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Crippen TL, Kim D, Poole TL, Swiger SL, Anderson RC. The bacterial and archaeal communities of flies, manure, lagoons, and troughs at a working dairy. Front Microbiol 2024; 14:1327841. [PMID: 38449879 PMCID: PMC10915237 DOI: 10.3389/fmicb.2023.1327841] [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: 10/25/2023] [Accepted: 12/19/2023] [Indexed: 03/08/2024] Open
Abstract
Background Fundamental investigations into the location, load, and persistence of microbes, whether beneficial or detrimental, are scarce. Many questions about the retention and survival of microbes on various surfaces, as well as the load necessary for spread, exist. To answer these questions, we must know more about where to find various microbes and in what concentrations, the composition of the microbial communities, and the extent of dissemination between various elements. This study investigated the diversity, composition, and relative abundance of the communities associated with manure, lagoons, troughs, house flies, and stable flies present at a dairy, implementing two different free-stall management systems: flow-through and cross-vent. Shotgun metagenomics at the community level was used to compare the microbiomes within the dairy, allowing confident interpretation at the species level. Results The results showed that there were significant difference in microbial composition between not only each of the dairy elements but also management styles. The primary exceptions were the microbiomes of the house fly and the stable fly. Their compositions heavily overlapped with one another, but interestingly, not with the other components sampled. Additionally, both species of flies carried more pathogens than the other elements of the dairy, indicating that they may not share these organisms with the other components, or that the environments offered by the other components are unsatisfactory for the survival of some pathogens.. Conclusion The lack of overlapping pathogen profiles suggests a lack of transfer from flies to other dairy elements. Dairy health data, showing a low incidence of disease, suggests minimal sharing of bacteria by the flies at a level required for infection, given the health program of this dairy. While flies did carry a multitude of pathogenic bacteria, the mere presence of the bacteria associated with the flies did not necessarily translate into high risk leading to morbidity and mortality at this dairy. Thus, using flies as the sole sentinel of dairy health may not be appropriate for all bacterial pathogens or dairies.
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Affiliation(s)
- Tawni L. Crippen
- Southern Plains Agricultural Research Center, Agricultural Research Service, US Department of Agriculture, College Station, TX, United States
| | - Dongmin Kim
- Department of Entomology, Texas A & M University, College Station, TX, United States
| | - Toni L. Poole
- Southern Plains Agricultural Research Center, Agricultural Research Service, US Department of Agriculture, College Station, TX, United States
| | - Sonja L. Swiger
- Entomology Extension, Texas AgriLife, Texas A & M University, College Station, TX, United States
| | - Robin C. Anderson
- Southern Plains Agricultural Research Center, Agricultural Research Service, US Department of Agriculture, College Station, TX, United States
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Chao J, Li J, Kong M, Shao K, Tang X. Bacterioplankton diversity and potential health risks in volcanic lakes: A study from Arxan Geopark, China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 342:123058. [PMID: 38042466 DOI: 10.1016/j.envpol.2023.123058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 10/29/2023] [Accepted: 11/26/2023] [Indexed: 12/04/2023]
Abstract
Bacterioplankton play a vital role in maintaining the functions and services of lake ecosystems. Understanding the diversity and distribution patterns of bacterioplankton, particularly the presence of potential pathogenic bacterial communities, is crucial for safeguarding human health. In this study, we employed 16S rRNA gene amplicon sequencing to investigate the diversity and geographic patterns of bacterioplankton communities, as well as potential pathogens, in eight volcanic lakes located in the Arxan UNESCO Global Geopark (in the Greater Khingan Mountains of China). Our results revealed that the bacterial communities primarily comprised Bacteroidota (45.3%), Proteobacteria (33.1%), and Actinobacteria (9.0%) at the phylum level. At the genus level, prominent taxa included Flavobacterium (31.5%), Acinetobacter (11.0%), Chryseobacterium (7.9%), and CL500-29 marine group (5.6%). Among the bacterioplankton, we identified 34 pathogen genera (165 amplicon sequence variants [ASVs]), with Acinetobacter (59.8%), Rahnella (18.3%), Brevundimonas (9.6%), and Pseudomonas (5.8%) being the most dominant. Our findings demonstrated distinct biogeographic patterns in the bacterial communities at the local scale, driven by a combination of dispersal limitation and environmental factors influenced by human activities. Notably, approximately 15.3% of the bacterioplankton reads in the Arxan lakes were identified as potential pathogens, underscoring the potential risks to public health in these popular tourist destinations. This study provides the first comprehensive insight into the diversity of bacterioplankton in mountain lake ecosystems affected by high tourist activity, laying the groundwork for effective control measures against bacterial pathogens.
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Affiliation(s)
- Jianying Chao
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, 210042, China
| | - Jian Li
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, 210042, China
| | - Ming Kong
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, 210042, China
| | - Keqiang Shao
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Xiangming Tang
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China.
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3
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Zhang Y, Li Z, Peng Y, Guo Z, Wang H, Wei T, Shakir Y, Jiang G, Deng Y. Microbiome in a ground-based analog cabin of China Space Station during a 50-day human occupation. ISME COMMUNICATIONS 2024; 4:ycae013. [PMID: 38495633 PMCID: PMC10942772 DOI: 10.1093/ismeco/ycae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/18/2024] [Accepted: 01/18/2024] [Indexed: 03/19/2024]
Abstract
Dead-corner areas in space station that untouched by the clean-up campaign often experience microorganisms outbreaks, but the microbiome of these areas has never been studied. In this study, the microbiome in a ground-based analog ``Tianhe'' core module of China Space Station was first investigated during a 50-day three-crew occupation. Dead-corner areas were receiving attention by adopting a new sampling method. Results indicate that the astronauts occupation did not affect the dominant bacteria community, but affected a small proportion. Due to the frequent activity of astronauts in the work and sleep areas, the biomarkers in these two areas are common human skin surface and gut microorganisms, respectively. For areas that astronaut rarely visits, the biomarkers in which are common environmental microbial groups. Fluorescence counting showed that 70.12-84.78% of bacteria were alive, with a quantity of 104-105 cells/100 cm2. With the occupation time extension, the number of microorganisms increased. At the same sampling time, there was no significant bioburden difference in various locations. The cultivable bioburden ranged from 101 to 104 colony forming unit (CFU)/100 cm2, which are the following eight genera Penicillium, Microsphaeropsis, Stachybotrys, Humicola, Cladosporium, Bacillus, Planomicrobium, and Acinetobacter. Chryseomicrobium genus may be a key focus for future microbial prevention and control work.
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Affiliation(s)
- Ying Zhang
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Zhidong Li
- Office of International Business and Technology Application, Beijing Institute of Spacecraft System Engineering, Beijing 100094, China
| | - Yuan Peng
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Zimu Guo
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Hong Wang
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Tao Wei
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Yasmeen Shakir
- Department of Biochemistry, Hazara University, Mansehra 21120, Pakistan
| | - Guohua Jiang
- School of Medical Technology, Beijing Institute of Technology, Beijing 100081, China
| | - Yulin Deng
- School of Medical Technology, Beijing Institute of Technology, Beijing 100081, China
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Avetisov SE, Rodina ES, Kravchik MV, Kosova JV, Fettser EI, Novikov IA. [Study of the growth temperature of ocular surface microorganisms in norm and in infectious keratitis]. Vestn Oftalmol 2024; 140:34-42. [PMID: 38962977 DOI: 10.17116/oftalma202414003134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
Standard bacteriological examinations, which involve culturing microorganisms at 37 °C, are commonly used in clinical practice for diagnosing infectious diseases. However, the growth temperature of microorganisms on the ocular surface (OS) during infectious keratitis (IK) may not coincide with the laboratory standard, which is due to the characteristic features of heat exchange in the eye. PURPOSE This exploratory study examines the distribution and properties of OS microorganisms isolated under different temperature cultivation conditions in patients with IK and healthy volunteers without ophthalmic pathology. MATERIAL AND METHODS Fifteen participants were divided into two groups. Group 1 (n=10) consisted of patients with signs of unilateral infectious keratitis, while group 2 (n=5) served as the control group. A novel microbiological method was employed to isolate pure cultures of microorganisms. This method involved cultivating microorganisms at two temperature regimes (37 °C and 24 °C) and subsequently identifying them using biochemical, immunological, and physicochemical techniques, including mass spectrometry. Scanning electron microscopy (SEM) with lanthanide staining used as the reference method. The temperature status of the ocular surface was assessed using non-contact infrared thermography. RESULTS The study demonstrated the presence of psychrotolerant microorganisms on the ocular surface, which exhibited growth at a relatively low temperature of 24 °C. These psychrotolerant microorganisms were found to be isolated from the ocular surface displaying signs of temperature dysregulation. Among such microorganisms are Acinetobacter lwoffii, Achromobacter xylosoxidans, Bacillus licheniformis, Enterococcus faecalis, Klebsiella oxytoca, Klebsiella pneumoniae, Micrococcus luteus, Pseudomonas luteola, Streptococcus spp. CONCLUSION When identifying the causative agent of infectious keratitis, it is crucial to consider the divergence of growth temperature of ocular surface microorganisms. The presence of psychrotolerant microorganisms on the ocular surface, which can effectively grow at room temperature, should be taken into account, especially in cases of temperature dysregulation.
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Affiliation(s)
- S E Avetisov
- I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
- Krasnov Research Institute of Eye Diseases, Moscow, Russia
| | - E S Rodina
- I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - M V Kravchik
- Krasnov Research Institute of Eye Diseases, Moscow, Russia
| | - J V Kosova
- Krasnov Research Institute of Eye Diseases, Moscow, Russia
| | - E I Fettser
- I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
- Krasnov Research Institute of Eye Diseases, Moscow, Russia
| | - I A Novikov
- Krasnov Research Institute of Eye Diseases, Moscow, Russia
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Wan X, Li J, Ao M, McLaughlin RW, Fan F, Wang D, Zheng J. The intestinal microbiota of a Risso's dolphin (Grampus griseus): possible relationships with starvation raised by macro-plastic ingestion. Int Microbiol 2023; 26:1001-1007. [PMID: 37059916 PMCID: PMC10104690 DOI: 10.1007/s10123-023-00355-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 03/29/2023] [Accepted: 04/05/2023] [Indexed: 04/16/2023]
Abstract
Ingesting marine plastics is increasingly common in cetaceans, but little is known about their potential effects. Here, by utilizing 16S rRNA gene sequencing, we profiled the intestinal bacterial communities of a stranded Risso's dolphin (Grampus griseus) which died because of the ingestion of rubber gloves. In this study, we explored the potential relationships between starvation raised by plastic ingestion with the dolphin gut microbiota. Our results showed significant differences in bacterial diversity and composition among the different anatomical areas along the intestinal tract, which may be related to the intestinal emptying process under starvation. In addition, the intestinal bacterial composition of the Risso's dolphin showed both similarity and divergence to that of other toothed whales, suggesting potential roles of both host phylogeny and habitat shaping of the cetacean intestinal microbiome. Perhaps, the microbiota is reflecting a potentially disordered intestinal microbial profile caused by the ingestion of macro-plastics which led to starvation. Moreover, two operational taxonomic units (0.17% of the total reads) affiliated with Actinobacillus and Acinetobacter lwoffii were detected along the intestinal tract. These bacterial species may cause infections in immunocompromised dolphins which are malnourished. This preliminary study profiles the intestinal microbiota of a Risso's dolphin, and provides an additional understanding of the potential relationships between starvation raised by ingesting macro-plastics with cetacean gut microbiota.
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Affiliation(s)
- Xiaoling Wan
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Jia Li
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Mengxue Ao
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | | | - Fei Fan
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- National Aquatic Biological Resource Center, Wuhan, 430072, China
| | - Ding Wang
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- National Aquatic Biological Resource Center, Wuhan, 430072, China
| | - Jinsong Zheng
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
- National Aquatic Biological Resource Center, Wuhan, 430072, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Zhang S, Liu X, Zhao Y, Wang P, Yu R, Xu P, Jiang Y, Cheng L. Microbiome characteristics description of COVID-19 patients based on bulk RNA-seq and scRNA-Seq data. Comput Biol Med 2023; 165:107400. [PMID: 37651767 DOI: 10.1016/j.compbiomed.2023.107400] [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: 07/16/2023] [Revised: 08/04/2023] [Accepted: 08/26/2023] [Indexed: 09/02/2023]
Abstract
After infection with SARS-CoV-2, the microbiome inside the human body changes dramatically. By re-annotating microbial sequences in bulk RNA-seq and scRNA-seq data of COVID-19 patients, we described the cellular microbial landscape of COVID-19 patients and identified characteristic microorganisms in various tissues. We found that Acinetobacter lwoffii was highly correlated with COVID-19 symptoms and might disrupt some pathways of patients by interacting with the host and other microbes, such as Klebsiella pneumoniae. We further identified characteristic microorganisms specific to cell type, indicating the enrichment preference of some microbes. We also revealed the co-infection of SARS-CoV-2 with hMPV, which may cause the development of COVID-19. Overall, we demonstrated that the presence of intracellular microorganisms in COVID-19 patients and the synergies between microorganisms were strongly correlated with disease progression, providing a theoretical basis for COVID-19 treatment in a certain extent.
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Affiliation(s)
- Sainan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
| | - Xingwang Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
| | - Yue Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
| | - Ping Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
| | - Rui Yu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
| | - Peigang Xu
- Chongqing Research Institute of Harbin Institute of Technology, China.
| | - Yue Jiang
- Cipher Gene, Ltd., Beijing, 100080, China.
| | - Liang Cheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China; NHC Key Laboratory of Molecular Probes and Targeted Diagnosis and Therapy, Harbin Medical University, Harbin, 150028, Heilongjiang, China.
