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Esposito E, Pace A, Affuso A, Oliviero M, Iaccarino D, Paduano G, Maffucci F, Fusco G, De Carlo E, Hochscheid S, Di Nocera F. Antibiotic Resistance of Bacteria Isolated from Clinical Samples and Organs of Rescued Loggerhead Sea Turtles ( Caretta caretta) in Southern Italy. Animals (Basel) 2024; 14:2103. [PMID: 39061565 PMCID: PMC11273476 DOI: 10.3390/ani14142103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 07/13/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
Antimicrobial resistance affects all environments, endangering the health of numerous species, including wildlife. Increasing anthropic pressure promotes the acquisition and dissemination of antibiotic resistance by wild animals. Sea turtles, being particularly exposed, are considered sentinels and carriers of potential zoonotic pathogens and resistant strains. Therefore, this study examined the antibiotic resistance profiles of bacteria isolated from loggerhead sea turtles hospitalised in a rescue centre of Southern Italy over a 9-year period. Resistance to ceftazidime, doxycycline, enrofloxacin, flumequine, gentamicin, oxytetracycline and sulfamethoxazole-trimethoprim was evaluated for 138 strains isolated from the clinical samples or organs of 60 animals. Gram-negative families were the most isolated: Vibrionaceae were predominant, followed by Shewanellaceae, Pseudomonadaceae, Enterobacteriaceae and Morganellaceae. These last three families exhibited the highest proportion of resistance and multidrug-resistant strains. Among the three Gram-positive families isolated, Enterococcaceae were the most represented and resistant. The opportunistic behaviour of all the isolated species is particularly concerning for diseased sea turtles, especially considering their resistance to commonly utilised antibiotics. Actually, the multiple antibiotic resistance was higher when the sea turtles were previously treated. Taken together, these findings highlight the need to improve antimicrobial stewardship and monitor antibiotic resistance in wildlife, to preserve the health of endangered species, along with public and environmental health.
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Affiliation(s)
- Emanuele Esposito
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute 2, 80055 Portici, Italy; (M.O.); (D.I.); (G.P.); (G.F.); (E.D.C.); (F.D.N.)
| | - Antonino Pace
- Department of Marine Animal Conservation and Public Engagement, Stazione Zoologica Anton Dohrn, Via Nuova Macello 16, 80055 Portici, Italy; (A.A.); (F.M.); (S.H.)
| | - Andrea Affuso
- Department of Marine Animal Conservation and Public Engagement, Stazione Zoologica Anton Dohrn, Via Nuova Macello 16, 80055 Portici, Italy; (A.A.); (F.M.); (S.H.)
| | - Maria Oliviero
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute 2, 80055 Portici, Italy; (M.O.); (D.I.); (G.P.); (G.F.); (E.D.C.); (F.D.N.)
| | - Doriana Iaccarino
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute 2, 80055 Portici, Italy; (M.O.); (D.I.); (G.P.); (G.F.); (E.D.C.); (F.D.N.)
| | - Gianluigi Paduano
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute 2, 80055 Portici, Italy; (M.O.); (D.I.); (G.P.); (G.F.); (E.D.C.); (F.D.N.)
| | - Fulvio Maffucci
- Department of Marine Animal Conservation and Public Engagement, Stazione Zoologica Anton Dohrn, Via Nuova Macello 16, 80055 Portici, Italy; (A.A.); (F.M.); (S.H.)
| | - Giovanna Fusco
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute 2, 80055 Portici, Italy; (M.O.); (D.I.); (G.P.); (G.F.); (E.D.C.); (F.D.N.)
| | - Esterina De Carlo
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute 2, 80055 Portici, Italy; (M.O.); (D.I.); (G.P.); (G.F.); (E.D.C.); (F.D.N.)
| | - Sandra Hochscheid
- Department of Marine Animal Conservation and Public Engagement, Stazione Zoologica Anton Dohrn, Via Nuova Macello 16, 80055 Portici, Italy; (A.A.); (F.M.); (S.H.)
| | - Fabio Di Nocera
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute 2, 80055 Portici, Italy; (M.O.); (D.I.); (G.P.); (G.F.); (E.D.C.); (F.D.N.)
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Han K, Yue J, Li J, Zhang J, Lin J, Zhuang Q, Li N, Li S, Rong C, Hua M, Liu Y, Yang D, Gu C, Chen L, Zeng H, Chen C. Emergence of mcr-4.3 genes in a novel Shewanella specie isolated from the Arctic environment. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 123:105636. [PMID: 38972619 DOI: 10.1016/j.meegid.2024.105636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 06/28/2024] [Accepted: 07/04/2024] [Indexed: 07/09/2024]
Abstract
Mobile colistin resistance (mcr) genes are pivotal contributors to last-line of antimicrobial resistance in human infections. Shewanella, historically recognized as a natural environmental bacterium with metal reduction capabilities, recently has been observed in clinical settings. However, limited knowledge has been explored on genetic differences between strains from non-clinical and clinical strains. In this study, we conducted the whole genome sequencing on six Arctic strains, illustrated the phylogenetic relationships on published 393 Shewanella strains that categorized the genus into four lineages (L1 to L4). Over 86.4% of clinical strain group (CG) strains belonged to L1 and L4, carrying mcr-4 genes and a complete metal-reduction pathways gene cluster. Remarkably, a novel Arctic Shewanella strain in L3, exhibits similar genetic characteristics with CG strains that carried both mcr-4 genes and a complete metal reduction pathway gene cluster. It raised concerns about the transmission ability from environment to clinic setting causing in the potential infections, and emphasized the need for monitoring the emerging strains with human infections.
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Affiliation(s)
- Kai Han
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Jinglin Yue
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Jiarui Li
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Jiuming Zhang
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Jing Lin
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Qinghui Zhuang
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Na Li
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Sha Li
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Chengbo Rong
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Mingxi Hua
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Yuwei Liu
- Emergency Department, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Duo Yang
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Chaoyang Gu
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Liang Chen
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Hui Zeng
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Chen Chen
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, China.
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Madrid NY, Mejia LF, Urrego JFG. Left knee septic monoarthritis in a pediatric patient due to shewanella putrefaciens: case report and literature review. Ann Clin Microbiol Antimicrob 2024; 23:43. [PMID: 38730467 PMCID: PMC11088002 DOI: 10.1186/s12941-024-00702-6] [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: 11/26/2023] [Accepted: 05/06/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Shewanella putrefaciens is a gram-negative, nonfermenting, oxidase-positive, hydrogen sulfide-producing bacillus and a halophilic bacterium, known for causing unusual infections in humans and often regarded as an opportunistic pathogen. Its diverse symptoms have a significant impact on human health, with 260 documented disorders reported in the literature over the last 40 years, highlighting its potential danger. CASE PRESENTATION We present the case of a previously healthy 15-year-old male patient who sustained a self-inflicted sharp-object injury while working in the field, resulting in secondary septic monoarthritis due to Shewanella putrefaciens. CONCLUSIONS This case highlights the bacteriological and clinical characteristics, as well as the antibiogram, of Shewanella spp. Given the recent increase in notifications of Shewanella infections, predominantly by S. algae and S. putrefaciens, it is essential to consider these pathogens in patients with a history of contact with bodies of water. Special attention must be paid to their resistance patterns in patient management to prevent the development of intrinsic antimicrobial resistance.
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Affiliation(s)
- Nathalie Yepes Madrid
- Pediatric specialty resident, Universidad Libre Sectional Cali, Valle del Cauca, Colombia.
- Pediatrics Specialty Research Group (GRINPED), Valle del Cauca, Colombia.
| | - Luis Fernando Mejia
- Fundación Clínica Infantil Club Noel, Pediatric Specialty Program, Universidad Libre Sectional Cali, Valle del Cauca, Colombia
- Pediatrics Specialty Research Group (GRINPED), Valle del Cauca, Colombia
| | - José Fernando Gomez Urrego
- Fundación Clínica Infantil Club Noel, Postgraduate coordinator of the Specialty Program, Universidad Libre Sectional Cali, Epidemiologist, Valle del Cauca, Colombia
- Pediatrics Specialty Research Group (GRINPED), Valle del Cauca, Colombia
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Xia X, Ma X, Liang N, Qin L, Huo W, Li Y. Damage of polyethylene microplastics on the intestine multilayer barrier, blood cell immune function and the repair effect of Leuconostoc mesenteroides DH in the large-scale loach (Paramisgurnus dabryanus). FISH & SHELLFISH IMMUNOLOGY 2024; 147:109460. [PMID: 38382690 DOI: 10.1016/j.fsi.2024.109460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 02/17/2024] [Accepted: 02/18/2024] [Indexed: 02/23/2024]
Abstract
Polyethylene microplastics (PE-MPs) has become a global concern due to their widespread distribution and hazardous properties in aquatic habitats. In this study, the accumulation effect of PE-MPs in the intestine of large-scale loach (Paramisgurnus dabryanus) was explored by adding different concentrations of PE-MPs to the water, the destination of PE-MPs after breaking the intestinal barrier and the effects caused. The collected data showed that PE-MPs accumulation for 21d altered the histomorphology and antioxidant enzyme activity of the intestine, induced dysbiosis of the intestinal flora. 10 mg/L of PE-MPs induced a significant increase in the transcript levels of intestinal immunity factors in loach after 21d of exposure. Moreover, the levels of diamine oxidase (DAO) and d-lactic acid (D-Lac) in the gut and serum of loach were significantly increased after exposure to PE-MPs at all concentrations (1, 5, 10 mg/L). Subsequently, the presence of PE-MPs was detected in the blood, suggesting that the disruption of the intestinal multilayer barrier allowed PE-MPs to spill into the circulation. The accumulation of PE-MPs (1,5,10 mg/L) in the blood led to massive apoptosis and necrosis of blood cells and activated phagocytosis in response to PE-MPs invasion. To alleviate the damage, this study further exposure the effect of probiotics on PE-MPs treated loach by adding Leuconostoc mesenteroides DH (109 CFU/g) to the feed. The results showed that DH significantly increased the intestinal index and reduced the levels of DAO and D-Lac. To investigate the reason, we followed the PE-MPs in the intestine and blood of the loach and found that the number of PE-MPs particles was significantly reduced in the probiotic group, while the PE-MPs content in the feces was elevated. Thus, we concluded that DH reducing the accumulation of PE-MPs in the intestinal by increases fecal PE-MPs, which in turn mitigates the damage to the intestinal barrier caused by PE-MPs, and reduces the amount of PE-MPs in the blood. This work offers a robust analysis to understand the mechanisms of damage to the intestinal barrier by MPs and the fate of MPs after escaping the intestinal barrier and provide a new perspective on the application of probiotics in mitigating PE-MPs toxicity.
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Affiliation(s)
- Xiaohua Xia
- College of Life Science, Henan Normal University, Xinxiang, Henan, 453007, China.
| | - Xiaoyu Ma
- College of Life Science, Henan Normal University, Xinxiang, Henan, 453007, China.
| | - Ning Liang
- College of Life Science, Henan Normal University, Xinxiang, Henan, 453007, China.
| | - Lu Qin
- College of Life Science, Henan Normal University, Xinxiang, Henan, 453007, China.
| | - Weiran Huo
- College of Life Science, Henan Normal University, Xinxiang, Henan, 453007, China.
| | - Yi Li
- College of Life Science, Henan Normal University, Xinxiang, Henan, 453007, China.
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Kang Y, Yu K, Huang Z, Pang B, Liu S, Peng T, Li Y, Wang D. Prevalence and molecular characteristics of Shewanella infection in diarrhea patients in Beijing, China 2017-2019. Front Microbiol 2024; 15:1293577. [PMID: 38357347 PMCID: PMC10866003 DOI: 10.3389/fmicb.2024.1293577] [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: 09/13/2023] [Accepted: 01/03/2024] [Indexed: 02/16/2024] Open
Abstract
Introduction Shewanella is an important opportunistic pathogen distributed in marine environments that has caused an increasing number of clinical infections. However, there are few reports on the distribution and characteristics of Shewanella in the diarrheal pathogen spectrum. In this study, we have systematically described the prevalence of Shewanella infections in diarrhea patients in Beijing, China 2017-2019, and genome characteristics and antimicrobial susceptibility of Shewanella isolates. Methods Stool samples were collected from diarrhea patients in a surveillance project from 2017 to 2019. Shewanella strains were isolated, and identified using VITEKR 2 COMPACT and MALDI-TOF MS. Average nucleotide identity (ANI) analysis, multi-locus sequence typing (MLST), phylogenetic analysis, virulence-associated genes and antimicrobial resistance genes analysis were used for genome characteristics description. The antibiotic susceptibility test was performed with microbroth dilution method. Results 1104 fecal samples were collected, and the Shewanella detection rate was 2.36% (26/1104). The main manifestations of infection caused by Shewanella spp. were diarrhea (100%, 26/26), abdominal pain (65.38%, 17/26), and vomiting (38.46%, 10/26). The 26 isolates were classified into 3 species (S. algae (n = 18), S. indica (n = 5), and S. chilikensis (n = 3)) and 22 sequence types. Core genome single nucleotide polymorphism-based evolutionary tree identified three clone groups corresponding to three infection events in the same months in 2017 and 2019. The putative virulence-associated gene pool consisted of 56 potential virulence genes, including 19 virulence gene factors. The resistance rates of the 26 isolates to 17 antibiotics from high to low were as follows: polymyxin E (76.92%), cefotaxime (57.69%), ampicillin (50%), ampicillin-sulbactam (34.62%), nalidixic acid (15.38%), ciprofloxacin (11.54%), selectrin (3.846%,1/26), and tetracycline (3.846%, 1/26). The rate of multidrug resistance was 38.46% (10/26). Discussion Monitoring for Shewanella spp. should be added to the routine surveillance of infectious diarrhea during the epidemic season.
