an important determinant of virulence.
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Affiliation(s)
- Naohisa Wada
- Biodiversity Research Center, Academia Sinica, No.128, Sec 2, Academia Rd, Nangang, Taipei, 11529, Taiwan
- Department of Marine Science and Resources, College of Bioresource Science, Nihon University, Fujisawa, Kanagawa, 252-0813, Japan
| | - Akira Iguchi
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8567, Japan
- Research Laboratory on Environmentally-conscious Developments and Technologies [E-code], National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8567, Japan
| | - Yuta Urabe
- Department of Marine Science and Resources, College of Bioresource Science, Nihon University, Fujisawa, Kanagawa, 252-0813, Japan
| | - Yuki Yoshioka
- Department of Bioresources Engineering, National Institute of Technology, Okinawa College, 905 Henoko, Nago-City, Okinawa, 905-2192, Japan
| | - Natsumi Abe
- Department of Marine Science and Resources, College of Bioresource Science, Nihon University, Fujisawa, Kanagawa, 252-0813, Japan
| | - Kazuki Takase
- Department of Marine Science and Resources, College of Bioresource Science, Nihon University, Fujisawa, Kanagawa, 252-0813, Japan
| | - Shuji Hayashi
- Department of Marine Science and Resources, College of Bioresource Science, Nihon University, Fujisawa, Kanagawa, 252-0813, Japan
| | - Saeko Kawanabe
- Department of Marine Science and Resources, College of Bioresource Science, Nihon University, Fujisawa, Kanagawa, 252-0813, Japan
| | - Yui Sato
- College of Science and Engineering, James Cook University, Townsville, Queensland, 4811, Australia
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, No.128, Sec 2, Academia Rd, Nangang, Taipei, 11529, Taiwan.
| | - Nobuhiro Mano
- Department of Marine Science and Resources, College of Bioresource Science, Nihon University, Fujisawa, Kanagawa, 252-0813, Japan.
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15
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Seidel L, Broman E, Nilsson E, Ståhle M, Ketzer M, Pérez-Martínez C, Turner S, Hylander S, Pinhassi J, Forsman A, Dopson M. Climate change-related warming reduces thermal sensitivity and modifies metabolic activity of coastal benthic bacterial communities. THE ISME JOURNAL 2023; 17:855-869. [PMID: 36977742 DOI: 10.1038/s41396-023-01395-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 03/01/2023] [Accepted: 03/10/2023] [Indexed: 03/30/2023]
Abstract
Besides long-term average temperature increases, climate change is projected to result in a higher frequency of marine heatwaves. Coastal zones are some of the most productive and vulnerable ecosystems, with many stretches already under anthropogenic pressure. Microorganisms in coastal areas are central to marine energy and nutrient cycling and therefore, it is important to understand how climate change will alter these ecosystems. Using a long-term heated bay (warmed for 50 years) in comparison with an unaffected adjacent control bay and an experimental short-term thermal (9 days at 6-35 °C) incubation experiment, this study provides new insights into how coastal benthic water and surface sediment bacterial communities respond to temperature change. Benthic bacterial communities in the two bays reacted differently to temperature increases with productivity in the heated bay having a broader thermal tolerance compared with that in the control bay. Furthermore, the transcriptional analysis showed that the heated bay benthic bacteria had higher transcript numbers related to energy metabolism and stress compared to the control bay, while short-term elevated temperatures in the control bay incubation experiment induced a transcript response resembling that observed in the heated bay field conditions. In contrast, a reciprocal response was not observed for the heated bay community RNA transcripts exposed to lower temperatures indicating a potential tipping point in community response may have been reached. In summary, long-term warming modulates the performance, productivity, and resilience of bacterial communities in response to warming.
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Affiliation(s)
- Laura Seidel
- Centre for ecology and evolution in microbial model systems (EEMiS), Linnaeus University, Kalmar, Sweden.
| | - Elias Broman
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- Baltic Sea Centre, Stockholm University, Stockholm, Sweden
| | - Emelie Nilsson
- Centre for ecology and evolution in microbial model systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Magnus Ståhle
- Centre for ecology and evolution in microbial model systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Marcelo Ketzer
- Centre for ecology and evolution in microbial model systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Clara Pérez-Martínez
- Centre for ecology and evolution in microbial model systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Stephanie Turner
- Centre for ecology and evolution in microbial model systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Samuel Hylander
- Centre for ecology and evolution in microbial model systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Jarone Pinhassi
- Centre for ecology and evolution in microbial model systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Anders Forsman
- Centre for ecology and evolution in microbial model systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Mark Dopson
- Centre for ecology and evolution in microbial model systems (EEMiS), Linnaeus University, Kalmar, Sweden
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16
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Mahmud MM, Kabir A, Hossain MZ, Mim SJ, Yeva IJ, Khatun M, Rahman MS, Dey MM, Nazir KHMNH. First report of Aliarcobacter cryaerophilus in ready-to-cook chicken meat samples from super shops in Bangladesh. J Adv Vet Anim Res 2023; 10:113-117. [PMID: 37155535 PMCID: PMC10122937 DOI: 10.5455/javar.2023.j659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/25/2023] [Accepted: 03/26/2023] [Indexed: 05/10/2023] Open
Abstract
Objective This study aimed to isolate Aliarcobacter cryaerophilus in ready-to-cook poultry meat in Bangladesh. Materials and Methods Thirty drumstick samples were collected from super shops in Dhaka city (n = 10), Mymensingh city (n = 10), and Patuakhali town (n = 10). After sample processing, they were cultured in Blood agar media with Campylobacter base using a microfilter (0.42 nm). Suspected colonies were subjected to DNA extraction and PCR assay targeting 16SrRNA genes. Then, sequencing was performed for confirmation. Results Of 30 samples, 3 (10%) were positive for A. cryaerophilus. Phylogenetic analysis shows that our isolate has strong similarities with one of the isolates from China. Conclusion The presence of this organism in ready-to-cook poultry meat is a significant concern for consumers as it bears zoonotic importance.
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Affiliation(s)
- Md. Muket Mahmud
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
- These two authors contributed equally
| | - Ajran Kabir
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
- These two authors contributed equally
| | - Md. Zawad Hossain
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Sanjida Jamal Mim
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Israt Jahan Yeva
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Minara Khatun
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Mohammad Saidur Rahman
- Department of Agricultural Economics, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Madan Mohan Dey
- Department of Agricultural Sciences, Texas State University, San Marcos, TX, USA
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17
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Buzzanca D, Alessandria V, Botta C, Seif Zadeh N, Ferrocino I, Houf K, Cocolin L, Rantsiou K. Transcriptome Analysis of Arcobacter butzleri Infection in a Mucus-Producing Human Intestinal In Vitro Model. Microbiol Spectr 2023; 11:e0207122. [PMID: 36622176 PMCID: PMC9927503 DOI: 10.1128/spectrum.02071-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Arcobacter butzleri is a foodborne pathogen belonging to the Arcobacteraceae family. This Gram-negative bacterium is found in water, food, and various organisms, including farm animals, clams, and fish. Moreover, A. butzleri has been isolated from human stool samples, where it was associated with gastrointestinal symptoms such as diarrhea. The present study focused on the transcriptome analysis of three A. butzleri strains isolated from human stools and displaying variable virulence potential in vitro. We used a mucus-producing human intestinal in vitro model (Caco-2/HT29-MTX-E12) to study the colonization and invasion abilities of the three A. butzleri strains. The ability of all three A. butzleri strains to colonize our in vitro model system was subsequently confirmed. Moreover, transcriptomics showed the upregulation of putative virulence genes. Among these genes, tonB, exbB, and exbD, which belong to the same operon, were upregulated in strain LMG 11119, which also had the greatest colonization ability. Moreover, genes not currently considered A. butzleri virulence genes were differentially expressed during cell model colonization. The main functions of these genes were linked to organic acid metabolism and iron transport and particularly to the function of the TonB complex. IMPORTANCE Recent advancements in the genomic characterization of A. butzleri revealed putative virulence genes and highlighted the possible pathogenic mechanisms used by this foodborne pathogen. It is therefore possible to study the transcriptomes of these bacteria to explore possible virulence mechanisms under conditions that mimic the infection process. The transcriptome and colonization/invasion analyses that we performed in this study enabled the evaluation of A. butzleri-mediated infection of the mucus-producing human intestinal in vitro model. We confirmed the upregulation of previously proposed virulence genes in the A. butzleri strains. In addition, we identified the differential expression of a number of other genes, which are not currently thought to be associated with virulence, in three A. butzleri strains during infection of mucus-producing human epithelial cells. Changes in the concentration of acetic acid and the upregulation of genes associated with organic acid metabolism during host-pathogen contact were also observed. These findings highlight the importance of previously unreported genes in the virulence mechanisms of A. butzleri.