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7
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Yang J, Li L, Zhu X, He C, Li T, Qin J, Wang Y. Microbial Community Characterization and Molecular Resistance Monitoring in Geriatric Intensive Care Units in China Using mNGS. Infect Drug Resist 2023; 16:5121-5134. [PMID: 37576519 PMCID: PMC10422961 DOI: 10.2147/idr.s421702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 07/29/2023] [Indexed: 08/15/2023] Open
Abstract
Background Surface pathogens in the ICU pose a global public health threat, especially to elderly patients who are immunocompromised. To detect these pathogens, unbiased methods such as metagenomic next-generation sequencing (mNGS) are increasingly utilized for environmental microbiological surveillance. Methods In a six-month study from January to July 2022, we investigated microbial communities in Chinese geriatric ICUs by regularly monitoring multiple surfaces at three-month intervals. Using mNGS sequencing, we analyzed microorganisms present at eight specific locations within the ICU. Additionally, we compared pathogen profiles and drug resistance genes between patient cultures and environmental samples collected during the same period. Results The microbial composition remained relatively stable over time, but significant differences in alpha diversities were observed among various surfaces such as floors, hands, pumps, trolleys, and ventilator inlets/outlets. Surfaces with high contact frequency for healthcare workers, including workstations, ventilator panels, trolleys, pumps, and beds, harbored pathogenic microorganisms such as Acinetobacter baumannii, Cutibacterium acnes, Staphylococcus haemolyticus, Pseudomonas aeruginosa, and Enterococcus faecium. Acinetobacter baumannii, particularly the carbapenem-resistant strain (CRAB), was the most frequently identified pathogen in geriatric ICU patients regardless of testing method used. The mNGS approach enabled detection of viruses, fungi, and parasites that are challenging to culture. Additionally, an abundance of drug resistance genes was found in almost all environmental samples. Conclusion The microbial composition and abundance in the ICU remained relatively constant over time. The floor exhibited the highest microbial diversity and abundance in the ICU environment. Drug-resistant genes in the ICU environment may migrate between patients. Overall, mNGS is an emerging and powerful tool for microbiological monitoring of the hospital environment.
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Affiliation(s)
- Jilin Yang
- Department of Critical Care Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, People’s Republic of China
| | - Lingyi Li
- Department of Medical, Hangzhou Matridx Biotechnology Company, Hangzhou, People’s Republic of China
| | - Xiaolin Zhu
- Department of Critical Care Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, People’s Republic of China
| | - Chen He
- Department of Critical Care Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, People’s Republic of China
| | - Ting Li
- Department of Critical Care Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, People’s Republic of China
| | - Jiahong Qin
- Department of Critical Care Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, People’s Republic of China
| | - Yijie Wang
- Department of Critical Care Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, People’s Republic of China
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Kisková J, Juhás A, Galušková S, Maliničová L, Kolesárová M, Piknová M, Pristaš P. Antibiotic Resistance and Genetic Variability of Acinetobacter spp. from Wastewater Treatment Plant in Kokšov-Bakša (Košice, Slovakia). Microorganisms 2023; 11:microorganisms11040840. [PMID: 37110263 PMCID: PMC10143558 DOI: 10.3390/microorganisms11040840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/20/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
This study investigated the genetic variability and antibiotic resistance of Acinetobacter community depending on the stage of wastewater treatment in Kokšov-Bakša for the city of Košice (Slovakia). After cultivation, bacterial isolates were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), and their sensitivity to ampicillin, kanamycin, tetracycline, chloramphenicol and ciprofloxacin was examined. Acinetobacter spp. and Aeromonas spp. dominated bacterial populations in all wastewater samples. We identified 12 different groups based on protein profiling, 14 genotypes by amplified ribosomal DNA restriction analysis and 11 Acinetobacter species using 16S rDNA sequence analysis within Acinetobacter community, which showed significant variability in their spatial distribution. While Acinetobacter population structure changed during the wastewater treatment, the prevalence of antibiotic-resistant strains did not significantly vary depending on the stage of wastewater treatment. The study highlights the role of a highly genetically diverse Acinetobacter community surviving in wastewater treatment plants as an important environmental reservoir assisting in the further dissemination of antibiotic resistance in aquatic systems.
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Chen W, Sang S, Shao L, Li Y, Li T, Gan L, Liu L, Wang D, Zhou L. Biogeographic Patterns and Community Assembly Processes of Bacterioplankton and Potential Pathogens in Subtropical Estuaries in China. Microbiol Spectr 2023; 11:e0368322. [PMID: 36507672 PMCID: PMC9927264 DOI: 10.1128/spectrum.03683-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/23/2022] [Indexed: 12/14/2022] Open
Abstract
Microbial communities in coastal waters are diverse and dynamic and play important roles in ecosystem functions and services. Despite the ecological impact of bacterioplankton or pathogens, little is known about whether bacterioplankton and pathogen communities exhibit similar patterns. Here, using 16S RNA gene amplicon sequencing, the geographic patterns and assembly processes of bacterioplankton and pathogen communities in 30 subtropical estuaries were studied. Results showed that the estuarine bacterioplankton communities mainly consisted of Proteobacteria (49.06%), Actinobacteria (17.62%), and Bacteroidetes (16.33%), among which 31 pathogen genera (186 amplicon sequence variants [ASVs]) were identified. Under the influence of salinity, bacterioplankton and pathogens showed similar biogeographic patterns. Redundancy and correlation analyses indicated that the bacterioplankton communities were strongly correlated with estuarine environmental factors, but potential pathogens were less influenced. Co-occurrence network analysis revealed a close relationship between bacterioplankton and potential pathogens, with two pathogens identified as connectors (i.e., ASV340 [Clostridium perfringens] and ASV1624 [Brevundimonas diminuta]), implying potential impacts of pathogens on structure, function, and stability of estuarine bacterioplankton communities. Null-model analysis revealed that deterministic processes (heterogeneous selection) dominated bacterioplankton community assembly, while stochastic processes (undominated effect) shaped the potential pathogen community. Our findings illustrate the biogeographic patterns and community assembly mechanisms of bacterioplankton and pathogens in estuaries, which should provide guidance and a reference for the control of potential pathogenic bacteria. IMPORTANCE Bacterioplankton play an important role in estuarine ecosystem functions and services; however, potentially pathogenic bacteria may exhibit infectivity and pose a serious threat to environmental and human health. In this study, geographic patterns and assembly processes of bacterioplankton communities in 30 subtropical estuaries were explored, and potential pathogenic bacteria in the estuaries were detected and profiled. Our results demonstrate here that bacterioplankton and pathogens show similar biogeographic patterns under the influence of salinity. Interestingly, heterogeneous selection dominated bacterioplankton assembly, while stochasticity dominated pathogen assembly. This study provides important information for future risk assessment of potential pathogenic bacteria as well as management in estuarine ecosystems.
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Affiliation(s)
- Wenjian Chen
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Shilei Sang
- State Environmental Protection Key Laboratory of Environmental Pollution Health Risk Assessment, South China Institute of Environmental Sciences, MEE, Guangzhou, China
| | - Liyi Shao
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Yusen Li
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, Guangxi, China
| | - Tongzhou Li
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Lihong Gan
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Li Liu
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Dapeng Wang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, Guangxi, China
| | - Lei Zhou
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
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Assessment of Bacterial Diversity of Industrial Poultry Wastewater by Denaturing Gradient Gel Electrophoresis (DGGE) and the Cultivation Method in Order to Inform Its Reuse in Agriculture. BIOMED RESEARCH INTERNATIONAL 2022; 2022:6065305. [PMID: 36177057 PMCID: PMC9514947 DOI: 10.1155/2022/6065305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 08/07/2022] [Accepted: 08/24/2022] [Indexed: 11/30/2022]
Abstract
Effluents discharged by poultry meat industries are heavily polluted with raw materials, such as fat, blood residues, and proteins. Thus, untreated effluents directly discharged into the environment may constitute a public health threat. This study aims to evaluate the bacterial diversity of three water qualities: industrial poultry wastewater (PWW), tap water (TW), and PWW diluted with TW (50 : 50) (V/V) (TWPWW) by the combination of culture-independent and culture-dependent approaches. The total bacterial DNA was extracted using phenol/chloroform method. The hypervariable 16S rRNA region V3-V5 was amplified by PCR using universal primers. The amplicons were separated by vertical electrophoresis on a polyacrylamide gel of increasing denaturing gradient according to their richness in GC bases. Selected bands were reamplified and sequenced. Pure isolated bacteria from nutrient agar medium were characterized according to their morphological and biochemical characteristics. Genomic DNA from pure strains was extracted by boiling method, and a molecular amplification of the 16S–23S ITS region of the 16S rRNA gene was performed using the universal primers. Selected isolates were identified by sequencing. Results showed a high bacterial load and diversity in PWW in comparison with TW and TWPWW. A collection of 44 strains was obtained, and 25 of them were identified by sequencing. Proteobacteria represented 76% of isolated bacteria Gamma-Proteobacteria was the predominate isolate (68%). Other isolates were Firmicutes (8%), Bacteroidetes (12%), and Actinobacteria (8%). These isolates belong to different genera, namely, Pseudomonas, Acinetobacter, Proteus, Empedobacter, Corynebacterium, Enterobacter, Comamonas, Frondibacter, Leclercia, Staphylococcus, Atlantibacter, Klebsiella, and Microbacterium.
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Perrone MR, Romano S, De Maria G, Tundo P, Bruno AR, Tagliaferro L, Maffia M, Fragola M. Simultaneous monitoring of SARS-CoV-2 and bacterial profiles from the air of hospital environments with COVID-19-affected patients. AEROBIOLOGIA 2022; 38:391-412. [PMID: 36097443 PMCID: PMC9453715 DOI: 10.1007/s10453-022-09754-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
UNLABELLED The SARS-CoV-2 presence and the bacterial community profile in air samples collected at the Intensive Care Unit (ICU) of the Operational Unit of Infectious Diseases of Santa Caterina Novella Hospital in Galatina (Lecce, Italy) have been evaluated in this study. Air samplings were performed in different rooms of the ICU ward with and without COVID-19 patients. No sample was found positive to SARS-CoV-2, according to Allplex 2019-nCoV Assay. The airborne bacterial community profiles determined by the 16S rRNA gene metabarcoding approach up to the species level were characterized by richness and biodiversity indices, Spearman correlation coefficients, and Principal Coordinate Analysis. Pathogenic and non-pathogenic bacterial species, also detected in outdoor air samples, were found in all collected indoor samples. Staphylococcus pettenkoferi, Corynebacterium tuberculostearicum, and others coagulase-negative staphylococci, detected at high relative abundances in all the patients' rooms, were the most abundant pathogenic species. The highest mean relative abundance of S. pettenkoferi and C. tuberculostearicum suggested that they were likely the main pathogens of COVID-19 patients at the ICU ward of this study. The identification of nosocomial pathogens representing potential patients' risks in ICU COVID-19 rooms and the still controversial airborne transmission of the SARS-CoV-2 are the main contributions of this study. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10453-022-09754-7.
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Affiliation(s)
- Maria Rita Perrone
- Department of Mathematics and Physics, University of Salento, 73100 Lecce, Italy
| | - Salvatore Romano
- Department of Mathematics and Physics, University of Salento, 73100 Lecce, Italy
| | - Giuseppe De Maria
- Presidio Ospedaliero Santa Caterina Novella, Azienda Sanitaria Locale Lecce, 73013 Galatina, Lecce, Italy
| | - Paolo Tundo
- Presidio Ospedaliero Santa Caterina Novella, Azienda Sanitaria Locale Lecce, 73013 Galatina, Lecce, Italy
| | - Anna Rita Bruno
- Presidio Ospedaliero Santa Caterina Novella, Azienda Sanitaria Locale Lecce, 73013 Galatina, Lecce, Italy
| | - Luigi Tagliaferro
- Presidio Ospedaliero Santa Caterina Novella, Azienda Sanitaria Locale Lecce, 73013 Galatina, Lecce, Italy
| | - Michele Maffia
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy
| | - Mattia Fragola
- Department of Mathematics and Physics, University of Salento, 73100 Lecce, Italy
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12
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Perrone MR, Romano S, De Maria G, Tundo P, Bruno AR, Tagliaferro L, Maffia M, Fragola M. Compositional Data Analysis of 16S rRNA Gene Sequencing Results from Hospital Airborne Microbiome Samples. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:10107. [PMID: 36011742 PMCID: PMC9408509 DOI: 10.3390/ijerph191610107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/05/2022] [Accepted: 08/06/2022] [Indexed: 06/15/2023]
Abstract
The compositional analysis of 16S rRNA gene sequencing datasets is applied to characterize the bacterial structure of airborne samples collected in different locations of a hospital infection disease department hosting COVID-19 patients, as well as to investigate the relationships among bacterial taxa at the genus and species level. The exploration of the centered log-ratio transformed data by the principal component analysis via the singular value decomposition has shown that the collected samples segregated with an observable separation depending on the monitoring location. More specifically, two main sample clusters were identified with regards to bacterial genera (species), consisting of samples mostly collected in rooms with and without COVID-19 patients, respectively. Human pathogenic genera (species) associated with nosocomial infections were mostly found in samples from areas hosting patients, while non-pathogenic genera (species) mainly isolated from soil were detected in the other samples. Propionibacterium acnes, Staphylococcus pettenkoferi, Corynebacterium tuberculostearicum, and jeikeium were the main pathogenic species detected in COVID-19 patients' rooms. Samples from these locations were on average characterized by smaller richness/evenness and diversity than the other ones, both at the genus and species level. Finally, the ρ metrics revealed that pairwise positive associations occurred either between pathogenic or non-pathogenic taxa.