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Affiliation(s)
- Ying Kang
- Shunyi District Center for Disease Control and Prevention, Beijing, China
- Workstation for Microbial Infectious Disease, Shunyi District Center for Disease Control and Prevention, Beijing, China
| | - Keyi Yu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Zhenzhou Huang
- Hangzhou Center for Disease Control and Prevention, Hangzhou, Zhejiang, China
| | - Bo Pang
- Workstation for Microbial Infectious Disease, Shunyi District Center for Disease Control and Prevention, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Shengtian Liu
- Shunyi District Center for Disease Control and Prevention, Beijing, China
| | - Tao Peng
- Shunyi District Center for Disease Control and Prevention, Beijing, China
| | - Ying Li
- Shunyi District Center for Disease Control and Prevention, Beijing, China
- Workstation for Microbial Infectious Disease, Shunyi District Center for Disease Control and Prevention, Beijing, China
| | - Duochun Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
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Wu X, Li Q, Cai J, Huang H, Ma S, Tan H. Longitudinal change of gut microbiota in hypertensive disorders in pregnancy: a nested case-control and Mendelian randomization study. Sci Rep 2023; 13:16986. [PMID: 37813882 PMCID: PMC10562506 DOI: 10.1038/s41598-023-43780-w] [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: 06/01/2023] [Accepted: 09/28/2023] [Indexed: 10/11/2023] Open
Abstract
Mounting evidence has shown that gut microbiota (GM) is related to hypertensive disorders in pregnancy (HDP), however, most studies only focused on one time point in pregnancy. In this study, we conducted a nested case-control study utilizing a follow-up cohort, resulting in the collection of 47 HDP patients and 30 healthy controls. The GM profiles were explored using 16S rRNA sequencing at three time points during pregnancy. The diversity analysis of GM showed no significant difference between HDP patients and controls, however, we found 21 differential GM during pregnancy. Trend analysis showed that there are statistical differences in the relative abundance of Thermomonas, Xanthomonas, and Phenylobacteriumat during pregnancy in the gestational hypertension group, and of Xanthomonas, Polycyclovorans, and Phenylobacterium in the control group. The correlation study found that six genera of GM are related to blood pressure. Furthermore, the MR analysis identified the causal relationship between Methanobrevibacter and pre-eclampsia (PE). This study first explored the longitudinal change of GM in HDP patients during pregnancy, found the differential GM, and detected the causal association. Our findings may promote the prevention and treatment of HDP from the perspective of GM and provide valuable insights into the pathogenesis of HDP.
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Affiliation(s)
- Xinrui Wu
- School of Medicine, Jishou University, Jishou, China
- Xiangya School of Public Health, Central South University, Changsha, China
| | - Qi Li
- Xiangxi Center for Disease Control and Prevention, Jishou, China
| | - Jiawang Cai
- School of Medicine, Jishou University, Jishou, China
| | | | - Shujuan Ma
- Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China.
| | - Hongzhuan Tan
- Xiangya School of Public Health, Central South University, Changsha, China.
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Jiang X, Miao B, Zhao X, Bai X, Yuan M, Chen X, Gong X, Liu Z, Li J, Meng S, Han X, Li J. Unveiling the Emergence and Genetic Diversity of OXA-48-like Carbapenemase Variants in Shewanella xiamenensis. Microorganisms 2023; 11:1325. [PMID: 37317299 DOI: 10.3390/microorganisms11051325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 05/09/2023] [Accepted: 05/15/2023] [Indexed: 06/16/2023] Open
Abstract
An increase in the carbapenem-hydrolyzing capacity of class D β-lactamase has been observed in strains of multiple species, posing a significant challenge to the control of antibiotic resistance. In this study, we aimed to investigate the genetic diversity and phylogenetic characteristics of new blaOXA-48-like variants derived from Shewanella xiamenensis. Three ertapenem-non-susceptible S. xiamenensis strains were identified, one isolated from the blood sample of an inpatient, the other two isolated from the aquatic environment. Phenotypic characterization confirmed that the strains were carbapenemase producers and exhibited antimicrobial resistance patterns to ertapenem, with some showing lower susceptibility to imipenem, chloramphenicol, ciprofloxacin, and tetracycline. No significant resistance to cephalosporins was observed. Sequence analysis revealed that one strain harbored blaOXA-181 and the other two strains harbored blaOXA-48-like genes, with open reading frame (ORF) similarities with blaOXA-48 ranging from 98.49% to 99.62%. The two novel blaOXA-48-like genes, named blaOXA-1038 and blaOXA-1039, respectively, were cloned and expressed in E. coli. The three OXA-48-like enzymes demonstrated significant hydrolysis activity against meropenem, and the classical β-lactamase inhibitor had no significant inhibitory effect. In conclusion, this study demonstrated the diversity of the blaOXA gene and highlighted the emergence of novel OXA carbapenemases in S. xiamenensis. Further attention to S. xiamenensis and OXA carbapenemases is recommended for the effective prevention and control of antibiotic-resistant bacteria.
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Affiliation(s)
- Xueqi Jiang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Beibei Miao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Xiaofei Zhao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Xuemei Bai
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Min Yuan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Xia Chen
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Xinyi Gong
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Zeliang Liu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Jie Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Shuang Meng
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Xiao Han
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Juan Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
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Lu J, Sha H, Chen J, Yi X, Xiong J. Characterizing sediment functional traits and ecological consequences respond to increasing antibiotic pollution. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12572-7. [PMID: 37191684 DOI: 10.1007/s00253-023-12572-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/28/2023] [Accepted: 05/05/2023] [Indexed: 05/17/2023]
Abstract
Current studies have shown that the taxonomic structures of ecologically important microbial communities are altered by antibiotic exposure, but the resulting effects on functional potentials and subsequent biogeochemical processes are poorly understood. However, this knowledge is indispensable for developing an accurate projection of nutrient dynamics in the future. Using metagenomic analyses, here we explored the responses of taxonomical and functional structures of a sediment microbial community, and their links with key biogeochemical processes to increasing antibiotic pollution from the pristine inlet to the outfall sites along an aquaculture discharge channel. We identified sharply contrasting sedimentary microbial communities and functional traits along increasing antibiotic pollution. Functional structures exhibited steeper distance-decay relationships than taxonomical structures along both the antibiotic distance and physicochemical distance, revealing higher functional sensitivity. Sediment enzyme activities were significantly and positively coupled with the relative abundances of their coding genes, thus the abundances of genes were indicative of functional potentials. The nitrogen cycling pathways were commonly inhibited by antibiotics, but not for the first step of nitrification, which could synergistically mitigate nitrous oxide emission. However, antibiotic pollution stimulated methanogens and inhibited methanotrophs, thereby promoting methane efflux. Furthermore, microbes could adapt to antibiotic pollution through enriched potential of sulfate uptake. Antibiotics indirectly affected taxonomic structures through alterations in network topological features, which in turn affected sediment functional structures and biogeochemical processes. Notably, only 13 antibiotics concentration-discriminatory genes contributed an overall 95.9% accuracy in diagnosing in situ antibiotic concentrations, in which just two indicators were antibiotic resistance genes. Our study comprehensively integrates sediment compositional and functional traits, biotic interactions, and enzymatic activities, thus generating a better understanding about ecological consequences of increasing antibiotics pollution. KEY POINTS: • Contrasting functional traits respond to increasing antibiotic pollution. • Antibiotics pollution stimulates CH4 efflux, while mitigating N2O emission and may drive an adaptive response of enriched sulfate uptake. • Indicator genes contribute 95.9% accuracy in diagnosing antibiotic concentrations.
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Affiliation(s)
- Jiaqi Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, 315211, Ningbo, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Haonan Sha
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, 315211, Ningbo, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, 315211, Ningbo, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Xianghua Yi
- Lanshion Marine Science and Technology Co., Ltd, Ningbo, 315715, China
| | - Jinbo Xiong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, 315211, Ningbo, China.
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
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Luo B, Su JY, Wang YN, Guan L, Dong KS, Niu HJ, Shen SF, Li Y. Shewanella subflava sp. nov., a novel multi-resistant bacterium, isolated from the estuary of the Fenhe River into the Yellow River. Antonie Van Leeuwenhoek 2023; 116:511-519. [PMID: 37022511 DOI: 10.1007/s10482-023-01829-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 03/29/2023] [Indexed: 04/07/2023]
Abstract
A aerobic, gram-negative, rod-shaped and polar-flagellum bacterial strain, designated as FYR11-62T, was isolated from the estuary of the Fenhe River into the Yellow River in Shanxi Province, China. The isolate was able to grow at 4-37 °C (optimum, 25 °C), pH 5.5-9.5 (optimum, pH 7.5) and in the presence of 0-7.0% (w/v) NaCl (optimum, 1.0% NaCl). Phylogenetic analyses based on 16S rRNA genes and 1597 single-copy orthologous clusters indicated that strain FYR11-62T affiliated with the genus Shewanella and shared the highest 16S rRNA gene sequence similarity to Shewanella aestuarii SC18T (98.3%) and Shewanella gaetbuli TF-27T (97.3%), respectively. The major fatty acids were summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), C16:0 and iso-C15:0. The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The main quinones were Q-7 and Q-8. The genomic DNA G + C content was 41.6%. Gene annotation showed that strain FYR11-62T possessed 30 antibiotic resistance genes, implying its multiple antidrug resistance. The average nucleotide identity and digital DNA-DNA hybridization values between strain FYR11-62T and its closely related species were all below the thresholds for species delineation. The phylogenetic position together with the results of the analysis of morphological, physiological and genomic features support the classification of strain FYR11-62T (= MCCC 1K07242T = KCTC 92244T) as a novel species of the genus Shewanella, for which the name Shewanella subflava sp. nov. is proposed.
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Affiliation(s)
- Bi Luo
- Financial Assets Department, Shanxi Agricultural University, Taigu, 030801, China
| | - Jing-Yun Su
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, China
| | - Ya-Nan Wang
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, China
| | - Li Guan
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, China
| | - Kai-Shi Dong
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, China
| | - Hui-Jing Niu
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Shao-Fei Shen
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, China.
| | - Yi Li
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, China.
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10
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Nelli A, Venardou B, Skoufos I, Voidarou C(C, Lagkouvardos I, Tzora A. An Insight into Goat Cheese: The Tales of Artisanal and Industrial Gidotyri Microbiota. Microorganisms 2023; 11:microorganisms11010123. [PMID: 36677415 PMCID: PMC9863150 DOI: 10.3390/microorganisms11010123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 12/22/2022] [Accepted: 12/29/2022] [Indexed: 01/06/2023] Open
Abstract
The purpose of this study was to determine for the first time the microbiota in artisanal-type and industrial-type Gidotyri cheeses and investigate the influence of the cheese-making practices on their composition using culture-independent techniques. The microbiota present in artisanal with commercial starters (Artisanal_CS, n = 15), artisanal with in-house starters (Artisanal_IHS, n = 10) and industrial (Ind., n = 9) Gidotyri cheese samples were analyzed using a targeted metagenomic approach (16S rRNA gene). The Ind. Gidotyri cheese microbiota were less complex, dominated by the Streptococcaceae family (91%) that was more abundant compared to the artisanal Gidotyri cheeses (p < 0.05). Artisanal cheeses were more diverse compositionally with specific bacterial species being prevalent to each subtype. Particularly, Loigolactobacillus coryniformis (OTU 175), Secundilactobacillus malefermentans (OTU 48), and Streptococcus parauberis (OTU 50) were more prevalent in Artisanal_IHS cheeses compared to Artisanal_CS (p ≤ 0.001) and Ind. (p < 0.01) Gidotyri cheeses. Carnobacterium maltaromaticum (OTU 23) and Enterobacter hormaechei subsp. hoffmannii (OTU 268) were more prevalent in Artisanal_CS cheeses compared to Artisanal_IHS cheeses (p < 0.05) and Ind. cheeses (p < 0.05). Hafnia alvei (OTU 13) and Acinetobacter colistiniresistens (OTU 111) tended to be more prevalent in Artisanal_CS compared to the other two cheese groups (p < 0.10). In conclusion, higher microbial diversity was observed in the artisanal-type Gidotyri cheeses, with possible bacterial markers specific to each subtype identified with potential application to traceability of the manufacturing processes’ authenticity and cheese quality.
