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Wang H, Xia F, Xia Y, Li J, Hu Y, Deng Y, Zou M. Pangenome analysis of Shewanella xiamenensis revealed important genetic traits concerning genetic diversity, pathogenicity and antibiotic resistance. BMC Genomics 2024; 25:216. [PMID: 38413855 PMCID: PMC10898099 DOI: 10.1186/s12864-024-10146-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 02/19/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Shewanella xiamenensis, widely distributed in natural environments, has long been considered as opportunistic pathogen. Recently, significant changes in the resistance spectrum have been observed in S. xiamenensis, due to acquired antibiotic resistance genes. Therefore, a pan-genome analysis was conducted to illuminate the genomic changes in S. xiamenensis. RESULTS Phylogenetic analysis revealed three major clusters and three singletons, among which close relationship between several strains was discovered, regardless of their host and niches. The "open" genomes with diversity of accessory and strain-specific genomes took advantage towards diversity environments. The purifying selection pressure was the main force on genome evolution, especially in conservative genes. Only 53 gene families were under positive selection pressure. Phenotypic resistance analysis revealed 21 strains were classified as multi-drug resistance (MDR). Ten types of antibiotic resistance genes and two heavy metal resistance operons were discovered in S. xiamenensis. Mobile genetic elements and horizontal gene transfer increased genome diversity and were closely related to MDR strains. S. xiamenensis carried a variety of virulence genes and macromolecular secretion systems, indicating their important roles in pathogenicity and adaptability. Type IV secretion system was discovered in 15 genomes with various sequence structures, indicating it was originated from different donors through horizontal gene transfer. CONCLUSIONS This study provided with a detailed insight into the changes in the pan-genome of S. xiamenensis, highlighting its capability to acquire new mobile genetic elements and resistance genes for its adaptation to environment and pathogenicity to human and animals.
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Affiliation(s)
- Haichen Wang
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 41008, Hunan Province, People's Republic of China
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
| | - Fengjun Xia
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 41008, Hunan Province, People's Republic of China
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
| | - Yubing Xia
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 41008, Hunan Province, People's Republic of China
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
| | - Jun Li
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 41008, Hunan Province, People's Republic of China
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
| | - Yongmei Hu
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 41008, Hunan Province, People's Republic of China
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
| | - Yating Deng
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 41008, Hunan Province, People's Republic of China
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
| | - Mingxiang Zou
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 41008, Hunan Province, People's Republic of China.
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China.
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2
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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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Liao YC, Huang YT, Tseng CH, Liu CW, Liu PY. Comparative Genomics Identified PenR E151V Substitution Associated with Carbapenem-Resistance Burkholderia cepacia Complex and a Novel Burkholderia cepacia Complex Specific OXA-1043 Subgroup. Infect Drug Resist 2023; 16:5627-5635. [PMID: 37662974 PMCID: PMC10473398 DOI: 10.2147/idr.s418969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 08/10/2023] [Indexed: 09/05/2023] Open
Abstract
Purpose Burkholderia cepacia complex (Bcc) is a known significant opportunistic pathogen causing morbidity and mortality, particularly in those with cystic fibrosis, chronic granulomatous disease, or immunocompromising host. Mortality of Bcc bloodstream infections among non-cystic fibrosis patients remained high. The antibiotic treatment for Bcc infection is quite challenging due to its intrinsic resistance to most antibiotics, and the resistance to carbapenems was the biggest concern among them. We aimed to realize the mechanism of carbapenem resistance in Bcc. Patients and Methods Ten strains of Bcc were identified by the MALDI-TOF MS, and the drug susceptibility test was using VITEK 2 system. The Burkholderia cepacia complex genomes were sequenced via Nanopore GridIon. We also downloaded another ninety-five strains of Bcc from the National Center for Biotechnology Information database to evaluate the divergence between carbapenem-resistance and carbapenem-sensitive strains. Results The genetic organization between carbapenem-sensitive and carbapenem-resistant strains of Bcc showed no difference. However, in the carbapenem-sensitive strain, E151V substitution in PenR was detected. In addition, a novel specific OXA family subgroup, blaOXA-1043 in Burkholderia cenocepacia was discovered. Conclusion The E151V substitution in PenR may be associated with carbapenem-sensitive in Bcc. Moreover, the V151E mutation in PenR may be related to the activation of PenB, leading to Bcc resistance to carbapenems. Besides, a novel OXA family subgroup, blaOXA-1043, was found in Burkholderia cenocepacia, which differs from the previous OXA family.
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Affiliation(s)
- Ya-Chun Liao
- 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, Chiayi, Taiwan
| | - Chien-Hao Tseng
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Chia-Wei Liu
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Po-Yu Liu
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
- Department of Post-Baccalaureate Medicine, National Chung Hsing University, Taichung, Taiwan
- Genome Center for Infectious Diseases, Taichung Veterans General Hospital, Taichung, Taiwan
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4
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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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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: 12] [Impact Index Per Article: 6.0] [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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6
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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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7
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Ng WWS, Shum HP, To KKW, Sridhar S. Emerging Infections Due to Shewanella spp.: A Case Series of 128 Cases Over 10 Years. Front Med (Lausanne) 2022; 9:850938. [PMID: 35573023 PMCID: PMC9100594 DOI: 10.3389/fmed.2022.850938] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundShewanella species are emerging pathogens that can cause severe hepatobiliary, skin and soft tissue, gastrointestinal, respiratory infections, and bacteremia. Here we reported the largest case series of infections caused by Shewanella species.AimTo identify the clinical features and risk factors predisposing to Shewanella infections. To evaluate resistance pattern of Shewanella species and appropriateness of antibiotic use in the study cohort.MethodsPatients admitted to a regional hospital in Hong Kong with Shewanella species infection from April 1, 2010 to December 31, 2020 were included. Demographics, antibiotics, microbiology, and outcomes were retrospectively analyzed.FindingsOver the 10 years, we identified 128 patients with Shewanella species infection. 61.7% were male with a median age of 78 (IQR 65–87). Important underlying diseases included hepatobiliary diseases (63.3%), malignancy (26.6%), chronic kidney disease or end-stage renal failure (25.8%), and diabetes mellitus (22.7%). Hepatobiliary infections (60.4%) were the most common clinical manifestation. Majority (92.2%) were infected with Shewanella algae, while 7.8% were infected with Shewanella putrefaciens. The identified organisms were usually susceptible to ceftazidime (98.7%), gentamicin (97.4%), cefoperazone-sulbactam (93.5%) and ciprofloxacin (90.3%). Imipenem-susceptible strains were only present in 76.6% of isolates.ConclusionThis largest case series suggested that Shewanella infections are commonly associated with underlying comorbidities, especially with hepatobiliary diseases and malignancy. Although Shewanella species remained largely susceptible to third and fourth generation cephalosporins and aminoglycosides, carbapenem resistance has been on a significant rise.
