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Sykes EME, Mateo-Estrada V, Muzaleva A, Zhanel G, Dettman J, Chapados J, Gerdis S, Akineden Ö, Castillo-Ramírez S, Khan IUH, Kumar A. Characterization of a colistin resistant, hypervirulent hospital isolate of Acinetobacter courvalinii from Canada. Eur J Clin Microbiol Infect Dis 2024; 43:1939-1949. [PMID: 39073669 DOI: 10.1007/s10096-024-04873-0] [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: 02/27/2024] [Accepted: 06/14/2024] [Indexed: 07/30/2024]
Abstract
Non-baumannii Acinetobacter spp. are becoming more prevalent in clinical settings including those that present resistance to last-resort antibiotics such as colistin. AB222-IK40 is an Acinetobacter courvalinii strain isolated from the Ottawa Hospital Research Institute located in Ottawa, Canada. To our knowledge, it is the first report of clinical A. courvalinii in Canada. Based on the susceptibility profile, AB222-IK40 is resistant to colistin and non-susceptible to ertapenem. Whole-genome sequencing allowed for genomic investigation into colistin resistance mechanisms. No previously identified mechanism(s) were observed, but a mobile colistin resistance (mcr)-like gene and a UDP-glucose dehydrogenase gene were identified. Based on phylogenomic analyses, the mcr-like gene is an intrinsic phosphoethanolamine transferase. This gene family is implicated in one of the many mechanisms responsible for colistin resistance in Acinetobacter baumannii as well as Acinetobacter modestus. UDP-glucose dehydrogenase is involved in colistin resistance in Enterobacterales and has been shown to be involved in capsule formation in A. baumannii. Global lipidomics revealed greater abundance of phosphatidyl-myo-inositol and lyso-phosphatidyl ethanolamine moieties in the membrane of A. courvalinii than in A. baumannii. Lipidomic profiles showed differences that were probably responsible for the colistin resistance phenotype in AB222-IK40. This isolate was also hypervirulent based on survival assays in Galleria mellonella. As this is the first report of A. courvalinii from a hospital in Canada, this species may be an emerging clinical pathogen, and therefore, it is important to understand this mechanism of its colistin resistance and hypervirulence.
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Affiliation(s)
- Ellen M E Sykes
- Department of Microbiology, University of Manitoba Winnipeg, Winnipeg, MB, R3T 2N2, Canada
| | - Valeria Mateo-Estrada
- Programa de Genómica Evolutiva, Centro de Ciencias Génomicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Anna Muzaleva
- Department of Microbiology, University of Manitoba Winnipeg, Winnipeg, MB, R3T 2N2, Canada
| | - George Zhanel
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Jeremy Dettman
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, Canada
| | - Julie Chapados
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, Canada
| | - Suzanne Gerdis
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, Canada
| | - Ömer Akineden
- Dairy Sciences, Institute of Veterinary Food Science, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Santiago Castillo-Ramírez
- Programa de Genómica Evolutiva, Centro de Ciencias Génomicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Izhar U H Khan
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, Canada
| | - Ayush Kumar
- Department of Microbiology, University of Manitoba Winnipeg, Winnipeg, MB, R3T 2N2, Canada.