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11
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Cerbino GN, Traglia GM, Ayala Nuñez T, Parmeciano Di Noto G, Ramírez MS, Centrón D, Iriarte A, Quiroga C. Comparative genome analysis of the genus Shewanella unravels the association of key genetic traits with known and potential pathogenic lineages. Front Microbiol 2023; 14:1124225. [PMID: 36925471 PMCID: PMC10011109 DOI: 10.3389/fmicb.2023.1124225] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/06/2023] [Indexed: 03/06/2023] Open
Abstract
Shewanella spp. are Gram-negative rods widely disseminated in aquatic niches that can also be found in human-associated environments. In recent years, reports of infections caused by these bacteria have increased significantly. Mobilome and resistome analysis of a few species showed that they are versatile; however, comprehensive comparative studies in the genus are lacking. Here, we analyzed the genetic traits of 144 genomes from Shewanella spp. isolates focusing on the mobilome, resistome, and virulome to establish their evolutionary relationship and detect unique features based on their genome content and habitat. Shewanella spp. showed a great diversity of mobile genetic elements (MGEs), most of them associated with monophyletic lineages of clinical isolates. Furthermore, 79/144 genomes encoded at least one antimicrobial resistant gene with their highest occurrence in clinical-related lineages. CRISPR-Cas systems, which confer immunity against MGEs, were found in 41 genomes being I-E and I-F the more frequent ones. Virulome analysis showed that all Shewanella spp. encoded different virulence genes (motility, quorum sensing, biofilm, adherence, etc.) that may confer adaptive advantages for survival against hosts. Our data revealed that key accessory genes are frequently found in two major clinical-related groups, which encompass the opportunistic pathogens Shewanella algae and Shewanella xiamenensis together with several other species. This work highlights the evolutionary nature of Shewanella spp. genomes, capable of acquiring different key genetic traits that contribute to their adaptation to different niches and facilitate the emergence of more resistant and virulent isolates that impact directly on human and animal health.
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Affiliation(s)
- Gabriela N Cerbino
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPAM), Facultad de Medicina, Buenos Aires, Argentina
| | - German M Traglia
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Teolincacihuatl Ayala Nuñez
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPAM), Facultad de Medicina, Buenos Aires, Argentina
| | - Gisela Parmeciano Di Noto
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPAM), Facultad de Medicina, Buenos Aires, Argentina
| | - María Soledad Ramírez
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University, Fullerton, Fullerton, CA, United States
| | - Daniela Centrón
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPAM), Facultad de Medicina, Buenos Aires, Argentina
| | - Andrés Iriarte
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Cecilia Quiroga
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPAM), Facultad de Medicina, Buenos Aires, Argentina
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12
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Chia-Wei L, Cheng JF, Tung KC, Hong YK, Lin JH, Lin YH, Tsai CA, Lin SP, Chen YC, Shi ZY, Huang YT, Liu PY. Evolution of trimethoprim/sulfamethoxazole resistance in Shewanella algae from the perspective of comparative genomics and global phylogenic analysis. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2022; 55:1195-1202. [PMID: 34732312 DOI: 10.1016/j.jmii.2021.09.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 08/22/2021] [Accepted: 09/15/2021] [Indexed: 12/27/2022]
Abstract
OBJECTIVE Shewanella algae is a zoonotic marine bacterium that causes a variety of infections in immunocompromised patients or those who have been exposed to seawater. The development of trimethoprim/sulfamethoxazole (TMP/SMX) resistance in S. algae are found in human and environment isolates during the past ten years, and thus the treatment options are decreasing. METHODOLOGY In the study, we conduct a comparative genomic study to identify the resistant mechanism of TMP/SMX-resistance in S. algae. RESULTS We found the resistance of TMP/SMX in S. algae is associated with the existence of sul1 and dfrA12 within the class 1 integron. The gene cassette dfra12-aadA2-qacEΔ1/sul1 within the class 1 integron is highly conserved. In addition, the class 1 integron and encapsulated sul1 are significantly enriched in Enterobacteriaceae in NCBI and UniProt databases. CONCLUSION Our study suggests that the horizontal transfer of TMP/SMX resistance via class 1 integron is most frequently occurred within Enterobacteriaceae and has spread to a wide range of sources including soil, poultry, and marine water.
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Affiliation(s)
- Liu Chia-Wei
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Jan-Fang Cheng
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Kwong-Chung Tung
- Department of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Yu-Kai Hong
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-Yi, Taiwan
| | - Jyun-Hong Lin
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-Yi, Taiwan
| | - Yu-Hui Lin
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Che-An Tsai
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Shih-Ping Lin
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Yung-Chun Chen
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Zhi-Yuan Shi
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Yao-Ting Huang
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-Yi, Taiwan.
| | - Po-Yu Liu
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan; Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung, Taiwan; Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung, Taiwan.
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13
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Yu K, Huang Z, Xiao Y, Wang D. Shewanella infection in humans: Epidemiology, clinical features and pathogenicity. Virulence 2022; 13:1515-1532. [PMID: 36065099 PMCID: PMC9481105 DOI: 10.1080/21505594.2022.2117831] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The genus Shewanella consists of Gram-negative proteobacteria that are ubiquitously distributed in environment. As the members of this genus have rapidly increased within the past decade, several species have become emerging pathogens worldwide, attracting the attention of the medical community. These species are also associated with severe community- and hospital-acquired infections. Patients infected with Shewanella spp. had experiences of occupational or recreational exposure; meanwhile, the process of infection is complex and the pathogenicity is influenced by a variety of factors. Here, an exhaustive internet-based literature search was carried out in PUBMED using terms “Achromobacter putrefaciens,” “Pseudomonas putrefaciens,” “Alteromonas putrefaciens” and “Shewanella” to search literatures published between 1978 and June 2022. We provided a comprehensive review on the epidemiology, clinical features and pathogenicity of Shewanella, which will contribute a better understanding of its clinical aetiology, and facilitate the timely diagnosis and effective treatment of Shewanella infection for clinicians and public health professionals.
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Affiliation(s)
- Keyi Yu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China.,Center for Human Pathogenic Culture Collection, China CDC, Beijing, China
| | - Zhenzhou Huang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China.,Center for Human Pathogenic Culture Collection, China CDC, Beijing, China
| | - Yue Xiao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China.,Center for Human Pathogenic Culture Collection, China CDC, Beijing, China
| | - Duochun Wang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China.,Center for Human Pathogenic Culture Collection, China CDC, Beijing, China
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14
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Li R, Zhang L, Lu X, Peng K, Liu Y, Xiao X, Song H, Wang Z. Occurrence and Characterization of NDM-1-Producing Shewanella spp. and Acinetobacter portensis Co-Harboring tet(X3) in a Chinese Dairy Farm. Antibiotics (Basel) 2022; 11:1422. [PMID: 36290080 PMCID: PMC9598548 DOI: 10.3390/antibiotics11101422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/12/2022] [Accepted: 10/14/2022] [Indexed: 08/15/2023] Open
Abstract
Bacteria with carbapenem or tigecycline resistance have been spreading widely among humans, animals and the environment globally, being great threats to public health. However, bacteria co-carrying drug resistance genes of carbapenem and tigecycline in Shewanella and Acinetobacter species remain to be investigated. Here, we detected nine blaNDM-1-carrying Shewanella spp. isolates as well as three A. portensis isolates co-harboring tet(X3) and blaNDM-1 from seventy-two samples collected from a dairy farm in China. To explore their genomic characteristic and transmission mechanism, we utilized various methods, including PCR, antimicrobial susceptibility testing, conjugation experiment, whole-genome sequencing, circular intermediate identification and bioinformatics analysis. Clonal dissemination was found among three A. portensis, of which tet(X3) and blaNDM-1 were located on a novel non-conjugative plasmid pJNE5-X3_NDM-1 (333,311 bp), and the circular intermediate ΔISCR2-tet(X3)-blaNDM-1 was identified. Moreover, there was another copy of tet(X3) on the chromosome of A. portensis. It was verified that blaNDM-1 could be transferred to Escherichia coli C600 from Shewanella spp. by conjugation, and self-transmissible IncA/C2 plasmids mediated the transmission of blaNDM-1 in Shewanella spp. strains. Stringent surveillance was warranted to curb the transmission of such vital resistance genes.
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Affiliation(s)
- Ruichao Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou 225009, China
| | - Lifei Zhang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
| | - Xiaoyu Lu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
| | - Kai Peng
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
| | - Yuan Liu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou 225009, China
| | - Xia Xiao
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
| | - Hongqin Song
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
| | - Zhiqiang Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
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Deng Z, Zeng S, Zhou R, Hou D, Bao S, Zhang L, Hou Q, Li X, Weng S, He J, Huang Z. Phage-prokaryote coexistence strategy mediates microbial community diversity in the intestine and sediment microhabitats of shrimp culture pond ecosystem. Front Microbiol 2022; 13:1011342. [PMID: 36212844 PMCID: PMC9537357 DOI: 10.3389/fmicb.2022.1011342] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 08/24/2022] [Indexed: 11/23/2022] Open
Abstract
Emerging evidence supports that the phage-prokaryote interaction drives ecological processes in various environments with different phage life strategies. However, the knowledge of phage-prokaryote interaction in the shrimp culture pond ecosystem (SCPE) is still limited. Here, the viral and prokaryotic community profiles at four culture stages in the intestine of Litopenaeus vannamei and cultural sediment microhabitats of SCPE were explored to elucidate the contribution of phage-prokaryote interaction in modulating microbial communities. The results demonstrated that the most abundant viral families in the shrimp intestine and sediment were Microviridae, Circoviridae, Inoviridae, Siphoviridae, Podoviridae, Myoviridae, Parvoviridae, Herelleviridae, Mimiviridae, and Genomoviridae, while phages dominated the viral community. The dominant prokaryotic genera were Vibrio, Formosa, Aurantisolimonas, and Shewanella in the shrimp intestine, and Formosa, Aurantisolimonas, Algoriphagus, and Flavobacterium in the sediment. The viral and prokaryotic composition of the shrimp intestine and sediment were significantly different at four culture stages, and the phage communities were closely related to the prokaryotic communities. Moreover, the phage-prokaryote interactions can directly or indirectly modulate the microbial community composition and function, including auxiliary metabolic genes and closed toxin genes. The interactional analysis revealed that phages and prokaryotes had diverse coexistence strategies in the shrimp intestine and sediment microhabitats of SCPE. Collectively, our findings characterized the composition of viral communities in the shrimp intestine and cultural sediment and revealed the distinct pattern of phage-prokaryote interaction in modulating microbial community diversity, which expanded our cognization of the phage-prokaryote coexistence strategy in aquatic ecosystems from the microecological perspective and provided theoretical support for microecological prevention and control of shrimp culture health management.
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Affiliation(s)
- Zhixuan Deng
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shenzheng Zeng
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Renjun Zhou
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Dongwei Hou
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shicheng Bao
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Linyu Zhang
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qilu Hou
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xuanting Li
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shaoping Weng
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Maoming, China
| | - Jianguo He
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Maoming, China
- *Correspondence: Jianguo He,
| | - Zhijian Huang
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Maoming, China
- Zhijian Huang,
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16
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Li S, Ondon BS, Ho SH, Jiang J, Li F. Antibiotic resistant bacteria and genes in wastewater treatment plants: From occurrence to treatment strategies. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156544. [PMID: 35679932 DOI: 10.1016/j.scitotenv.2022.156544] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 06/02/2022] [Accepted: 06/03/2022] [Indexed: 06/15/2023]
Abstract
This study aims to discuss the following: (1) occurrence and proliferation of antibiotic resistance in wastewater treatment plants (WWTPs); (2) factors influencing antibiotic resistance bacteria and genes in WWTPs; (3) tools to assess antibiotic resistance in WWTPs; (4) environmental contamination of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) from WWTPs; (5) effects of ARB and ARGs from WWTPs on human health; and (6) treatment strategies. In general, resistant and multi-resistant bacteria, including Enterobacteriaceae, Pseudomonas aeruginosa, and Escherichia coli, exist in various processes of WWTPs. The existence of ARB and ARGs results from the high concentration of antibiotics in wastewater, which promote selective pressures on the local bacteria present in WWTPs. Thus, improving wastewater treatment technology and avoiding the misuse of antibiotics is critical to overcoming the threat of proliferation of ARBs and ARGs. Numerous factors can affect the development of ARB and ARGs in WWTPs. Abiotic factors can affect the bacterial community dynamics, thereby, affecting the applicability of ARB during the wastewater treatment process. Furthermore, the organic loads and other nutrients influence bacterial survival and growth. Specifically, molecular methods for the rapid characterization and detection of ARBs or their genes comprise DNA sequencing, real-time PCR, simple and multiplex PCR, and hybridization-based technologies, including micro- and macro-arrays. The reuse of effluent from WWTPs for irrigation is an efficient method to overcome water scarcity. However, there are also some potential environmental risks associated with this practice, such as increase in the levels of antibiotic resistance in the soil microbiome. Human mortality rates may significantly increase, as ARB can lead to resistance among several types of antibiotics or longer treatment times. Some treatment technologies, such as anaerobic and aerobic treatment, coagulation, membrane bioreactors, and disinfection processes, are considered potential techniques to restrict antibiotic resistance in the environment.
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Affiliation(s)
- Shengnan Li
- Key Laboratory of Pollution Processes and Environmental Criteria of the Ministry of Education, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China
| | - Brim Stevy Ondon
- Key Laboratory of Pollution Processes and Environmental Criteria of the Ministry of Education, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Shih-Hsin Ho
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China
| | - Jiwei Jiang
- Key Laboratory of Pollution Processes and Environmental Criteria of the Ministry of Education, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Fengxiang Li
- Key Laboratory of Pollution Processes and Environmental Criteria of the Ministry of Education, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China.