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Affiliation(s)
- Maria Rita Perrone
- Department of Mathematics and Physics, University of Salento, 73100 Lecce, Italy
| | - Salvatore Romano
- Department of Mathematics and Physics, University of Salento, 73100 Lecce, Italy
| | - Giuseppe De Maria
- Presidio Ospedaliero Santa Caterina Novella, Azienda Sanitaria Locale Lecce, 73013 Galatina, Italy
| | - Paolo Tundo
- Presidio Ospedaliero Santa Caterina Novella, Azienda Sanitaria Locale Lecce, 73013 Galatina, Italy
| | - Anna Rita Bruno
- Presidio Ospedaliero Santa Caterina Novella, Azienda Sanitaria Locale Lecce, 73013 Galatina, Italy
| | - Luigi Tagliaferro
- Presidio Ospedaliero Santa Caterina Novella, Azienda Sanitaria Locale Lecce, 73013 Galatina, Italy
| | - Michele Maffia
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy
| | - Mattia Fragola
- Department of Mathematics and Physics, University of Salento, 73100 Lecce, Italy
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13
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Jiang S, Sun B, Zhu R, Che C, Ma D, Wang R, Dai H. Airborne microbial community structure and potential pathogen identification across the PM size fractions and seasons in the urban atmosphere. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 831:154665. [PMID: 35314242 DOI: 10.1016/j.scitotenv.2022.154665] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/14/2022] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
As a vital component of airborne bioaerosols, bacteria and fungi seriously endanger human health as pathogens and allergens. However, comprehensive effects of environmental variables on airborne microbial community structures remain poorly understood across the PM sizes and seasons. We collected atmospheric PM1.0, PM2.5, and PM10 samples in Hefei, a typical rapidly-developing city in East China, across three seasons, and performed a comprehensive analysis of airborne microbial community structures using qPCR and high-throughput sequencing. Overall the bacterial and fungal abundances in PM1.0 were one to two orders of magnitude higher than those in PM2.5 and PM10 across seasons, but their α-diversity tended to increase from PM1.0 to PM10. The bacterial gene abundances showed a strong positive correlation (P < 0.05) with atmospheric SO2 and NO2 concentrations and air quality index. The bacterial gene abundances were significantly higher (P = 0.001) than fungi, and the bacterial diversity showed stronger seasonality. The PM sizes influenced distribution patterns for airborne microbial communities within the same season. Source-tracking analysis indicated that soils, plants, human and animal feces represented important sources of airborne bacteria with a total relative abundance of more than 60% in summer, but total abundance from the unidentified sources surpassed in fall and winter. Total 10 potential bacterial and 12 potential fungal pathogens were identified at the species level with the highest relative abundances in summer, and their abundances increased with the PM sizes. Together, our results indicated that a complex set of environmental factors, including water-soluble ions in PM, changes in air pollutant levels and meteorological conditions, and shifts in the relative importance of available microbial sources, acted to control the seasonal compositions of microbial communities in the urban atmosphere.
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Affiliation(s)
- Shaoyi Jiang
- Institute of Polar Environment & Anhui Key Laboratory of Polar Environment and Global Change, School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Bowen Sun
- Institute of Polar Environment & Anhui Key Laboratory of Polar Environment and Global Change, School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Renbin Zhu
- Institute of Polar Environment & Anhui Key Laboratory of Polar Environment and Global Change, School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China.
| | - Chenshuai Che
- Institute of Polar Environment & Anhui Key Laboratory of Polar Environment and Global Change, School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Dawei Ma
- State Grid Anhui Electric Power Research Institute, Hefei 230601, China
| | - Runfang Wang
- State Grid Anhui Electric Power Research Institute, Hefei 230601, China
| | - Haitao Dai
- Institute of Polar Environment & Anhui Key Laboratory of Polar Environment and Global Change, School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
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14
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Cui J, Hou S, Liu B, Yang M, Wei L, Du S, Li S. Species composition and overall diversity are significantly correlated between the tongue coating and gastric fluid microbiomes in gastritis patients. BMC Med Genomics 2022; 15:60. [PMID: 35300688 PMCID: PMC8932003 DOI: 10.1186/s12920-022-01209-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 03/01/2022] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND In traditional Chinese medicine, it is believed that the "tongue coating is produced by fumigation of stomach gas", and that tongue coating can reflect the health status of humans, especially stomach health. Therefore, studying the relationship between the microbiome of the tongue coating and the gastric fluid is of great significance for understanding the biological basis of tongue diagnosis. METHODS This paper detected the microbiomes of the tongue coating and the gastric fluid in 35 gastritis patients using metagenomic sequencing technology, systematically constructed the microbial atlas of tongue coating and gastric juice, and first described the similar characteristics between the two sites. RESULTS There was a significant correlation between tongue coating and gastric juice in terms of microbial species composition and overall diversity. In terms of species composition, it was found that the two sites were dominated by five phyla, namely, Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria and Proteobacteria, and that most of the gastric microbial species could be detected from the patient's own tongue coating. In terms of overall diversity, a significant correlation was found between the alpha diversity of the tongue coating microbiome and the gastric juice microbiome. Furthermore, in terms of abundance, 4 classes, 2 orders, 4 families, 18 genera and 46 species were found to significantly correlate between the tongue coating and the gastric fluid. CONCLUSIONS The results provide microbiome-based scientific evidence for tongue diagnosis, and offer a new perspective for understanding the biological basis of tongue diagnosis.
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Affiliation(s)
- Jiaxing Cui
- Institute of TCM-X, MOE Key Laboratory of Bioinformatics / Bioinformatics Division, BNRist / Department of Automation, Tsinghua University, Beijing, 100084, China.,China Industrial Control Systems Cyber Emergency Response Team, Beijing, 100040, China
| | - Siyu Hou
- Institute of TCM-X, MOE Key Laboratory of Bioinformatics / Bioinformatics Division, BNRist / Department of Automation, Tsinghua University, Beijing, 100084, China
| | - Bing Liu
- Beijing Lotus BioMedical Technology Co., Ltd., Beijing, 102206, China
| | - Mingran Yang
- Institute of TCM-X, MOE Key Laboratory of Bioinformatics / Bioinformatics Division, BNRist / Department of Automation, Tsinghua University, Beijing, 100084, China
| | - Lai Wei
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, 510060, China
| | - Shiyu Du
- China-Japan Friendship Hospital, Beijing, 100029, China.
| | - Shao Li
- Institute of TCM-X, MOE Key Laboratory of Bioinformatics / Bioinformatics Division, BNRist / Department of Automation, Tsinghua University, Beijing, 100084, China. .,School of Life Sciences and Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China.
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15
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Liang J, Zhou K, Li Q, Dong X, Zhang P, Liu H, Lin H, Zhang X, Lu J, Lin X, Li K, Xu T, Zhang H, Bao Q, Zhu M, Hu Y, Ren P. Identification and Characterization of a Novel Aminoglycoside 3''-Nucleotidyltransferase, ANT(3'')-IId, From Acinetobacter lwoffii. Front Microbiol 2021; 12:728216. [PMID: 34531844 PMCID: PMC8438517 DOI: 10.3389/fmicb.2021.728216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/06/2021] [Indexed: 11/19/2022] Open
Abstract
A novel plasmid-encoded aminoglycoside 3''-nucleotidyltransferase ANT(3")-IId, was discovered in Acinetobacter lwoffi strain H7 isolated from a chick on an animal farm in Wenzhou, China. The whole-genome of A. lwoffii H7 consisted of one chromosome and five plasmids (pH7-250, pH7-108, pH7-68, pH7-48, and pH7-11). ant(3")-IId was identified as being encoded on pH7-250, sharing the highest amino acid identity of 50.64% with a function-known resistance gene, ant(3")-IIb (KB849358.1). Susceptibility testing and enzyme kinetic parameter analysis were conducted to determine the function of the aminoglycoside 3"-nucleotidyltransferase. The ant(3")-IId gene conferred resistance to spectinomycin and streptomycin [the minimum inhibitory concentration (MIC) levels of both increased 16-fold compared with the control strain]. Consistent with the MIC data, kinetic analysis revealed a narrow substrate profile including spectinomycin and streptomycin, with Kcat/Km ratios of 4.99 and 4.45×103M−1 S−1, respectively. Sequencing analysis revealed that the ant(3")-IId gene was associated with insertion sequences (IS) element [ΔISAba14-ΔISAba14-hp-orf-orf-orf1-ant(3")-IId], and ant(3")-IId were identified in plasmids from various Acinetobacter species. This study of the novel aminoglycoside 3"-nucleotidyltranferase ANT(3")-IId helps us further understand the functional and sequence characteristics of aminoglycoside 3"-nucleotidyltranferases, highlights the risk of resistance gene transfer among Acinetobacter species and suggests that attention should be given to the emergence of new aminoglycoside 3"-nucleotidyltranferase genes.
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Affiliation(s)
- Jialei Liang
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Kexin Zhou
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Qiaoling Li
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xu Dong
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Peiyao Zhang
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Hongmao Liu
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Hailong Lin
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xueya Zhang
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Junwan Lu
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xi Lin
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Kewei Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Teng Xu
- Institute of Translational Medicine, Baotou Central Hospital, Baotou, China
| | - Hailin Zhang
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Qiyu Bao
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Mei Zhu
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou, China
| | - Yunliang Hu
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Ping Ren
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
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16
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Gomez-Ramirez U, Valencia-Mayoral P, Mendoza-Elizalde S, Murillo-Eliosa JR, Solórzano Santos F, Contreras-Rodríguez A, Zúñiga G, Aguilar-Rodea P, Jiménez-Rojas VL, Vigueras Galindo JC, Salazar-García M, Velázquez-Guadarrama N. Role of Helicobacter pylori and Other Environmental Factors in the Development of Gastric Dysbiosis. Pathogens 2021; 10:1203. [PMID: 34578235 PMCID: PMC8467233 DOI: 10.3390/pathogens10091203] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/26/2021] [Accepted: 09/08/2021] [Indexed: 11/17/2022] Open
Abstract
Microbiomes are defined as complex microbial communities, which are mainly composed of bacteria, fungi, and viruses residing in diverse regions of the human body. The human stomach consists of a unique and heterogeneous habitat of microbial communities owing to its anatomical and functional characteristics, that allow the optimal growth of characteristic bacteria in this environment. Gastric dysbiosis, which is defined as compositional and functional alterations of the gastric microbiota, can be induced by multiple environmental factors, such as age, diet, multiple antibiotic therapies, proton pump inhibitor abuse, H. pylori status, among others. Although H. pylori colonization has been reported across the world, chronic H. pylori infection may lead to serious consequences; therefore, the infection must be treated. Multiple antibiotic therapy improvements are not always successful because of the lack of adherence to the prescribed antibiotic treatment. However, the abuse of eradication treatments can generate gastric dysbiotic states. Dysbiosis of the gastric microenvironment induces microbial resilience, due to the loss of relevant commensal bacteria and simultaneous colonization by other pathobiont bacteria, which can generate metabolic and physiological changes or even initiate and develop other gastric disorders by non-H. pylori bacteria. This systematic review opens a discussion on the effects of multiple environmental factors on gastric microbial communities.
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Affiliation(s)
- Uriel Gomez-Ramirez
- Laboratorio de Investigación en Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Mexico City 06720, Mexico; (U.G.-R.); (S.M.-E.); (F.S.S.); (P.A.-R.); (V.L.J.-R.); (J.C.V.G.)
- Posgrado en Ciencias Quimicobiológicas, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Pedro Valencia-Mayoral
- Departamento de Patología Clínica y Experimental, Hospital Infantil de México Federico Gómez, Mexico City 06720, Mexico; (P.V.-M.); (J.R.M.-E.)
| | - Sandra Mendoza-Elizalde
- Laboratorio de Investigación en Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Mexico City 06720, Mexico; (U.G.-R.); (S.M.-E.); (F.S.S.); (P.A.-R.); (V.L.J.-R.); (J.C.V.G.)
| | - Juan Rafael Murillo-Eliosa
- Departamento de Patología Clínica y Experimental, Hospital Infantil de México Federico Gómez, Mexico City 06720, Mexico; (P.V.-M.); (J.R.M.-E.)
| | - Fortino Solórzano Santos
- Laboratorio de Investigación en Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Mexico City 06720, Mexico; (U.G.-R.); (S.M.-E.); (F.S.S.); (P.A.-R.); (V.L.J.-R.); (J.C.V.G.)
| | - Araceli Contreras-Rodríguez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico;
| | - Gerardo Zúñiga
- Laboratorio de Variación Biológica y Evolución, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico;
| | - Pamela Aguilar-Rodea
- Laboratorio de Investigación en Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Mexico City 06720, Mexico; (U.G.-R.); (S.M.-E.); (F.S.S.); (P.A.-R.); (V.L.J.-R.); (J.C.V.G.)
| | - Verónica Leticia Jiménez-Rojas
- Laboratorio de Investigación en Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Mexico City 06720, Mexico; (U.G.-R.); (S.M.-E.); (F.S.S.); (P.A.-R.); (V.L.J.-R.); (J.C.V.G.)
| | - Juan Carlos Vigueras Galindo
- Laboratorio de Investigación en Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Mexico City 06720, Mexico; (U.G.-R.); (S.M.-E.); (F.S.S.); (P.A.-R.); (V.L.J.-R.); (J.C.V.G.)
| | - Marcela Salazar-García
- Laboratorio de Investigación en Biología del Desarrollo y Teratogénesis Experimental, Hospital Infantil de México Federico Gómez, Mexico City 06720, Mexico;
| | - Norma Velázquez-Guadarrama
- Laboratorio de Investigación en Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Mexico City 06720, Mexico; (U.G.-R.); (S.M.-E.); (F.S.S.); (P.A.-R.); (V.L.J.-R.); (J.C.V.G.)
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17
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Xu N, Qiu C, Yang Q, Zhang Y, Wang M, Ye C, Guo M. Analysis of Phenol Biodegradation in Antibiotic and Heavy Metal Resistant Acinetobacter lwoffii NL1. Front Microbiol 2021; 12:725755. [PMID: 34566929 PMCID: PMC8461059 DOI: 10.3389/fmicb.2021.725755] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/23/2021] [Indexed: 11/30/2022] Open
Abstract
Phenol is a common environmental contaminant. The purpose of this study was to isolate phenol-degrading microorganisms from wastewater in the sections of the Chinese Medicine Manufactory. The phenol-degrading Acinetobacter lwoffii NL1 was identified based on a combination of biochemical characteristics and 16S rRNA genes. To analyze the molecular mechanism, the whole genome of A. lwoffii NL1 was sequenced, yielding 3499 genes on one circular chromosome and three plasmids. Enzyme activity analysis showed that A. lwoffii NL1 degraded phenol via the ortho-cleavage rather than the meta-cleavage pathway. Key genes encoding phenol hydroxylase and catechol 1,2-dioxygenase were located on a megaplasmid (pNL1) and were found to be separated by mobile genetic elements; their function was validated by heterologous expression in Escherichia coli and quantitative real-time PCR. A. lwoffii NL1 could degrade 0.5 g/L phenol within 12 h and tolerate a maximum of 1.1 g/L phenol, and showed resistance against multiple antibiotics and heavy metal ions. Overall, this study shows that A. lwoffii NL1 can be potentially used for efficient phenol degradation in heavy metal wastewater treatment.