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Affiliation(s)
- Davide Buzzanca
- Department of Agricultural, Forest and Food Sciences, University of Turin, Turin, Italy
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Valentina Alessandria
- Department of Agricultural, Forest and Food Sciences, University of Turin, Turin, Italy
| | - Cristian Botta
- Department of Agricultural, Forest and Food Sciences, University of Turin, Turin, Italy
| | - Negin Seif Zadeh
- Department of Agricultural, Forest and Food Sciences, University of Turin, Turin, Italy
| | - Ilario Ferrocino
- Department of Agricultural, Forest and Food Sciences, University of Turin, Turin, Italy
| | - Kurt Houf
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Luca Cocolin
- Department of Agricultural, Forest and Food Sciences, University of Turin, Turin, Italy
| | - Kalliopi Rantsiou
- Department of Agricultural, Forest and Food Sciences, University of Turin, Turin, Italy
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18
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Fairén AG, Rodríguez N, Sánchez-García L, Rojas P, Uceda ER, Carrizo D, Amils R, Sanz JL. Ecological successions throughout the desiccation of Tirez lagoon (Spain) as an astrobiological time-analog for wet-to-dry transitions on Mars. Sci Rep 2023; 13:1423. [PMID: 36755119 PMCID: PMC9908944 DOI: 10.1038/s41598-023-28327-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 01/17/2023] [Indexed: 02/10/2023] Open
Abstract
Tirez was a small and seasonal endorheic athalassohaline lagoon that was located in central Spain. In recent years, the lagoon has totally dried out, offering for the first time the opportunity to analyze its desiccation process as a "time-analog" to similar events occurred in paleolakes with varying salinity during the wet-to-dry transition on early Mars. On the martian cratered highlands, an early period of water ponding within enclosed basins evolved to a complete desiccation of the lakes, leading to deposition of evaporitic sequences during the Noachian and into the Late Hesperian. As Tirez also underwent a process of desiccation, here we describe (i) the microbial ecology of Tirez when the lagoon was still active 20 years ago, with prokaryotes adapted to extreme saline conditions; (ii) the composition of the microbial community in the dried lake sediments today, in many case groups that thrive in sediments of extreme environments; and (iii) the molecular and isotopic analysis of the lipid biomarkers that can be recovered from the sediments today. We discuss the implications of these results to better understanding the ecology of possible Martian microbial communities during the wet-to-dry transition at the end of the Hesperian, and how they may inform about research strategies to search for possible biomarkers in Mars after all the water was lost.
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Affiliation(s)
- Alberto G Fairén
- Centro de Astrobiología (CSIC-INTA), 28850, Torrejón de Ardoz, Spain. .,Department of Astronomy, Cornell University, Ithaca, NY, 14853, USA.
| | - Nuria Rodríguez
- Centro de Astrobiología (CSIC-INTA), 28850, Torrejón de Ardoz, Spain.,Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain
| | | | - Patricia Rojas
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain
| | - Esther R Uceda
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain
| | - Daniel Carrizo
- Centro de Astrobiología (CSIC-INTA), 28850, Torrejón de Ardoz, Spain
| | - Ricardo Amils
- Centro de Astrobiología (CSIC-INTA), 28850, Torrejón de Ardoz, Spain.,Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain.,Departamento de Biología Molecular, Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain
| | - José L Sanz
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain.
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19
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Gungor C, Hizlisoy H, Ertas Onmaz N, Gundog DA, Barel M, Disli HB, Dishan A, Al S, Yildirim Y, Gonulalan Z. Profile of Aliarcobacter spp. from edible giblets: Genetic diversity, antibiotic resistance, biofilm formation. Int J Food Microbiol 2023; 386:110047. [PMID: 36512969 DOI: 10.1016/j.ijfoodmicro.2022.110047] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 11/18/2022] [Accepted: 11/29/2022] [Indexed: 12/10/2022]
Abstract
Aliarcobacter spp. are recognized as emerging foodborne pathogens and consumption of foods contaminated with them can be a hazard to human and animal health. This study was conducted to investigate the prevalence of Aliarcobacter spp. in edible internal organs of different animal species from retail markets and giblet sellers. Additionally, this study was focused on the antimicrobial resistance, virulence profiles, biofilm-forming capabilities, and phylogenetic relationships of obtained isolates. A total of 270 samples were analyzed from which, 28 (10.4 %) were isolated as Aliarcobacter spp. by conventional methods. Within the 28 Aliarcobacter spp. isolates, 17 (60.7 %) were identified as A. butzleri, 10 (35.7 %) were A. cryaerophilus and one (3.5 %) was A. skirrowii by PCR method. The disc diffusion method showed that the highest resistance rate of Aliarcobacter spp. was seen against oxacillin (78.5 %), and 20 (71.4 %) out of the 28 isolates exhibited multidrug resistance (MDR). Out of the 28 isolates, mviN, pldA, tlyA, and hecB virulence genes were detected in 85.7 %, 46.4 %, 46.4 %, and 3.5 %, respectively, but irgA, Cj1349, ciaB, cadF, and hecA genes were not detected. According to the microplate test, 27 (96.4 %) isolates had weak biofilm ability while one A. cryaerophilus isolate (3.6 %) exhibited strong biofilm formation. ERIC-PCR band patterns suggested that isolated Aliarcobacter spp. from giblets, have different contamination sources. The presence of pathogenic and multidrug-resistant Aliarcobacter spp. in food poses a potential risk to public health and control measures throughout the food chain are necessary to prevent the spread of these strains.
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Affiliation(s)
- Candan Gungor
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Türkiye.
| | - Harun Hizlisoy
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Türkiye
| | - Nurhan Ertas Onmaz
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Türkiye
| | - Dursun Alp Gundog
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Türkiye
| | - Mukaddes Barel
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Türkiye
| | - H Burak Disli
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Türkiye
| | - Adalet Dishan
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Türkiye
| | - Serhat Al
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Türkiye
| | - Yeliz Yildirim
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Türkiye
| | - Zafer Gonulalan
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Türkiye
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Farrington W, Farahani F, Tayon KG, Rudzinski J, Feldman M, Sharma K. Multiple coinfections and Guillain Barré syndrome following outdoor travel to the American Northeast. Proc AMIA Symp 2023; 36:386-388. [PMID: 37091769 PMCID: PMC10120553 DOI: 10.1080/08998280.2023.2167049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
A 66-year-old immunocompetent man with preceding travel through the Northeastern United States developed Guillain-Barré syndrome. A broad search for infections revealed intraerythrocytic parasites on blood smear and positive polymerase chain reaction for Babesia microti; elevated IgM/IgG serologies for Ehrlichia chaffeensis; elevated IgM/IgG serologies and qualitative polymerase chain reaction for Epstein-Barr virus; and fecal culture growth of Arcobacter butzleri. In this report, we discuss the known or suspected association of these infectious agents with Guillain-Barré syndrome. This case also highlights the importance, in the setting of endemic exposure, of screening for multiple coinfections that can be transmitted by the same arthropod vector.
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Affiliation(s)
- William Farrington
- Department of Internal Medicine, Texas Health Dallas Presbyterian Hospital, Dallas, Texas
| | - Farzam Farahani
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Kevin Garrett Tayon
- Department of Internal Medicine, Texas Health Dallas Presbyterian Hospital, Dallas, Texas
| | - Jaclyn Rudzinski
- North Dallas Pathology Services, Texas Health Dallas Presbyterian Hospital, Dallas, Texas
| | - Mark Feldman
- Department of Internal Medicine, Texas Health Dallas Presbyterian Hospital, Dallas, Texas
| | - Kartavya Sharma
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, Texas
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21
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Hines IS, Markov Madanick J, Smith SA, Kuhn DD, Stevens AM. Analysis of the core bacterial community associated with consumer-ready Eastern oysters (Crassostrea virginica). PLoS One 2023; 18:e0281747. [PMID: 36812164 PMCID: PMC9946220 DOI: 10.1371/journal.pone.0281747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 01/30/2023] [Indexed: 02/24/2023] Open
Abstract
Shellfish, such as the Eastern oyster (Crassostrea virginica), are an important agricultural commodity. Previous research has demonstrated the importance of the native microbiome of oysters against exogenous challenges by non-native pathogens. However, the taxonomic makeup of the oyster microbiome and the impact of environmental factors on it are understudied. Research was conducted quarterly over a calendar year (February 2020 through February 2021) to analyze the taxonomic diversity of bacteria present within the microbiome of consumer-ready-to-eat live Eastern oysters. It was hypothesized that a core group of bacterial species would be present in the microbiome regardless of external factors such as the water temperature at the time of harvest or post-harvesting processing. At each time point, 18 Chesapeake Bay (eastern United States) watershed aquacultured oysters were acquired from a local grocery store, genomic DNA was extracted from the homogenized whole oyster tissues, and the bacterial 16S rRNA gene hypervariable V4 region was PCR-amplified using barcoded primers prior to sequencing via Illumina MiSeq and bioinformatic analysis of the data. A core group of bacteria were identified to be consistently associated with the Eastern oyster, including members of the phyla Firmicutes and Spirochaetota, represented by the families Mycoplasmataceae and Spirochaetaceae, respectively. The phyla Cyanobacterota and Campliobacterota became more predominant in relation to warmer or colder water column temperature, respectively, at the time of oyster harvest.