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Affiliation(s)
- Wincy Wing-Sze Ng
- Department of Intensive Care, Pamela Youde Nethersole Eastern Hospital, Hong Kong, Hong Kong SAR, China
- *Correspondence: Wincy Wing-Sze Ng
| | - Hoi-Ping Shum
- Department of Intensive Care, Pamela Youde Nethersole Eastern Hospital, Hong Kong, Hong Kong SAR, China
| | - Kelvin Kai-Wang To
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Siddharth Sridhar
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
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Araújo S, Azenha SR, Henriques I, Tacão M. qnrA gene diversity in Shewanella spp. MICROBIOLOGY (READING, ENGLAND) 2021; 167. [PMID: 34914577 DOI: 10.1099/mic.0.001118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Members of Shewanella are ubiquitous in aquatic environments, some of which have been implicated in human infections. The progenitors of antibiotic resistance genes with clinical relevance, such as qnrA genes, have been identified in Shewanella. qnrA code for a pentapeptide repeat protein that protects type II topoisomerases, decreasing susceptibility to quinolones and fluoroquinolones. In this study, 248 genomes of 49 Shewanella species were analysed as well as 33 environmental isolates belonging to 10 Shewanella species. The presence of the qnrA gene was detected in 22.9% of the genomes and 15.2% of the isolates. The gene was more often detected in Shewanella algae, but was also detected in Shewanella carassii, Shewanella chilikensis, Shewanella haliotis and Shewanella indica. The identified genes encoded the previously described variants QnrA3 (in 22 genomes of one species), QnrA2 (eight genomes and three species), QnrA1 (six genomes and two species), QnrA7 (five genomes and two species), QnrA10 (two genomes of one species) and QnrA4 (one genome). In addition, 11 novel variants with 3 to 7 amino acid substitutions were identified (in 13 genomes and one environmental isolate). The presence of this gene appears to be species-specific although within some species several variants were detected. The study presents a previously unknown diversity of qnrA in Shewanella, highlighting the role of this genus as progenitor and reservoir of these genes. Further studies are needed to determine the phenotypes conferred by the new variants and the mechanisms that may mediate the transfer of these genes to new hosts.
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Affiliation(s)
- S Araújo
- Biology Department, University of Aveiro, Aveiro, Portugal.,CESAM, University of Aveiro, Aveiro, Portugal
| | - S R Azenha
- Biology Department, University of Aveiro, Aveiro, Portugal
| | - I Henriques
- Biology Department, University of Aveiro, Aveiro, Portugal.,CESAM, University of Aveiro, Aveiro, Portugal.,University of Coimbra, Department of Life Sciences, Faculty of Sciences and Technology, Coimbra, Portugal
| | - M Tacão
- Biology Department, University of Aveiro, Aveiro, Portugal.,CESAM, University of Aveiro, Aveiro, Portugal
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9
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Abstract
Class D β-lactamases are composed of 14 families and the majority of the member enzymes are included in the OXA family. The genes for class D β-lactamases are frequently identified in the chromosome as an intrinsic resistance determinant in environmental bacteria and a few of these are found in mobile genetic elements carried by clinically significant pathogens. The most dominant OXA family among class D β-lactamases is superheterogeneous and the family needs to have an updated scheme for grouping OXA subfamilies through phylogenetic analysis. The OXA enzymes, even the members within a subfamily, have a diverse spectrum of resistance. Such varied activity could be derived from their active sites, which are distinct from those of the other serine β-lactamases. Their substrate profile is determined according to the size and position of the P-, Ω- and β5-β6 loops, assembling the active-site channel, which is very hydrophobic. Also, amino acid substitutions occurring in critical structures may alter the range of hydrolysed substrates and one subfamily could include members belonging to several functional groups. This review aims to describe the current class D β-lactamases including the functional groups, occurrence types (intrinsic or acquired) and substrate spectra and, focusing on the major OXA family, a new model for subfamily grouping will be presented.
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Affiliation(s)
- Eun-Jeong Yoon
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
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10
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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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Rivera-Izquierdo M, Láinez-Ramos-Bossini AJ, Rivera-Izquierdo C, López-Gómez J, Fernández-Martínez NF, Redruello-Guerrero P, Martín-delosReyes LM, Martínez-Ruiz V, Moreno-Roldán E, Jiménez-Mejías E. OXA-48 Carbapenemase-Producing Enterobacterales in Spanish Hospitals: An Updated Comprehensive Review on a Rising Antimicrobial Resistance. Antibiotics (Basel) 2021; 10:antibiotics10010089. [PMID: 33477731 PMCID: PMC7832331 DOI: 10.3390/antibiotics10010089] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/07/2021] [Accepted: 01/16/2021] [Indexed: 12/14/2022] Open
Abstract
Carbapenemase-producing Enterobacterales (CPE) are significant contributors to the global public health threat of antimicrobial resistance. OXA-48-like enzymes and their variants are unique carbapenemases with low or null hydrolytic activity toward carbapenems but no intrinsic activity against expanded-spectrum cephalosporins. CPEs have been classified by the WHO as high-priority pathogens given their association with morbidity and mortality and the scarce number of effective antibiotic treatments. In Spain, the frequency of OXA-48 CPE outbreaks is higher than in other European countries, representing the major resistance mechanism of CPEs. Horizontal transfer of plasmids and poor effective antibiotic treatment are additional threats to the correct prevention and control of these hospital outbreaks. One of the most important risk factors is antibiotic pressure, specifically carbapenem overuse. We explored the use of these antibiotics in Spain and analyzed the frequency, characteristics and prevention of CPE outbreaks. Future antibiotic stewardship programs along with specific preventive measures in hospitalized patients must be reinforced and updated in Spain.
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Affiliation(s)
- Mario Rivera-Izquierdo
- Department of Preventive Medicine and Public Health, University of Granada, 18016 Granada, Spain; (C.R.-I.); (L.M.M.-d.); (V.M.-R.); (E.M.-R.); (E.J.-M.)