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Affiliation(s)
- Nan Xu
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Chong Qiu
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Qiyuan Yang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Yunzeng Zhang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Mingqi Wang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Minliang Guo
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
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18
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Yu M, Wang X, Yan A. Microbial Profiles of Retail Pacific Oysters ( Crassostrea gigas) From Guangdong Province, China. Front Microbiol 2021; 12:689520. [PMID: 34305851 PMCID: PMC8292972 DOI: 10.3389/fmicb.2021.689520] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/31/2021] [Indexed: 12/26/2022] Open
Abstract
Oysters are one of the main aquatic products sold in coastal areas worldwide and are popular among consumers because of their delicious taste and nutritional value. However, the microorganisms present in oysters may pose health risks to consumers. In this study, the microbial communities of Pacific oysters (Crassostrea gigas) collected from aquatic product markets in three cities (Guangzhou, Zhuhai, and Jiangmen) of Guangdong Province, China, where raw oysters are popular, were investigated. The plate counts of viable bacteria in oysters collected in the three cities were all approximately 2 log colony-forming units/g. High-throughput sequencing analysis of the V3–V4 region of the 16Sribosomal DNA gene showed a high level of microbial diversity in oysters, as evidenced by both alpha and beta diversity analysis. Proteobacteria, Bacteroidetes, and Firmicutes were the dominant phyla of the microorganisms present in these samples. A variety of pathogenic bacteria, including the fatal foodborne pathogen Vibrio vulnificus, were found, and Vibrio was the dominant genus. Additionally, the relationship between other microbial species and pathogenic microorganisms may be mostly symbiotic in oysters. These data provide insights into the microbial communities of retail oysters in the Guangdong region and indicate a considerable risk related to the consumption of raw oysters.
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Affiliation(s)
- Mingjia Yu
- Department of Food Science, Foshan Polytechnic, Foshan, China
| | - Xiaobo Wang
- Department of Food Science, Foshan Polytechnic, Foshan, China
| | - Aixian Yan
- Department of Food Science, Foshan Polytechnic, Foshan, China
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19
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Durán C, Ciucci S, Palladini A, Ijaz UZ, Zippo AG, Sterbini FP, Masucci L, Cammarota G, Ianiro G, Spuul P, Schroeder M, Grill SW, Parsons BN, Pritchard DM, Posteraro B, Sanguinetti M, Gasbarrini G, Gasbarrini A, Cannistraci CV. Nonlinear machine learning pattern recognition and bacteria-metabolite multilayer network analysis of perturbed gastric microbiome. Nat Commun 2021; 12:1926. [PMID: 33771992 PMCID: PMC7997970 DOI: 10.1038/s41467-021-22135-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 02/24/2021] [Indexed: 12/11/2022] Open
Abstract
The stomach is inhabited by diverse microbial communities, co-existing in a dynamic balance. Long-term use of drugs such as proton pump inhibitors (PPIs), or bacterial infection such as Helicobacter pylori, cause significant microbial alterations. Yet, studies revealing how the commensal bacteria re-organize, due to these perturbations of the gastric environment, are in early phase and rely principally on linear techniques for multivariate analysis. Here we disclose the importance of complementing linear dimensionality reduction techniques with nonlinear ones to unveil hidden patterns that remain unseen by linear embedding. Then, we prove the advantages to complete multivariate pattern analysis with differential network analysis, to reveal mechanisms of bacterial network re-organizations which emerge from perturbations induced by a medical treatment (PPIs) or an infectious state (H. pylori). Finally, we show how to build bacteria-metabolite multilayer networks that can deepen our understanding of the metabolite pathways significantly associated to the perturbed microbial communities.
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Affiliation(s)
- Claudio Durán
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Center for Systems Biology Dresden (CSBD), Cluster of Excellence Physics of Life (PoL), Department of Physics, Technische Universität Dresden, Dresden, Germany
| | - Sara Ciucci
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Center for Systems Biology Dresden (CSBD), Cluster of Excellence Physics of Life (PoL), Department of Physics, Technische Universität Dresden, Dresden, Germany
| | - Alessandra Palladini
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Center for Systems Biology Dresden (CSBD), Cluster of Excellence Physics of Life (PoL), Department of Physics, Technische Universität Dresden, Dresden, Germany
- Paul Langerhans Institute Dresden, Helmholtz Zentrum Munchen, Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Umer Z Ijaz
- Department of Infrastructure and Environment University of Glasgow, School of Engineering, Glasgow, UK
| | - Antonio G Zippo
- Institute of Neuroscience, Consiglio Nazionale delle Ricerche, Milan, Italy
| | | | - Luca Masucci
- Institute of Microbiology, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Giovanni Cammarota
- Internal Medicine and Gastroenterology Unit, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Gianluca Ianiro
- Internal Medicine and Gastroenterology Unit, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Pirjo Spuul
- Department of Chemistry and Biotechnology, Division of Gene Technology, Tallinn University of Technology, Tallinn, 12618, Estonia
| | - Michael Schroeder
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Dresden, Germany
| | - Stephan W Grill
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Bryony N Parsons
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - D Mark Pritchard
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
- Department of Gastroenterology, Royal Liverpool and Broadgreen University Hospitals NHS Trust, Liverpool, UK
| | - Brunella Posteraro
- Institute of Microbiology, Università Cattolica del Sacro Cuore, Rome, Italy
| | | | - Giovanni Gasbarrini
- Internal Medicine and Gastroenterology Unit, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Antonio Gasbarrini
- Internal Medicine and Gastroenterology Unit, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Carlo Vittorio Cannistraci
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Center for Systems Biology Dresden (CSBD), Cluster of Excellence Physics of Life (PoL), Department of Physics, Technische Universität Dresden, Dresden, Germany.
- Center for Complex Network Intelligence (CCNI) at Tsinghua Laboratory of Brain and Intelligence (THBI), Department of Biomedical Engineering, Tsinghua University, Beijing, China.
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20
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Pulami D, Schauss T, Eisenberg T, Wilharm G, Blom J, Goesmann A, Kämpfer P, Glaeser SP. Acinetobacter baumannii in manure and anaerobic digestates of German biogas plants. FEMS Microbiol Ecol 2021; 96:5896450. [PMID: 32832994 DOI: 10.1093/femsec/fiaa176] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 08/20/2020] [Indexed: 12/19/2022] Open
Abstract
Studies considering environmental multidrug-resistant Acinetobacter spp. are scarce. The application of manure on agricultural fields is one source of multidrug-resistant bacteria from livestock into the environment. Here, Acinetobacter spp. were quantified by quantitative polymerase chain reaction in manure applied to biogas plants and in the output of the anaerobic digestion, and Acinetobacter spp. isolated from those samples were comprehensively characterized. The concentration of Acinetobacter 16S ribosomal ribonucleic acid (rRNA) gene copies per g fresh weight was in range of 106-108 in manure and decreased (partially significantly) to a still high concentration (105-106) in digestates. 16S rRNA, gyrB-rpoB and blaOXA51-like gene sequencing identified 17 different Acinetobacter spp., including six A. baumannii strains. Multilocus sequence typing showed no close relation of the six strains with globally relevant clonal complexes; however, they represented five novel sequence types. Comparative genomics and physiological tests gave an explanation how Acinetobacter could survive the anaerobic biogas process and indicated copper resistance and the presence of intrinsic beta-lactamases, efflux-pump and virulence genes. However, the A. baumannii strains lacked acquired resistance against carbapenems, colistin and quinolones. This study provided a detailed characterization of Acinetobacter spp. including A. baumannii released via manure through mesophilic or thermophilic biogas plants into the environment.
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Affiliation(s)
- Dipen Pulami
- Institute of Applied Microbiology, Justus Liebig University Giessen, D-35392 Giessen, Germany
| | - Thorsten Schauss
- Institute of Applied Microbiology, Justus Liebig University Giessen, D-35392 Giessen, Germany
| | - Tobias Eisenberg
- Department of Veterinary Medicine, Hessian State Laboratory (LHL), D-35392 Giessen, Germany; Institute of Hygiene and Infectious Diseases of Animals, Justus-Liebig-University Giessen, D-35392, Giessen, Germany
| | - Gottfried Wilharm
- Project Group P2, Robert Koch Institute, Wernigerode Branch, D-38855 Wernigerode, Germany
| | - Jochen Blom
- Institute for Bioinformatics and Systems Biology, D-35392 Giessen, Germany
| | - Alexander Goesmann
- Institute for Bioinformatics and Systems Biology, D-35392 Giessen, Germany
| | - Peter Kämpfer
- Institute of Applied Microbiology, Justus Liebig University Giessen, D-35392 Giessen, Germany
| | - Stefanie P Glaeser
- Institute of Applied Microbiology, Justus Liebig University Giessen, D-35392 Giessen, Germany
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21
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Rybitwa D, Wawrzyk A, Rahnama M. Application of a Medical Diode Laser (810 nm) for Disinfecting Small Microbiologically Contaminated Spots on Degraded Collagenous Materials for Improved Biosafety in Objects of Exceptional Historical Value From the Auschwitz-Birkenau State Museum and Protection of Human Health. Front Microbiol 2020; 11:596852. [PMID: 33391215 PMCID: PMC7775414 DOI: 10.3389/fmicb.2020.596852] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 11/27/2020] [Indexed: 11/20/2022] Open
Abstract
The research aim was to optimize the operating parameters of a diode laser irradiation for the effective disinfection of degraded collagenous materials. Historical leather shoes stored at the Auschwitz-Birkenau State Museum in Oświęcim (Poland) were the main study objects. Surfaces of contaminated small spots occurring on the degraded materials were sampled with moistened swabs and microbiologically examined using the molecular techniques MALDI-TOF MS, 16S rRNA, and NGS sequencing. The surfaces were colonized by bacteria with 106 CFU/100 cm2 and 104 CFU/100 cm2 by fungi, on average. Microorganisms of the genera Bacillus and Penicillium were predominant. The effectiveness of the laser treatment was assessed for the new and degraded collagenous materials against isolated environmental strains using four variants of exposure time and number of repetitions. 0.3 W/CW 2 × 2 min variant was the most effective and also did not noticeably change the color of the treated samples. The variant caused a reduction in the numbers of microorganisms by 96–100%. After 1 month, four types of leather were subjected to comprehensive physico-chemical analyses. SEM and FTIR techniques confirmed that laser irradiation in the selected optimal variant did not affect the surface morphology and collagen structure, while XPS technique enabled detection of subtle changes in non-historical protective coatings on the surfaces of tested degraded historical materials.
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Affiliation(s)
- Dorota Rybitwa
- Preservation Department, Auschwitz-Birkenau State Museum, Oświęcim, Poland
| | - Anna Wawrzyk
- Preservation Department, Auschwitz-Birkenau State Museum, Oświęcim, Poland.,Sanitary-Epidemiological Station, Kraków, Poland
| | - Mansur Rahnama
- The Chair and Department of Oral Surgery, Medical University of Lublin, Lublin, Poland
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22
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Carvalheira A, Silva J, Teixeira P. Acinetobacter spp. in food and drinking water - A review. Food Microbiol 2020; 95:103675. [PMID: 33397609 DOI: 10.1016/j.fm.2020.103675] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 01/01/2023]
Abstract
Acinetobacter spp. has emerged as a pathogen of major public health concern due to their increased resistance to antibiotics and their association with a wide range of nosocomial infections, community-acquired infections and war and natural disaster-related infections. It is recognized as a ubiquitous organism however, information about the prevalence of different pathogenic species of this genus in food sources and drinking water is scarce. Since the implementation of molecular techniques, the role of foods as a source of several species, including the Acinetobacter baumannii group, has been elucidated. Multidrug resistance was also detected among Acinetobacter spp. isolated from food products. This highlights the importance of foods as potential sources of dissemination of Acinetobacter spp. between the community and clinical environments and reinforces the need for further investigations on the potential health risks of Acinetobacter spp. as foodborne pathogens. The aim of this review was to summarize the published data on the occurrence of Acinetobacter spp. in different food sources and drinking water. This information should be taken into consideration by those responsible for infection control in hospitals and other healthcare facilities.
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Affiliation(s)
- Ana Carvalheira
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal
| | - Joana Silva
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal
| | - Paula Teixeira
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal.
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23
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Chen YC, Miao ZF, Yip KL, Cheng YA, Liu CJ, Li LH, Lin CY, Wang JW, Wu DC, Cheng TL, Wang JY. Gut Fecal Microbiota Transplant in a Mouse Model of Orthotopic Rectal Cancer. Front Oncol 2020; 10:568012. [PMID: 33194651 PMCID: PMC7658813 DOI: 10.3389/fonc.2020.568012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/06/2020] [Indexed: 12/12/2022] Open
Abstract
The gut microbiota is reported to play an important role in carcinogenesis and the treatment of CRC. SW480 and SW620 colon cancer cells integrated with infrared fluorescent proteins were injected into the rectal submucosa of nude mice. In the subsequent 30 days, we observed tumor growth weekly using an in vivo imaging system. The bacterial solution was infused anally into the mice to perform bacterial transplant. Phosphate-buffered saline, Acinetobacter lwoffii, and Bifidobacterium longum solutions were infused individually. The 16S ribosomal DNA (rDNA) and polymerase chain reaction of murine feces were investigated to confirm the colonization of target bacteria. In the SW620 orthotopic xenograft rectal cancer model, 4 of 5 mice developed rectal cancer by 30 days after submucosal injection. In the SW480 orthotopic xenograft rectal cancer model, 2 of 6 mice developed rectal cancer by 30 days after submucosal injection. For the 16S rDNA analysis, the mice receiving the bacterial solution infusion demonstrated positive findings for A. lwoffii and B. longum. With the successful establishment of a mouse model of orthotopic rectal cancer and transplant of target bacteria, we can further explore the relationship between gut microbiota and CRC. The role of fecal microbiota transplant in the treatment and alleviation of adverse events of chemotherapy in CRC could be clarified in subsequent studies.