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Affiliation(s)
- Ian S. Hines
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Justin Markov Madanick
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Stephen A. Smith
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, Virginia, United States of America
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, Blacksburg, Virginia, United States of America
| | - David D. Kuhn
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, Virginia, United States of America
- Department of Food Science and Technology, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Ann M. Stevens
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, Virginia, United States of America
- * E-mail:
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Du J, Liu Y, Zhu H. Genome-based analyses of the genus Acidovorax: proposal of the two novel genera Paracidovorax gen. nov., Paenacidovorax gen. nov. and the reclassification of Acidovorax antarcticus as Comamonas antarctica comb. nov. and emended description of the genus Acidovorax. Arch Microbiol 2022; 205:42. [PMID: 36574033 DOI: 10.1007/s00203-022-03379-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/12/2022] [Accepted: 12/15/2022] [Indexed: 12/28/2022]
Abstract
The genus Acidovorax is a genetically heterogeneous species clustering that comprises many environmental and plant-pathogenic taxa. To better understand the evolutionary relationships among the Acidovorax species, 22 available genome sequences of type strains including the genera Acidovorax and Comamonas were used to conduct the genome-based analyses. Three well-supported monophyletic clusters of the Acidovorax species were determined based on the phylogenomic tree reconstructed using core genes, while they were not grouped in the 16S rRNA gene-based phylogenetic tree. The species arrangements of the genus Acidovorax were further confirmed by the comparisons of the digital DNA-DNA hybridization and average nucleotide identity (ANI) values. The ANI, average amino acid identity, and the percentage of conserved proteins values among the inter-clusters were approximately 83, 81, and 61%, respectively, and thus were proposed as practical thresholds for genus delineation. Besides, Acidovorax antarcticus was much closer to members of the genus Comamonas rather than those of the genus Acidovorax based on the genome-based analysis. Taken together, we propose the division of the current genus Acidovorax into the emended genus Acidovorax and the two novel genera Paracidovorax gen. nov., Paenacidovorax gen. nov. and the transfer of Acidovorax antarcticus into the genus Comamonas as Comamonas antarctica comb. nov.
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Affiliation(s)
- Juan Du
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Building 66, Xianlie Middle Road 100, Guangzhou, 510070, Guangdong Province, People's Republic of China
| | - Yang Liu
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Building 66, Xianlie Middle Road 100, Guangzhou, 510070, Guangdong Province, People's Republic of China
| | - Honghui Zhu
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Building 66, Xianlie Middle Road 100, Guangzhou, 510070, Guangdong Province, People's Republic of China.
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23
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Effect of Atmospheric Conditions on Pathogenic Phenotypes of Arcobacter butzleri. Microorganisms 2022; 10:microorganisms10122409. [PMID: 36557662 PMCID: PMC9785646 DOI: 10.3390/microorganisms10122409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Arcobacter butzleri is an emergent gram-negative enteropathogenic bacterium widespread in different environments and hosts. During the colonization of the gastrointestinal tract, bacteria face a variety of environmental conditions to successfully establish infection in a new host. One of these challenges is the fluctuation of oxygen concentrations encountered not only throughout the host gastrointestinal tract and defences but also in the food industry. Oxygen fluctuations can lead to modulations in the virulence of the bacterium and possibly increase its pathogenic potential. In this sense, eight human isolates of A. butzleri were studied to evaluate the effects of microaerobic and aerobic atmospheric conditions in stressful host conditions, such as oxidative stress, acid survival, and human serum survival. In addition, the effects on the modulation of virulence traits, such as haemolytic activity, bacterial motility, biofilm formation ability, and adhesion and invasion of the Caco-2 cell line, were also investigated. Overall, aerobic conditions negatively affected the susceptibility to oxygen reactive species and biofilm formation ability but improved the isolates' haemolytic ability and motility while other traits showed an isolate-dependent response. In summary, this work demonstrates for the first time that oxygen levels can modulate the potential pathogenicity of A. butzleri, although the response to stressful conditions was very heterogeneous among different strains.
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24
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Phylogenomic analysis of a metagenome-assembled genome indicates a new taxon of an anoxygenic phototroph bacterium in the family Chromatiaceae and the proposal of “Candidatus Thioaporhodococcus” gen. nov. Arch Microbiol 2022; 204:688. [DOI: 10.1007/s00203-022-03298-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/28/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022]
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Zhou G, Wang M, Wang H, Chen X, Gu Y, Shao Z, Zhang J, Zhang M. Species classification and novel plasmid identifications in Arcobacter cryaerophilus and Arcobacter cryaerophilus-like organisms. Front Microbiol 2022; 13:984450. [PMID: 36212879 PMCID: PMC9535334 DOI: 10.3389/fmicb.2022.984450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 09/01/2022] [Indexed: 11/24/2022] Open
Abstract
The Arcobacter is a globally emerging foodborne and zoonotic pathogen that can cause diarrhea in humans. It is relatively homogenous and clearly distinguishes the group from other Epsilonproteobacteria. Arcobacter cryaerophilus (A. cryaerophilus) is a heterogeneous species and little is known about its genomic characterization in China. This study aims to determine the genetic and plasmid features of A. cryaerophilus based on whole-genome sequence (WGS). Average Nucleotide Identity (ANI) and in silico DNA–DNA hybridization (isDDH) were used for the species classification for 90 initially identified A. cryaerophilus strains. One complete genome and 42 draft genomes were obtained by whole genome sequencing. The genomic characteristics were determined using various bioinformatics software. The genomes of the strains examined were estimated to vary from 1.81 to 2.28 Mb in length, with a G + C content of around 27%. ANI and isDDH results indicated that 90 initially identified A. cryaerophilus strains should be reclassified into four new species (ANI > 96% or isDDH > 70%). Two clades (four subclades) were identified among 90 genomes with the phylogenetic analysis. The phylogenetic tree indicated these 90 genomes exhibited a high intra-species genomic diversity. No clustering was assorted with the host or geographic location among these genomes. Aminoglycoside resistance genes, such as aph(2’’)-Ih, AAC(6’)-Ie-APH(2’’)-Ia, aac(6’)-IIa, ant(6), and streptothricin resistance gene SAT-4 were detected in the chromosomes from a third of the Chinese strains. Virulence-related genes were identified in all the sequenced strains. A novel large multiple drug-resistant plasmid (named pCNAC48 with 161,992 bp in length) was identified in strain ICDCAC48. Two antibiotic-resistance islands were found in the plasmid with lengths of 7,950 and 25,137 bp and G + C content of 38.23 and 32.39%, respectively. The drug resistance genes and some transposable elements were cross-distributed among the islands in the plasmid. Antimicrobial susceptibility tests indicated these resistance genes in the plasmid were functional. Plasmid conjugation and curing experiments proved pCNAC48 was stable in strain ICDCAC48. It was the first identified multiple drug resistance plasmid in A. cryaerophilus-like.
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26
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Roguet A, Newton RJ, Eren AM, McLellan SL. Guts of the Urban Ecosystem: Microbial Ecology of Sewer Infrastructure. mSystems 2022; 7:e0011822. [PMID: 35762794 PMCID: PMC9426572 DOI: 10.1128/msystems.00118-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 05/25/2022] [Indexed: 11/20/2022] Open
Abstract
Microbes have inhabited the oceans and soils for millions of years and are uniquely adapted to their habitat. In contrast, sewer infrastructure in modern cities dates back only ~150 years. Sewer pipes transport human waste and provide a view into public health, but the resident organisms that likely modulate these features are relatively unexplored. Here, we show that the bacterial assemblages sequenced from untreated wastewater in 71 U.S. cities were highly coherent at a fine sequence level, suggesting that urban infrastructure separated by great spatial distances can give rise to strikingly similar communities. Within the overall microbial community structure, temperature had a discernible impact on the distribution patterns of closely related amplicon sequence variants, resulting in warm and cold ecotypes. Two bacterial genera were dominant in most cities regardless of their size or geographic location; on average, Arcobacter accounted for 11% and Acinetobacter 10% of the entire community. Metagenomic analysis of six cities revealed these highly abundant resident organisms carry clinically important antibiotic resistant genes blaCTX-M, blaOXA, and blaTEM. In contrast, human fecal bacteria account for only ~13% of the community; therefore, antibiotic resistance gene inputs from human sources to the sewer system could be comparatively small, which will impact measurement capabilities when monitoring human populations using wastewater. With growing awareness of the metabolic potential of microbes within these vast networks of pipes and the ability to examine the health of human populations, it is timely to increase our understanding of the ecology of these systems. IMPORTANCE Sewer infrastructure is a relatively new habitat comprised of thousands of kilometers of pipes beneath cities. These wastewater conveyance systems contain large reservoirs of microbial biomass with a wide range of metabolic potential and are significant reservoirs of antibiotic resistant organisms; however, we lack an adequate understanding of the ecology or activity of these communities beyond wastewater treatment plants. The striking coherence of the sewer microbiome across the United States demonstrates that the sewer environment is highly selective for a particular microbial community composition. Therefore, results from more in-depth studies or proven engineering controls in one system could be extrapolated more broadly. Understanding the complex ecology of sewer infrastructure is critical for not only improving our ability to treat human waste and increasing the sustainability of our cities but also to create scalable and effective sewage microbial observatories, which are inevitable investments of the future to monitor health in human populations.