- Service of Preventive Medicine and Public Health, Hospital Clínico San Cecilio, 18016 Granada, Spain
- Biosanitary Institute of Granada, ibs.GRANADA, 18012 Granada, Spain
- Correspondence:
| | | | - Carlos Rivera-Izquierdo
- Department of Preventive Medicine and Public Health, University of Granada, 18016 Granada, Spain; (C.R.-I.); (L.M.M.-d.); (V.M.-R.); (E.M.-R.); (E.J.-M.)
- Service of Ginecology and Obstetrics, Hospital Universitario Virgen de las Nieves, 18014 Granada, Spain
| | - Jairo López-Gómez
- Service of Internal Medicine, San Cecilio University Hospital, 18016 Granada, Spain;
| | - Nicolás Francisco Fernández-Martínez
- Department of Preventive Medicine and Public Health, Reina Sofía University Hospital, 14004 Córdoba, Spain;
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), 14001 Córdoba, Spain
| | | | - Luis Miguel Martín-delosReyes
- Department of Preventive Medicine and Public Health, University of Granada, 18016 Granada, Spain; (C.R.-I.); (L.M.M.-d.); (V.M.-R.); (E.M.-R.); (E.J.-M.)
| | - Virginia Martínez-Ruiz
- Department of Preventive Medicine and Public Health, University of Granada, 18016 Granada, Spain; (C.R.-I.); (L.M.M.-d.); (V.M.-R.); (E.M.-R.); (E.J.-M.)
- Biosanitary Institute of Granada, ibs.GRANADA, 18012 Granada, Spain
- CIBER of Epidemiology and Public Health of Spain (CIBERESP), 28029 Madrid, Spain
| | - Elena Moreno-Roldán
- Department of Preventive Medicine and Public Health, University of Granada, 18016 Granada, Spain; (C.R.-I.); (L.M.M.-d.); (V.M.-R.); (E.M.-R.); (E.J.-M.)
- Biosanitary Institute of Granada, ibs.GRANADA, 18012 Granada, Spain
| | - Eladio Jiménez-Mejías
- Department of Preventive Medicine and Public Health, University of Granada, 18016 Granada, Spain; (C.R.-I.); (L.M.M.-d.); (V.M.-R.); (E.M.-R.); (E.J.-M.)
- Biosanitary Institute of Granada, ibs.GRANADA, 18012 Granada, Spain
- CIBER of Epidemiology and Public Health of Spain (CIBERESP), 28029 Madrid, Spain
- Teaching and Research in Family Medicine SEMERGEN-UGR, University of Granada, 18016 Granada, Spain
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12
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Successful use of culture and enrichment for the detection of OXA-181-producing Escherichia coli from rectal swab samples falsely categorized as negative by Xpert® Carba-R. Diagn Microbiol Infect Dis 2020; 96:114909. [DOI: 10.1016/j.diagmicrobio.2019.114909] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 10/02/2019] [Accepted: 10/06/2019] [Indexed: 11/22/2022]
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13
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Dellière S, Gits-Muselli M, Bretagne S, Alanio A. Outbreak-Causing Fungi: Pneumocystis jirovecii. Mycopathologia 2019; 185:783-800. [PMID: 31782069 DOI: 10.1007/s11046-019-00408-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 11/15/2019] [Indexed: 12/17/2022]
Abstract
Pneumocystis jirovecii pneumonia (PCP) is an important cause of morbidity in immunocompromised patients, with a higher mortality in non-HIV than in HIV patients. P. jirovecii is one of the rare transmissible pathogenic fungi and the only one that depends fully on the host to survive and proliferate. Transmissibility among humans is one of the main specificities of P. jirovecii. Hence, the description of multiple outbreaks raises questions regarding preventive care management of the disease, especially in the non-HIV population. Indeed, chemoprophylaxis is well codified in HIV patients but there is a trend for modifications of the recommendations in the non-HIV population. In this review, we aim to discuss the mode of transmission of P. jirovecii, identify published outbreaks of PCP and describe molecular tools available to study these outbreaks. Finally, we discuss public health and infection control implications of PCP outbreaks in hospital setting for in- and outpatients.
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Affiliation(s)
- Sarah Dellière
- Laboratoire de Parasitologie-Mycologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Université de Paris, Paris, France
- Molecular Mycology Unit, CNRS UMR2000, Institut Pasteur, 25 rue du Dr Roux, 75724, Paris Cedex 15, France
| | - Maud Gits-Muselli
- Laboratoire de Parasitologie-Mycologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Université de Paris, Paris, France
- Molecular Mycology Unit, CNRS UMR2000, Institut Pasteur, 25 rue du Dr Roux, 75724, Paris Cedex 15, France
| | - Stéphane Bretagne
- Laboratoire de Parasitologie-Mycologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Université de Paris, Paris, France
- Molecular Mycology Unit, CNRS UMR2000, Institut Pasteur, 25 rue du Dr Roux, 75724, Paris Cedex 15, France
- National Reference Center for Invasive Mycoses and Antifungals (NRCMA), Institut Pasteur, Paris, France
| | - Alexandre Alanio
- Laboratoire de Parasitologie-Mycologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Université de Paris, Paris, France.
- Molecular Mycology Unit, CNRS UMR2000, Institut Pasteur, 25 rue du Dr Roux, 75724, Paris Cedex 15, France.
- National Reference Center for Invasive Mycoses and Antifungals (NRCMA), Institut Pasteur, Paris, France.
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14
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Abstract
Surveillance studies have shown that OXA-48-like carbapenemases are the most common carbapenemases in Enterobacterales in certain regions of the world and are being introduced on a regular basis into regions of nonendemicity, where they are responsible for nosocomial outbreaks. OXA-48, OXA-181, OXA-232, OXA-204, OXA-162, and OXA-244, in that order, are the most common enzymes identified among the OXA-48-like carbapenemase group. OXA-48 is associated with different Tn1999 variants on IncL plasmids and is endemic in North Africa and the Middle East. OXA-162 and OXA-244 are derivatives of OXA-48 and are present in Europe. OXA-181 and OXA-232 are associated with ISEcp1, Tn2013 on ColE2, and IncX3 types of plasmids and are endemic in the Indian subcontinent (e.g., India, Bangladesh, Pakistan, and Sri Lanka) and certain sub-Saharan African countries. Overall, clonal dissemination plays a minor role in the spread of OXA-48-like carbapenemases, but certain high-risk clones (e.g., Klebsiella pneumoniae sequence type 147 [ST147], ST307, ST15, and ST14 and Escherichia coli ST38 and ST410) have been associated with the global dispersion of OXA-48, OXA-181, OXA-232, and OXA-204. Chromosomal integration of bla OXA-48 within Tn6237 occurred among E. coli ST38 isolates, especially in the United Kingdom. The detection of Enterobacterales with OXA-48-like enzymes using phenotypic methods has improved recently but remains challenging for clinical laboratories in regions of nonendemicity. Identification of the specific type of OXA-48-like enzyme requires sequencing of the corresponding genes. Bacteria (especially K. pneumoniae and E. coli) with bla OXA-48, bla OXA-181, and bla OXA-232 are emerging in different parts of the world and are most likely underreported due to problems with the laboratory detection of these enzymes. The medical community should be aware of the looming threat that is posed by bacteria with OXA-48-like carbapenemases.