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Affiliation(s)
- Yen-Cheng Chen
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Zhi-Feng Miao
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Kwan-Ling Yip
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yi-An Cheng
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan.,Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chung-Jung Liu
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Ling-Hui Li
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Chung-Yen Lin
- Institute of Information Science, Academia Sinica, Taipei, Taiwan
| | - Jiunn-Wei Wang
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,Department of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Deng-Chyang Wu
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,Department of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Tian-Lu Cheng
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan.,Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan.,College of Medicine, Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Jaw-Yuan Wang
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.,College of Medicine, Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Surgery, Faculty of Medicine, College of Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.,Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Center for Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan.,Center for Liquid Biopsy and Cohort Research, Kaohsiung Medical University, Kaohsiung, Taiwan
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24
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Wilson G, Jackson V, Boyken L, Puig-Asensio M, Marra AR, Perencevich E, Schweizer ML, Diekema D, Breheny P, Petersen C. A randomized control trial evaluating efficacy of antimicrobial impregnated hospital privacy curtains in an intensive care setting. Am J Infect Control 2020; 48:862-868. [PMID: 32139090 DOI: 10.1016/j.ajic.2019.12.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 12/27/2019] [Accepted: 12/27/2019] [Indexed: 01/05/2023]
Abstract
BACKGROUND Acquisition of pathogens into health care settings from prior room occupants has been documented. Hospital room privacy curtains are at high risk for pathogenic bacterial contamination. Antimicrobial impregnated curtains could be effective in reducing contamination. METHODS Rooms within an intensive care unit at The University of Iowa Hospitals and Clinics were randomized to 3 arms. The 2 intervention arms: (1) halamine antimicrobial curtains (BioSmart curtain [BSC]) and (2) halamine antimicrobial curtains sprayed twice weekly with a sodium hypochlorite-based disinfecting spray (BSC-pre and BSC-post) and a third control arm (standard curtain [SC]). Samples were collected twice weekly for 3 weeks to assess pathogenic bacterial contamination. RESULTS The likelihood of remaining uncontaminated was 38% for SC, 37% for BSC, and 60% for the BSC-pre group. Time to event (contamination) analysis found no statistically significant difference between pathogenic contamination between the SC, BSC, and BSC-pre groups (P value = .1921). There was a decrease in average colony count for BSC curtains compared with control, however, this difference was not statistically significant. Hypochlorite spray was found to transiently decontaminate curtains, but effects dissipated after 72 hours. CONCLUSIONS BSC did not show a significant reduction in pathogenic contamination compared with control. Antimicrobial curtains could have a role in reducing environmental contamination in the health care setting. Future studies should be done to determine the long-term effects of using antimicrobial curtains in health care.
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25
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Chen XY, Fan HN, Zhang HK, Qin HW, Shen L, Yu XT, Zhang J, Zhu JS. Rewiring of Microbiota Networks in Erosive Inflammation of the Stomach and Small Bowel. Front Bioeng Biotechnol 2020; 8:299. [PMID: 32478040 PMCID: PMC7237573 DOI: 10.3389/fbioe.2020.00299] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/20/2020] [Indexed: 12/12/2022] Open
Abstract
The development of non-invasive, inexpensive, and effective early diagnosis tests for gastric and small-bowel lesions is an urgent requirement. The introduction of magnetically guided capsule endoscopy (MGCE) has aided examination of the small bowel for diagnoses. However, the distribution of the fecal microbiome in abnormal erosions of the stomach and small bowel remains unclear. Herein, alternations in the fecal microbiome in three groups [normal, small-bowel inflammation, and chronic gastritis (CG)] were analyzed by metagenomics and our well-developed method [individual-specific edge-network analysis (iENA)]. In addition to the dominant microbiota identified by the conventional differential analysis, iENA could recognize novel network biomarkers of microbiome communities, such as the genus Bacteroide in CG and small-bowel inflammation. Combined with differential network analysis, the network-hub microbiota within rewired microbiota networks revealed high-ranked iENA microbiota markers, which were disease specific and had particular pathogenic functions. Our findings illuminate the components of the fecal microbiome and the importance of specific bacteria in CG and small-bowel erosions, and could be employed to develop preventive and non-invasive therapeutic strategies.
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Affiliation(s)
- Xiao-Yu Chen
- Department of Gastroenterology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Hui-Ning Fan
- Department of Gastroenterology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Huang-Kai Zhang
- Aginome-XMU Joint Laboratory, Xiamen University, Xiamen, China
| | - Huang-Wen Qin
- Department of Gastroenterology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Li Shen
- Clinical Research Center, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Xiang-Tian Yu
- Clinical Research Center, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Jing Zhang
- Department of Gastroenterology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Jin-Shui Zhu
- Department of Gastroenterology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
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26
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Palmisano S, Campisciano G, Iacuzzo C, Bonadio L, Zucca A, Cosola D, Comar M, de Manzini N. Role of preoperative gut microbiota on colorectal anastomotic leakage: preliminary results. Updates Surg 2020; 72:1013-1022. [PMID: 32062786 DOI: 10.1007/s13304-020-00720-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 02/04/2020] [Indexed: 12/25/2022]
Abstract
BACKGROUND The dysbiosis is defined as a disturbed symbiotic relationship between microbiota and the host and can cause a pro-inflammatory imbalance impairing the healing process at anastomotic level. The aim of this study is to detect, in fecal samples collected in the preoperative time, a peculiar microbiota composition that could predict the onset of colorectal anastomotic leakage. MATERIALS AND METHODS We compared gut microbiota of healthy patients (Group A) and patients with colorectal cancer eligible for surgery (Group B). Group B was divided into patients who developed anastomotic leak (Group BL) and patients who had uneventful recovery (Group BNL). Stool samples were collected before surgery and after neoadjuvant treatment. RESULTS We analyzed stool samples from 48 patients, 27 belonging to Group A and 21 to Group B. In Group B, five patients developed anastomotic leakage (Group BL). Compared to healthy subjects, Group B showed a moderate increase of Bacteroidetes and Proteobacteria, a moderate reduction of Firmicutes and Actinobacteria, and a statistically significant reduction of Faecalibacterium prausnitzii. Group BL patients showed an array of bacterial species which promoted dysbiosis, such as Acinetobacter lwoffii and Hafnia alvei. Group BNL patients showed that bacterial species like Faecalibacterium prausnitzii and Barnesiella intestinihominis have a protective function. CONCLUSIONS The bacterial flora in subjects with colorectal cancer is statistically different compared to healthy patients. The presence of preoperative aggressive bacteria and the lack of protective strains has strengthened the hypothesis that a peculiar microbiota composition could represent a risk factor for the occurrence of anastomotic leakage.
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Affiliation(s)
- Silvia Palmisano
- Department of Medical, Surgical and Health Sciences, University of Trieste, Piazzale Europa 1, 34127, Trieste, Italy.
- Surgical Clinic Unit, Cattinara Hospital, ASUITS, Strada di Fiume 447, 34149, Trieste, Italy.
| | - Giuseppina Campisciano
- Institute for Maternal and Child Health IRCCS, Burlo Garofolo, Via dell' Istria 65/1, 34149, Trieste, Italy
| | - Cristiana Iacuzzo
- Department of Medical, Surgical and Health Sciences, University of Trieste, Piazzale Europa 1, 34127, Trieste, Italy
| | - Laura Bonadio
- Department of Medical, Surgical and Health Sciences, University of Trieste, Piazzale Europa 1, 34127, Trieste, Italy
| | - Annalisa Zucca
- Department of Medical, Surgical and Health Sciences, University of Trieste, Piazzale Europa 1, 34127, Trieste, Italy
| | - Davide Cosola
- Surgical Clinic Unit, Cattinara Hospital, ASUITS, Strada di Fiume 447, 34149, Trieste, Italy
| | - Manola Comar
- Department of Medical, Surgical and Health Sciences, University of Trieste, Piazzale Europa 1, 34127, Trieste, Italy
- Institute for Maternal and Child Health IRCCS, Burlo Garofolo, Via dell' Istria 65/1, 34149, Trieste, Italy
| | - Nicolò de Manzini
- Department of Medical, Surgical and Health Sciences, University of Trieste, Piazzale Europa 1, 34127, Trieste, Italy
- Surgical Clinic Unit, Cattinara Hospital, ASUITS, Strada di Fiume 447, 34149, Trieste, Italy
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27
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Yang Y, Hou Y, Ma M, Zhan A. Potential pathogen communities in highly polluted river ecosystems: Geographical distribution and environmental influence. AMBIO 2020; 49:197-207. [PMID: 31020611 PMCID: PMC6888796 DOI: 10.1007/s13280-019-01184-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 03/13/2019] [Accepted: 04/03/2019] [Indexed: 05/03/2023]
Abstract
Risks of pathogenic bacteria to the health of both human beings and water ecosystems have been widely acknowledged. However, traditional risk assessment methods based on fecal indicator bacteria and/or pure culture are not comprehensive at the community level, mainly owing to the limited taxonomic coverage. Here, we combined the technique of high-throughput sequencing and the concept of metacommunity to assess the potential pathogenic bacterial communities in an economically and ecologically crucial but highly polluted river-the North Canal River (NCR) in Haihe River Basin located in North China. NCR presented a significant environmental gradient, with the highest, moderate, and lowest levels of pollution in the up-, middle, and downstream. After multiple analyses, we successfully identified 48 genera, covering nine categories of potential pathogens (mainly human pathogens). The most abundant genus was Acinetobacter, which was rarely identified as a pathogen bacterium in previous studies of NCR. At the community level, we observed significant geographical variation of community composition and structure. Such a high level of geographical variation was mainly derived from differed abundance of species among sections along the river, especially the top seven Operational Taxonomic Units (OTUs). For example, relative abundance of OTU1 (Gammaproteobacteria/Acinetobacter) increased significantly from upstream towards downstream. Regarding the underlying mechanisms driving community geographical variation, environmental filtering was identified as the dominant ecological process and total nitrogen as the most influential environmental variable. Altogether, this study provided a comprehensive profile of potential pathogenic bacteria in NCR and revealed the underlying mechanisms of community succession. Owing to their high abundance and wide geographical distribution, we suggest that potential pathogens identified in this study should be incorporated into future monitoring and management programs in NCR. By revealing the correlation between environmental factors and community composition, the results obtained in this study have significant implications for early warning and risk assessment of potential pathogen bacteria, as well as management practices in highly polluted river ecosystems.
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Affiliation(s)
- Yuzhan Yang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085 China
| | - Yang Hou
- Beijing Dongcheng District Food and Drug Safety Monitoring Center, 12-14 Zhushikou Street East, Beijing, 100050 China
| | - Min Ma
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085 China
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085 China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing, 100049 China
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28
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Leaf-associated microbiota on perilla (Perilla frutescens var. frutescens) cultivated in South Korea to detect the potential risk of food poisoning. Food Res Int 2019; 126:108664. [DOI: 10.1016/j.foodres.2019.108664] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 08/28/2019] [Accepted: 09/09/2019] [Indexed: 12/13/2022]
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29
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Gallini SH, Cole SD, DiGeronimo PM. In vitro inhibition of shell flora by a commercial probiotic marketed for use in captive hermit crabs (Coenobita spp.). J Exot Pet Med 2019. [DOI: 10.1053/j.jepm.2019.07.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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30
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Abstract
Nickel is an essential cofactor for some pathogen virulence factors. Due to its low availability in hosts, pathogens must efficiently transport the metal and then balance its ready intracellular availability for enzyme maturation with metal toxicity concerns. The most notable virulence-associated components are the Ni-enzymes hydrogenase and urease. Both enzymes, along with their associated nickel transporters, storage reservoirs, and maturation enzymes have been best-studied in the gastric pathogen Helicobacter pylori, a bacterium which depends heavily on nickel. Molecular hydrogen utilization is associated with efficient host colonization by the Helicobacters, which include both gastric and liver pathogens. Translocation of a H. pylori carcinogenic toxin into host epithelial cells is powered by H2 use. The multiple [NiFe] hydrogenases of Salmonella enterica Typhimurium are important in host colonization, while ureases play important roles in both prokaryotic (Proteus mirabilis and Staphylococcus spp.) and eukaryotic (Cryptoccoccus genus) pathogens associated with urinary tract infections. Other Ni-requiring enzymes, such as Ni-acireductone dioxygenase (ARD), Ni-superoxide dismutase (SOD), and Ni-glyoxalase I (GloI) play important metabolic or detoxifying roles in other pathogens. Nickel-requiring enzymes are likely important for virulence of at least 40 prokaryotic and nine eukaryotic pathogenic species, as described herein. The potential for pathogenic roles of many new Ni-binding components exists, based on recent experimental data and on the key roles that Ni enzymes play in a diverse array of pathogens.
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Alharbi JS, Alawadhi Q, Leather SR. Monomorium ant is a carrier for pathogenic and potentially pathogenic bacteria. BMC Res Notes 2019; 12:230. [PMID: 30992046 PMCID: PMC6469133 DOI: 10.1186/s13104-019-4266-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 04/11/2019] [Indexed: 11/26/2022] Open
Abstract
Objectives Household ants are regarded as a major household pest and their close association with microorganisms and people means that they may constitute a disease risk. Our study is the first to provide information on the pathogenicity of Monomorium spp. a common insect in Kuwait by quantifying and identifying the exoskeleton bacterial burden. Samples of Monomorium were collected in June from indoor and outdoor sites of 30 houses located in two residential districts. Results The study identified a total of 16 different species of Gram-negative bacteria of which the indoor isolates were 75% greater in species count than the outdoor samples. Indoor isolates identified from both districts were more frequent than the outdoors and similar trends were obtained for a single district. Outdoor ant samples on the other hand carried a high percentage of bacteria but with less diversity in both districts. There was a significant variability in bacterial species in relation to sample sources, indoor and outdoor, and discrete geographical location. The presence of a high percentage of pathogenic and potentially pathogenic bacteria indoor poses a great threat to domestic households, which would be further exacerbated in places with poor standards of hygiene.