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Affiliation(s)
- Adélaïde Roguet
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Ryan J. Newton
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - A. Murat Eren
- Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Sandra L. McLellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
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27
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Švarcová K, Hofmeisterová L, Švecová B, Šilha D. In Vitro Activity of Water Extracts of Olive Oil against Planktonic Cells and Biofilm Formation of Arcobacter-like Species. Molecules 2022; 27:molecules27144509. [PMID: 35889378 PMCID: PMC9318941 DOI: 10.3390/molecules27144509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/11/2022] [Accepted: 07/13/2022] [Indexed: 01/27/2023] Open
Abstract
Extra-virgin olive oils contain many bioactive substances that are phenolic compounds. The survival of Arcobacter-like strains in non-buffered (WEOO) and buffered (BEOO) extracts of olive oils were studied. Time kill curves of different strains were measured in the environment of olive oil extracts of different grades. The activity of the extracts was also monitored for biofilm formation using the Christensen method. In vitro results revealed that extra-virgin olive oil extracts exhibited the strongest antimicrobial effects, especially non-buffered extracts, which exhibited strain inhibition after only 5 min of exposure. The weakest inhibitory effects were observed for olive oil extracts. A decrease in biofilm formation was observed in the environment of higher WEOO concentrations, although at lower concentrations of extracts, increased biofilm formation occurred due to stress conditions. The dialdehydic forms of oleuropein derivatives, hydroxytyrosol, and tyrosol were the main compounds detected by HPLC-CoulArray. The results indicate that not all olive oils had a similar bactericidal effect, and that bioactivity primarily depended on the content of certain phenolic compounds.
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Affiliation(s)
- Karolína Švarcová
- Department of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Studentská 573, 532 10 Pardubice, Czech Republic; (K.Š.); (L.H.)
| | - Leona Hofmeisterová
- Department of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Studentská 573, 532 10 Pardubice, Czech Republic; (K.Š.); (L.H.)
| | - Blanka Švecová
- Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, 532 10 Pardubice, Czech Republic;
| | - David Šilha
- Department of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Studentská 573, 532 10 Pardubice, Czech Republic; (K.Š.); (L.H.)
- Correspondence: ; Tel.: +420-466-037-765
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28
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Arcobacter Butzleri in an AIDS Patient. Case Rep Infect Dis 2022; 2022:6983094. [PMID: 35847602 PMCID: PMC9279096 DOI: 10.1155/2022/6983094] [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: 03/10/2022] [Revised: 06/09/2022] [Accepted: 06/22/2022] [Indexed: 11/17/2022] Open
Abstract
Background Arcobacter butzleri (A. butzleri) is an emerging enteric pathogen increasingly identified in Europe and is likely under-reported in other global regions. We describe to our knowledge the first case report of A. butzleri in an AIDS patient, along with the first documented local (Singapore) case of A. butzleri infection. Case Presentation. A 38-year-old AIDS patient presented with diarrhoea of 2 weeks' duration. Stool cultures yielded A. butzleri. The patient was treated with 3 days of ciprofloxacin with clinical resolution of diarrhoea. Conclusion A. butzleri is likely to be present, although under-reported in AIDS patients, and it should be noted as a pathogen of increasing significance.
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Chuan J, Belov A, Cloutier M, Li X, Khan IUH, Chen W. Comparative genomics analysis and virulence-related factors in novel Aliarcobacter faecis and Aliarcobacter lanthieri species identified as potential opportunistic pathogens. BMC Genomics 2022; 23:471. [PMID: 35761183 PMCID: PMC9235176 DOI: 10.1186/s12864-022-08663-w] [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: 02/09/2022] [Accepted: 05/19/2022] [Indexed: 12/30/2022] Open
Abstract
Abstract
Background
Emerging pathogenic bacteria are an increasing threat to public health. Two recently described species of the genus Aliarcobacter, A. faecis and A. lanthieri, isolated from human or livestock feces, are closely related to Aliarcobacter zoonotic pathogens (A. cryaerophilus, A. skirrowii, and A. butzleri). In this study, comparative genomics analysis was carried out to examine the virulence-related, including virulence, antibiotic, and toxin (VAT) factors in the reference strains of A. faecis and A. lanthieri that may enable them to become potentially opportunistic zoonotic pathogens.
Results
Our results showed that the genomes of the reference strains of both species have flagella genes (flaA, flaB, flgG, flhA, flhB, fliI, fliP, motA and cheY1) as motility and export apparatus, as well as genes encoding the Twin-arginine translocation (Tat) (tatA, tatB and tatC), type II (pulE and pulF) and III (fliF, fliN and ylqH) secretory pathways, allowing them to secrete proteins into the periplasm and host cells. Invasion and immune evasion genes (ciaB, iamA, mviN, pldA, irgA and fur2) are found in both species, while adherence genes (cadF and cj1349) are only found in A. lanthieri. Acid (clpB), heat (clpA and clpB), osmotic (mviN), and low-iron (irgA and fur2) stress resistance genes were observed in both species, although urease genes were not found in them. In addition, arcB, gyrA and gyrB were found in both species, mutations of which may mediate the resistance to quaternary ammonium compounds (QACs). Furthermore, 11 VAT genes including six virulence (cadF, ciaB, irgA, mviN, pldA, and tlyA), two antibiotic resistance [tet(O) and tet(W)] and three cytolethal distending toxin (cdtA, cdtB, and cdtC) genes were validated with the PCR assays. A. lanthieri tested positive for all 11 VAT genes. By contrast, A. faecis showed positive for ten genes except for cdtB because no PCR assay for this gene was available for this species.
Conclusions
The identification of the virulence, antibiotic-resistance, and toxin genes in the genomes of A. faecis and A. lanthieri reference strains through comparative genomics analysis and PCR assays highlighted the potential zoonotic pathogenicity of these two species. However, it is necessary to extend this study to include more clinical and environmental strains to explore inter-species and strain-level genetic variations in virulence-related genes and assess their potential to be opportunistic pathogens for animals and humans.
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Kobayashi M, Zhang Q, Segawa T, Maeda M, Hirano R, Okabe S, Ishii S. Temporal dynamics of Campylobacter and Arcobacter in a freshwater lake that receives fecal inputs from migratory geese. WATER RESEARCH 2022; 217:118397. [PMID: 35421690 DOI: 10.1016/j.watres.2022.118397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/26/2022] [Accepted: 04/01/2022] [Indexed: 06/14/2023]
Abstract
Migratory geese could influence the microbiological water quality; however, their impacts on pathogen dynamics remain largely unknown. In this study, we analyzed the population dynamics of Campylobacter and Arcobacter group bacteria (AGB) in a freshwater lake in Japan over two years. The bacteria were quantified by using both culture-dependent and -independent methods. The potential sources of these bacteria were examined by a high-throughput flaA sequencing approach. Campylobacter was abundantly detected both by culture-dependent and -independent methods in the lake, especially when migratory geese were present in the lake. High-throughput flaA sequencing suggests that geese were the likely source of Campylobacter in the lake. The viable population of Campylobacter exceeds the concentrations that can potentially cause 10-4 infections per person per year when water is used to grow fresh vegetables. The occurrence of AGB, on the other hand, was not directly related to the population of migratory geese. AGB were not detected in geese fecal samples. Diverse AGB flaA genotypes occurred in the lake over multiple seasons. Our results suggest that AGB likely comprise a part of the indigenous microbial population of the lake and grow in response to high nutrient, warm temperature, and low dissolved oxygen concentrations in the lake. Geese therefore can indirectly impact the AGB population by providing nutrients to cause eutrophication and lower the dissolved oxygen concentration. Since geese travel long-distance and disperse their fecal microbiota and nutrients to wide areas, they may have significant impacts on water quality and public health.
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Affiliation(s)
- Mayumi Kobayashi
- Division of Environmental Engineering, Graduate School of Engineering, Hokakido University, Sapporo, Japan; BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Qian Zhang
- BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Takahiro Segawa
- Center for Life Science Research, University of Yamanashi, Yamanashi, Japan
| | - Mitsuto Maeda
- Division of Environmental Engineering, Graduate School of Engineering, Hokakido University, Sapporo, Japan
| | - Reiko Hirano
- Division of Environmental Engineering, Graduate School of Engineering, Hokakido University, Sapporo, Japan
| | - Satoshi Okabe
- Division of Environmental Engineering, Graduate School of Engineering, Hokakido University, Sapporo, Japan
| | - Satoshi Ishii
- Division of Environmental Engineering, Graduate School of Engineering, Hokakido University, Sapporo, Japan; BioTechnology Institute, University of Minnesota, St. Paul, MN, USA; Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN, USA.