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15
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Characterization of Chromosome-Mediated BlaOXA-894 in Shewanella xiamenensis Isolated from Pig Wastewater. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16193768. [PMID: 31597235 PMCID: PMC6801428 DOI: 10.3390/ijerph16193768] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/01/2019] [Accepted: 10/03/2019] [Indexed: 11/20/2022]
Abstract
A new variant of the blaOXA-546 gene, namely blaOXA-894, was identified on the chromosome of Shewanella xiamenensis isolated from pig wastewater in rural China. OXA-894 differs from OXA-546 (A46V, I219del) and OXA-48 (T167I, I219del) with two amino acid substitutions, respectively. The isolate was resistant to ampicillin, aztreonam, imipenem, meropenem and fosfomycin. Carba NP test confirmed S. xiamenensis strain sx20 as a carbapenemase-producer. The blaOXA-894 gene was located between the gene encoding a LysR family transcriptional regulator and the C15 gene. Its gene environment was similar to other S. xiamenensis with chromosome-located blaOXA-48-like genes. The T24H and T94V amino acid substitutions of LuxS protein were predicted to be deleterious, which may affect the virulence phenotype. The occurrence and potential health risk of carbapenem-resistant S. xiamenensis in a water environment is of concern.
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16
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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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17
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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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18
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Huang YT, Cheng JF, Wu ZY, Tung KC, Chen YJ, Hong YK, Chen SY, Liu PY. Genomic and phylogenetic characterization of Shewanella xiamenensis isolated from giant grouper (Epinephelus lanceolatus) in Taiwan. Zoonoses Public Health 2019; 66:679-685. [PMID: 30977595 DOI: 10.1111/zph.12580] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 02/16/2019] [Accepted: 03/24/2019] [Indexed: 11/30/2022]
Abstract
Shewanella xiamenensis is an emerging pathogen causing intra-abdominal infection and intestinal colonization. Epidemiologic clues suggest its role as a potential food-borne zoonotic agent. To date, four genome sequences of S. xiamenensis have been made publicly available. All of them were isolated from water samples. In this study, we characterized the genome of a S. xiamenensis strain isolated from a giant grouper in Taiwan. The genome of S. xiamenensis ZYW1 is 4,827,717 bp in length and encodes 4,239 open reading frames. Its genomic sequence shares high homology with other S. xiamenensis strains. blaOXA-416 was identified. This is the first detection of S. xiamenensis in Taiwan. These genomic data and analyses contribute to our understanding of S. xiamenensis and may help to elucidate disease-causing mechanisms in future studies.
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Affiliation(s)
- Yao-Ting Huang
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-Yi, Taiwan
| | - Jan-Fang Cheng
- Department of Energy, Joint Genome Institute, Walnut Creek, California
| | - Zong-Yen Wu
- Department of Energy, Joint Genome Institute, Walnut Creek, California.,Department of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Kwong-Chung Tung
- Department of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Ying-Ju Chen
- Department of Food and Nutrition, Providence University, Taichung, Taiwan
| | - Yu-Kai Hong
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-Yi, Taiwan
| | - Shi-Yu Chen
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-Yi, Taiwan
| | - Po-Yu Liu
- Department of Optometry, Shu-Zen Junior College of Medicine and Management, Kaohsiung City, 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.,Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
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19
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Jousset AB, Bernabeu S, Bonnin RA, Creton E, Cotellon G, Sauvadet A, Naas T, Dortet L. Development and validation of a multiplex polymerase chain reaction assay for detection of the five families of plasmid-encoded colistin resistance. Int J Antimicrob Agents 2019; 53:302-309. [DOI: 10.1016/j.ijantimicag.2018.10.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 10/09/2018] [Accepted: 10/30/2018] [Indexed: 12/13/2022]
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20
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Genetic and Biochemical Characterization of OXA-535, a Distantly Related OXA-48-Like β-Lactamase. Antimicrob Agents Chemother 2018; 62:AAC.01198-18. [PMID: 30082287 DOI: 10.1128/aac.01198-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 07/30/2018] [Indexed: 01/15/2023] Open
Abstract
OXA-535 is a chromosome-encoded carbapenemase of Shewanella bicestrii JAB-1 that shares only 91.3% amino acid sequence identity with OXA-48. Catalytic efficiencies are similar to those of OXA-48 for most β-lactams, except for ertapenem, where a 2,000-fold-higher efficiency was observed with OXA-535. OXA-535 and OXA-436, a plasmid-encoded variant of OXA-535 differing by three amino acids, form a novel cluster of distantly related OXA-48-like carbapenemases. Comparison of blaOXA-535 and blaOXA-436 genetic environments suggests that an ISCR1 may be responsible for blaOXA-436 gene mobilization from the chromosome of Shewanella spp. to plasmids.