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Madan K, Goel A, Singh O, Gupta A, Tarai B, Juneja D. Shewanella algae: A Rare Cause of Sepsis and Septic Shock. INDIAN JOURNAL OF CRITICAL CARE CASE REPORT 2022; 1:9-10. [DOI: 10.5005/jp-journals-11006-0003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
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18
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A Pilot Study: Favorable Effects of Clostridium butyricum on Intestinal Microbiota for Adjuvant Therapy of Lung Cancer. Cancers (Basel) 2022; 14:cancers14153599. [PMID: 35892858 PMCID: PMC9332558 DOI: 10.3390/cancers14153599] [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: 05/27/2022] [Revised: 06/22/2022] [Accepted: 07/20/2022] [Indexed: 02/01/2023] Open
Abstract
Probiotics as medications have previously been shown to change intestinal microbial characteristics, potentially influencing cancer therapy efficacy. Patients with non-squamous non-small cell lung cancer (NS-NSCLC) treated by bevacizumab plus platinum-based chemotherapy were randomized to obtain Clostridium butyricum supplement (CBS) or receive a placebo as adjuvant therapy. Clinical efficacy and safety were assessed using progression-free survival (PFS), overall survival (OS), and adverse events (AE). Intestinal microbiota was longitudinally explored between CBS and placebo groups over time. Patients who took CBS had significantly decreased bacterial richness and abundance, as well as increased the total richness of the genus Clostridium, Bifidobacterium, and Lactobacillus compared to the placebo group (p < 0.05). Beta diversity and the interactional network of intestinal microbiota were distinctly different between CBS and placebo group. However, there were no significant variations between them in terms of microbial taxonomical taxa and alpha diversity. The potential opportunistic pathogen Shewanella was still detectable after treatment in the placebo group, while no distinguishing microbial markers were found in the CBS group. In terms of clinical efficacy, the CBS group had a significantly reduced AE compare to the placebo group (p < 0.05), although no significantly longer PFS and OS. Therefore, favorable modifications in intestinal microbiota and significant improvements in drug safety make probiotics be promising adjunctive therapeutic avenues for lung cancer treatment.
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Ayala Nuñez T, Cerbino GN, Rapisardi MF, Quiroga C, Centrón D. Novel Mobile Integrons and Strain-Specific Integrase Genes within Shewanella spp. Unveil Multiple Lateral Genetic Transfer Events within The Genus. Microorganisms 2022; 10:microorganisms10061102. [PMID: 35744620 PMCID: PMC9229058 DOI: 10.3390/microorganisms10061102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 11/16/2022] Open
Abstract
Shewanella spp. are Gram-negative bacteria that thrive in aquatic niches and also can cause infectious diseases as opportunistic pathogens. Chromosomal (CI) and mobile integrons (MI) were previously described in some Shewanella isolates. Here, we evaluated the occurrence of integrase genes, the integron systems and their genetic surroundings in the genus. We identified 22 integrase gene types, 17 of which were newly described, showing traits of multiple events of lateral genetic transfer (LGT). Phylogenetic analysis showed that most of them were strain-specific, except for Shewanella algae, where SonIntIA-like may have co-evolved within the host as typical CIs. It is noteworthy that co-existence of up to five different integrase genes within a strain, as well as their wide dissemination to Alteromonadales, Vibrionales, Chromatiales, Oceanospirillales and Enterobacterales was observed. In addition, identification of two novel MIs suggests that continuous LGT events may have occurred resembling the behavior of class 1 integrons. The constant emergence of determinants associated to antimicrobial resistance worldwide, concomitantly with novel MIs in strains capable to harbor several types of integrons, may be an alarming threat for the recruitment of novel antimicrobial resistance gene cassettes in the genus Shewanella, with its consequent contribution towards multidrug resistance in clinical isolates.
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Affiliation(s)
- Teolincacihuatl Ayala Nuñez
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires CP1121, Argentina; (T.A.N.); (G.N.C.); (M.F.R.)
| | - Gabriela N. Cerbino
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires CP1121, Argentina; (T.A.N.); (G.N.C.); (M.F.R.)
| | - María Florencia Rapisardi
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires CP1121, Argentina; (T.A.N.); (G.N.C.); (M.F.R.)
| | - Cecilia Quiroga
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires CP1121, Argentina; (T.A.N.); (G.N.C.); (M.F.R.)
- Laboratorio de Investigación en Biología del ARN Bacteriano IMPaM (UBA/CONICET), Faculty of Medicine, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires CP1121, Argentina
- Correspondence: or (C.Q.); (D.C.); Tel.: +54-11-5285-3500 (C.Q.); +54-911-50987496 (D.C.)
| | - Daniela Centrón
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires CP1121, Argentina; (T.A.N.); (G.N.C.); (M.F.R.)
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos IMPaM (UBA/CONICET), Faculty of Medicine, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires CP1121, Argentina
- Correspondence: or (C.Q.); (D.C.); Tel.: +54-11-5285-3500 (C.Q.); +54-911-50987496 (D.C.)
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20
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Kaliyeva SS, Lavrinenko AV, Tishkambayev Y, Zhussupova G, Issabekova A, Begesheva D, Simokhina N. Microbial Landscape and Antibiotic Susceptibility Dynamics of Skin and Soft Tissue Infections in Kazakhstan 2018–2020. Antibiotics (Basel) 2022; 11:antibiotics11050659. [PMID: 35625303 PMCID: PMC9137831 DOI: 10.3390/antibiotics11050659] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/04/2022] [Accepted: 05/11/2022] [Indexed: 02/04/2023] Open
Abstract
Skin and soft tissue inflammatory diseases of bacterial origin occupy a significant part of hospitalizations to emergency departments. One of the most common causes of sepsis is soft tissue infection, which accounts for about a quarter of all nosocomial infections. The aim of this study was to determine the differences in microbial landscape and antibiotic susceptibility of soft tissue infection pathogens among adults and children during the period 2018–2020. We studied 110 samples of pus admitted to the Scientific Research laboratory of the Karaganda Medical University from 2018 to 2020. Each sample was studied using the standard and express methods. The antibiotic susceptibility was determined by using the diffuse disk method in accordance with the CLSI 2018 recommendations. As such, 50% of S. epidermidis strains in children and 30% in adults were methicillin resistant. Differences in the resistance of S. aureus strains in children and adults were insignificant. Thus, methicillin-resistant S. aureus (MRSA) was not detected in children, but in adults, on the other hand, their percentage was 12.5%. The third cause of infection in adults was E. coli (13.72%), among which 75% were multidrug resistant. A. baumanii was found in 4.9% of adult patients’ samples, of which 60% were multidrug resistant. The effectiveness of the most prescribed antibiotics decreased due to the isolated strain resistance.
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Affiliation(s)
- Sholpan S. Kaliyeva
- Department of Clinical Pharmacology and Evidence-Based Medicine, NCJSC Karaganda Medical University, Karaganda 100000, Kazakhstan; (S.S.K.); (N.S.)
| | - Alyona V. Lavrinenko
- Scientific Research Laboratory, NCJSC Karaganda Medical University, Karaganda 100000, Kazakhstan;
| | - Yerbol Tishkambayev
- Department of Surgery, NCJSC Karaganda Medical University, Karaganda 100000, Kazakhstan;
| | - Gulzira Zhussupova
- Salidat Kairbekova National Research Center for Health Development, Nur-Sultan 010000, Kazakhstan
- Correspondence: (G.Z.); (A.I.); Tel.: +77-(07)-953-8148 (G.Z.); +77-(08)-625-4901 (A.I.)
| | - Aissulu Issabekova
- Department of Clinical Pharmacology and Evidence-Based Medicine, NCJSC Karaganda Medical University, Karaganda 100000, Kazakhstan; (S.S.K.); (N.S.)
- Correspondence: (G.Z.); (A.I.); Tel.: +77-(07)-953-8148 (G.Z.); +77-(08)-625-4901 (A.I.)
| | - Dinara Begesheva
- National Center for Rational Use of Medicines, Nur-Sultan 010000, Kazakhstan;
| | - Natalya Simokhina
- Department of Clinical Pharmacology and Evidence-Based Medicine, NCJSC Karaganda Medical University, Karaganda 100000, Kazakhstan; (S.S.K.); (N.S.)
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21
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Yan Y, Chai X, Chen Y, Zhang X. The Fulminating Course of Infection Caused by Shewanella algae: A Case Report. Infect Drug Resist 2022; 15:1645-1650. [PMID: 35422640 PMCID: PMC9005229 DOI: 10.2147/idr.s357181] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/26/2022] [Indexed: 11/23/2022] Open
Abstract
Shewanella algae, a Gram-negative bacillus found in warm saltwater environments, has been increasingly recognized as a human pathogen that can cause infection of the skin and soft tissue, ear, blood, and intra-abdominal. In this case, we report a Shewanella algae infection that caused sepsis, renal insufficiency, cardiac dysfunction, fistula and massive pleural effusion after surgery in a 73-year-old man with cancer of the esophagus and cardia.
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Affiliation(s)
- Yun Yan
- Department of Critical Care Medicine, Xijing Hospital, The Fourth Military Medical University, Xi’an, People’s Republic of China
| | - Xin Chai
- Department of Critical Care Medicine, Xijing Hospital, The Fourth Military Medical University, Xi’an, People’s Republic of China
| | - Yu Chen
- Department of Critical Care Medicine, Xijing Hospital, The Fourth Military Medical University, Xi’an, People’s Republic of China
- Correspondence: Yu Chen; Xijing Zhang, Department of Critical Care Medicine, Xijing Hospital, The Fourth Military Medical University, Xi’an, People’s Republic of China, Tel +862984775344, Fax +862983244986, Email ;
| | - Xijing Zhang
- Department of Critical Care Medicine, Xijing Hospital, The Fourth Military Medical University, Xi’an, People’s Republic of China
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22
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Lizárraga WC, Mormontoy CG, Calla H, Castañeda M, Taira M, Garcia R, Marín C, Abanto M, Ramirez P. Complete genome sequence of Shewanella algae strain 2NE11, a decolorizing bacterium isolated from industrial effluent in Peru. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2022; 33:e00704. [PMID: 35145887 PMCID: PMC8816663 DOI: 10.1016/j.btre.2022.e00704] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/28/2021] [Accepted: 01/19/2022] [Indexed: 12/14/2022]
Abstract
Shewanella is a microbial group with high potential to be applied in textile effluents bioremediation due to its ability to use a wide variety of substrates as a final electron acceptor in respiration. The present research aimed to describe a new strain, Shewanella algae 2NE11, a decolorizing bacterium isolated from industrial effluent in Peru. S. algae 2NE11 showed an optimal growth under pH 6-9, temperature between 30-40 °C, and 0-4 % NaCl. It can tolerate high concentrations of NaCl until 10% and low temperatures as 4 °C. It decolorizes azo and anthraquinone dyes with a decolorization rate of 89-97%. We performed next-generation sequencing (Pacific Bioscience®) and achieved its complete genome sequence with a length of 5,030,813bp and a GC content of 52.98%. Genomic characterization revealed the presence of protein-coding genes related to decolorization like azoreductase, dyp-peroxidase, oxidoreductases, and the complete Mtr respiratory pathway. Likewise, we identified other properties such as the presence of metal resistant genes, and genes related to lactate and N-acetylglucosamine metabolism. These results highlight its potential to be applied in the bioremediation of textile effluents and guide future research on decolorization metabolic pathways.
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Affiliation(s)
- Wendy C Lizárraga
- Laboratory of Molecular Microbiology and Biotechnology, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima, Perú
| | - Carlo G Mormontoy
- Laboratory of Molecular Microbiology and Biotechnology, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima, Perú
| | - Hedersson Calla
- Laboratory of Molecular Microbiology and Biotechnology, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima, Perú
| | - Maria Castañeda
- Laboratory of Molecular Microbiology and Biotechnology, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima, Perú
| | - Mario Taira
- Laboratory of Molecular Microbiology and Biotechnology, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima, Perú
| | - Ruth Garcia
- Laboratory of Molecular Microbiology and Biotechnology, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima, Perú
| | - Claudia Marín
- Laboratory of Molecular Microbiology and Biotechnology, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima, Perú
| | - Michel Abanto
- Núcleo Científico y Tecnológico en Biorecursos - BIOREN, Universidad de La Frontera, Temuco, Chile
| | - Pablo Ramirez
- Laboratory of Molecular Microbiology and Biotechnology, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima, Perú
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23
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Shewanella jiangmenensis sp. nov., isolated from aquaculture water. Arch Microbiol 2022; 204:198. [PMID: 35218433 DOI: 10.1007/s00203-022-02761-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 11/02/2022]
Abstract
A Gram-stain-negative and facultatively anaerobic bacterial strain designated as JM162201T was isolated from aquaculture water for farming Pacific white shrimp (Litopenaeus vannamei). The genome size of strain JM162201T was 4,436,316 bp, and the genomic DNA G + C content was 55.0%. Phylogenetic analysis based on 16S rRNA gene sequences and genomes showed that strain JM162201T belonged to the genus Shewanella and was closely related to Shewanella litorisediminis SMK1-12T (97.1%), Shewanella khirikhana TH2012T (97.0%), and Shewanella amazonensis SB2BT (96.0%). The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain JM162201T and three reference type strains were below the recognized thresholds of 95.0-96.0% (for ANI) and 70.0% (for dDDH) for species delineation. Growth occurred at 10-40 °C (optimum, 30 °C), at pH 4.0-10.0 (optimum, 7.0-8.0), and in 0-6.0% NaCl (w/v, optimum, 0-0.1%). The major cellular fatty acids of strain JM162201T were summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), C17:1 ω8c, iso-C15:0, C16:0, and C15:0. The predominant quinones were MK7, Q-7, and Q-8. The major polar lipids were phosphatidylethanolamine (PE) and phosphatidylglycerol (PG). Based on the polyphasic taxonomical analyses, strain JM162201T represents a novel species of the genus Shewanella, for which the name Shewanella jiangmenensis sp. nov. is proposed, with the type strain JM162201T (= GDMCC 1.2006T = KCTC 82340T).