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Luo D, Zhang K, Song T, Xie J. Enhancing microbial electrosynthesis by releasing extracellular polymeric substances: Novel strategy through extracellular electron transfer improvement. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Park MJ, Kim YJ, Park M, Yu J, Namirimu T, Roh YR, Kwon KK. Establishment of Genome Based Criteria for Classification of the Family Desulfovibrionaceae and Proposal of Two Novel Genera, Alkalidesulfovibrio gen. nov. and Salidesulfovibrio gen. nov. Front Microbiol 2022; 13:738205. [PMID: 35694308 PMCID: PMC9174804 DOI: 10.3389/fmicb.2022.738205] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 04/11/2022] [Indexed: 01/14/2023] Open
Abstract
Bacteria in the Desulfovibrionaceae family, which contribute to S element turnover as sulfate-reducing bacteria (SRB) and disproportionation of partially oxidized sulfoxy anions, have been extensively investigated since the importance of the sulfur cycle emerged. Novel species belonging to this taxon are frequently reported, because they exist in various environments and are easy to culture using established methods. Due to the rapid expansion of the taxon, correction and reclassification have been conducted. The development of high-throughput sequencing facilitated rapid expansion of genome sequence database. Genome-based criteria, based on these databases, proved to be potential classification standard by overcoming the limitations of 16S rRNA-based phylogeny. Although standards methods for taxogenomics are being established, the addition of a novel genus requires extensive calculations with taxa, including many species, such as Desulfovibrionaceae. Thus, the genome-based criteria for classification of Desulfovibrionaceae were established and validated in this study. The average amino-acid identity (AAI) cut-off value, 63.43 ± 0.01, was calculated to be an appropriate criterion for genus delineation of the family Desulfovibrionaceae. By applying the AAI cut-off value, 88 genomes of the Desulfovibrionaceae were divided into 27 genera, which follows the core gene phylogeny results. In this process, two novel genera (Alkalidesulfovibrio and Salidesulfovibrio) and one former invalid genus (“Psychrodesulfovibrio”) were officially proposed. Further, by applying the 95–96% average nucleotide identity (ANI) standard and the 70% digital DNA–DNA hybridization standard values for species delineation of strains that were classified as the same species, five strains have the potential to be newly classified. After verifying that the classification was appropriately performed through relative synonymous codon usage analysis, common characteristics were listed by group. In addition, by detecting metal resistance related genes via in silico analysis, it was confirmed that most strains display metal tolerance.
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Affiliation(s)
- Mi-Jeong Park
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
- Department of Applied Ocean Science, University of Science and Technology, Daejeon, South Korea
| | - Yun Jae Kim
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
| | - Myeongkyu Park
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea
| | - Jihyun Yu
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
- Department of Applied Ocean Science, University of Science and Technology, Daejeon, South Korea
| | - Teddy Namirimu
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
- Department of Applied Ocean Science, University of Science and Technology, Daejeon, South Korea
| | - Yoo-Rim Roh
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
- Department of Applied Ocean Science, University of Science and Technology, Daejeon, South Korea
| | - Kae Kyoung Kwon
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
- Department of Applied Ocean Science, University of Science and Technology, Daejeon, South Korea
- *Correspondence: Kae Kyoung Kwon,
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Kerkhof PJ, Peruzy MF, Murru N, Houf K. Wild boars as reservoir for Campylobacter and Arcobacter. Vet Microbiol 2022; 270:109462. [DOI: 10.1016/j.vetmic.2022.109462] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 05/03/2022] [Accepted: 05/11/2022] [Indexed: 12/16/2022]
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Xu XJ, Wu YN, Xiao QY, Xie P, Ren NQ, Yuan YX, Lee DJ, Chen C. Simultaneous removal of NO X and SO 2 from flue gas in an integrated FGD-CABR system by sulfur cycling-mediated Fe(II)EDTA regeneration. ENVIRONMENTAL RESEARCH 2022; 205:112541. [PMID: 34915032 DOI: 10.1016/j.envres.2021.112541] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 11/29/2021] [Accepted: 12/05/2021] [Indexed: 06/14/2023]
Abstract
Chemical absorption-biological reduction (CABR) process is an attractive method for NOX removal and Fe(II)EDTA regeneration is important to sustain high NOX removal. In this study a sustainable and eco-friendly sulfur cycling-mediated Fe(II)EDTA regeneration method was incorporated in the integrated biological flue gas desulfurization (FGD)-CABR system. Here, we investigated the NOX and SO2 removal efficiency of the system under three different flue gas flows (100 mL/min, 500 mL/min, and 1000 mL/min) and evaluated the feasibility of chemical Fe(III)EDTA reduction by sulfide in series of batch tests. Our results showed that complete SO2 removal was achieved at all the tested scenarios with sulfide, thiosulfate and S0 accumulation in the solution. Meanwhile, the total removal efficiency of NOX achieved ∼100% in the system, of which 3.2%-23.3% was removed in spray scrubber and 76.7%-96.5% in EGSB reactor along with no N2O emission. The optimal pH and S2-/Fe(III)EDTA for Fe(II)EDTA regeneration and S0 recovery was 8.0 and 1:2. The microbial community analysis results showed that the cooperation of heterotrophic denitrifier (Saprospiraceae_uncultured and Dechloromonas) and iron-reducing bacteria (Klebsiella and Petrimonas) in EGSB reactor and sulfide-oxidizing, nitrate-reducing bacteria (Azoarcus and Pseudarcobacter) in spray scrubber contributed to the efficient removal of NOX in flue gas.
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Affiliation(s)
- Xi-Jun Xu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province, 150090, China
| | - Yi-Ning Wu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province, 150090, China.
| | - Qing-Yang Xiao
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province, 150090, China
| | - Peng Xie
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province, 150090, China
| | - Nan-Qi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province, 150090, China
| | - Yi-Xing Yuan
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province, 150090, China
| | - Duu-Jong Lee
- Department of Chemical Engineering, National Taiwan University, Taipei, 106, Taiwan; Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei, 106, Taiwan
| | - Chuan Chen
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province, 150090, China.
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DNA- and RNA-based bacterial communities and geochemical zonation under changing sediment porewater dynamics on the Aldabra Atoll. Sci Rep 2022; 12:4257. [PMID: 35277525 PMCID: PMC8917147 DOI: 10.1038/s41598-022-07980-0] [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: 07/08/2021] [Accepted: 02/28/2022] [Indexed: 11/26/2022] Open
Abstract
The remote Aldabra Atoll, Seychelles, provides the rare opportunity to study bacterial communities in pristine carbonate sediments across an entire biome. The four sampled sites cover sand with high porewater exchange, bioturbated silt and mud with intermediate exchange, as well as a seasonally and episodically desiccated landlocked pool. As sediments harbour dead cells and environmental DNA alongside live cells, we used bacterial 16S rRNA gene and transcript analysis to distinguish between past and present inhabitants. Previously described laminated sediments mirroring past conditions in the Cerin, France could not be retrieved. Thus, the aim was adjusted to determine whether bacterial community composition and diversity follow typical geochemical zonation patterns at different locations of the atoll. Our data confirm previous observations that diversity decreases with depth. In the lagoon, the bacterial community composition changed from Pseudomonas dominating in the sand to diverse mixed surface and sulphate reduction zones in the anaerobic mud with strongly negative Eh. The latter correlated with high total alkalinity, ammonia, and total sulphide, alongside a decrease in SO42−/Cl− and high relative abundances of sulphate reducing (Halo-) Desulfovibrio, sulphur oxidizing Arcobacteraceae, photo(hetero)troph Cyanobacteria, Alphaproteobacteria, and fermenting Propionigenium. In contrast to expectations, deeper mud and pool sediments harboured high abundances of Halomonas or Alphaproteobacteria alongside high C/N and increased salinity. We believe that this atypical community shift may be driven by a change in the complexity of available organic matter.
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Venâncio I, Luís Â, Domingues F, Oleastro M, Pereira L, Ferreira S. The Prevalence of Arcobacteraceae in Aquatic Environments: A Systematic Review and Meta-Analysis. Pathogens 2022; 11:244. [PMID: 35215187 PMCID: PMC8880612 DOI: 10.3390/pathogens11020244] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 01/31/2022] [Accepted: 02/10/2022] [Indexed: 11/17/2022] Open
Abstract
Members of the family Arcobacteraceae are distributed widely in aquatic environments, and some of its species have been associated with human and animal illness. However, information about the diversity and distribution of Arcobacteraceae in different water bodies is still limited. In order to better characterize the health risk posed by members in the family Arcobacteraceae, a systematic review and meta-analysis-based method was used to investigate the prevalence of Arcobacteraceae species in aquatic environments based on available data published worldwide. The database search was performed using related keywords and considering studies up to February 2021. The pooled prevalence in aquatic environments was 69.2%, ranging from 0.6 to 99.9%. These bacteria have a wide geographical distribution, being found in diverse aquatic environments with the highest prevalence found in raw sewage and wastewater treatment plants (WWTP), followed by seawater, surface water, ground water, processing water from food processing plants and water for human consumption. Assessing the effectiveness of treatments in WWTP in eliminating this contamination, it was found that the wastewater treatment may not be efficient in the removal of Arcobacteraceae. Among the analyzed Arcobacteraceae species, Al. butzleri was the most frequently found species. These results highlight the high prevalence and distribution of Arcobacteraceae in different aquatic environments, suggesting a risk to human health. Further, it exposes the importance of identifying and managing the sources of contamination and taking preventive actions to reduce the burden of members of the Arcobacteraceae family.