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Affiliation(s)
- Jenan S Alharbi
- Science Department, College of Basic Education, Public Authority for Applied Education and Training (PAAET) , Alardyia, PO Box: 23167, Safat, Kuwait.
| | - Qaderya Alawadhi
- Science Department, College of Basic Education, Public Authority for Applied Education and Training (PAAET) , Alardyia, PO Box: 23167, Safat, Kuwait
| | - Simon R Leather
- Crop & Environment Sciences, Harper Adams University, Edgmond, Newport, TF10 8NB, UK
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Cao S, Geng Y, Yu Z, Deng L, Gan W, Wang K, Ou Y, Chen D, Huang X, Zuo Z, He M, Lai W. Acinetobacter lwoffii, an emerging pathogen for fish in Schizothorax genus in China. Transbound Emerg Dis 2018; 65:1816-1822. [PMID: 30239149 DOI: 10.1111/tbed.12957] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 06/14/2018] [Accepted: 06/18/2018] [Indexed: 11/27/2022]
Abstract
Acinetobacter lwoffii, a serious human pathogen, has been identified as a cause of nosocomial infections such as bacteremia, pneumonia and meningitis. There are only a few studies reporting A. lwoffii as a pathogen of fish. During 2016 and 2017, six bacterial strains, isolated from diseased fish of the Schizothorax genus, were identified as A. lwoffii by morphology, biochemical tests, 16S rDNA and gyrB gene sequencing analysis. One of these isolates was selected for experimental infection of Sclizothorax prenanti, Schizothorax davidi and Schizothorax wangchiachii, to confirm its pathogenicity. Experimentally infected fish showed similar symptoms to those observed in fish after natural outbreaks. Susceptibility of the isolates to 14 antibiotics was tested using a disc diffusion method; all isolates were resistant to cephalothin, aminoglycosides and β-lactams, and sensitive only to some fluoroquinolones and tetracyclines. Histological examination revealed that A. lwoffii infection could cause pathological lesions in multiple organs and tissues, especially in liver, kidney, spleen and heart. These lesions included extensive haemorrhage, vacuolar degeneration, necrosis and inflammatory cell infiltration. To our knowledge, this is the first report on A. lwoffii as a virulent pathogen for fish of the Schizothorax genus.
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Affiliation(s)
- Shiqi Cao
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Sichuan, China
| | - Yi Geng
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Sichuan, China
| | - Zehui Yu
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Sichuan, China
| | - Longjun Deng
- Yalong River Hydropower Development Company Ltd., Chengdu, Sichuan, China
| | - Weixiong Gan
- Yalong River Hydropower Development Company Ltd., Chengdu, Sichuan, China
| | - Kaiyu Wang
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Sichuan, China
| | - Yangping Ou
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Sichuan, China
| | - Defang Chen
- Department of Aquaculture, Sichuan Agricultural University, Wenjiang, Sichuan, China
| | - Xiaoli Huang
- Department of Aquaculture, Sichuan Agricultural University, Wenjiang, Sichuan, China
| | - Zhicai Zuo
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Sichuan, China
| | - Min He
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Sichuan, China
| | - Weiming Lai
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Sichuan, China
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Han Y, Wang Y, Li L, Xu G, Liu J, Yang K. Bacterial population and chemicals in bioaerosols from indoor environment: Sludge dewatering houses in nine municipal wastewater treatment plants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 618:469-478. [PMID: 29136598 DOI: 10.1016/j.scitotenv.2017.11.071] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 11/06/2017] [Accepted: 11/07/2017] [Indexed: 05/04/2023]
Abstract
Municipal wastewater treatment plants (MWTPs) are regarded as sources of airborne microorganisms. Sludge dewatering house (SDH) is one of the most serious indoor bioaerosol pollution treatment sectors in MWTPs. In this study, properties of bioaerosols from SDHs of nine MWTPs were investigated in China. Results suggested that bioaerosols were generated mainly from the mixed liquor and will be promoted by the mechanical motion of belts of dewatering devices. They will accumulate in the SDHs due to the treatment devices placed inside. Levels of airborne bacteria and chemicals showed regional variations. In Hefei and Yixing, the emissions of total suspended particles (TSP) and airborne bacteria were higher than those in Beijing and Guangzhou. Results of bacterial population showed that bacterial species in bioaerosols from SDHs also presented significant regional disparity; these regional disparities were closely related with the source of bioaerosols in SDHs. Among these identified bacterial species, some common potential pathogens were detected in all SDHs, such as Aeromonas caviae, Flavobacterium sp., and Staphylococcus lentus. Relative humidity (RH) and temperature were the major parameters on bioaerosols to survive. As shown in this study, SDHs in wastewater treatment plants should be provided considerable attention for being an emission source of indoor bioaerosols.
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Affiliation(s)
- Yunping Han
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; National Engineering Laboratory for VOCs Pollution Control Material & Technology, University of Chinese Academy of Sciences, Beijing 101408, China.
| | - Yanjie Wang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; National Engineering Laboratory for VOCs Pollution Control Material & Technology, University of Chinese Academy of Sciences, Beijing 101408, China.
| | - Lin Li
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; National Engineering Laboratory for VOCs Pollution Control Material & Technology, University of Chinese Academy of Sciences, Beijing 101408, China.
| | - Guangsu Xu
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; National Engineering Laboratory for VOCs Pollution Control Material & Technology, University of Chinese Academy of Sciences, Beijing 101408, China.
| | - Junxin Liu
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Kaixiong Yang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; National Engineering Laboratory for VOCs Pollution Control Material & Technology, University of Chinese Academy of Sciences, Beijing 101408, China.
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KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples. mSystems 2018; 3:mSystems00218-17. [PMID: 29577086 PMCID: PMC5864415 DOI: 10.1128/msystems.00218-17] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 02/06/2018] [Indexed: 01/15/2023] Open
Abstract
Various indoor, outdoor, and host-associated environments contain small quantities of microbial biomass and represent a niche that is often understudied because of technical constraints. Many studies that attempt to evaluate these low-biomass microbiome samples are riddled with erroneous results that are typically false positive signals obtained during the sampling process. We have investigated various low-biomass kits and methods to determine the limit of detection of these pipelines. Here we present KatharoSeq, a high-throughput protocol combining laboratory and bioinformatic methods that can differentiate a true positive signal in samples with as few as 50 to 500 cells. We demonstrate the application of this method in three unique low-biomass environments, including a SAF, a hospital NICU, and an abalone-rearing facility. Microbiome analyses of low-biomass samples are challenging because of contamination and inefficiencies, leading many investigators to employ low-throughput methods with minimal controls. We developed a new automated protocol, KatharoSeq (from the Greek katharos [clean]), that outperforms single-tube extractions while processing at least five times as fast. KatharoSeq incorporates positive and negative controls to reveal the whole bacterial community from inputs of as few as 50 cells and correctly identifies 90.6% (standard error, 0.013%) of the reads from 500 cells. To demonstrate the broad utility of KatharoSeq, we performed 16S rRNA amplicon and shotgun metagenome analyses of the Jet Propulsion Laboratory spacecraft assembly facility (SAF; n = 192, 96), 52 rooms of a neonatal intensive care unit (NICU; n = 388, 337), and an endangered-abalone-rearing facility (n = 192, 123), obtaining spatially resolved, unique microbiomes reproducible across hundreds of samples. The SAF, our primary focus, contains 32 sOTUs (sub-OTUs, defined as exact sequence matches) and their inferred variants identified by the deblur algorithm, with four (Acinetobacter lwoffii, Paracoccus marcusii, Mycobacterium sp., and Novosphingobium) being present in >75% of the samples. According to microbial spatial topography, the most abundant cleanroom contaminant, A. lwoffii, is related to human foot traffic exposure. In the NICU, we have been able to discriminate environmental exposure related to patient infectious disease, and in the abalone facility, we show that microbial communities reflect the marine environment rather than human input. Consequently, we demonstrate the feasibility and utility of large-scale, low-biomass metagenomic analyses using the KatharoSeq protocol. IMPORTANCE Various indoor, outdoor, and host-associated environments contain small quantities of microbial biomass and represent a niche that is often understudied because of technical constraints. Many studies that attempt to evaluate these low-biomass microbiome samples are riddled with erroneous results that are typically false positive signals obtained during the sampling process. We have investigated various low-biomass kits and methods to determine the limit of detection of these pipelines. Here we present KatharoSeq, a high-throughput protocol combining laboratory and bioinformatic methods that can differentiate a true positive signal in samples with as few as 50 to 500 cells. We demonstrate the application of this method in three unique low-biomass environments, including a SAF, a hospital NICU, and an abalone-rearing facility.
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35
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Hogan NS, Thorpe KL, van den Heuvel MR. Opportunistic disease in yellow perch in response to decadal changes in the chemistry of oil sands-affected waters. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 234:769-778. [PMID: 29247939 DOI: 10.1016/j.envpol.2017.11.091] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 11/23/2017] [Accepted: 11/27/2017] [Indexed: 06/07/2023]
Abstract
Oil sands-affected water from mining must eventually be incorporated into the reclaimed landscape or treated and released. However, this material contains petrogenic organic compounds, such as naphthenic acids and traces of polycyclic aromatic hydrocarbons. This has raised concerns for impacts of oil sands process-affected waters on the heath of wildlife and humans downstream of receiving environments. The objective of this study was to evaluate the temporal association of disease states in fish with water chemistry of oil sands-affected waters over more than a decade and determine the pathogens associated with disease pathologies. Yellow perch (Perca flavescens) captured from nearby lakes were stocked into two experimental ponds during 1995-1997 and 2008-2010. South Bison Pond is a drainage basin that has received unextracted oil sands-contaminated material. Demonstration Pond is a constructed pond containing mature fine tailings capped with fresh water. Two disease pathologies, fin erosion for which a suspected bacterial pathogen (Acinetobacter Iwoffi) is identified, and lymphocystis (confirmed using a real-time PCR) were associated with oil sands-affected water exposure. From 1995 to 1997 pathologies were most prevalent in the South Bison Pond; however, from 2008 to 2009, disease was more frequently observed in the Demonstration Pond. CYP1A activity was 3-16 fold higher in fish from experimental ponds as compared to reference populations and this pattern was consistent across all sampling years. Bile fluorescence displayed a gradient of exposure with experimental ponds being elevated over local perch populations. Naphthenic acids decreased in the Bison Pond from approximately 12 mg/L to <4 mg/L while naphthenic acids increased in the Demonstration Pond from 6 mg/L to 12 mg/L due to tailings densification. Temporal changes in naphthenic acid levels, CYP1A activity and bile fluorescent metabolites correlate positively with incidence of disease pathologies whereas all inorganic water quality changes (major ions, pH, metals) were not associated with disease responses.
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Affiliation(s)
- Natacha S Hogan
- Toxicology Centre, University of Saskatchewan, 44 Campus Drive, Saskatoon, Saskatchewan, S7N 5B3, Canada; Department of Animal and Poultry Science, University of Saskatchewan, 51 Campus Drive, Saskatoon, Saskatchewan, S7N 5A8, Canada.
| | - Karen L Thorpe
- Environmental Department, Wentworth Way, University of York, Heslington, York, YO10 5NG, United Kingdom
| | - Michael R van den Heuvel
- Canadian Rivers Institute, University of Prince Edward Island, 550 University Ave, Charlottetown, Prince Edward Island, C1A 4P3, Canada
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36
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Bashir M, Ahmed M, Weinmaier T, Ciobanu D, Ivanova N, Pieber TR, Vaishampayan PA. Functional Metagenomics of Spacecraft Assembly Cleanrooms: Presence of Virulence Factors Associated with Human Pathogens. Front Microbiol 2016; 7:1321. [PMID: 27667984 PMCID: PMC5017214 DOI: 10.3389/fmicb.2016.01321] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 08/10/2016] [Indexed: 01/09/2023] Open
Abstract
Strict planetary protection practices are implemented during spacecraft assembly to prevent inadvertent transfer of earth microorganisms to other planetary bodies. Therefore, spacecraft are assembled in cleanrooms, which undergo strict cleaning and decontamination procedures to reduce total microbial bioburden. We wanted to evaluate if these practices selectively favor survival and growth of hardy microorganisms, such as pathogens. Three geographically distinct cleanrooms were sampled during the assembly of three NASA spacecraft: The Lockheed Martin Aeronautics' Multiple Testing Facility during DAWN, the Kennedy Space Center's Payload Hazardous Servicing Facility (KSC-PHSF) during Phoenix, and the Jet Propulsion Laboratory's Spacecraft Assembly Facility during Mars Science Laboratory. Sample sets were collected from the KSC-PHSF cleanroom at three time points: before arrival of the Phoenix spacecraft, during the assembly and testing of the Phoenix spacecraft, and after removal of the spacecraft from the KSC-PHSF facility. All samples were subjected to metagenomic shotgun sequencing on an Illumina HiSeq 2500 platform. Strict decontamination procedures had a greater impact on microbial communities than sampling location Samples collected during spacecraft assembly were dominated by Acinetobacter spp. We found pathogens and potential virulence factors, which determine pathogenicity in all the samples tested during this study. Though the relative abundance of pathogens was lowest during the Phoenix assembly, potential virulence factors were higher during assembly compared to before and after assembly, indicating a survival advantage. Decreased phylogenetic and pathogenic diversity indicates that decontamination and preventative measures were effective against the majority of microorganisms and well implemented, however, pathogen abundance still increased over time. Four potential pathogens, Acinetobacter baumannii, Acinetobacter lwoffii, Escherichia coli and Legionella pneumophila, and their corresponding virulence factors were present in all cleanroom samples. This is the first functional metagenomics study describing presence of pathogens and their corresponding virulence factors in cleanroom environments. The results of this study should be considered for microbial monitoring of enclosed environments such as schools, homes, hospitals and more isolated habitation such the International Space Station and future manned missions to Mars.