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Yasin A, Begum MK, Eshik MME, Punom NJ, Ahmmed S, Rahman MS. Molecular identification and antibiotic resistance patterns of diverse bacteria associated with shrimp PL nurseries of Bangladesh: suspecting Acinetobacter venetianus as future threat. PeerJ 2022; 10:e12808. [PMID: 35223199 PMCID: PMC8868018 DOI: 10.7717/peerj.12808] [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: 08/04/2021] [Accepted: 12/27/2021] [Indexed: 01/11/2023] Open
Abstract
Shrimp aquaculture has been accomplished with breeding and nursing of shrimp in an artificial environment to fulfill the increasing demand of shrimp consumption worldwide. However, the microbial diseases appear as a serious problem in this industry. The study was designed to identify the diverse bacteria from shrimp PL (post-larvae) nurseries and to profile antibiotic resistance patterns. The rearing water (raw seawater, treated and outlet water) and shrimp PL were collected from eight nurseries of south-west Bangladesh. Using selective agar plates, thirty representative isolates were selected for 16S rRNA gene sequencing, antibiotic susceptibility test and MAR index calculation. Representative isolates were identified as Aeromonas caviae, Pseudomonas monteilii, Shewanella algae, Vibrio alginolyticus, V. brasiliensis, V. natriegens, V. parahaemolyticus, V. shilonii, V. xuii, Zobellella denitrificans which are Gram-negative, and Bacillus licheniformis and B. pumilus which are Gram-positive. Notably, six strains identified as Acinetobacter venetianus might be a concern of risk for shrimp industry. The antibiotic resistance pattern reveals that the strain YWO8-97 (identified as P. monteilii) was resistant to all twelve antibiotics. Ceftazidime was the most powerful antibiotic since most of the studied strains were sensitive against it. The six strains of A. venetianus showed multiple antibiotic resistance patterns. MAR index were ranged from 0.08 to 1.0, and values of 26 isolates were more than 0.2 which means prior high exposure to the antibiotics. From the present study, it can be concluded that shrimp PL nurseries in southern part of Bangladesh are getting contaminated with antibiotic resistant pathogenic bacteria.
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Affiliation(s)
- Abdullah Yasin
- Aquatic Animal Health Group, Department of Fisheries, Faculty of Biological Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Mst. Khadiza Begum
- Aquatic Animal Health Group, Department of Fisheries, Faculty of Biological Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Md. Mostavi Enan Eshik
- Aquatic Animal Health Group, Department of Fisheries, Faculty of Biological Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Nusrat Jahan Punom
- Aquatic Animal Health Group, Department of Fisheries, Faculty of Biological Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Shawon Ahmmed
- Aquatic Animal Health Group, Department of Fisheries, Faculty of Biological Sciences, University of Dhaka, Dhaka, Bangladesh,Brackishwater Station, Bangladesh Fisheries Research Institute (BFRI), Khulna, Bangladesh
| | - Mohammad Shamsur Rahman
- Aquatic Animal Health Group, Department of Fisheries, Faculty of Biological Sciences, University of Dhaka, Dhaka, Bangladesh
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25
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Huang Z, Yu K, Fu S, Xiao Y, Wei Q, Wang D. Genomic analysis reveals high intra-species diversity of Shewanella algae. Microb Genom 2022; 8. [PMID: 35143386 PMCID: PMC8942018 DOI: 10.1099/mgen.0.000786] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Shewanella algae is widely distributed in marine and freshwater habitats, and has been proved to be an emerging marine zoonotic and human pathogen. However, the genomic characteristics and pathogenicity of Shewanella algae are unclear. Here, the whole-genome features of 55 S. algae strains isolated from different sources were described. Pan-genome analysis yielded 2863 (19.4 %) genes shared among all strains. Functional annotation of the core genome showed that the main functions are focused on basic lifestyle such as metabolism and energy production. Meanwhile, the phylogenetic tree of the single nucleotide polymorphisms (SNPs) of core genome divided the 55 strains into three clades, with the majority of strains from China falling into the first two clades. As for the accessory genome, 167 genomic islands (GIs) and 65 phage-related elements were detected. The CRISPR-Cas system with a high degree of confidence was predicted in 23 strains. The GIs carried a suite of virulence genes and mobile genetic elements, while prophages contained several transposases and integrases. Horizontal genes transfer based on homology analysis indicated that these GIs and prophages were parts of major drivers for the evolution and the environmental adaptation of S. algae. In addition, a rich putative virulence-associated gene pool was found. Eight classes of antibiotic-associated resistance genes were detected, and the carriage rate of β-lactam resistance genes was 100 %. In conclusion, S. algae exhibits a high intra-species diversity in the aspects of population structure, virulence-associated genes and potential drug resistance, which is helpful for its evolution in pathogenesis and environmental adaptability.
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Affiliation(s)
- Zhenzhou Huang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, PR China.,Center for Human Pathogenic Culture Collection, China CDC, Beijing 102206, PR China
| | - Keyi Yu
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, PR China.,Center for Human Pathogenic Culture Collection, China CDC, Beijing 102206, PR China
| | - Songzhe Fu
- Key Laboratory of Environment Controlled Aquaculture (KLECA), Ministry of Education, Dalian, PR China.,College of Marine Science and Environment, Dalian Ocean University, Dalian, PR China
| | - Yue Xiao
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, PR China.,Center for Human Pathogenic Culture Collection, China CDC, Beijing 102206, PR China
| | - Qiang Wei
- Center for Human Pathogenic Culture Collection, China CDC, Beijing 102206, PR China
| | - Duochun Wang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, PR China.,Center for Human Pathogenic Culture Collection, China CDC, Beijing 102206, PR China
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26
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Liao G, Wu Q, Mo B, Zhou J, Li J, Zou J, Fan L. Intestinal morphology and microflora to Vibrio alginolyticus in pacific white shrimp (Litopenaeus vannamei). FISH & SHELLFISH IMMUNOLOGY 2022; 121:437-445. [PMID: 35065276 DOI: 10.1016/j.fsi.2022.01.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/15/2022] [Accepted: 01/16/2022] [Indexed: 06/14/2023]
Abstract
In recent years, the shrimp farming industry encountered significant economic losses induced by Vibrio alginolyticus. In this study, the influence of Vibrio alginolyticus on intestinal histomorphology and microbiome composition in Litopenaeus vannamei were studied. The results showed that the intestinal mucosal epithelial cells of Vibrio group (VA group) injected only with Vibrio alginolyticus showed large area exfoliation at 12 h, and the tissue morphology of intestine recovered at 48 h. Compared with the control group (CK group), the abundance of Proteobacteria was significantly higher (P < 0.05), while the abundance of Actinobacteria was significantly lower after infection with Vibrio alginolyticus. The abundance of Shewanella in intestinal microbiome of Litopenaeus vannamei was significantly higher at 12 h (P < 0.05), but the abundance of Candidatus_Bacilloplasma was significantly lower at 48 h after infection (P < 0.05). In VA group, the diversity of intestinal microbiome was significantly lower at 12 h, which could be caused by the proliferation of Candidatus_Bacilloplasma and Shewanella. All above findings suggested that the stability of the dynamic balance of microbiome in the intestine helped Litopenaeus vannamei to resist pathogen colonization.
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Affiliation(s)
- Guowei Liao
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Qiuping Wu
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Binhua Mo
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Jiang Zhou
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Junyi Li
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Jixing Zou
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Lanfen Fan
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China; Research Center for Green Development of Agriculture, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China.
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27
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Metagenomic and Recombination Analyses of Antimicrobial Resistance Genes from Recreational Waters of Black Sea Coastal Areas and Other Marine Environments Unveil Extensive Evidence for Their both Intrageneric and Intergeneric Transmission across Genetically Very Diverse Microbial Communities. Mar Genomics 2021; 61:100916. [PMID: 34922301 DOI: 10.1016/j.margen.2021.100916] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 12/04/2021] [Accepted: 12/06/2021] [Indexed: 11/20/2022]
Abstract
Microbial communities of marine coastal recreation waters have become large reservoirs of AMR genes (ARGs), contributing to the emergence and transmission of various zoonotic, foodborne and other infections that exhibit resistance to various antibiotics. Thus, it is highly imperative to determine ARGs assemblages as well as mechanisms and trajectories of their transmission across these microbial communities for our better understanding of the evolutionary trends of AMR (AMR). In this study, using metagenomics approaches, we screened for ARGs in recreation waters of the Black Sea coastal areas of the Batumi City (Georgia). Also, a large array of the recombination detection algorithms of the SplitsTree, RDP4, and GARD was applied to elucidate genetic recombination of ARGs and trajectories of their transmission across various marine microbial communities. The metagenomics analyses of sea water samples, obtained from across the above marine sites, could identify putative ARGs encoding for multidrug resistance efflux transporters mainly from the Major Facilitator and Resistance Nodulation Division superfamilies. The data, generated by SplitsTree (fit ≥95.619; bootstrap values ≥ 95; Phi p ≤ 0.0494), RDP4 (p ≤ 0.0490), and GARD, provided strong statistical evidence not only for intrageneric recombination of these ARGs, but also for their intergeneric recombination across fairly large and diverse microbial communities of marine environment. These bacteria included both human pathogenic and nonpathogenic species, exhibiting collectively the genera of Vibrio, Aeromonas, Synechococcus, Citromicrobium, Rhodobacteraceae, Pseudoalteromonas, Altererythrobacter, Erythrobacter, Altererythrobacter, Marivivens, Xuhuaishuia, and Loktanella. The above nonpathogenic bacteria are strongly suggested to contribute to ARGs transmission in marine ecosystems.
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28
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Jia PP, Junaid M, Xin GY, Wang Y, Ma YB, Pei DS. Disruption of Intestinal Homeostasis Through Altered Responses of the Microbial Community, Energy Metabolites, and Immune System in Zebrafish After Chronic Exposure to DEHP. Front Microbiol 2021; 12:729530. [PMID: 34675901 PMCID: PMC8524448 DOI: 10.3389/fmicb.2021.729530] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/02/2021] [Indexed: 01/09/2023] Open
Abstract
Di-(2-ethylhexyl) phthalate (DEHP) is ubiquitously reported in global water bodies and exhibits various environmental and human health risks. However, the effects of DEHP chronic exposure on the intestinal microbiota and associated host health concerns in aquatic species are still largely unexplored. In this study, chronic exposure to DEHP at environmental levels significantly increased the body weight, length, and body mass index (BMI), especially in male fish. The microbial community was disrupted with the relative abundance of phylum Firmicutes and genera diversity for Prevotella-7, Deefgea, PeM15, Halomonas, Akkermansia, Chitinibacter, and Roseomonas, which are significantly activated in zebrafish after exposure to DEHP. The height of the gut villus, the thickness of muscularis layer, and the number of goblet cells per villus were significantly decreased, as well as showed differences between female and male zebrafish. Further, the levels of energy-related metabolites in gut tissues were increased, compared to the control group. The expression levels of immune-related genes (interleukin 8, il-8, also referred to as cxcl8a), microbial defense-related genes (lysozyme, lyz, interleukin 10, and il-10), and obesity-related genes (aquaporin 8a, aqp8, mucin 2.1, muc2.1, fibroblast growth factor 2, fgf2, and proopiomelanocortin a, pomca) were significantly up-regulated in zebrafish, except the down-regulated expressions of toll-like receptor-5 (tlr-5) and interleukin 1β (il-1β) in the females and pomca in the males, respectively. Importantly, Spearman's correlation analyses revealed that the levels of metabolites and gene expressions in the gut were closely related to the dominant microbial genera, such as Aeromonas, Deefgea, Akkermansia, PeM15, Mycobacterium, and Rhodobacter. Taken together, chronic exposure to DEHP at environmental levels disturbed bacterial composition accompanied by the altered expressions of intestinal metabolites and the critical immune and intestinal function-related genes, which provided novel insights into DEHP effects on perturbation of gut microbiota and metabolic homeostasis in zebrafish.