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Affiliation(s)
- Igor Venâncio
- CICS-UBI-Health Sciences Research Centre, University of Beira Interior, 6200-506 Covilhã, Portugal; (I.V.); (Â.L.); (F.D.)
| | - Ângelo Luís
- CICS-UBI-Health Sciences Research Centre, University of Beira Interior, 6200-506 Covilhã, Portugal; (I.V.); (Â.L.); (F.D.)
- Grupo de Revisões Sistemáticas (GRUBI), Faculdade de Ciências da Saúde, Universidade da Beira Interior, 6200-506 Covilhã, Portugal;
| | - Fernanda Domingues
- CICS-UBI-Health Sciences Research Centre, University of Beira Interior, 6200-506 Covilhã, Portugal; (I.V.); (Â.L.); (F.D.)
| | - Mónica Oleastro
- National Reference Laboratory for Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal;
| | - Luísa Pereira
- Grupo de Revisões Sistemáticas (GRUBI), Faculdade de Ciências da Saúde, Universidade da Beira Interior, 6200-506 Covilhã, Portugal;
- CMA-UBI-Centro de Matemática e Aplicações, Universidade da Beira Interior, 6200-001 Covilhã, Portugal
- C4-UBI, Cloud Computing Competence Centre, University of Beira Interior, 6200-284 Covilhã, Portugal
| | - Susana Ferreira
- CICS-UBI-Health Sciences Research Centre, University of Beira Interior, 6200-506 Covilhã, Portugal; (I.V.); (Â.L.); (F.D.)
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Orel N, Fadeev E, Klun K, Ličer M, Tinta T, Turk V. Bacterial Indicators Are Ubiquitous Members of Pelagic Microbiome in Anthropogenically Impacted Coastal Ecosystem. Front Microbiol 2022; 12:765091. [PMID: 35111137 PMCID: PMC8801744 DOI: 10.3389/fmicb.2021.765091] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/25/2021] [Indexed: 01/18/2023] Open
Abstract
Coastal zones are exposed to various anthropogenic impacts, such as different types of wastewater pollution, e.g., treated wastewater discharges, leakage from sewage systems, and agricultural and urban runoff. These various inputs can introduce allochthonous organic matter and microbes, including pathogens, into the coastal marine environment. The presence of fecal bacterial indicators in the coastal environment is usually monitored using traditional culture-based methods that, however, fail to detect their uncultured representatives. We have conducted a year-around in situ survey of the pelagic microbiome of the dynamic coastal ecosystem, subjected to different anthropogenic pressures to depict the seasonal and spatial dynamics of traditional and alternative fecal bacterial indicators. To provide an insight into the environmental conditions under which bacterial indicators thrive, a suite of environmental factors and bacterial community dynamics were analyzed concurrently. Analyses of 16S rRNA amplicon sequences revealed that the coastal microbiome was primarily structured by seasonal changes regardless of the distance from the wastewater pollution sources. On the other hand, fecal bacterial indicators were not affected by seasons and accounted for up to 34% of the sequence proportion for a given sample. Even more so, traditional fecal indicator bacteria (Enterobacteriaceae) and alternative wastewater-associated bacteria (Lachnospiraceae, Ruminococcaceae, Arcobacteraceae, Pseudomonadaceae and Vibrionaceae) were part of the core coastal microbiome, i.e., present at all sampling stations. Microbial source tracking and Lagrangian particle tracking, which we employed to assess the potential pollution source, revealed the importance of riverine water as a vector for transmission of allochthonous microbes into the marine system. Further phylogenetic analysis showed that the Arcobacteraceae in our data set was affiliated with the pathogenic Arcobacter cryaerophilus, suggesting that a potential exposure risk for bacterial pathogens in anthropogenically impacted coastal zones remains. We emphasize that molecular analyses combined with statistical and oceanographic models may provide new insights for environmental health assessment and reveal the potential source and presence of microbial indicators, which are otherwise overlooked by a cultivation approach.
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Affiliation(s)
- Neža Orel
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
- *Correspondence: Neža Orel,
| | - Eduard Fadeev
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Katja Klun
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
| | - Matjaž Ličer
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
- Office for Meteorology, Hydrology and Oceanography, Slovenian Environment Agency, Ljubljana, Slovenia
| | - Tinkara Tinta
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
- Tinkara Tinta,
| | - Valentina Turk
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
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Prevalence, antimicrobial susceptibility and virulence gene profiles of Arcobacter species isolated from human stool samples, foods of animal origin, ready-to-eat salad mixes and environmental water. Gut Pathog 2021; 13:76. [PMID: 34930425 PMCID: PMC8686351 DOI: 10.1186/s13099-021-00472-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 12/07/2021] [Indexed: 12/11/2022] Open
Abstract
Background Members of the genus Arcobacter are considered as emerging zoonotic food and waterborne pathogens that cause gastroenteritis and bacteremia in humans. However, the potential risk that Arcobacter species pose to public health remains unassessed in various countries, including Baltic states. Therefore, the aim of this study was to determine the prevalence, antimicrobial susceptibility and presence of putative virulence genes of Arcobacter isolates recovered from humans, food products and environmental water in Lithuania. Results A total of 1862 samples were collected and examined from 2018 to 2020 in the city of Kaunas. Overall, 11.2% (n = 208) of the samples were positive for the presence of Arcobacter spp. The highest prevalence was detected in chicken meat (36%), followed by environmental water (28.1%), raw cow milk (25%), ready-to-eat salad mixes (7.1%) and human stool (1.7%). A. butzleri was the most frequently isolated species (n = 192; 92.3%), followed by A. cryaerophilus (n = 16; 7.7%). Arcobacter spp. antimicrobial susceptibility testing revealed unimodally distributed aggregated minimal inhibitory concentrations (MICs) for gentamicin, tetracycline, ciprofloxacin, ampicillin and erythromycin. However, a bimodal distribution for azithromycin was found with 96.2% of determined MICs above the epidemiological cut-off value (ECOFF) defined for Campylobacter jejuni (0.25 µg/ml). Majority of the Arcobacter isolates (n = 187; 89.9%) showed high susceptibility to ciprofloxacin with MICs below or equal to the ECOFF value of 0.5 µg/ml. The putative virulence genes cadF (100%), ciaB (100%), cj1349 (99%), tlyA (99%), mviN (97.9%) and pldA (95.8%) were the predominant genes detected among A. butzleri isolates. In contrast, the mviN and ciaB genes were present in all, whereas cj1349 (12.5%), tlyA (25%) and hecA (12.5%) were only detected in few A. cryaerophilus isolates. Conclusions Our results demonstrate that food products and environmental water in Lithuania are frequently contaminated with Arcobacter spp. that carry multiple putative virulence genes. Furthermore, A. butzleri were isolated from 1.7% of inpatients. Fluoroquinolones and aminoglycosides were found to be more effective against Arcobacter in comparison to other antimicrobial agents. However, further studies are needed to determine the pathogenic mechanisms and factors that facilitate the spread of Arcobacter infections.
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Kerkhof PJ, On SLW, Houf K. Arcobacter vandammei sp. nov., isolated from the rectal mucus of a healthy pig. Int J Syst Evol Microbiol 2021; 71. [PMID: 34797211 DOI: 10.1099/ijsem.0.005113] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
A study on the polyphasic taxonomic classification of an Arcobacter strain, R-73987T, isolated from the rectal mucus of a porcine intestinal tract, was performed. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the strain could be assigned to the genus Arcobacter and suggested that strain R-73987T belongs to a novel undescribed species. Comparative analysis of the rpoB gene sequence confirmed the findings. Arcobacter faecis LMG 28519T was identified as its closest neighbour in a multigene analysis based on 107 protein- encoding genes. Further, whole-genome sequence comparisons by means of average nucleotide identity and in silico DNA-DNA hybridization between the genome of strain R-73987T and the genomes of validly named Arcobacter species resulted in values below 95-96 and 70 %, respectively. In addition, a phenotypic analysis further corroborated the conclusion that strain R-73987T represents a novel Arcobacter species, for which the name Arcobacter vandammei sp. nov. is proposed. The type strain is R-73987T (=LMG 31429T=CCUG 75005T). This appears to be the first Arcobacter species recovered from porcine intestinal mucus.