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Affiliation(s)
- Mina Bashir
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of TechnologyPasadena, CA, USA; Division of Endocrinology and Diabetology, Medical University of GrazGraz, Austria
| | - Mahjabeen Ahmed
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of TechnologyPasadena, CA, USA; Department of Biological Sciences, California State Polytechnic UniversityPomona, CA, USA
| | - Thomas Weinmaier
- Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna Vienna, Austria
| | - Doina Ciobanu
- Department of Energy, Joint Genome Institute Walnut Creek, CA, USA
| | - Natalia Ivanova
- Department of Energy, Joint Genome Institute Walnut Creek, CA, USA
| | - Thomas R Pieber
- Division of Endocrinology and Diabetology, Medical University of Graz Graz, Austria
| | - Parag A Vaishampayan
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology Pasadena, CA, USA
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Escallón C, Becker MH, Walke JB, Jensen RV, Cormier G, Belden LK, Moore IT. Testosterone levels are positively correlated with cloacal bacterial diversity and the relative abundance of Chlamydiae in breeding male rufous‐collared sparrows. Funct Ecol 2016. [DOI: 10.1111/1365-2435.12696] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Camilo Escallón
- Department of Biological Sciences Virginia Tech 2119 Derring Hall Blacksburg Virginia 24061 USA
| | - Matthew H. Becker
- Department of Biological Sciences Virginia Tech 2119 Derring Hall Blacksburg Virginia 24061 USA
| | - Jenifer B. Walke
- Department of Biological Sciences Virginia Tech 2119 Derring Hall Blacksburg Virginia 24061 USA
| | - Roderick V. Jensen
- Department of Biological Sciences Virginia Tech 2119 Derring Hall Blacksburg Virginia 24061 USA
| | - Guy Cormier
- Georgia Advanced Computing Resource Center The University of Georgia 4098C Stegeman Coliseum Athens Georgia 30602 USA
| | - Lisa K. Belden
- Department of Biological Sciences Virginia Tech 2119 Derring Hall Blacksburg Virginia 24061 USA
| | - Ignacio T. Moore
- Department of Biological Sciences Virginia Tech 2119 Derring Hall Blacksburg Virginia 24061 USA
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Draft Genome Sequence and Complete Plasmid Sequence of Acinetobacter lwoffii F78, an Isolate with Strong Allergy-Protective Properties. GENOME ANNOUNCEMENTS 2016; 4:4/4/e00685-16. [PMID: 27445377 PMCID: PMC4956450 DOI: 10.1128/genomea.00685-16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The hygiene hypothesis states that the tremendous increase in atopic diseases correlates significantly with less contact to microbes in childhood. Here, we report the draft genome sequence of Acinetobacter lwoffii F78, a rural cowshed isolate with strong allergy-protective properties that contains an 8,579-bp plasmid.
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Comparative genomic analysis of novel Acinetobacter symbionts: A combined systems biology and genomics approach. Sci Rep 2016; 6:29043. [PMID: 27378055 PMCID: PMC4932630 DOI: 10.1038/srep29043] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 06/08/2016] [Indexed: 12/20/2022] Open
Abstract
The increasing trend of antibiotic resistance in Acinetobacter drastically limits the range of therapeutic agents required to treat multidrug resistant (MDR) infections. This study focused on analysis of novel Acinetobacter strains using a genomics and systems biology approach. Here we used a network theory method for pathogenic and non-pathogenic Acinetobacter spp. to identify the key regulatory proteins (hubs) in each strain. We identified nine key regulatory proteins, guaA, guaB, rpsB, rpsI, rpsL, rpsE, rpsC, rplM and trmD, which have functional roles as hubs in a hierarchical scale-free fractal protein-protein interaction network. Two key hubs (guaA and guaB) were important for insect-associated strains, and comparative analysis identified guaA as more important than guaB due to its role in effective module regulation. rpsI played a significant role in all the novel strains, while rplM was unique to sheep-associated strains. rpsM, rpsB and rpsI were involved in the regulation of overall network topology across all Acinetobacter strains analyzed in this study. Future analysis will investigate whether these hubs are useful as drug targets for treating Acinetobacter infections.
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40
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Singh NP, Sagar T, Nirmal K, Kaur IR. Pyogenic Liver Abscess Caused by Acinetobacter lwoffii: A Case Report. J Clin Diagn Res 2016; 10:DD01-2. [PMID: 27504286 DOI: 10.7860/jcdr/2016/18256.7943] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Accepted: 04/18/2016] [Indexed: 11/24/2022]
Abstract
Acinetobacter lwoffii is a gram negative aerobic non-fermenter bacilli. It is considered as an important emerging pathogen after Acinetobacter baumannii in patients with impaired immune system and in nosocomial infections. Here, we present a case of community acquired pyogenic liver Abscess caused by Acinetobacter lwoffii in a diabetic patient.
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Affiliation(s)
- N Pal Singh
- Professor, Department of Microbiology, University College of Medical Sciences and Guru Tag Bahadur Hospital , East Delhi, India
| | - Tanu Sagar
- Senior Resident, Department of Microbiology, University College of Medical Sciences and Guru Tag Bahadur Hospital , East Delhi, India
| | - Kirti Nirmal
- Post Graduate Student, Department of Microbiology, University College of Medical, Sciences and Guru Tag Bahadur, Hospital , East Delhi, India
| | - I Rajender Kaur
- Professor and Head, Department of Microbiology, University College of Medical Sciences and Guru Tag Bahadur Hospital , East Delhi, India
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Chng KR, Chan SH, Ng AHQ, Li C, Jusakul A, Bertrand D, Wilm A, Choo SP, Tan DMY, Lim KH, Soetinko R, Ong CK, Duda DG, Dima S, Popescu I, Wongkham C, Feng Z, Yeoh KG, Teh BT, Yongvanit P, Wongkham S, Bhudhisawasdi V, Khuntikeo N, Tan P, Pairojkul C, Ngeow J, Nagarajan N. Tissue Microbiome Profiling Identifies an Enrichment of Specific Enteric Bacteria in Opisthorchis viverrini Associated Cholangiocarcinoma. EBioMedicine 2016; 8:195-202. [PMID: 27428430 PMCID: PMC4919562 DOI: 10.1016/j.ebiom.2016.04.034] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 04/13/2016] [Accepted: 04/25/2016] [Indexed: 01/06/2023] Open
Abstract
Cholangiocarcinoma (CCA) is the primary cancer of the bile duct system. The role of bile duct tissue microbiomes in CCA tumorigenesis is unestablished. To address this, sixty primary CCA tumors and matched normals, from both liver fluke (Opisthorchis viverrini) associated (OVa, n = 28) and non-O. viverrini associated (non-OVa, n = 32) cancers, were profiled using high-throughput 16S rRNA sequencing. A distinct, tissue-specific microbiome dominated by the bacterial families Dietziaceae, Pseudomonadaceae and Oxalobacteraceae was observed in bile duct tissues. Systemic perturbation of the microbiome was noted in tumor and paired normal samples (vs non-cancer normals) for several bacterial families with a significant increase in Stenotrophomonas species distinguishing tumors vs paired normals. Comparison of parasite associated (OVa) vs non-associated (non-OVa) groups identified enrichment for specific enteric bacteria (Bifidobacteriaceae, Enterobacteriaceae and Enterococcaceae). One of the enriched families, Bifidobacteriaceae, was found to be dominant in the O. viverrini microbiome, providing a mechanistic link to the parasite. Functional analysis and comparison of CCA microbiomes revealed higher potential for producing bile acids and ammonia in OVa tissues, linking the altered microbiota to carcinogenesis. These results define how the unique microbial communities resident in the bile duct, parasitic infections and the tissue microenvironment can influence each other, and contribute to cancer. Stenotrophomonas, implicated in bile duct infections, is enriched in tumor tissues of non-fluke related cholangiocarcinoma. O. viverrini infection may alter composition of bile duct tissue microbiomes. Enteric bacteria with metabolic outputs linked to carcinogenesis are enriched in O. viverrini associated tissue microbiomes.
The link between microbiota and cancer of the gastrointestinal (GI) tract has been extensively studied. However, the role of tissue microbiome in cholangiocarcinoma (CCA), cancer of the bile duct (an organ connected to the GI tract), is largely unknown. In this study, we detected intriguing compositional differences in the tissue microbiomes of liver fluke related and non-related CCA. Taken together, our data suggests a connection between parasitic infections, tissue microbiome alterations, tissue micro-environment changes and CCA development.
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Affiliation(s)
| | - Sock Hoai Chan
- Division of Medical Oncology, National Cancer Centre Singapore, 11 Hospital Drive, 169610, Singapore
| | | | - Chenhao Li
- Genome Institute of Singapore, 138672, Singapore
| | - Apinya Jusakul
- Laboratory of Cancer Epigenome, National Cancer Centre Singapore, 11 Hospital Drive, 169610, Singapore
| | | | - Andreas Wilm
- Genome Institute of Singapore, 138672, Singapore
| | - Su Pin Choo
- Division of Medical Oncology, National Cancer Centre Singapore, 11 Hospital Drive, 169610, Singapore
| | - Damien Meng Yew Tan
- Department of Gastroenterology and Hepatology, Singapore General Hospital, Outram Road, 169608, Singapore
| | - Kiat Hon Lim
- Department of Pathology, Singapore General Hospital, Outram Road, 169608, Singapore
| | - Roy Soetinko
- Department of Gastroenterology and Hepatology, Singapore General Hospital, Outram Road, 169608, Singapore
| | - Choon Kiat Ong
- Laboratory of Cancer Epigenome, National Cancer Centre Singapore, 11 Hospital Drive, 169610, Singapore
| | - Dan G Duda
- Edwin L. Steele Laboratories for Tumor Biology, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Simona Dima
- Center of Digestive Diseases and Liver Transplantation, Fundeni Clinical Institute, Bucharest, Romania
| | - Irinel Popescu
- Center of Digestive Diseases and Liver Transplantation, Fundeni Clinical Institute, Bucharest, Romania
| | - Chaisiri Wongkham
- Liver Fluke and Cholangiocarcinoma Research Center, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Zhu Feng
- Dept. of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Khay Guan Yeoh
- Dept. of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Dept. of Gastroenterology and Hepatology, National University Health System, Singapore
| | - Bin Tean Teh
- Laboratory of Cancer Epigenome, National Cancer Centre Singapore, 11 Hospital Drive, 169610, Singapore; Cancer Science and Stem Cell Biology, Duke-NUS Graduate Medical School, 8 College Road, 169857, Singapore
| | - Puangrat Yongvanit
- Liver Fluke and Cholangiocarcinoma Research Center, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Sopit Wongkham
- Liver Fluke and Cholangiocarcinoma Research Center, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Vajaraphongsa Bhudhisawasdi
- Liver Fluke and Cholangiocarcinoma Research Center, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Narong Khuntikeo
- Liver Fluke and Cholangiocarcinoma Research Center, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Patrick Tan
- Genome Institute of Singapore, 138672, Singapore; Cancer Science and Stem Cell Biology, Duke-NUS Graduate Medical School, 8 College Road, 169857, Singapore
| | - Chawalit Pairojkul
- Liver Fluke and Cholangiocarcinoma Research Center, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand.
| | - Joanne Ngeow
- Division of Medical Oncology, National Cancer Centre Singapore, 11 Hospital Drive, 169610, Singapore; Oncology Academic Clinical Program, Duke-NUS Graduate Medical School, 8 College Road, 169857, Singapore.
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Angeletti S, Ceccarelli G, Vita S, Dicuonzo G, Lopalco M, Dedej E, Blasi A, Antonelli F, Conti A, De Cesaris M, Farchi F, Lo Presti A, Ciccozzi M. Unusual microorganisms and antimicrobial resistances in a group of Syrian migrants: Sentinel surveillance data from an asylum seekers centre in Italy. Travel Med Infect Dis 2016; 14:115-22. [PMID: 26987764 DOI: 10.1016/j.tmaid.2016.03.005] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 02/18/2016] [Accepted: 03/08/2016] [Indexed: 11/25/2022]
Abstract
BACKGROUND Three years of civil war in Syria have caused death and increase of communicable diseases. The suffering population has been forced to migrate creating a fertile condition for epidemic spread of infection within the refugee camps. METHODS Forty-eight Syrian migrants, upon their arrival in Italy, were accommodated at the asylum seekers centre of Castelnuovo di Porto. They received a physical examination and were subjected to microbiological surveillance by blood, rectal, pharyngeal and nasal swabs collection and delivering to the Clinical Pathology and Microbiology Laboratory of the University Campus Bio-Medico of Rome. RESULTS All refugees resulted negative for HBV, HCV and HIV infections. In swabs a large number of unusual gram-negative bacteria species were isolated, such as Pseudomonas putida, Pseudomonas monteilii, Pseudomonas fulva, Pseudomonas moselii, Aeromonas veronii, Aeromonas caviae, Aeromonas hydrophila, Acinteobacter guilloviae, Acinteobacter lowffii; Acinetobacter johnsonii; Acinteobacter tjernbergae; Pantoea agglomerans; Pantoea calida. Among isolates, strains resistant to carbapenems, ESBL producers and methicillin resistant were found. CONCLUSIONS The microbiological surveillance performed represents a useful action to understand refugees health status and to trace unusual microorganisms movement even carriers of antimicrobial resistance during migrants traveling.