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Affiliation(s)
- Pan-Pan Jia
- School of Public Health and Management, Chongqing Medical University, Chongqing, China.,Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Muhammad Junaid
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Guang-Yuan Xin
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Yan Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Yan-Bo Ma
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - De-Sheng Pei
- School of Public Health and Management, Chongqing Medical University, Chongqing, China
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Sanz-García F, Gil-Gil T, Laborda P, Ochoa-Sánchez LE, Martínez JL, Hernando-Amado S. Coming from the Wild: Multidrug Resistant Opportunistic Pathogens Presenting a Primary, Not Human-Linked, Environmental Habitat. Int J Mol Sci 2021; 22:8080. [PMID: 34360847 PMCID: PMC8347278 DOI: 10.3390/ijms22158080] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/22/2021] [Accepted: 07/24/2021] [Indexed: 12/24/2022] Open
Abstract
The use and misuse of antibiotics have made antibiotic-resistant bacteria widespread nowadays, constituting one of the most relevant challenges for human health at present. Among these bacteria, opportunistic pathogens with an environmental, non-clinical, primary habitat stand as an increasing matter of concern at hospitals. These organisms usually present low susceptibility to antibiotics currently used for therapy. They are also proficient in acquiring increased resistance levels, a situation that limits the therapeutic options for treating the infections they cause. In this article, we analyse the most predominant opportunistic pathogens with an environmental origin, focusing on the mechanisms of antibiotic resistance they present. Further, we discuss the functions, beyond antibiotic resistance, that these determinants may have in the natural ecosystems that these bacteria usually colonize. Given the capacity of these organisms for colonizing different habitats, from clinical settings to natural environments, and for infecting different hosts, from plants to humans, deciphering their population structure, their mechanisms of resistance and the role that these mechanisms may play in natural ecosystems is of relevance for understanding the dissemination of antibiotic resistance under a One-Health point of view.
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Affiliation(s)
| | | | | | | | - José L. Martínez
- Centro Nacional de Biotecnología, CSIC, 28049 Madrid, Spain; (F.S.-G.); (T.G.-G.); (P.L.); (L.E.O.-S.); (S.H.-A.)
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30
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Yu K, Huang Z, Li Y, Fu Q, Lin L, Wu S, Dai H, Cai H, Xiao Y, Lan R, Wang D. Establishment and Application of Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry for Detection of Shewanella Genus. Front Microbiol 2021; 12:625821. [PMID: 33679644 PMCID: PMC7930330 DOI: 10.3389/fmicb.2021.625821] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/04/2021] [Indexed: 01/28/2023] Open
Abstract
Shewanella species are widely distributed in the aquatic environment and aquatic organisms. They are opportunistic human pathogens with increasing clinical infections reported in recent years. However, there is a lack of a rapid and accurate method to identify Shewanella species. We evaluated here matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for rapid identification of Shewanella. A peptide mass reference spectra (PMRS) database was constructed for the type strains of 36 Shewanella species. The main spectrum projection (MSP) cluster dendrogram showed that the type strains of Shewanella species can be effectively distinguished according to the different MS fingerprinting. The PMRS database was validated using 125 Shewanella test strains isolated from various sources and periods; 92.8% (n = 116) of the strains were correctly identified at the species level, compared with the results of multilocus sequence analysis (MLSA), which was previously shown to be a method for identifying Shewanella at the species level. The misidentified strains (n = 9) by MALDI-TOF MS involved five species of two groups, i.e., Shewanella algae-Shewanella chilikensis-Shewanella indica and Shewanella seohaensis-Shewanella xiamenensis. We then identified and defined species-specific biomarker peaks of the 36 species using the type strains and validated these selected biomarkers using 125 test strains. Our study demonstrated that MALDI-TOF MS was a reliable and powerful tool for the rapid identification of Shewanella strains at the species level.
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Affiliation(s)
- Keyi Yu
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), State Key Laboratory for Infectious Disease Prevention and Control, Beijing, China
- Center for Human Pathogenic Culture Collection, China CDC, Beijing, China
| | - Zhenzhou Huang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), State Key Laboratory for Infectious Disease Prevention and Control, Beijing, China
- Center for Human Pathogenic Culture Collection, China CDC, Beijing, China
| | - Ying Li
- Workstation for Microbial Infectious Disease, Shunyi District Center for Disease Control and Prevention, Beijing, China
| | | | | | | | - Hang Dai
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), State Key Laboratory for Infectious Disease Prevention and Control, Beijing, China
- Center for Human Pathogenic Culture Collection, China CDC, Beijing, China
| | - Hongyan Cai
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), State Key Laboratory for Infectious Disease Prevention and Control, Beijing, China
- Center for Human Pathogenic Culture Collection, China CDC, Beijing, China
| | - Yue Xiao
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), State Key Laboratory for Infectious Disease Prevention and Control, Beijing, China
- Center for Human Pathogenic Culture Collection, China CDC, Beijing, China
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Duochun Wang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), State Key Laboratory for Infectious Disease Prevention and Control, Beijing, China
- Center for Human Pathogenic Culture Collection, China CDC, Beijing, China
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Comparative genomics of two Shewanella xiamenensis strains isolated from a pilgrim before and during travels to the Hajj. Gut Pathog 2021; 13:9. [PMID: 33563327 PMCID: PMC7871542 DOI: 10.1186/s13099-021-00404-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/02/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Shewanella xiamenensis has been reported in water environment and in patients and can act as the originator of oxacillinase in gram-negative bacteria. In order to assess genome plasticity and its functional properties related diarrhea symptoms in pilgrim, comparisons of draft genome sequences of the two isolates were conducted with other closely related genomes. RESULTS We isolated S. xiamenensis 111B and 111D strains from a pilgrim before travels to the Hajj and during travels with diarrhea symptom, respectively. Whole-genome sequencing showed that draft genome size of 111B strain was 5,008,191 bp, containing 49 kb of a putative plasmid. The genome size of 111D was 4,964,295 bp containing 225 kb of a putative plasmid that shared the backbone sequences with the hospital wastewater strain T17. Comparatively, two Hajj strains are identical at 97.3% identity and 98.7% coverage. They are closely related to river water strain, AS58 by SNPs analysis. Notably, a novel blaOXA-48 allele blaOXA-547 was identified in 111D, sharing 99.5% identity with blaOXA-546 and blaOXA-894. Multiple copies of virulence specific genes, such as capsular polysaccharide biosynthesis, O-antigen and lasB (vibriolysin related gene) have been identified specifically in 111D, but absent in 111B strain. CONCLUSIONS The whole genome sequences of S. xiamenensis strain 111B and 111D, including comparative genomic analysis, highlight here the potential for virulence factors that might be related to the cause of diarrhea in humans and also indicate the possible acquisition of pathogenic bacteria, including antibiotic resistance genes or plasmids during the Hajj.
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Ojha N, Walsh K, Hess MJ. Non-Necrotizing Bullous Cellulitis and Bacteremia: A Rare Presentation of the Shewanella Algae Infection. Cureus 2021; 13:e12776. [PMID: 33628648 PMCID: PMC7889438 DOI: 10.7759/cureus.12776] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
A 58-year-old male with severe psoriasis on Risankizumab presented with painful, left leg swelling with erythema and blisters concerning for necrotizing fasciitis. Intraoperative findings showed non-necrotizing bullous cellulitis. The blood and tissue cultures grew Shewanella algae. A handful case of non-necrotizing bullous cellulitis has been reported but this is the first documented case of non-necrotizing bullous cellulitis and bacteremia in PubMed.
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Affiliation(s)
- Niranjan Ojha
- Internal Medicine, Upstate University Hospital, Syracuse, USA
| | - Kevin Walsh
- Internal Medicine, Upstate University Hospital, Syracuse, USA
| | - Matthew J Hess
- Hospital Medicine, Upstate University Hospital, Syracuse, USA
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Searching for putative virulence factors in the genomes of Shewanella indica and Shewanella algae. Arch Microbiol 2020; 203:683-692. [PMID: 33040180 DOI: 10.1007/s00203-020-02060-1] [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: 07/02/2020] [Revised: 09/12/2020] [Accepted: 09/30/2020] [Indexed: 12/16/2022]
Abstract
Bacterial pathogens are a major threat to both humans and animals worldwide. It is crucial to understand the mechanisms of various disease processes at the molecular level. Shewanella species are widespread in the environment and some are considered as emerging opportunistic human and marine mammal pathogens. In this study, putative virulence factors on the genome of Shewanella indica BW, a bacterium isolated from the Bryde's whale (Balaenoptera edeni), were determined. Additionally, for comparative purposes, putative virulence factors from two other S. indica and ten S. algae strains were also determined using the Pathosystems Resource Integration Center (PATRIC) pipeline. We confirmed the presence of previously reported virulence factors and we are proposing several new candidate virulence factors. Interestingly, the putative virulence factors were very similar between the two species with the exception of microbial collagenase which was present in all S. algae genomes, but absent in all S. indica genomes.
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34
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Kreienbaum M, Dörrich AK, Brandt D, Schmid NE, Leonhard T, Hager F, Brenzinger S, Hahn J, Glatter T, Ruwe M, Briegel A, Kalinowski J, Thormann KM. Isolation and Characterization of Shewanella Phage Thanatos Infecting and Lysing Shewanella oneidensis and Promoting Nascent Biofilm Formation. Front Microbiol 2020; 11:573260. [PMID: 33072035 PMCID: PMC7530303 DOI: 10.3389/fmicb.2020.573260] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 08/27/2020] [Indexed: 01/21/2023] Open
Abstract
Species of the genus Shewanella are widespread in nature in various habitats, however, little is known about phages affecting Shewanella sp. Here, we report the isolation of phages from diverse freshwater environments that infect and lyse strains of Shewanella oneidensis and other Shewanella sp. Sequence analysis and microscopic imaging strongly indicate that these phages form a so far unclassified genus, now named Shewanella phage Thanatos, which can be positioned within the subfamily of Tevenvirinae (Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Tevenvirinae). We characterized one member of this group in more detail using S. oneidensis MR-1 as a host. Shewanella phage Thanatos-1 possesses a prolate icosahedral capsule of about 110 nm in height and 70 nm in width and a tail of about 95 nm in length. The dsDNA genome exhibits a GC content of about 34.5%, has a size of 160.6 kbp and encodes about 206 proteins (92 with an annotated putative function) and two tRNAs. Out of those 206, MS analyses identified about 155 phage proteins in PEG-precipitated samples of infected cells. Phage attachment likely requires the outer lipopolysaccharide of S. oneidensis, narrowing the phage's host range. Under the applied conditions, about 20 novel phage particles per cell were produced after a latent period of approximately 40 min, which are stable at a pH range from 4 to 12 and resist temperatures up to 55°C for at least 24 h. Addition of Thanatos to S. oneidensis results in partial dissolution of established biofilms, however, early exposure of planktonic cells to Thanatos significantly enhances biofilm formation. Taken together, we identified a novel genus of Myophages affecting S. oneidensis communities in different ways.
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Affiliation(s)
- Maximilian Kreienbaum
- Department of Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Anja K Dörrich
- Department of Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
| | - David Brandt
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Nicole E Schmid
- Department of Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Tabea Leonhard
- Department of Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Fabian Hager
- Department of Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Susanne Brenzinger
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, Netherlands
| | - Julia Hahn
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Timo Glatter
- Facility for Mass Spectrometry and Proteomics, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Matthias Ruwe
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Ariane Briegel
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, Netherlands
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Kai M Thormann
- Department of Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
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Chen YJ, He GC, Cheng JF, Lee YT, Hung YH, Chen WH, Huang YT, Liu PY. Comparative genomics reveals insights into characterization and distribution of quorum sensing-related genes in Shewanella algae from marine environment and clinical sources. Comp Immunol Microbiol Infect Dis 2020; 73:101545. [PMID: 32927298 DOI: 10.1016/j.cimid.2020.101545] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 08/05/2020] [Accepted: 08/28/2020] [Indexed: 11/26/2022]
Abstract
Shewanella algae is not only the most commonly reported species in Shewanella human infections but also capable to inhabit a wide variety of habitats. Although there is evidence that quorum sensing is associated with bacterial adaptation to changing environmental conditions, little is known of the quorum sensing system in S. algae. In this study, we conducted the whole genome sequencing of S. algae strains and applied comparative genomics to reveal the core genome. Genes related to the quorum sensing system were identified by integrated bioinformatics analysis. S. algae harbor genes involved in all three main types of autoinducer systems. This study provides insights into the quorum sensing systems in S. algae, which might be valuable in the future study of cell behavior in S. algae.
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Affiliation(s)
- Ying-Ju Chen
- Bachelor Program in Health Care and Social Work for Indigenous Students, College of Humanities & Social Sciences, Providence University, Taichung 43301, Taiwan
| | - Guo-Cheng He
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-Yi 62102, Taiwan
| | - Jan-Fang Cheng
- Department of Energy, Joint Genome Institute, CA 94598, USA
| | - Yi-Tzu Lee
- Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei 11221, Taiwan; Department of Emergency Medicine, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Yu-Hsuan Hung
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-Yi 62102, Taiwan
| | - Wen-Huei Chen
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-Yi 62102, Taiwan
| | - Yao-Ting Huang
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-Yi 62102, Taiwan.
| | - Po-Yu Liu
- Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung 40227, Taiwan; Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung 40227, Taiwan; Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung 40705, Taiwan.