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Affiliation(s)
- Pieter-Jan Kerkhof
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Stephen L W On
- Department of Wine, Food and Molecular Biosciences, Lincoln University, Springs Road, Lincoln 7467, New Zealand
| | - Kurt Houf
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium.,Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium, 9000 Ghent, Belgium
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Wang P, Mao Y, Su Y, Wang J. Comparative analysis of transcriptomic data shows the effects of multiple evolutionary selection processes on codon usage in Marsupenaeus japonicus and Marsupenaeus pulchricaudatus. BMC Genomics 2021; 22:781. [PMID: 34717552 PMCID: PMC8557549 DOI: 10.1186/s12864-021-08106-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 10/19/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Kuruma shrimp, a major commercial shrimp species in the world, has two cryptic or sibling species, Marsupenaeus japonicus and Marsupenaeus pulchricaudatus. Codon usage analysis would contribute to our understanding of the genetic and evolutionary characteristics of the two Marsupenaeus species. In this study, we analyzed codon usage and related indices using coding sequences (CDSs) from RNA-seq data. RESULTS Using CodonW 1.4.2 software, we performed the codon bias analysis of transcriptomes obtained from hepatopancreas tissues, which indicated weak codon bias. Almost all parameters had similar correlations for both species. The gene expression level (FPKM) was negatively correlated with A/T3s. We determined 12 and 14 optimal codons for M. japonicus and M. pulchricaudatus, respectively, and all optimal codons have a C/G-ending. The two Marsupenaeus species had different usage frequencies of codon pairs, which contributed to further analysis of transcriptional differences between them. Orthologous genes that underwent positive selection (ω > 1) had a higher correlation coefficient than that of experienced purifying selection (ω < 1). Parity Rule 2 (PR2) and effective number of codons (ENc) plot analysis showed that the codon usage patterns of both species were influenced by both mutations and selection. Moreover, the average observed ENc value was lower than the expected value for both species, suggesting that factors other than GC may play roles in these phenomena. The results of multispecies clustering based on codon preference were consistent with traditional classification. CONCLUSIONS This study provides a relatively comprehensive understanding of the correlations among codon usage bias, gene expression, and selection pressures of CDSs for M. japonicus and M. pulchricaudatus. The genetic evolution was driven by mutations and selection pressure. Moreover, the results point out new insights into the specificities and evolutionary characteristics of the two Marsupenaeus species.
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Affiliation(s)
- Panpan Wang
- Jiangsu Key Laboratory of Marine Bioresources and Environment/ Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, 222005, China
- Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China
- The Jiangsu Provincial Infrastructure for Conservation and Utilization of Agricultural Germplasm, Nanjing, 210014, China
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Yong Mao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, Fujian, China.
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, 361102, China.
| | - Yongquan Su
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Jun Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, Fujian, China
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Bell RL, Kase JA, Harrison LM, Balan KV, Babu U, Chen Y, Macarisin D, Kwon HJ, Zheng J, Stevens EL, Meng J, Brown EW. The Persistence of Bacterial Pathogens in Surface Water and Its Impact on Global Food Safety. Pathogens 2021; 10:1391. [PMID: 34832547 PMCID: PMC8617848 DOI: 10.3390/pathogens10111391] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/15/2021] [Accepted: 10/19/2021] [Indexed: 11/17/2022] Open
Abstract
Water is vital to agriculture. It is essential that the water used for the production of fresh produce commodities be safe. Microbial pathogens are able to survive for extended periods of time in water. It is critical to understand their biology and ecology in this ecosystem in order to develop better mitigation strategies for farmers who grow these food crops. In this review the prevalence, persistence and ecology of four major foodborne pathogens, Shiga toxin-producing Escherichia coli (STEC), Salmonella, Campylobacter and closely related Arcobacter, and Listeria monocytogenes, in water are discussed. These pathogens have been linked to fresh produce outbreaks, some with devastating consequences, where, in a few cases, the contamination event has been traced to water used for crop production or post-harvest activities. In addition, antimicrobial resistance, methods improvements, including the role of genomics in aiding in the understanding of these pathogens, are discussed. Finally, global initiatives to improve our knowledge base of these pathogens around the world are touched upon.
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Affiliation(s)
- Rebecca L. Bell
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD 20740, USA; (J.A.K.); (Y.C.); (D.M.); (H.J.K.); (J.Z.); (E.W.B.)
| | - Julie A. Kase
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD 20740, USA; (J.A.K.); (Y.C.); (D.M.); (H.J.K.); (J.Z.); (E.W.B.)
| | - Lisa M. Harrison
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, Food and Drug Administration, Laurel, MD 20708, USA; (L.M.H.); (K.V.B.); (U.B.)
| | - Kannan V. Balan
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, Food and Drug Administration, Laurel, MD 20708, USA; (L.M.H.); (K.V.B.); (U.B.)
| | - Uma Babu
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, Food and Drug Administration, Laurel, MD 20708, USA; (L.M.H.); (K.V.B.); (U.B.)
| | - Yi Chen
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD 20740, USA; (J.A.K.); (Y.C.); (D.M.); (H.J.K.); (J.Z.); (E.W.B.)
| | - Dumitru Macarisin
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD 20740, USA; (J.A.K.); (Y.C.); (D.M.); (H.J.K.); (J.Z.); (E.W.B.)
| | - Hee Jin Kwon
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD 20740, USA; (J.A.K.); (Y.C.); (D.M.); (H.J.K.); (J.Z.); (E.W.B.)
| | - Jie Zheng
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD 20740, USA; (J.A.K.); (Y.C.); (D.M.); (H.J.K.); (J.Z.); (E.W.B.)
| | - Eric L. Stevens
- Office of the Center Director, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD 20740, USA;
| | - Jianghong Meng
- Joint Institute for Food Safety and Applied Nutrition, Center for Food Safety and Security Systems, University of Maryland, College Park, MD 20742, USA;
| | - Eric W. Brown
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD 20740, USA; (J.A.K.); (Y.C.); (D.M.); (H.J.K.); (J.Z.); (E.W.B.)
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Yu Q, Sun W, Gao H. Thiosulfate oxidation in sulfur-reducing Shewanella oneidensis and its unexpected influences on the cytochrome c content. Environ Microbiol 2021; 23:7056-7072. [PMID: 34664382 DOI: 10.1111/1462-2920.15807] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/04/2021] [Accepted: 10/07/2021] [Indexed: 12/13/2022]
Abstract
Thiosulfate, an important form of sulfur compounds, can serve as both electron donor and acceptor in various microorganisms. In Shewanella oneidensis, a bacterium renowned for respiratory versatility, thiosulfate reduction has long been recognized but whether it can catalyse thiosulfate oxidation remains elusive. In this study, we discovered that S. oneidensis is capable of thiosulfate oxidation, a process specifically catalysed by two periplasmic cytochrome c (cyt c) proteins, TsdA and TsdB, which act as the catalytic subunit and the electron transfer subunit respectively. In the presence of oxygen, oxidation of thiosulfate has priority over reduction. Intriguingly, thiosulfate oxidation negatively regulates the cyt c content in S. oneidensis cells, largely by reducing intracellular levels of cAMP, which as the cofactor modulates activity of global regulator Crp required for transcription of many cyt c genes. This unexpected finding provides an additional dimension to interplays between the respiration regulator and the respiratory pathways in S. oneidensis. Moreover, the data presented here identified S. oneidensis as the first bacterium known to date owning both functional thiosulfate reductase and dehydrogenase, and importantly, genomics analyses suggested that the number of bacterial species possessing this feature is rather limited.
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Affiliation(s)
- Qingzi Yu
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou, 310058, China
| | - Weining Sun
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou, 310058, China
| | - Haichun Gao
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou, 310058, China
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Mateus C, Martins R, Luís Â, Oleastro M, Domingues F, Pereira L, Ferreira S. Prevalence of Arcobacter: From farm to retail – A systematic review and meta-analysis. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.108177] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Biofilm Formation Ability of Arcobacter-like and Campylobacter Strains under Different Conditions and on Food Processing Materials. Microorganisms 2021; 9:microorganisms9102017. [PMID: 34683338 PMCID: PMC8538277 DOI: 10.3390/microorganisms9102017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/09/2021] [Accepted: 09/21/2021] [Indexed: 11/23/2022] Open
Abstract
Campylobacter jejuni is the most frequent cause of bacterial gastrointestinal food-borne infection worldwide. The transmission of Campylobacter and Arcobacter-like species is often made possible by their ability to adhere to various abiotic surfaces. This study is focused on monitoring the biofilm ability of 69 strains of Campylobacter spp. and lesser described species of the Arcobacteraceae family isolated from food, water, and clinical samples within the Czech Republic. Biofilm formation was monitored and evaluated under an aerobic/microaerophilic atmosphere after cultivation for 24 or 72 h depending on the surface material. An overall higher adhesion ability was observed in arcobacters. A chi-squared test showed no association between the origin of the strains and biofilm activity (p > 0.05). Arcobacter-like species are able to form biofilms under microaerophilic and aerobic conditions; however, they prefer microaerophilic environments. Biofilm formation has already been demonstrated at refrigerator temperatures (5 °C). Arcobacters also showed higher biofilm formation ability at the temperature of 30 °C. This is in contrast to Campylobacter jejuni NP 2896, which showed higher biofilm formation ability at temperatures of 5–30 °C. Overall, the results demonstrated the biofilm formation ability of many strains, which poses a considerable risk to the food industry, medical practice, and human health.