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Affiliation(s)
- Silvia Angeletti
- Clinical Pathology and Microbiology Laboratory, University Hospital Campus Bio-Medico of Rome, Italy
| | - Giancarlo Ceccarelli
- Department of Public Health and Infectious Diseases. University of Rome, "Sapienza," Policlinico Umberto I", Rome, Italy; Migrant Health Research Organisation (Mi-HeRO) - Centro di Ricerca sulla Salute delle Popolazioni Mobili e Globale, Italy
| | - Serena Vita
- Department of Public Health and Infectious Diseases. University of Rome, "Sapienza," Policlinico Umberto I", Rome, Italy; Migrant Health Research Organisation (Mi-HeRO) - Centro di Ricerca sulla Salute delle Popolazioni Mobili e Globale, Italy
| | - Giordano Dicuonzo
- Clinical Pathology and Microbiology Laboratory, University Hospital Campus Bio-Medico of Rome, Italy
| | - Maurizio Lopalco
- Sanitary Bureau of Asylum Seekers Center of Castelnuovo di Porto, Rome, Italy; Auxilium Società Cooperativa Sociale, Senise (PZ), Italy
| | - Etleva Dedej
- Clinical Pathology and Microbiology Laboratory, University Hospital Campus Bio-Medico of Rome, Italy
| | - Aletheia Blasi
- Clinical Pathology and Microbiology Laboratory, University Hospital Campus Bio-Medico of Rome, Italy
| | - Francesca Antonelli
- Clinical Pathology and Microbiology Laboratory, University Hospital Campus Bio-Medico of Rome, Italy
| | - Alessia Conti
- Clinical Pathology and Microbiology Laboratory, University Hospital Campus Bio-Medico of Rome, Italy
| | - Marina De Cesaris
- Clinical Pathology and Microbiology Laboratory, University Hospital Campus Bio-Medico of Rome, Italy
| | - Francesca Farchi
- Department of Infectious, Parasitic, and Immune-Mediated Diseases, Epidemiology Unit, Reference Centre on Phylogeny, Molecular Epidemiology, and Microbial Evolution (FEMEM), National Institute of Health, Rome, Italy
| | - Alessandra Lo Presti
- Department of Infectious, Parasitic, and Immune-Mediated Diseases, Epidemiology Unit, Reference Centre on Phylogeny, Molecular Epidemiology, and Microbial Evolution (FEMEM), National Institute of Health, Rome, Italy
| | - Massimo Ciccozzi
- Clinical Pathology and Microbiology Laboratory, University Hospital Campus Bio-Medico of Rome, Italy; Department of Infectious, Parasitic, and Immune-Mediated Diseases, Epidemiology Unit, Reference Centre on Phylogeny, Molecular Epidemiology, and Microbial Evolution (FEMEM), National Institute of Health, Rome, Italy.
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Sharifi-Rad J, Hoseini-Alfatemi SM, Sharifi-Rad M, Teixeira da Silva JA. Antibacterial, antioxidant, antifungal and anti-inflammatory activities of crude extract from Nitraria schoberi fruits. 3 Biotech 2015; 5:677-684. [PMID: 28324518 PMCID: PMC4569636 DOI: 10.1007/s13205-014-0266-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 10/31/2014] [Indexed: 01/30/2023] Open
Abstract
This study is the first comprehensive investigation of the antibacterial, antioxidant, antifungal and anti-inflammatory activities of a crude extract from Nitraria schoberi L. (Zygophyllaceae) fruits. The extract was tested against four Gram-negative (Pseudomonas aeruginosa, Enterobacter aerogenes, Klebsiella pneumoniae and Acinetobacter lwoffii) and one Gram-positive (Staphylococcus aureus) bacteria using the agar disc diffusion and microdilution methods. P. aeruginosa was inhibited the most (widest inhibition zone) while K. pneumonia showed the largest MIC value. The antioxidant activity of fruits (0.02 mg/mL vs. 0.04, 0.06 and 1.00 mg/mL for α-tocopherol, butylated hydroxyanisole and ascorbic acid, respectively) was determined by the paired diene method. The antifungal activity of N. schoberi fruits was tested against different fungi, including Aspergillus niger and Candida albicans, with 300 µg/mL of fruit extract being the most effective concentration. The percentage of anti-inflammatory activity assayed for N. schoberi fruit extract at 100, 200 and 500 µg/mL was 36.12, 59.89 and 88.33 %, respectively. N. schoberi fruits possess potent antibacterial, antioxidant, antifungal and anti-inflammatory properties, and may be used as an antibacterial and antifungal to treat diseases and/or as a protective agent against disorders associated with oxidative stress and inflammation.
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Affiliation(s)
- Javad Sharifi-Rad
- Zabol Medicinal Plants Research Center, Zabol University of Medical Sciences, Zabol, Iran.
- Department of Pharmacognosy, Faculty of Pharmacy, Zabol University of Medical Sciences, Zabol, Iran.
| | - Seyedeh Mahsan Hoseini-Alfatemi
- Pediatric Infections Research Center, Mofid Children Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Majid Sharifi-Rad
- Department of Range and Watershed Management, Faculty of Natural Resources, University of Zabol, Zabol, Iran
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Kim MG, Jeon JW, Ryu IH, Lee JJ, Kim JS, Choi JW, Cho BS, Yoon HJ. Mycotic abdominal aortic aneurysm caused by bacteroides thetaiotaomicron and acinetobacter lwoffii: the first case in Korea. Infect Chemother 2014; 46:54-8. [PMID: 24693472 PMCID: PMC3970306 DOI: 10.3947/ic.2014.46.1.54] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 09/09/2013] [Accepted: 09/10/2013] [Indexed: 11/24/2022] Open
Abstract
Mycotic aneurysms are uncommon, but are fatal without appropriate management. Previous reports have shown that anaerobes and gram-negative organisms are less common but more dangerous than other causative agents of mycotic aneurysm. We report the case of a 60-year-old man with poorly controlled diabetes mellitus and atherosclerosis in the aorta, and a 10-day of history of lower abdominal pain and fever. This man was diagnosed with an uncommon abdominal aorta mycotic aneurysm caused by Bacteroides thetaiotaomicron and Acinetobacter lwoffii. The aneurysm was successfully treated with antibiotics therapy and aorto-bi-external iliac artery bypass with debridement of the infected aortic wall. We present this case together with a review of the relevant literature.
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Affiliation(s)
- Min Gyu Kim
- Division of Infectious Diseases, Department of Internal Medicine, Eulji University Hospital, Eulji University College of Medicine, Daejeon, Korea
| | - Jae Woong Jeon
- Division of Infectious Diseases, Department of Internal Medicine, Eulji University Hospital, Eulji University College of Medicine, Daejeon, Korea
| | - Il Hwan Ryu
- Division of Infectious Diseases, Department of Internal Medicine, Eulji University Hospital, Eulji University College of Medicine, Daejeon, Korea
| | - Jae Joon Lee
- Division of Infectious Diseases, Department of Internal Medicine, Eulji University Hospital, Eulji University College of Medicine, Daejeon, Korea
| | - Joo Seok Kim
- Division of Infectious Diseases, Department of Internal Medicine, Eulji University Hospital, Eulji University College of Medicine, Daejeon, Korea
| | - Ji Wook Choi
- Division of Infectious Diseases, Department of Internal Medicine, Eulji University Hospital, Eulji University College of Medicine, Daejeon, Korea
| | - Byung-Sun Cho
- Division of Infectious Diseases, Department of Internal Medicine, Eulji University Hospital, Eulji University College of Medicine, Daejeon, Korea
| | - Hee Jung Yoon
- Division of Infectious Diseases, Department of Internal Medicine, Eulji University Hospital, Eulji University College of Medicine, Daejeon, Korea
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Turowski EE, Shen Z, Ducore RM, Parry NMA, Kirega A, Dewhirst FE, Fox JG. Isolation of a Campylobacter lanienae-like bacterium from laboratory chinchillas (Chinchilla laniger). Zoonoses Public Health 2014; 61:571-80. [PMID: 24628887 DOI: 10.1111/zph.12107] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Indexed: 11/26/2022]
Abstract
Routine necropsies of 27 asymptomatic juvenile chinchillas revealed a high prevalence of gastric ulcers with microscopic lymphoplasmacytic gastroenteritis and typhlocolitis. Polymerase chain reaction (PCR) analysis using Campylobacter genus-specific partial 16S rRNA primers revealed the presence of Campylobacter spp. DNA in the faeces of 12 of 27 animals (44.4%). Species-specific partial 16S rRNA PCR and sequencing confirmed that these animals were colonized with Campylobacter lanienae, a gram-negative, microaerophilic bacterium that was first identified on routine faecal screening of slaughterhouse employees and subsequently isolated from faeces of livestock. Campylobacter lanienae was isolated from the faeces of six PCR-positive animals and identified with species-specific PCR and full 16S rRNA sequencing. Phylogenetic analysis showed that these isolates clustered with C. lanienae strain NCTC 13004. PCR analysis of DNA extracted from gastrointestinal tissues revealed the presence of C. lanienae DNA in the caecum and colon of these chinchillas. Gastrointestinal lesions were scored and compared between C. lanienae-positive and C. lanienae-negative animals. There was no correlation between colonization status and lesion severity in the stomach, liver, duodenum, or colon. Possible routes of C. lanienae infection in chinchillas could include waterborne transmission and faecal-oral transmission from wild mice and rats or livestock. Based on these findings, the authors conclude that C. lanienae colonizes the lower bowel of chinchillas in the absence of clinical disease. This is the first report of C. lanienae in any rodent species. Campylobacter lanienae isolates from different mammalian species demonstrate heterogeneity by 16S rRNA sequence comparison. Analysis using rpoB suggests that isolates and clones currently identified as C. lanienae may represent multiple species or subspecies.
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Affiliation(s)
- E E Turowski
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
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Geller BL, Marshall-Batty K, Schnell FJ, McKnight MM, Iversen PL, Greenberg DE. Gene-silencing antisense oligomers inhibit acinetobacter growth in vitro and in vivo. J Infect Dis 2013; 208:1553-60. [PMID: 24130069 DOI: 10.1093/infdis/jit460] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Peptide-conjugated phosphorodiamidate morpholino oligomers (PPMOs) are synthetic DNA/RNA analogues that silence expression of specific genes. We studied whether PPMOs targeted to essential genes in Acinetobacter lwoffii and Acinetobacter baumannii are active in vitro and in vivo. METHODS PPMOs were evaluated in vitro using minimum inhibitory concentration (MIC) and viability assays, and in vivo using murine pulmonary infection models with intranasal PPMO treatment. RESULTS MICs of PPMOs ranged from 0.1 to 64 µM (approximately 0.6-38 µg/mL). The most effective PPMO tested was (RXR)4-AcpP, which is targeted to acpP. (RXR)4-AcpP reduced viability of A. lwoffii and A. baumannii by >10(3) colony-forming units/mL at 5-8 times MIC. Mice treated with ≥0.25 mg/kg of (RXR)4-AcpP survived longer and had less inflammation and bacterial lung burden than mice treated with a scrambled-sequence PPMO or phosphate-buffered saline. Treatment could be delayed after infection and still increase survival. CONCLUSIONS PPMOs targeted to essential genes of A. lwoffii and A. baumannii were bactericidal and had MICs in a clinically relevant range. (RXR)4-AcpP increased survival of mice infected with A. lwoffii or A. baumannii, even when initial treatment was delayed after infection. PPMOs could be a viable therapeutic approach in dealing with multidrug-resistant Acinetobacter species.
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Liu YM, Chen YS, Toh HS, Huang CC, Lee YL, Ho CM, Lu PL, Ko WC, Chen YH, Wang JH, Tang HJ, Yu KW, Liu YC, Chuang YC, Xu Y, Ni Y, Liu CE, Hsueh PR. In vitro susceptibilities of non-Enterobacteriaceae isolates from patients with intra-abdominal infections in the Asia-Pacific region from 2003 to 2010: results from the Study for Monitoring Antimicrobial Resistance Trends (SMART). Int J Antimicrob Agents 2012; 40 Suppl:S11-7. [DOI: 10.1016/s0924-8579(12)70004-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Comparison of the virulence potential of Acinetobacter strains from clinical and environmental sources. PLoS One 2012; 7:e37024. [PMID: 22655033 PMCID: PMC3360037 DOI: 10.1371/journal.pone.0037024] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 04/12/2012] [Indexed: 12/19/2022] Open
Abstract
Several Acinetobacter strains have utility for biotechnology applications, yet some are opportunistic pathogens. We compared strains of seven Acinetobacter species (baumannii, Ab; calcoaceticus, Ac; guillouiae, Ag; haemolyticus, Ah; lwoffii, Al; junii, Aj; and venetianus, Av-RAG-1) for their potential virulence attributes, including proliferation in mammalian cell conditions, haemolytic/cytolytic activity, ability to elicit inflammatory signals, and antibiotic susceptibility. Only Ah grew at 102 and 104 bacteria/well in mammalian cell culture medium at 37°C. However, co-culture with colonic epithelial cells (HT29) improved growth of all bacterial strains, except Av-RAG-1. Cytotoxicity of Ab and Ah toward HT29 was at least double that of other test bacteria. These effects included bacterial adherence, loss of metabolism, substrate detachment, and cytolysis. Only Ab and Ah exhibited resistance to killing by macrophage-like J774A.1 cells. Haemolytic activity of Ah and Av-RAG-1 was strong, but undetectable for other strains. When killed with an antibiotic, Ab, Ah, Aj and Av-RAG-1 induced 3 to 9-fold elevated HT29 interleukin (IL)-8 levels. However, none of the strains altered levels of J774A.1 pro-inflammatory cytokines (IL-1β, IL-6 and tumor necrosis factor-α). Antibiotic susceptibility profiling showed that Ab, Ag and Aj were viable at low concentrations of some antibiotics. All strains were positive for virulence factor genes ompA and epsA, and negative for mutations in gyrA and parC genes that convey fluoroquinolone resistance. The data demonstrate that Av-RAG-1, Ag and Al lack some potentially harmful characteristics compared to other Acinetobacter strains tested, but the biotechnology candidate Av-RAG-1 should be scrutinized further prior to widespread use.
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Nakphaichit M, Thanomwongwattana S, Phraephaisarn C, Sakamoto N, Keawsompong S, Nakayama J, Nitisinprasert S. The effect of including Lactobacillus reuteri KUB-AC5 during post-hatch feeding on the growth and ileum microbiota of broiler chickens. Poult Sci 2011; 90:2753-65. [DOI: 10.3382/ps.2011-01637] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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