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36
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Shewanella harboring antimicrobial and copper resistance genes in sea urchins (Paracentrotus lividus) from the Crozon peninsula (Brittany, France). INFECTION GENETICS AND EVOLUTION 2020; 85:104437. [PMID: 32574704 DOI: 10.1016/j.meegid.2020.104437] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 06/08/2020] [Accepted: 06/17/2020] [Indexed: 12/21/2022]
Abstract
Shewanella is a genus of aquatic non-fermenting Gram-negative bacteria with increasing numbers of reports of infections in humans and appearance of antimicrobial resistant strains. Cases of infection show a relatively strong association with seafood consumption or exposure to seawater. This study aimed to analyze Shewanella spp. isolated from the sea urchin Paracentrotus lividus collected from the Crozon peninsula (France) with the intention of obtaining insights into the role of this genus as a reservoir of antimicrobial and heavy metal resistance genes. Five among seven Shewanella isolates were resistant to antimicrobials, mainly to broad spectrum beta-lactams. Four isolates displayed multiple resistance to at least three of these antimicrobial classes: broad spectrum beta-lactams, aminoglycosides, macrolide, quinolones and/or tetracycline. Three antimicrobial resistance genes were detected in just one isolate encoding resistance to beta-lactam (blaSHV and blaTEM-1) and macrolide (ermB). In addition, the copper resistance gene cusB, was observed in this isolate which is also a plasmid carrier. Another copper resistance encoding gene, copA, was found among the isolates. These results indicate that the multidrug-resistant (MDR) Shewanella isolates and resistance genes could be potential risks to public health, due to the carrying of these MDR bacteria by sea urchins through human consumption.
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37
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Watterson WJ, Tanyeri M, Watson AR, Cham CM, Shan Y, Chang EB, Eren AM, Tay S. Droplet-based high-throughput cultivation for accurate screening of antibiotic resistant gut microbes. eLife 2020; 9:e56998. [PMID: 32553109 PMCID: PMC7351490 DOI: 10.7554/elife.56998] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 06/14/2020] [Indexed: 12/16/2022] Open
Abstract
Traditional cultivation approaches in microbiology are labor-intensive, low-throughput, and yield biased sampling of environmental microbes due to ecological and evolutionary factors. New strategies are needed for ample representation of rare taxa and slow-growers that are often outcompeted by fast-growers in cultivation experiments. Here we describe a microfluidic platform that anaerobically isolates and cultivates microbial cells in millions of picoliter droplets and automatically sorts them based on colony density to enhance slow-growing organisms. We applied our strategy to a fecal microbiota transplant (FMT) donor stool using multiple growth media, and found significant increase in taxonomic richness and larger representation of rare and clinically relevant taxa among droplet-grown cells compared to conventional plates. Furthermore, screening the FMT donor stool for antibiotic resistance revealed 21 populations that evaded detection in plate-based assessment of antibiotic resistance. Our method improves cultivation-based surveys of diverse microbiomes to gain deeper insights into microbial functioning and lifestyles.
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Affiliation(s)
- William J Watterson
- Pritzker School of Molecular Engineering, The University of ChicagoChicagoUnited States
- Institute for Genomics and Systems Biology, The University of ChicagoChicagoUnited States
| | - Melikhan Tanyeri
- Pritzker School of Molecular Engineering, The University of ChicagoChicagoUnited States
- Institute for Genomics and Systems Biology, The University of ChicagoChicagoUnited States
- Department of Engineering, Duquesne UniversityPittsburghUnited States
| | - Andrea R Watson
- Department of Medicine, The University of ChicagoChicagoUnited States
| | - Candace M Cham
- Department of Medicine, The University of ChicagoChicagoUnited States
| | - Yue Shan
- Department of Medicine, The University of ChicagoChicagoUnited States
| | - Eugene B Chang
- Department of Medicine, The University of ChicagoChicagoUnited States
| | - A Murat Eren
- Department of Medicine, The University of ChicagoChicagoUnited States
- Graduate Program in the Biophysical Sciences, The University of ChicagoChicagoUnited States
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological LaboratoryWoods HoleUnited States
| | - Savaş Tay
- Pritzker School of Molecular Engineering, The University of ChicagoChicagoUnited States
- Institute for Genomics and Systems Biology, The University of ChicagoChicagoUnited States
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Tseng CH, Cheng JF, Chen SY, Chen WH, Shi ZY, Lin YH, Tsai CA, Lin SP, Chen YC, Lin YC, Huang YT, Liu PY. Detection of S83V GyrA mutation in quinolone-resistant Shewanella algae using comparative genomics. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2020; 54:658-664. [PMID: 32507618 DOI: 10.1016/j.jmii.2020.04.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 04/13/2020] [Accepted: 04/29/2020] [Indexed: 12/23/2022]
Abstract
BACKGROUND Shewanella algae is a zoonotic pathogen that poses a serious health threat to immunocompromised hosts. Treatment of S. algae infections is challenging due to the pathogen's intrinsic resistance to a variety of β-lactam antibiotics. Therapeutic options have become further limited by the emergence of quinolone-resistant strains. Currently, there are few studies concerning the genetic and molecular mechanisms underlying acquired quinolones resistance in S. algae. qnrA was once proposed as the candidate gene related to quinolones resistance in S. algae. However, recent studies demonstrated qnrA are highly conservative and does not confer resistance to quinolones in S. algae. METHODS A total of 27 non-duplicated isolates of S. algae strains were examined. MICs of ciprofloxacin were determined using Vitek 2. Whole genome sequencing was performed using MiSeq platform. Comprehensive Antibiotic Resistance Database and ResFinder were used for annotation of quinolones resistance genes. Multiple sequence alignment by EMBOSS Clustal Omega were used to identified mutation in quinolone resistance-determining regions. To investigation of the alteration of protein structure induced by mutation, in silico molecular docking studies was conducted using Accryl Discovery studio visualizer. RESULTS All S. algae harbored the quinolone-resistance associated genes (qnrA, gyrA, gyrB, parC, and parE) regardless its resistance to ciprofloxacin. Comparison of these genomes identified a nonsynonymous mutation (S83V) in chromosome-encoded gyrase subunits (GyrA) in quinolone-resistant strain. We found this mutation disrupts the water-metal ion bridge, reduces the affinity of the quinolone-enzyme complex for the metal ions and therefore decrease the capability of quinolones to stabilize cleavage complexes. CONCLUSIONS The study provides insight into the quinolone resistance mechanisms in S. algae, which would be helpful for the evolution of antibiotic resistance in this bacterium.
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Affiliation(s)
- Chien-Hao Tseng
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Jan-Fang Cheng
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Shi-Yu Chen
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-Yi, Taiwan
| | - Wen-Huei Chen
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-Yi, Taiwan
| | - Zhi-Yuan Shi
- Infection Control Center, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Yu-Hui Lin
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Che-An Tsai
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Shih-Ping Lin
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Yung-Chun Chen
- Department of Critical Care Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Yu-Chia Lin
- Division of Infectious Diseases, Chiayi Branch, Taichung Veterans General Hospital, Chia-Yi, 600, Taiwan
| | - Yao-Ting Huang
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-Yi, Taiwan.
| | - Po-Yu Liu
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan; Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung, Taiwan; Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung, Taiwan.
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Prachumwat A, Wechprasit P, Srisala J, Kriangsaksri R, Flegel TW, Thitamadee S, Sritunyalucksana K. Shewanella khirikhana sp. nov. - a shrimp pathogen isolated from a cultivation pond exhibiting early mortality syndrome. Microb Biotechnol 2020; 13:781-795. [PMID: 31991524 PMCID: PMC7111104 DOI: 10.1111/1751-7915.13538] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 01/04/2020] [Accepted: 01/10/2020] [Indexed: 11/28/2022] Open
Abstract
Early mortality syndrome (EMS) in cultivated shrimp is of complex aetiology. One of the causes is acute hepatopancreatic necrosis disease (AHPND) caused by unique Vibrio isolates that carry two Pirvp toxin genes, but other causes of EMS remain mostly unexplained. Here, we describe the discovery of a Shewanella isolate TH2012T from an EMS/AHPND outbreak pond and demonstrate its virulence for shrimp (the mean lethal concentration of 105 colony-forming units per millilitre by immersion challenge) accompanied by distinctive histopathology, particularly of the ventral nerve cord and lymphoid organ but also including the digestive tract. On the basis of its complete genome sequence, multilocus phylogenetic trees, digital DNA-DNA hybridization analysis and differential phenotypic characteristics, we propose that Shewanella isolate TH2012T represents a novel species, separated sufficiently from the type strains S. litorisediminis and S. amazonensis to justify naming it Shewanella khirikhana sp. nov. Analysis of the TH2012T genome revealed no homologues of the Pirvp toxin genes but revealed a number of other potential virulence factors. It constitutes the first Shewanella isolate reported to be pathogenic to shrimp.
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Affiliation(s)
- Anuphap Prachumwat
- Aquatic Animal Health Research TeamIntegrative Aquaculture Biotechnology Research GroupNational Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development Agency (NSTDA)Pathum ThaniThailand
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp)Faculty of ScienceMahidol UniversityBangkokThailand
| | - Piyanuch Wechprasit
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp)Faculty of ScienceMahidol UniversityBangkokThailand
- Department of BiotechnologyFaculty of ScienceMahidol UniversityBangkokThailand
| | - Jiraporn Srisala
- Aquatic Animal Health Research TeamIntegrative Aquaculture Biotechnology Research GroupNational Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development Agency (NSTDA)Pathum ThaniThailand
| | - Ruttanaporn Kriangsaksri
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp)Faculty of ScienceMahidol UniversityBangkokThailand
- Department of BiotechnologyFaculty of ScienceMahidol UniversityBangkokThailand
| | - Timothy W. Flegel
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp)Faculty of ScienceMahidol UniversityBangkokThailand
- National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development Agency (NSTDA)Pathum ThaniThailand
| | - Siripong Thitamadee
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp)Faculty of ScienceMahidol UniversityBangkokThailand
- Department of BiotechnologyFaculty of ScienceMahidol UniversityBangkokThailand
| | - Kallaya Sritunyalucksana
- Aquatic Animal Health Research TeamIntegrative Aquaculture Biotechnology Research GroupNational Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development Agency (NSTDA)Pathum ThaniThailand
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40
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Zago V, Veschetti L, Patuzzo C, Malerba G, Lleo MM. Shewanella algae and Vibrio spp. strains isolated in Italian aquaculture farms are reservoirs of antibiotic resistant genes that might constitute a risk for human health. MARINE POLLUTION BULLETIN 2020; 154:111057. [PMID: 32174504 DOI: 10.1016/j.marpolbul.2020.111057] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/28/2020] [Accepted: 03/07/2020] [Indexed: 05/27/2023]
Abstract
The aquatic environment can represent a reservoir of antimicrobial resistance genes. In the present study, phenotypical, biochemical and molecular techniques were used to screen a collection of marine strains isolated in Italian aquaculture farms to investigate their beta-lactam resistance profiles. The genome of 12 carbapenemase and/or beta-lactamase producing strains was sequenced and a phylogenetic analysis of the beta-lactamases found in their chromosomes was performed. Gene annotation and prediction revealed the presence of blaAmpC and blaOXA-55-like in all the Shewanella algae isolates whereas in Vibrio anguillarum and Vibrio parahaemolyticus strains, blaAmpC and blaCARB-19 were found, respectively. Multiple alignments of OXA-55-like and AmpC protein sequences showed different point mutations. Finally, comparisons between enzyme phylogeny and strain clusterization based on sampling sites and dates indicate the diffusion of specific Multi Drug Resistant (MDR) Shewanella algae clones along the Italian Adriatic coast.
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Affiliation(s)
- Vanessa Zago
- Department of Diagnostics and Public Health, University of Verona, Italy
| | - Laura Veschetti
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Italy
| | - Cristina Patuzzo
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Italy
| | - Giovanni Malerba
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Italy
| | - Maria M Lleo
- Department of Diagnostics and Public Health, University of Verona, Italy.
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Whole-Genome Characterization of a Shewanella algae Strain Coharboring bla CTX-M-15 and armA Genes on a Novel IncC Plasmid. Antimicrob Agents Chemother 2020; 64:AAC.00267-20. [PMID: 32179520 DOI: 10.1128/aac.00267-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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Zago V, Veschetti L, Patuzzo C, Malerba G, Lleo MM. Resistome, Mobilome and Virulome Analysis of Shewanella algae and Vibrio spp. Strains Isolated in Italian Aquaculture Centers. Microorganisms 2020; 8:microorganisms8040572. [PMID: 32326629 PMCID: PMC7232470 DOI: 10.3390/microorganisms8040572] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/02/2020] [Accepted: 04/13/2020] [Indexed: 12/27/2022] Open
Abstract
Antimicrobial resistance is a major public health concern restricted not only to healthcare settings but also to veterinary and environmental ones. In this study, we analyzed, by whole genome sequencing (WGS) the resistome, mobilome and virulome of 12 multidrug-resistant (MDR) marine strains belonging to Shewanellaceae and Vibrionaceae families collected at aquaculture centers in Italy. The results evidenced the presence of several resistance mechanisms including enzyme and efflux pump systems conferring resistance to beta-lactams, quinolones, tetracyclines, macrolides, polymyxins, chloramphenicol, fosfomycin, erythromycin, detergents and heavy metals. Mobilome analysis did not find circular elements but class I integrons, integrative and conjugative element (ICE) associated modules, prophages and different insertion sequence (IS) family transposases. These mobile genetic elements (MGEs) are usually present in other aquatic bacteria but also in Enterobacteriaceae suggesting their transferability among autochthonous and allochthonous bacteria of the resilient microbiota. Regarding the presence of virulence factors, hemolytic activity was detected both in the Shewanella algae and in Vibrio spp. strains. To conclude, these data indicate the role as a reservoir of resistance and virulence genes in the environment of the aquatic microbiota present in the examined Italian fish farms that potentially might be transferred to bacteria of medical interest.