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21
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Tafoukt R, Leangapichart T, Hadjadj L, Bakour S, Diene SM, Rolain JM, Touati A. Characterisation of bla OXA-538 , a new variant of bla OXA-48 , in Shewanella xiamenensis isolated from river water in Algeria. J Glob Antimicrob Resist 2018; 13:70-73. [DOI: 10.1016/j.jgar.2017.11.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 10/28/2017] [Accepted: 11/16/2017] [Indexed: 10/18/2022] Open
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22
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Giani T, Antonelli A, Caltagirone M, Mauri C, Nicchi J, Arena F, Nucleo E, Bracco S, Pantosti A, Luzzaro F, Pagani L, Rossolini GM. Evolving beta-lactamase epidemiology in Enterobacteriaceae from Italian nationwide surveillance, October 2013: KPC-carbapenemase spreading among outpatients. ACTA ACUST UNITED AC 2018; 22:30583. [PMID: 28797330 PMCID: PMC5553057 DOI: 10.2807/1560-7917.es.2017.22.31.30583] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 12/20/2016] [Indexed: 12/31/2022]
Abstract
Extended-spectrum beta-lactamases (ESBLs), AmpC-type beta-lactamases (ACBLs) and carbapenemases are among the most important resistance mechanisms in Enterobacteriaceae. This study investigated the presence of these resistance mechanisms in consecutive non-replicate isolates of Escherichia coli (n = 2,352), Klebsiella pneumoniae (n = 697), and Proteus mirabilis (n = 275) from an Italian nationwide cross-sectional survey carried out in October 2013. Overall, 15.3% of isolates were non-susceptible to extended-spectrum cephalosporins but susceptible to carbapenems (ESCR-carbaS), while 4.3% were also non-susceptible to carbapenems (ESCR-carbaR). ESCR-carbaS isolates were contributed by all three species, with higher proportions among isolates from inpatients (20.3%) but remarkable proportions also among those from outpatients (11.1%). Most ESCR-carbaS isolates were ESBL-positive (90.5%), and most of them were contributed by E. coli carrying blaCTX-M group 1 genes. Acquired ACBLs were less common and mostly detected in P. mirabilis. ESCR-carbaR isolates were mostly contributed by K. pneumoniae (25.1% and 7.7% among K. pneumoniae isolates from inpatients and outpatients, respectively), with blaKPC as the most common carbapenemase gene. Results showed an increasing trend for both ESBL and carbapenemase producers in comparison with previous Italian surveys, also among outpatients.
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Affiliation(s)
- Tommaso Giani
- Department of Medical Biotechnologies, University of Siena, Siena, Italy.,These authors contributed equally to this work
| | - Alberto Antonelli
- These authors contributed equally to this work.,Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Mariasofia Caltagirone
- Department of Clinical, Surgical, Diagnostic, and Paediatric Sciences, Section of Microbiology, University of Pavia, Pavia, Italy
| | - Carola Mauri
- Microbiology and Virology Unit, Department of Laboratory Medicine, A. Manzoni Hospital, Lecco, Italy
| | - Jessica Nicchi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Fabio Arena
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Elisabetta Nucleo
- Department of Clinical, Surgical, Diagnostic, and Paediatric Sciences, Section of Microbiology, University of Pavia, Pavia, Italy
| | - Silvia Bracco
- Microbiology and Virology Unit, Department of Laboratory Medicine, A. Manzoni Hospital, Lecco, Italy
| | - Annalisa Pantosti
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Italian National Health Institute, Rome, Italy
| | -
- The AMCLI-CoSA survey participants are listed at the end of the article
| | - Francesco Luzzaro
- Microbiology and Virology Unit, Department of Laboratory Medicine, A. Manzoni Hospital, Lecco, Italy
| | - Laura Pagani
- Department of Clinical, Surgical, Diagnostic, and Paediatric Sciences, Section of Microbiology, University of Pavia, Pavia, Italy
| | - Gian Maria Rossolini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy.,Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Clinical Microbiology, Virology and Serology Unit, Florence Careggi University Hospital, Florence, Italy
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23
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CTX-M-15-Producing Shewanella Species Clinical Isolate Expressing OXA-535, a Chromosome-Encoded OXA-48 Variant, Putative Progenitor of the Plasmid-Encoded OXA-436. Antimicrob Agents Chemother 2017; 62:AAC.01879-17. [PMID: 29038283 DOI: 10.1128/aac.01879-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Accepted: 10/11/2017] [Indexed: 11/20/2022] Open
Abstract
Shewanella spp. constitute a reservoir of antibiotic resistance determinants. In a bile sample, we identified three extended-spectrum-β-lactamase (ESBL)-producing bacteria (Escherichia coli, Klebsiella pneumoniae, and Shewanella sp. strain JAB-1) isolated from a child suffering from cholangitis. Our objectives were to characterize the genome and the resistome of the first ESBL-producing isolate of the genus Shewanella and determine whether plasmidic exchange occurred between the three bacterial species. Bacterial isolates were characterized using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), standard biochemical tools, and antimicrobial susceptibility testing. Shewanella sp. JAB-1 and ESBL gene-encoding plasmids were characterized using PacBio and Illumina whole-genome sequencing, respectively. The Shewanella sp. JAB-1 chromosome-encoded OXA-48 variant was cloned and functionally characterized. Whole-genome sequencing (WGS) of the Shewanella sp. clinical isolate JAB-1 revealed the presence of a 193-kb plasmid belonging to the IncA/C incompatibility group and harboring two ESBL genes, blaCTX-M-15 and blaSHV-2ablaCTX-M-15 gene-carrying plasmids belonging to the IncY and IncR incompatibility groups were also found in the E. coli and K. pneumoniae isolates from the same patient, respectively. A comparison of the blaCTX-M-15 genetic environment indicated the independent origin of these plasmids and dismissed in vivo transfers. Furthermore, characterization of the resistome of Shewanella sp. JAB-1 revealed the presence of a chromosome-carried blaOXA-535 gene, likely the progenitor of the plasmid-carried blaOXA-436 gene, a novel blaOXA-48-like gene. The expression of blaOXA-535 in E. coli showed the carbapenem-hydrolyzing activity of OXA-535. The production of OXA-535 in Shewanella sp. JAB-1 could be evidenced using molecular and immunoenzymatic tests, but not with biochemical tests that monitor carbapenem hydrolysis. In this study, we have identified a CTX-M-15-producing Shewanella species that was responsible for a hepatobiliary infection and that is likely the progenitor of OXA-436, a novel plasmid-encoded OXA-48-like class D carbapenemase.
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24
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Martín-Rodríguez AJ, Martín-Pujol O, Artiles-Campelo F, Bolaños-Rivero M, Römling U. Shewanella spp. infections in Gran Canaria, Spain: retrospective analysis of 31 cases and a literature review. JMM Case Rep 2017; 4:e005131. [PMID: 29623211 PMCID: PMC5857365 DOI: 10.1099/jmmcr.0.005131] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 11/14/2017] [Indexed: 01/09/2023] Open
Abstract
INTRODUCTION Shewanella spp. can cause severe skin and soft-tissue infections, gastrointestinal infections, otitis and bacteraemia, generally upon contact with seawater or consumption of raw seafood. Recently, a new condition termed 'patera foot' characterized by acute skin and soft-tissue infection has been described in irregular immigrants arriving to the Canary Islands, Spain, in rudimentary boats. Most infections are caused by a single species, Shewanella algae. The improvement of the diagnostic capabilities in clinical microbiology laboratories has resulted in a growing number of cases being reported worldwide, most of them coming from warm regions. CASE PRESENTATION In this work, we reviewed the medical records of all the patients with Shewanella infections in the two university hospitals of Gran Canaria (the Canary Islands, Spain) during the period 2000-2016, resulting in the identification of 31 cases. We also conducted a literature review of Shewanella infections reported worldwide in recent years. CONCLUSION This case series suggests that Shewanella infections are nosocomially acquired more frequently than previously thought. In addition, the unexpectedly high proportion of multidrug-resistant isolates raises concerns.