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Attili AR, Nocera FP, Sisto M, Linardi M, Gigli F, Ngwa VN, Fiorito F, Cerracchio C, Meligrana MCT, Bonacucina E, Cuteri V, De Martino L. Evidence and antibiotic resistance profiles of clinical Acinetobacter calcoaceticus-Acinetobacter baumannii (ACB) and non-ACB complex members in companion animals: A 2020-2022 retrospective study. Comp Immunol Microbiol Infect Dis 2024; 109:102185. [PMID: 38663213 DOI: 10.1016/j.cimid.2024.102185] [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: 02/02/2024] [Revised: 04/09/2024] [Accepted: 04/16/2024] [Indexed: 05/21/2024]
Abstract
To evaluate the frequency of Acinetobacter spp., belonging to both Acinetobacter calcoaceticus-baumannii (ACB) and non-ACB complex, and their antibiotic resistance profiles in veterinary medicine, a three-year (2020-2022) retrospective study was carried out on sick companion animals. Epidemiological data from different clinical canine, feline, and equine samples, were acquired. For each strain, MALDI-TOF MS identification and susceptibility to a panel of 11 antibiotics, by Kirby-Bauer and E-test methods, were performed. Out of 628 bacteriological examinations, 2.5% resulted positive for strains belonging to Acinetobacter genus. Frequencies of 2.3%, 1.9%, and 3% were obtained from both in-visiting and hospitalized dogs, cats, and horses, respectively. Members of ACB-complex accounted for 50% of isolates. Since all strains resulted susceptible to aminoglycosides and polymyxins, no pandrug-resistant (PDR) species were recorded. While 12.5% A. baumannii resulted extensively-drug resistant (XDR), a higher percentage of multidrug-resistant strains was recorded among non-ACB strains (35.5%) than ACB strains (25%). Susceptibility was observed in the same percentage in both groups (62.5%). All ACB strains confirmed their intrinsic resistances. Non-ACB species showed lower resistances against antipseudomonal penicillins plus beta-lactamase inhibitors (P=0.1306), III generation cephalosporins (P=0.0547), and tetracyclines (P=0.0209) than ACB species. Carbapenem-resistance was observed for XDR A. baumannii (12.5%) and, in particular for MDR non-ACB complex members (25%). To our knowledge, A. lactucae represents the first description in two sick dogs in Italy. Furthermore, our results emphasize the role of non-ACB-complex species as important zoonotic pathogens, which could be reservoirs of clinically relevant resistance profiles.
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Affiliation(s)
- Anna-Rita Attili
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Circonvallazione 93/95, Macerata, Matelica 62024, Italy
| | - Francesca Paola Nocera
- Department of Veterinary Medicine and Animal Production, University of Naples "Federico II", Via F. Delpino n. 1, Naples 80137, Italy.
| | - Martina Sisto
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Circonvallazione 93/95, Macerata, Matelica 62024, Italy
| | - Martina Linardi
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Circonvallazione 93/95, Macerata, Matelica 62024, Italy
| | - Francesca Gigli
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Circonvallazione 93/95, Macerata, Matelica 62024, Italy
| | - Victor Ngu Ngwa
- School of Veterinary Medicine and Sciences, University of Ngaoundéré, P.O. Box 454, Ngaoundéré, Cameroon
| | - Filomena Fiorito
- Department of Veterinary Medicine and Animal Production, University of Naples "Federico II", Via F. Delpino n. 1, Naples 80137, Italy
| | - Claudia Cerracchio
- Department of Veterinary Medicine and Animal Production, University of Naples "Federico II", Via F. Delpino n. 1, Naples 80137, Italy
| | - Marina C T Meligrana
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Circonvallazione 93/95, Macerata, Matelica 62024, Italy
| | - Eleonora Bonacucina
- Veterinary Practitioner Freelance, Via Monte d'Aria, Castelraimondo, Macerata 62022, Italy
| | - Vincenzo Cuteri
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Circonvallazione 93/95, Macerata, Matelica 62024, Italy
| | - Luisa De Martino
- Department of Veterinary Medicine and Animal Production, University of Naples "Federico II", Via F. Delpino n. 1, Naples 80137, Italy
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Gu D, Wu Y, Chen K, Zhang Y, Ju X, Yan Z, Xie M, Chan EWC, Chen S, Ruan Z, Zhang R, Zhang J. Recovery and genetic characterization of clinically-relevant ST2 carbapenem-resistant Acinetobacter baumannii isolates from untreated hospital sewage in Zhejiang Province, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 916:170058. [PMID: 38218490 DOI: 10.1016/j.scitotenv.2024.170058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 01/15/2024]
Abstract
The global transmission of carbapenem-resistant Acinetobacter baumannii (CRAB) poses a significant and grave threat to human health. To investigate the potential relationship between hospital sewage and the transmission of CRAB within healthcare facilities, isolates of Acinetobacter spp. obtained from untreated hospital sewage samples were subjected to antimicrobial susceptibility tests, genome sequencing, and bioinformatic and phylogenetic tree analysis, and that data were matched with those of the clinical isolates. Among the 70 Acinetobacter spp. sewage isolates tested, A. baumannii was the most prevalent and detectable in 5 hospitals, followed by A. nosocomialis and A. gerneri. Worryingly, 57.14 % (40/70) of the isolates were MDR, with 25.71 % (18/70) being resistant to carbapenem. When utilizing the Pasteur scheme, ST2 was the predominant type among these CRAB isolates, with Tn2006 (ΔISAba1-blaOXA-23-ATPase-yeeB-yeeA-ΔISAba1) and Tn2009 (ΔISAba1-blaOXA-23-ATPase-hp-parA-yeeC-hp-yeeB-ΔISAba1) being the key mobile genetic elements that encode carbapenem resistance. Seven A. gerneri isolates which harbored Tn2008 (ISAba1-blaOXA-23 -ATPase) and the blaPER-1 gene were also identified. Besides, an A. soil isolate was found to exhibit high-level of meropenem resistance (MIC ≥128 mg/L) and harbor a blaNDM-1 gene located in a core genetic structure of ISAba125-blaNDM-1-ble-trpF-dsbC-cutA. To investigate the genetic relatedness between isolates recovered from hospital sewage and those collected from ICUs, a phylogenetic tree was constructed for 242 clinical isolates and 9 sewage isolates. The results revealed the presence of two evolutionary clades, each containing isolates from both ICU and sewage water, suggesting that CRAB isolates in untreated sewage water were also the transmission clones or closely related evolutionary isolates recoverable in hospital settings. Findings in this work confirm that hospital sewage is a potential reservoir of CRAB.