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Simaluiza RJ, Ambuludi DR, Fernández H. First case of diarrhea due to Aliarcobacter butzleri (formerly Arcobacter butzleri) in Ecuador. Infect Dis Now 2021; 51:564-566. [PMID: 34486524 DOI: 10.1016/j.idnow.2020.12.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 12/07/2020] [Indexed: 10/22/2022]
Abstract
The first case of acute watery diarrhea disease due to Aliarcobacter butzleri (formerly Arcobacter butzleri) in Ecuador is reported. An infant presented with moderate protein-calorie malnutrition, dehydration and anemia. A curved Gram-negative organism was isolated from stools, having been preliminarily identified by phenotypic characteristics. Definitive identification was achieved by multiplex PCR. Aliarcobacter butzleri was the only pathogenic microorganism isolated. No other entero-pathogens, enterovirus or parasites were found. Our findings strongly suggest that in this specific case, A. butzleri was the etiological agent. Further investigations are needed to develop standardized diagnostic protocols and to establish the prevalence and significance of Aliarcobacter infections in humans.
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Affiliation(s)
| | | | - Heriberto Fernández
- Institute of Clinical Microbiology, Universidad Austral de Chile, Valdivia, Chile.
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Mudadu A, Salza S, Melillo R, Mara L, Piras G, Spanu C, Terrosu G, Fadda A, Virgilio S, Tedde T. Prevalence and pathogenic potential of Arcobacter spp. isolated from edible bivalve molluscs in Sardinia. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.108139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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47
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Iwanowicz DD, Jonas RB, Schill WB, Marano-Briggs K. Novel microbiome dominated by Arcobacter during anoxic excurrent flow from an ocean blue hole in Andros Island, The Bahamas. PLoS One 2021; 16:e0256305. [PMID: 34411155 PMCID: PMC8375975 DOI: 10.1371/journal.pone.0256305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 08/03/2021] [Indexed: 11/18/2022] Open
Abstract
Andros Island, The Bahamas, composed of porous carbonate rock, has about 175 inland blue holes and over 50 known submerged ocean caves along its eastern barrier reef. These ocean blue holes can have both vertical and horizontal zones that penetrate under the island. Tidal forces drive water flow in and out of these caves. King Kong Cavern has a vertical collapse zone and a deep penetration under Andros Island that emits sulfidic, anoxic water and masses of thin, mucoid filaments ranging to meters in length and off-white turbid water during ebb flow. Our objective was to determine the microbial composition of this mucoid material and the unconsolidated water column turbidity based on the concept that they represent unique lithoautotrophic microbial material swept from the cave into the surrounding ocean. Bacterial DNA extracted from these filaments and surrounding turbid water was characterized using PCR that targeted a portion of the 16S rRNA gene. The genus Arcobacter dominated both the filaments and the water column above the cave entrance. Arcobacter nitrofigilis and Arcobacter sp. UDC415 in the mucoid filaments accounted for as much as 80% of mapped DNA reads. In the water column Arcobacter comprised from 65% to over 85% of the reads in the depth region from about 18 m to 34 m. Bacterial species diversity was much higher in surface water and in water deeper than 36 m than in the intermediate zone. Community composition indicates that ebb flow from the cavern influences the entire water column at least to within 6 m of the surface and perhaps the near surface as well.
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Affiliation(s)
- Deborah D. Iwanowicz
- Eastern Ecological Science Center, United States Geological Survey, Kearneysville, West Virginia, United States of America
| | - Robert B. Jonas
- Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, United States of America
- * E-mail:
| | - William B. Schill
- Eastern Ecological Science Center, United States Geological Survey, Kearneysville, West Virginia, United States of America
| | - Kay Marano-Briggs
- Eastern Ecological Science Center, United States Geological Survey, Kearneysville, West Virginia, United States of America
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48
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Characterization of AreABC, an RND-Type Efflux System Involved in Antimicrobial Resistance of Aliarcobacter butzleri. Antimicrob Agents Chemother 2021; 65:e0072921. [PMID: 34152822 DOI: 10.1128/aac.00729-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Aliarcobacter butzleri is an emergent enteropathogen for which resistance to several classes of antimicrobial agents has been described, although the underlying mechanisms have been poorly addressed. We aimed to evaluate the contribution of the resistance-nodulation-division-type (RND) efflux system, AreABC, to drug resistance in A. butzleri. A. butzleri strains were first tested against several antimicrobials with and without an efflux pump inhibitor. Then, erythromycin-resistant strains were screened for the presence of a premature stop codon in a putative transcriptional regulator of the AreABC system, areR. Lastly, antimicrobial susceptibility and ethidium bromide (EtBr) accumulation were evaluated using an areB knockout strain and a strain overexpressing the AreABC system through areR truncation. The presence of the efflux pump inhibitor resulted in increased susceptibility to most of the antimicrobials tested. A correlation between erythromycin resistance and the presence of premature stop codons in areR was observed. The truncation of areR resulted in increased expression of the AreABC system and decreased susceptibility to various antimicrobials. In contrast, areB inactivation resulted in increased susceptibility and a higher intracellular accumulation of EtBr. In conclusion, the AreABC efflux pump plays a role in the resistance of A. butzleri to multiple drugs and is regulated by a putative transcriptional repressor, areR. Our results support the importance of efflux pumps in this bacterium's resistance to major classes of antibiotics and other antimicrobials.
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Johnson MD, Scott JJ, Leray M, Lucey N, Bravo LMR, Wied WL, Altieri AH. Rapid ecosystem-scale consequences of acute deoxygenation on a Caribbean coral reef. Nat Commun 2021; 12:4522. [PMID: 34312399 PMCID: PMC8313580 DOI: 10.1038/s41467-021-24777-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/30/2021] [Indexed: 02/07/2023] Open
Abstract
Loss of oxygen in the global ocean is accelerating due to climate change and eutrophication, but how acute deoxygenation events affect tropical marine ecosystems remains poorly understood. Here we integrate analyses of coral reef benthic communities with microbial community sequencing to show how a deoxygenation event rapidly altered benthic community composition and microbial assemblages in a shallow tropical reef ecosystem. Conditions associated with the event precipitated coral bleaching and mass mortality, causing a 50% loss of live coral and a shift in the benthic community that persisted a year later. Conversely, the unique taxonomic and functional profile of hypoxia-associated microbes rapidly reverted to a normoxic assemblage one month after the event. The decoupling of ecological trajectories among these major functional groups following an acute event emphasizes the need to incorporate deoxygenation as an emerging stressor into coral reef research and management plans to combat escalating threats to reef persistence.
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Affiliation(s)
- Maggie D Johnson
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama.
- Tennenbaum Marine Observatories Network, MarineGEO, Smithsonian Institution, Edgewater, MD, USA.
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
| | - Jarrod J Scott
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama
| | - Matthieu Leray
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama
| | - Noelle Lucey
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama
| | - Lucia M Rodriguez Bravo
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Ensenada, Mexico
| | - William L Wied
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama
- Department of Biological Sciences, Center for Coastal Oceans Research, Florida International University, Miami, FL, USA
| | - Andrew H Altieri
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama
- Department of Environmental Engineering Sciences, University of Florida, Gainesville, FL, USA
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50
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Liguori R, Rommel SH, Bengtsson-Palme J, Helmreich B, Wurzbacher C. Microbial retention and resistances in stormwater quality improvement devices treating road runoff. FEMS MICROBES 2021. [DOI: 10.1093/femsmc/xtab008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
ABSTRACT
Current knowledge about the microbial communities that occur in urban road runoff is scarce. Road runoff of trafficked roads can be heavily polluted and is treated by stormwater quality improvement devices (SQIDs). However, microbes may influence the treatment process of these devices or could lead to stress resistant opportunistic microbial strains. In this study, the microbial community in the influent, effluent and the filter materials used to remove dissolved heavy metals from two different SQIDs were analyzed to determine microbial load, retention, composition, and mobile resistance genes. Although the microbes were replaced by new taxa in the effluent, there was no major retention of microbial genera. Further, the bacterial abundance of the SQIDs effluent was relatively stable over time. The heavy metal content correlated with intl1 and with microbial genera. The filter media itself was enriched with Intl1 gene cassettes, carrying several heavy metal and multidrug resistance genes (e.g. czrA, czcA, silP, mexW and mexI), indicating that this is a hot spot for horizontal gene transfer. Overall, the results shed light on road runoff microbial communities, and pointed to distinct bacterial communities within the SQIDs, which subsequently influence the microbial community and the genes released with the treated water.
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Affiliation(s)
- Renato Liguori
- Technical University of Munich, Chair of Urban Water Systems Engineering, Am Coulombwall 3, 85748 Garching, Germany
- Department of Science and Technology, Parthenope University of Naples, Centro direzionale Isola –C4, 80143, Napoli, Italy
| | - Steffen H Rommel
- Technical University of Munich, Chair of Urban Water Systems Engineering, Am Coulombwall 3, 85748 Garching, Germany
| | - Johan Bengtsson-Palme
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10A, SE-413 46, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Guldhedsgatan 10, SE-413 46, Gothenburg, Sweden
| | - Brigitte Helmreich
- Technical University of Munich, Chair of Urban Water Systems Engineering, Am Coulombwall 3, 85748 Garching, Germany
| | - Christian Wurzbacher
- Technical University of Munich, Chair of Urban Water Systems Engineering, Am Coulombwall 3, 85748 Garching, Germany
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