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Affiliation(s)
- Vanessa Zago
- Department of Diagnostics and Public Health, University of Verona, Strada Le Grazie 8, 37134 Verona, Italy;
| | - Laura Veschetti
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Strada Le Grazie 8, 37134 Verona, Italy; (L.V.); (C.P.); (G.M.)
| | - Cristina Patuzzo
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Strada Le Grazie 8, 37134 Verona, Italy; (L.V.); (C.P.); (G.M.)
| | - Giovanni Malerba
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Strada Le Grazie 8, 37134 Verona, Italy; (L.V.); (C.P.); (G.M.)
| | - Maria M. Lleo
- Department of Diagnostics and Public Health, University of Verona, Strada Le Grazie 8, 37134 Verona, Italy;
- Correspondence: ; Tel.: +39-045-802-7194
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Comparative Genomics Reveals Pathogenicity-Related Loci in Shewanella algae. CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY 2020; 2020:9205197. [PMID: 32318128 PMCID: PMC7149415 DOI: 10.1155/2020/9205197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 02/20/2020] [Indexed: 11/21/2022]
Abstract
Shewanella algae is an emerging marine zoonotic pathogen and accounts for considerable mortality and morbidity in compromised hosts. However, there is scarce literature related to the understanding of the genetic background of virulence determinants in S. algae. In this study, we aim to determine the occurrence of common virulence genes in S. algae using whole-genome sequence and comparative genomic analysis. Comparative genomics reveals putative-virulence genes related to bile resistance, chemotaxis, hemolysis, and motility. We detected the existence of hlyA, hlyD, and hlyIII involved in hemolysis. We also found chemotaxis gene cluster cheYZA operon and cheW gene. The results provide insights into the genetic basis underlying pathogenicity in S. algae.
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Hammad DBM, Hider SL, Liyanapathirana VC, Tonge DP. Molecular Characterization of Circulating Microbiome Signatures in Rheumatoid Arthritis. Front Cell Infect Microbiol 2020; 9:440. [PMID: 32039040 PMCID: PMC6987042 DOI: 10.3389/fcimb.2019.00440] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 12/09/2019] [Indexed: 12/12/2022] Open
Abstract
Rheumatoid Arthritis (RA) has been increasingly associated with perturbations to the microbial communities that reside in and on the body (the microbiome), in both human and animal studies. To date, such studies have mainly focused on the microbial communities that inhabit the gut and oral cavity. Mounting evidence suggests that microbial DNA can be detected in the blood circulation using a range of molecular methods. This DNA may represent an untapped pool of biomarkers that have the potential to report on changes to the microbiome of distant sites (e.g., example, the gut and oral cavity). To this end, through amplification and sequencing of the bacterial 16S rRNA variable region four, we evaluated the presence and identity of microbial DNA in blood samples obtained from RA patients (both prior to and 3 months following the instigation of treatment) in comparison to a small number of healthy control subjects and samples obtained from patients with ankylosing spondylitis (AS) and psoriatic arthritis (PA). Bacterial-derived DNA was identified in the majority of our patient samples. Taxonomic classification revealed that the microbiome community in RA was distinct from AS, PA, and the healthy state. Through analysis of paired patient samples obtained prior to and 3 months following treatment (V0 vs. V3), we found the microbiome to be modulated by treatment, and in many cases, this shift reduced the distance between these samples and the healthy control samples, suggesting a partial normalization following treatment in some patients. This effect was especially evident in seronegative arthritis patients. Herein, we provide further evidence for the existence of a blood microbiome in health and identify specific taxa modulated in disease and following treatment. These blood-derived signatures may have significant utility as disease biomarkers and suggest this area warrants further investigation.
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Affiliation(s)
- Dargham B M Hammad
- Faculty of Natural Sciences, School of Life Sciences, Keele University, Keele, United Kingdom
| | - S L Hider
- Arthritis Research UK Primary Care Centre, Research Institute for Primary Care and Health Sciences, Keele University, Keele, United Kingdom.,Haywood Academic Rheumatology Group, Midlands Partnership Foundation Trust, Staffordshire, United Kingdom
| | | | - Daniel P Tonge
- Faculty of Natural Sciences, School of Life Sciences, Keele University, Keele, United Kingdom
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Bauer MJ, Stone-Garza KK, Croom D, Andreoli C, Woodson P, Graf PCF, Maves RC. Shewanella algae Infections in United States Naval Special Warfare Trainees. Open Forum Infect Dis 2019; 6:ofz442. [PMID: 31696143 DOI: 10.1093/ofid/ofz442] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 10/04/2019] [Indexed: 11/12/2022] Open
Abstract
Shewanella infections are uncommon in immunocompetent hosts. We report 6 cases of Shewanella algae infection in young, healthy Naval Special Warfare trainees in San Diego during 2 consecutive El Niño seasons, defining a unique population at risk and adding to the epidemiologic understanding of this potentially virulent organism.
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Affiliation(s)
- Matthew J Bauer
- Division of Infectious Diseases, Department of Internal Medicine, Naval Medical Center, San Diego, California, USA
| | - Kristi K Stone-Garza
- Division of Infectious Diseases, Department of Internal Medicine, Naval Medical Center, San Diego, California, USA
| | - Daniel Croom
- Naval Special Warfare Center, Naval Amphibious Base Coronado, California, USA
| | - Cheryl Andreoli
- Navy Environmental and Preventive Medicine Unit FIVE, San Diego, California, USA
| | - Peter Woodson
- Naval Special Warfare Center, Naval Amphibious Base Coronado, California, USA
| | - Paul C F Graf
- Division of Microbiology, Department of Laboratory Medicine, Naval Medical Center, San Diego, California, USA
| | - Ryan C Maves
- Division of Infectious Diseases, Department of Internal Medicine, Naval Medical Center, San Diego, California, USA
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46
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Latif A, Kapoor V, Vivekanandan R, Reddy JT. A rare case of Shewanella septicemia: risk factors, environmental associations and management. BMJ Case Rep 2019; 12:12/9/e230252. [PMID: 31537604 DOI: 10.1136/bcr-2019-230252] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Shewanella species are Gram-negative, saprophytic, motile bacilli. Exposure to aquatic environment and raw fish ingestion have been defined as significant associated risk factors. The two species most commonly associated with human infections are Shewanella algae and Shewanella putrefaciens and major portion of infections (80%) caused by the former. Herein, we report a case of Shewanella septicaemia in a 70-year-old man in Omaha, NE who had no exposure to aquatic environment. To date, no defined treatment guidelines are present due to rarity of Shewanella infections, which is contributing to emerging antibiotic resistance.
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Affiliation(s)
- Azka Latif
- Internal Medicine, CHI Health Creighton University Medical Center Bergan Mercy, Omaha, Nebraska, USA
| | - Vikas Kapoor
- Internal Medicine, CHI Health Creighton University Medical Center Bergan Mercy, Omaha, Nebraska, USA
| | - Renuga Vivekanandan
- Infectious Diseases, Alegent-Creighton University Medical Center, Omaha, Nebraska, USA
| | - Joseph Thilumala Reddy
- Internal Medicine, CHI Health Creighton University Medical Center Bergan Mercy, Omaha, Nebraska, USA
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47
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Wang JH, Tseng SY, Tung KC. Genomic investigation of emerging zoonotic pathogen Shewanella xiamenensis. Tzu Chi Med J 2019; 32:162-166. [PMID: 32269948 PMCID: PMC7137373 DOI: 10.4103/tcmj.tcmj_69_19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 03/19/2019] [Accepted: 03/28/2019] [Indexed: 11/12/2022] Open
Abstract
Objective: Shewanella xiamenensis is an emerging zoonotic pathogen commonly found in aquatic ecosystem. Clustered regularly interspaced short palindromic repeats (CRISPR) and (CRISPR)-associated gene systems act as adaptive immune system of prokaryotes. Recently, growing evidence suggested their role in bacterial virulence and resistance. Despite its medical importance, little is known about the genomic characteristics of S. xiamenensis. Materials and Methods: Strain ZYW6 was isolated from Epinephelus awoara. We sequenced the 16S rRNA gene and blast against the GenBank bacterial database. Antibiotic susceptibility tests and interpretation were performed by automatic VITEK 2 system. We extracted the genomic DNA with QIAGEN Genomic-tip 100/G kit and QIAGEN Genomic DNA Buffer Set. Whole-genome shotgun sequencing was performed using the Illumina MiSeq sequencer. To identify the CRISPR-Cas System in the genome of S. xiamenensis ZYW6, the Integrated Microbial Genomes and Microbiomes and CRISPRFinder were used. Results: We characterized the genome of a S. xiamenensis strain. The genome is 4,765,190 bp in length and encodes 4262 open-reading frames. Type I CRISPR-Cas system and serine biosynthesis genes were identified. Conclusion: Our results demonstrate the genetic structure of CRISPR-Cas system, l-serine synthesis, and oxacillinase in S. xiamenensis. The report of antibiotics resistance genes in the study might indicate a possible reservoir of antimicrobial drug resistance determinants in food animal, resulting in potential infection source. The findings provide insights into the structure and composition of CRISPR-Cas system in S. xiamenensis and foundation for future biological validation.
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Affiliation(s)
- Jui-Hsing Wang
- Division of Infectious Disease, Department of Internal Medicine, Taichung Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taichung, Taiwan.,Department of Internal Medicine, School of Medicine, Tzu Chi University, Hualien, Taiwan
| | - Shu-Ying Tseng
- Department of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Kwong-Chung Tung
- Department of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
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Genome Sequence of Colistin-Resistant Bacteremic Shewanella algae Carrying the Beta-Lactamase Gene bla OXA-55. CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY 2019; 2019:3840563. [PMID: 31281553 PMCID: PMC6590586 DOI: 10.1155/2019/3840563] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 04/06/2019] [Accepted: 05/22/2019] [Indexed: 12/16/2022]
Abstract
Shewanella algae is an emerging pathogen widely distributed in aquatic environment. Bacteremia is a major manifestation of S. algae infections, and there are increasing reports of antibiotic-resistant strains. However, little is known about the genomic characteristics of human bacteremic S. algae. Here, we report the results of the whole-genome sequencing of colistin-resistant S. algae TYL, a blood isolate. Chromosome-encoded pmrC associated with colistin resistance and blaOXA-55 gene intrinsic to S. algae was identified. Continuous surveillance for the emergence of S. algae is needed.
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Zhang H, Wei W, Huang M, Umar Z, Feng Y. Definition of a Family of Nonmobile Colistin Resistance (NMCR-1) Determinants Suggests Aquatic Reservoirs for MCR-4. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1900038. [PMID: 31179218 PMCID: PMC6548957 DOI: 10.1002/advs.201900038] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 02/20/2019] [Indexed: 06/09/2023]
Abstract
Polymyxins, a family of cationic antimicrobial peptides, are recognized as a last-resort clinical option used in the treatment of lethal infections with carbapenem-resistant pathogens. A growing body of mobile colistin resistance (MCR) determinants renders colistin ineffective in the clinical and human sectors, posing a challenge to human health and food security. However, the origin and reservoir of the MCR family enzymes is poorly understood. Herein, a new family of nonmobile colistin resistance (from nmcr-1 to nmcr-1.8) from the aquatic bacterium Shewanella is reported. NMCR-1 (541aa) displays 62.78% identity to MCR-4. Genetic and structural analyses reveal that NMCR-1 shares a similar catalytic mechanism and functional motifs, both of which are required for MCR action and its resultant phenotypic resistance to polymyxin. Phylogeny and domain-swapping demonstrate that NMCR-1 is a progenitor of MCR-4 rather than MCR-1/2. Additionally, the experiment of bacterial growth and viability reveals that NMCR-1 promotes fitness cost as MCR-1/4 does in the recipient Escherichia coli. In summary, the finding suggests that the aquatic bacterium Shewanella (and even its associated aquaculture) is a reservoir for MCR-4 mobile colistin resistance.
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Affiliation(s)
- Huimin Zhang
- Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
- Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIL61801USA
| | - Wenhui Wei
- Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
| | - Man Huang
- Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
| | - Zeeshan Umar
- Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
| | - Youjun Feng
- Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
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ICE SXT vs. ICESh95: Co-existence of Integrative and Conjugative Elements and Competition for a New Host. Sci Rep 2019; 9:8045. [PMID: 31142760 PMCID: PMC6541609 DOI: 10.1038/s41598-019-44312-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 05/15/2019] [Indexed: 01/15/2023] Open
Abstract
Integrative and conjugative elements (ICEs) are mobile genetic elements that contribute to horizontal gene transfer. The aim of this work was to study different types of ICEs in clinical isolates of the emergent pathogen Shewanella spp., to compare their transfer efficiency and their ability to integrate a new host. Here we show that 3 out of 10 clinical isolates contained an ICE. Two of these elements were similar to ICEs from the SXT/R391 family and the other one was similar to ICESh95, a hybrid platform. Mating assays showed that these elements co-exist for several generations in the same host. Furthermore, transfer rates and competition assays between ICESh95 and ICESh392, an SXT-like element, suggest that the latter has evolved into a well-oiled machine that efficiently spread to different bacteria. Our results provide strong evidence of the role that ICEs play in the dissemination of genetic traits in nature and the implications that they have in the global threat of antimicrobial resistance.
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