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Affiliation(s)
- Danxia Gu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China; Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Yuchen Wu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China
| | - Kaichao Chen
- Department of Food Science and Nutrition, Faculty of Science, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Yanyan Zhang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China
| | - Xiaoyang Ju
- Department of Clinical Laboratory, The Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China
| | - Zelin Yan
- Department of Clinical Laboratory, The Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China
| | - Miaomiao Xie
- Department of Food Science and Nutrition, Faculty of Science, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Edward Wai Chi Chan
- Department of Food Science and Nutrition, Faculty of Science, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Sheng Chen
- Department of Food Science and Nutrition, Faculty of Science, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Zhi Ruan
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, China
| | - Rong Zhang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China.
| | - Jun Zhang
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, China.
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Sheikh AA, Schneiderman D, Sykes EME, Kumar A, Chen W, Lapen DR, Khan IUH. Three novel multiplex PCR assays for rapid detection of virulence, antimicrobial resistance, and toxin genes in Acinetobacter calcoaceticus-baumannii complex species. Lett Appl Microbiol 2024; 77:ovae027. [PMID: 38460955 DOI: 10.1093/lambio/ovae027] [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: 01/18/2024] [Revised: 03/01/2024] [Accepted: 03/08/2024] [Indexed: 03/11/2024]
Abstract
The Acinetobacter calcoaceticus-baumannii (ACB) complex is an often-overlooked group of nosocomial pathogens with a significant environmental presence. Rapid molecular screening methods for virulence, antimicrobial resistance, and toxin (VAT) genes are required to investigate the potential pathogenicity of environmental isolates. This study aimed to develop and apply novel ACB complex-specific multiplex PCR (mPCR) primers and protocols for the rapid detection of eight VAT genes. We optimized three single-tube mPCR assays using reference DNA from ACB complex and other Acinetobacter species. These assays were then applied to detect VAT genes in cultured ACB complex isolates recovered from clinical and environmental sources. Widespread detection of VAT genes in environmental isolates confirmed the validity, functionality, and applicability of these novel assays. Overall, the three newly developed ACB complex species-specific mPCR assays are rapid and simple tools that can be adopted in diagnostic and clinical lab settings. The detection of VAT genes in environmental isolates suggests that environmental niches could serve as a reservoir for potentially pathogenic ACB complex and warrants further investigation. The newly developed mPCR assays are specific, sensitive, and efficient, making them well-suited for high-throughput screening in epidemiological studies and evaluating the potential pathogenicity of ACB complex recovered from various sources.