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Affiliation(s)
- Alberto J. Martín-Rodríguez
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Instituto Universitario de Biorgánica “Antonio González”, Universidad de La Laguna, Tenerife, Spain
- Present address: Swedish Medical Nanoscience Center, Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | | | | | | | - Ute Römling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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A Decade of Development of Chromogenic Culture Media for Clinical Microbiology in an Era of Molecular Diagnostics. Clin Microbiol Rev 2017; 30:449-479. [PMID: 28122803 DOI: 10.1128/cmr.00097-16] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
In the last 25 years, chromogenic culture media have found widespread application in diagnostic clinical microbiology. In the last decade, the range of media available to clinical laboratories has expanded greatly, allowing specific detection of additional pathogens, including Pseudomonas aeruginosa, group B streptococci, Clostridium difficile, Campylobacter spp., and Yersinia enterocolitica. New media have also been developed to screen for pathogens with acquired antimicrobial resistance, including vancomycin-resistant enterococci, carbapenem-resistant Acinetobacter spp., and Enterobacteriaceae with extended-spectrum β-lactamases and carbapenemases. This review seeks to explore the utility of chromogenic media in clinical microbiology, with particular attention given to media that have been commercialized in the last decade. The impact of laboratory automation and complementary technologies such as matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is also assessed. Finally, the review also seeks to demarcate the role of chromogenic media in an era of molecular diagnostics.
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Tacão M, Silva I, Henriques I. Culture-independent methods reveal high diversity of OXA-48-like genes in water environments. JOURNAL OF WATER AND HEALTH 2017; 15:519-525. [PMID: 28771149 DOI: 10.2166/wh.2017.260] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The carbapenemase OXA-48 was identified for the first time in 2001 and is now one of the greatest concerns in terms of antibiotic resistance. While many studies report clinical OXA-48-like producers, few reports refer blaOXA-48-like genes in environmental bacteria. The main goal of this study was to evaluate the diversity of blaOXA-48-like genes in aquatic systems, using culture-independent approaches. For that, environmental DNA was obtained from riverine and estuarine water and used to construct clone libraries of blaOXA-48-like gene polymerase chain reaction amplicons. blaOXA-48-like libraries from river and estuarine water DNA comprised 75 and 70 clones, respectively. Sequence analysis showed that environmental blaOXA-48-like genes show a broader diversity than that so far observed in clinical settings. In total, 50 new OXA-48 variants were identified as well as sequences identical to previously reported OXA-48, OXA-181, OXA-199, OXA-204 and OXA-162. Though we have no evidence that these genes were carried by bacteria that are members of the natural heterotrophic flora or bacteria that have entered this particular water environment through anthropogenic sources, these results reinforce the role of aquatic systems as antibiotic resistance reservoirs. The variants of blaOXA-48 here described should be taken into account when designing molecular strategies for detecting this gene.
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Affiliation(s)
- Marta Tacão
- Biology Department & CESAM, University of Aveiro, Campus Universitário Santiago, Aveiro 3810-193, Portugal E-mail:
| | - Isabel Silva
- Biology Department & CESAM, University of Aveiro, Campus Universitário Santiago, Aveiro 3810-193, Portugal E-mail:
| | - Isabel Henriques
- Biology Department & CESAM, University of Aveiro, Campus Universitário Santiago, Aveiro 3810-193, Portugal E-mail:
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Genetic analysis of a PER-2-producing Shewanella sp. strain harbouring a variety of mobile genetic elements and antibiotic resistance determinants. J Glob Antimicrob Resist 2017; 11:81-86. [PMID: 28760680 DOI: 10.1016/j.jgar.2017.06.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 06/07/2017] [Accepted: 06/10/2017] [Indexed: 11/23/2022] Open
Abstract
The objective of this study was to investigate the molecular mechanisms explaining the multidrug-resistant (MDR) phenotype found in a novel clinical Shewanella sp. strain (Shew256) recovered from a diabetic patient. Whole-genome shotgun sequencing was performed using Illumina MiSeq-I and Nextera XT DNA library. De novo assembly was performed with SPAdes. RAST Server was used to predict the open-reading frames and the predictions were confirmed using BLAST. Further genomic analysis was carried out using average nucleotide identity (ANI), ACT (Artemis), OrthoMCL, ARG-ANNOT, ISfinder, PHAST, tRNAscan-SE, plasmidSPAdes, PlasmidFinder and MAUVE. PCR and plasmid extraction were also performed. Genomic analysis revealed a total of 456 predicted genes unique to Shew256 compared with other Shewanella genomes. Moreover, the presence of different resistance genes, including blaPER-2, was found. A complex class 1 integron containing the ISCR1 gene, disrupted by two putative transposase genes, was identified. Furthermore, other resistance genes, a transposon containing aph(3'), insertion sequences, phages and non-coding RNAs were also found. In conclusion, evidence of acquisition of resistance genes and mobile elements that could explain the MDR phenotype were observed. This Shewanella sp. represents a prime example of how antibiotic resistance determinants can be acquired by uncommon pathogens.