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Affiliation(s)
- Alexander A Sheikh
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, K1A 0C6, ON, Canada
| | - Danielle Schneiderman
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, K1A 0C6, ON, Canada
| | - Ellen M E Sykes
- Department of Microbiology, University of Manitoba, Winnipeg, R3T 2N2, MB, Canada
| | - Ayush Kumar
- Department of Microbiology, University of Manitoba, Winnipeg, R3T 2N2, MB, Canada
| | - Wen Chen
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, K1A 0C6, ON, Canada
| | - David R Lapen
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, K1A 0C6, ON, Canada
| | - Izhar U H Khan
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, K1A 0C6, ON, Canada
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Chuai X, Zhou Y, Feng J, Yu M, Wu Y, Han L, Zhao Y, Qiao H, Gao Z, Li J, Xie L, Zhao W, Wang C. Analysis of multidrug-resistant determinants of clinically isolated Acinetobacter baumannii CYZ via whole genome sequencing. Microbiol Immunol 2023; 67:396-403. [PMID: 37403254 DOI: 10.1111/1348-0421.13087] [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: 02/01/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/06/2023]
Abstract
Acinetobacter baumannii is a multidrug-resistant coccobacillus responsible for severe nosocomial infectious diseases. This study mainly focuses on investigating the antimicrobial resistance features of a clinically isolated strain (A. baumannii CYZ) using the PacBio Sequel II sequencing platform. The chromosomal size of A. baumannii CYZ is 3,960,760 bp, which contains a total of 3803 genes with a G + C content of 39.06%. Functional analysis performed using the Clusters of Orthologous Groups of Proteins (COGs), Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, as well as the Comprehensive Antibiotic Resistance Database (CARD) revealed a complicated set of antimicrobial resistance determinants in the genome of A. baumannii CYZ, which were mainly classified into multidrug efflux pumps and transport systems, β-lactamase relative and penicillin-binding proteins, aminoglycoside modification enzymes, alternation of antibiotic target sites, lipopolysaccharide relative, and other mechanisms. A total of 35 antibiotics were tested for the antimicrobial susceptibility of A. baumannii CYZ, and the organism exhibited a stronger antimicrobial resistance ability. The phylogenetic relationship indicated that A. baumannii CYZ has high homology with A. baumannii ATCC 17978; however, the former also exhibited its specific genome characteristics. Our research results give insight into the genetic antimicrobial-resistant features of A. baumannii CYZ as well as provide a genetic basis for the further study of the phenotype.
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Affiliation(s)
- Xia Chuai
- Department of Pathogenic Biology, Hebei Medical University, Shijiazhuang, PR China
| | - Yaya Zhou
- School of Basic Medical Sciences, Hebei Medical University, Shijiazhuang, PR China
| | - Junhua Feng
- Clinical Laboratory, The Fourth Hospital, Hebei Medical University, Shijiazhuang, PR China
| | - Menghan Yu
- Department of Pathogenic Biology, Hebei Medical University, Shijiazhuang, PR China
| | - Yan Wu
- Department of Pathogenic Biology, Hebei Medical University, Shijiazhuang, PR China
| | - Lujuan Han
- Department of Pathogenic Biology, Hebei Medical University, Shijiazhuang, PR China
| | - Yan Zhao
- Department of Pathogenic Biology, Hebei Medical University, Shijiazhuang, PR China
| | - Hongxiu Qiao
- Department of Pathogenic Biology, Hebei Medical University, Shijiazhuang, PR China
- Department of Experimental Center of Teaching, Hebei Medical University, Shijiazhuang, PR China
| | - Zhiyun Gao
- Department of Pathogenic Biology, Hebei Medical University, Shijiazhuang, PR China
| | - Jian Li
- Department of Pathogenic Biology, Hebei Medical University, Shijiazhuang, PR China
| | - Lixin Xie
- Department of Pathogenic Biology, Hebei Medical University, Shijiazhuang, PR China
| | - Wenting Zhao
- Department of Pathogenic Biology, Hebei Medical University, Shijiazhuang, PR China
| | - Changle Wang
- Department of Pathogenic Biology, Hebei Medical University, Shijiazhuang, PR China
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Sheck E, Romanov A, Shapovalova V, Shaidullina E, Martinovich A, Ivanchik N, Mikotina A, Skleenova E, Oloviannikov V, Azizov I, Vityazeva V, Lavrinenko A, Kozlov R, Edelstein M. Acinetobacter Non- baumannii Species: Occurrence in Infections in Hospitalized Patients, Identification, and Antibiotic Resistance. Antibiotics (Basel) 2023; 12:1301. [PMID: 37627721 PMCID: PMC10451542 DOI: 10.3390/antibiotics12081301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/05/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND Acinetobacter species other than A. baumannii are becoming increasingly more important as opportunistic pathogens for humans. The primary aim of this study was to assess the prevalence, species distribution, antimicrobial resistance patterns, and carbapenemase gene content of clinical Acinetobacter non-baumannii (Anb) isolates that were collected as part of a sentinel surveillance program of bacterial