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28
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Tacão M, Araújo S, Vendas M, Alves A, Henriques I. Shewanella species as the origin of bla OXA-48 genes: insights into gene diversity, associated phenotypes and possible transfer mechanisms. Int J Antimicrob Agents 2017; 51:340-348. [PMID: 28666748 DOI: 10.1016/j.ijantimicag.2017.05.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 05/15/2017] [Accepted: 05/27/2017] [Indexed: 11/30/2022]
Abstract
Chromosome-encoded beta-lactamases of Shewanella spp. have been indicated as probable progenitors of blaOXA-48-like genes. However, these have been detected in few Shewanella spp. and dissemination mechanisms are unclear. Thus, our main objective was to confirm the role of Shewanella species as progenitors of blaOXA-48-like genes. In silico analysis of Shewanella genomes was performed to detect blaOXA-48-like genes and context, and 43 environmental Shewanella spp. were characterised. Clonal relatedness was determined by BOX-PCR. Phylogenetic affiliation was assessed by 16S rDNA and gyrB sequencing. Antibiotic susceptibility phenotypes were determined. The blaOXA-48-like genes and genetic context were inspected by PCR, hybridisation and sequence analysis. Gene variants were cloned in Escherichia coli and MICs were determined. Shewanella isolates were screened for integrons, plasmids and insertion sequences. Analysis of Shewanella spp. genomes showed that putative blaOXA-48-like is present in the majority and in an identical context. Isolates presenting unique BOX profiles affiliated with 11 Shewanella spp. blaOXA-48-like genes were detected in 22 isolates from 6 species. Genes encoded enzymes identical to OXA-48, OXA-204, OXA-181, and 7 new variants differing from OXA-48 from 2 to 82 amino acids. IS1999 was detected in 24 isolates, although not in the vicinity of blaOXA-48 genes. Recombinant E. coli strains presented altered MICs. The presence/absence of blaOXA-48-like genes was species-related. Gene variants encoded enzymes with hydrolytic spectra similar to OXA-48-like from non-shewanellae. From the mobile elements previously described in association with blaOXA-48-like genes, only the IS1999 was found in Shewanella, which indicates its relevance in blaOXA-48-like genes transfer to other hosts.
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Affiliation(s)
- Marta Tacão
- Biology Department & CESAM, University of Aveiro, Aveiro, Portugal.
| | - Susana Araújo
- Biology Department & CESAM, University of Aveiro, Aveiro, Portugal
| | - Maria Vendas
- Biology Department & CESAM, University of Aveiro, Aveiro, Portugal
| | - Artur Alves
- Biology Department & CESAM, University of Aveiro, Aveiro, Portugal
| | - Isabel Henriques
- Biology Department & CESAM, University of Aveiro, Aveiro, Portugal
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29
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Yousfi K, Touati A, Lefebvre B, Fournier É, Côté JC, Soualhine H, Walker M, Bougdour D, Tremblay C, Bekal S. A Novel Plasmid, pSx1, Harboring a New Tn1696 Derivative from Extensively Drug-Resistant Shewanella xiamenensis Encoding OXA-416. Microb Drug Resist 2017; 23:429-436. [DOI: 10.1089/mdr.2016.0025] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Khadidja Yousfi
- Laboratoire d'Écologie Microbienne, FSNV, Université A/MIRA de Bejaia, Bejaia, Algérie
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Canada
| | - Abdelaziz Touati
- Laboratoire d'Écologie Microbienne, FSNV, Université A/MIRA de Bejaia, Bejaia, Algérie
| | - Brigitte Lefebvre
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Canada
| | - Éric Fournier
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Canada
| | - Jean-Charles Côté
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Canada
| | - Hafid Soualhine
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Canada
| | - Matthew Walker
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Djamila Bougdour
- Laboratoire d'Écologie Microbienne, FSNV, Université A/MIRA de Bejaia, Bejaia, Algérie
| | - Cécile Tremblay
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Canada
| | - Sadjia Bekal
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Canada
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30
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Coppi M, Antonelli A, Giani T, Spanu T, Liotti FM, Fontana C, Mirandola W, Gargiulo R, Barozzi A, Mauri C, Principe L, Rossolini GM. Multicenter evaluation of the RAPIDEC® CARBA NP test for rapid screening of carbapenemase-producing Enterobacteriaceae and Gram-negative nonfermenters from clinical specimens. Diagn Microbiol Infect Dis 2017; 88:207-213. [PMID: 28502395 DOI: 10.1016/j.diagmicrobio.2017.04.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 04/18/2017] [Accepted: 04/20/2017] [Indexed: 12/21/2022]
Abstract
The rapid diagnosis of carbapenemase-producing (CP) bacteria is essential for the management of therapy and infection control. In this study, RAPIDEC® CARBA NP (RCNP) was evaluated for the rapid screening of CP Enterobacteriaceae, Acinetobacter baumannii complex, and Pseudomonas aeruginosa from clinical specimens collected at five Italian hospitals. Firstly, each site tested 20 well-characterized strains in a blinded fashion. Secondly, each center prospectively tested 25 isolates from blood cultures processed with a rapid workflow (6h after subculture) and 25 isolates from other specimens processed after an overnight culture. The presence of carbapenemases was confirmed by multiplex real-timePCRs targeting carbapenemase genes. RCNP presented an overall sensitivity, specificity, positive predictive value, and negative predictive value of 70%, 94%, 82%, and 89%, respectively, with a higher performance in detection of CP Enterobacteriaceae and a poorer performance in detection of CP A. baumannii complex. With isolates from blood cultures, RCNP could significantly reduce the time required for identification of CP Enterobacteriaceae (less than 9h since the positivization of blood cultures).
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Affiliation(s)
- Marco Coppi
- Department of Experimental and Clinical Medicine, University of Florence, Italy
| | - Alberto Antonelli
- Department of Experimental and Clinical Medicine, University of Florence, Italy
| | - Tommaso Giani
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Teresa Spanu
- Institute of Microbiology, Catholic University of the Sacred Heart, Agostino Gemelli Hospital, Rome, Italy
| | - Flora Marzia Liotti
- Institute of Microbiology, Catholic University of the Sacred Heart, Agostino Gemelli Hospital, Rome, Italy
| | - Carla Fontana
- Department of Experimental Medicine and Surgery, Tor Vergata University of Rome, Rome, Italy; Clinical Microbiology Laboratories, Polyclinic of Tor Vergata Foundation, Rome, Italy
| | - Walter Mirandola
- Clinical Microbiology Laboratories, Polyclinic of Tor Vergata Foundation, Rome, Italy
| | - Raffaele Gargiulo
- Provincial Laboratory of Clinical Microbiology, S. Agostino-Estense Hospital, Modena, Italy
| | - Agostino Barozzi
- Provincial Laboratory of Clinical Microbiology, S. Agostino-Estense Hospital, Modena, Italy
| | - Carola Mauri
- Microbiology and Virology Unit, A. Manzoni Hospital, Lecco, Italy
| | - Luigi Principe
- Microbiology and Virology Unit, A. Manzoni Hospital, Lecco, Italy
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, Italy; Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy.
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31
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Yousfi K, Bekal S, Usongo V, Touati A. Current trends of human infections and antibiotic resistance of the genus Shewanella. Eur J Clin Microbiol Infect Dis 2017; 36:1353-1362. [PMID: 28299457 DOI: 10.1007/s10096-017-2962-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 03/05/2017] [Indexed: 10/20/2022]
Abstract
Shewanella spp. are commonly known as environmental bacteria and are most frequently isolated from aquatic areas. Currently, diseases syndromes and multidrug resistance have increasingly been reported in the genus Shewanella. Some species are associated with various infections, such as skin and soft tissue infections, as well as bacteremia. Generally, these bacteria are opportunistic and mostly affect people with an impaired immune system. This genus is also a probable vehicle and progenitor of antibiotic resistance genes. In fact, several resistance genes and mobile genetic elements have been identified in some resistant species isolated from environmental or clinical settings. These genes confer resistance to different antibiotic classes, including those used in therapies such as β-lactams and quinolones, and are generally located on the chromosome. Recently, a multidrug-resistant (MDR) plasmid harboring several drug resistance genes associated with transposons and integrons has been identified in Shewanella xiamenensis. These antibiotic resistance genes can circulate in the environment and contribute to the emergence of antibiotic resistance. This review describes different aspects of Shewanella, focusing on the infections caused by this genus, as well as their role in the propagation of antibiotic resistance via mobile genetic elements.
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Affiliation(s)
- K Yousfi
- Laboratoire d'Écologie Microbienne, FSNV, Université de Bejaia, Bejaia, 06000, Algeria.,Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada
| | - S Bekal
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada
| | - V Usongo
- Laboratoire d'Écologie Microbienne, FSNV, Université de Bejaia, Bejaia, 06000, Algeria.,Department of Food Science and Agricultural Chemistry, McGill University, Montreal, QC, Canada
| | - A Touati
- Laboratoire d'Écologie Microbienne, FSNV, Université de Bejaia, Bejaia, 06000, Algeria.
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Decousser JW, Poirel L, Nordmann P. Recent advances in biochemical and molecular diagnostics for the rapid detection of antibiotic-resistant Enterobacteriaceae: a focus on ß-lactam resistance. Expert Rev Mol Diagn 2017; 17:327-350. [DOI: 10.1080/14737159.2017.1289087] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Jean-Winoc Decousser
- Department of Virology, Bacteriology - Infection Control, Parasitology - Mycology, Assistance Publique - Hôpitaux de Paris, University Hospital Henri Mondor, Créteil, France
- IAME, UMR 1137, INSERM, Paris, France
| | - Laurent Poirel
- Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Department of Medicine, University of Fribourg, Fribourg, Switzerland
- French INSERM European Unit, University of Fribourg (LEA-IAME), Fribourg, Switzerland
- National Reference Center for Emerging Antibiotic Resistance, University of fribourg, fribourg, switzerland
| | - Patrice Nordmann
- Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Department of Medicine, University of Fribourg, Fribourg, Switzerland
- French INSERM European Unit, University of Fribourg (LEA-IAME), Fribourg, Switzerland
- National Reference Center for Emerging Antibiotic Resistance, University of fribourg, fribourg, switzerland
- Institute for Microbiology, University of Lausanne and University hospital Center, Lausanne, Switzerland
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Chromosome-Based blaOXA-48-Like Variants in Shewanella Species Isolates from Food-Producing Animals, Fish, and the Aquatic Environment. Antimicrob Agents Chemother 2017; 61:AAC.01013-16. [PMID: 27855066 DOI: 10.1128/aac.01013-16] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 11/03/2016] [Indexed: 01/23/2023] Open
Abstract
Carbapenems are considered last-resort antibiotics in health care. Increasing reports of carbapenemase-producing bacteria in food-producing animals and in the environment indicate the importance of this phenomenon in public health. Surveillance for carbapenemase genes and carbapenemase-producing bacteria in Dutch food-producing animals, environmental freshwater, and imported ornamental fish revealed several chromosome-based blaOXA-48-like variants in Shewanella spp., including two new alleles, blaOXA-514 and blaOXA-515 Carbapenemase genes were not associated with mobile genetic elements or Enterobacteriaceae.
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34
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Complete Genome Sequence of an Extensively Drug-Resistant Shewanella xiamenensis Strain Isolated from Algerian Hospital Effluents. GENOME ANNOUNCEMENTS 2016; 4:4/6/e01236-16. [PMID: 27834700 PMCID: PMC5105093 DOI: 10.1128/genomea.01236-16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In this study, we present the first complete genome of an extensively drug-resistant strain of Shewanella xiamenensis, collected from hospital effluents in Algeria. This genome includes the chromosome and a large new plasmid harboring several drug-resistance genes.
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Performance of the BD MAX™ instrument with Check-Direct CPE real-time PCR for the detection of carbapenemase genes from rectal swabs, in a setting with endemic dissemination of carbapenemase-producing Enterobacteriaceae. Diagn Microbiol Infect Dis 2016; 86:30-4. [PMID: 27345126 DOI: 10.1016/j.diagmicrobio.2016.06.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 06/01/2016] [Accepted: 06/02/2016] [Indexed: 11/23/2022]
Abstract
Carbapenemase-producing Enterobacteriaceae (CPE) represent an increasing public health issue and the early detection of colonization by CPE can help the implementation of infection control measures among inpatients. In this study, BD MAX Check-Direct CPE screen, with two different Master Mixes (BDMix and CPMix), using the automatic BD MAX(™) instrument, was evaluated for the detection of blaKPC, blaOXA-48, blaVIM and blaNDM genes, in comparison to selective broth enrichment and direct culture from rectal swabs. Among a total of 557 rectal swabs samples, 29 (5.2%) tested positive for CPE (23 for blaKPC, 5 for blaVIM and one for blaOXA-48). The sensitivity, specificity, positive and negative likelihood ratios values were 93.1%, 97.3%, 34.5 and 0.07, for BMix, and 100%, 97.1 %, 34.5 and 0 for CPMix, respectively. Five samples were positive with molecular methods only. The turn-around time was reduced from 18-24 hours (direct culture), or 48 h (broth enrichment) to only 3 h.
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36
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Zhao JY, Mu XD, Zhu YQ, Xi L, Xiao Z. Identification of an integron containing the quinolone resistance geneqnrA1inShewanella xiamenensis. FEMS Microbiol Lett 2015; 362:fnv146. [DOI: 10.1093/femsle/fnv146] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2015] [Indexed: 01/03/2023] Open
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