infections in hospitalized patients. The secondary aim was to evaluate the performance of MALDI-TOF MS systems for the species-level identification of Anb isolates. METHODS Clinical bacterial isolates were collected from multiple sites across Russia and Kazakhstan in 2016-2022. Species identification was performed by means of MALDI-TOF MS, with the Autobio and Bruker systems used in parallel. The PCR detection of the species-specific blaOXA-51-like gene was used as a means of differentiating A. baumannii from Anb species, and the partial sequencing of the rpoB gene was used as a reference method for Anb species identification. The susceptibility of isolates to antibiotics (amikacin, cefepime, ciprofloxacin, colistin, gentamicin, imipenem, meropenem, sulbactam, tigecycline, tobramycin, and trimethoprim-sulfamethoxazole) was determined using the broth microdilution method. The presence of the most common in Acinetobacter-acquired carbapenemase genes (blaOXA-23-like, blaOXA-24/40-like, blaOXA-58-like, blaNDM, blaIMP, and blaVIM) was assessed using real-time PCR. RESULTS In total, 234 isolates were identified as belonging to 14 Anb species. These comprised 6.2% of Acinetobacter spp. and 0.7% of all bacterial isolates from the observations. Among the Anb species, the most abundant were A. pittii (42.7%), A. nosocomialis (13.7%), the A. calcoaceticus/oleivorans group (9.0%), A. bereziniae (7.7%), and A. geminorum (6.0%). Notably, two environmental species, A. oleivorans and A. courvalinii, were found for the first time in the clinical samples of patients with urinary tract infections. The prevalence of resistance to different antibiotics in Anb species varied from <4% (meropenem and colistin) to 11.2% (gentamicin). Most isolates were susceptible to all antibiotics; however, sporadic isolates of A. bereziniae, A. johnsonii, A. nosocomialis, A. oleivorans, A. pittii, and A. ursingii were resistant to carbapenems. A. bereziniae was more frequently resistant to sulbactam, aminoglycosides, trimethoprim-sulfamethoxazole, and tigecycline than the other species. Four (1.7%) isolates of A. bereziniae, A. johnsonii, A. pittii were found to carry carbapenemase genes (blaOXA-58-like and blaNDM, either alone or in combination). The overall accuracy rates of the species-level identification of Anb isolates with the Autobio and Bruker systems were 80.8% and 88.5%, with misidentifications occurring in 5 and 3 species, respectively. CONCLUSIONS This study provides important new insights into the methods of identification, occurrence, species distribution, and antibiotic resistance traits of clinical Anb isolates.
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Affiliation(s)
- Eugene Sheck
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia; (E.S.); (I.A.)
| | - Andrey Romanov
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia; (E.S.); (I.A.)
| | - Valeria Shapovalova
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia; (E.S.); (I.A.)
| | - Elvira Shaidullina
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia; (E.S.); (I.A.)
| | - Alexey Martinovich
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia; (E.S.); (I.A.)
| | - Natali Ivanchik
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia; (E.S.); (I.A.)
| | - Anna Mikotina
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia; (E.S.); (I.A.)
| | - Elena Skleenova
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia; (E.S.); (I.A.)
| | - Vladimir Oloviannikov
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia; (E.S.); (I.A.)
| | - Ilya Azizov
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia; (E.S.); (I.A.)
| | - Vera Vityazeva
- Republican Children’s Hospital, 185000 Petrozavodsk, Republic of Karelia, Russia
| | - Alyona Lavrinenko
- Shared Resource Laboratory, Karaganda Medical University, 100008 Karaganda, Kazakhstan
| | - Roman Kozlov
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia; (E.S.); (I.A.)
| | - Mikhail Edelstein
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia; (E.S.); (I.A.)
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7
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Pulami D, Kämpfer P, Glaeser SP. High diversity of the emerging pathogen Acinetobacter baumannii and other Acinetobacter spp. in raw manure, biogas plants digestates, and rural and urban wastewater treatment plants with system specific antimicrobial resistance profiles. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160182. [PMID: 36395844 DOI: 10.1016/j.scitotenv.2022.160182] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 06/16/2023]
Abstract
Carbapenem-resistant Acinetobacter baumannii causing immense treatment problems in hospitals. There is still a knowledge gap on the abundance and stability of acquired resistances and the diversity of resistant Acinetobacter in the environment. The aim of the study was to investigate the diversity and antimicrobial resistances of Acinetobacter spp. released from livestock and human wastewater into the environment. Raw and digested manure of small scale on farm biogas plants as well as untreated and treated wastewater and sewage sludge of rural and urban wastewater treatment plants (WWTPs) were studied comparatively. A total of 132 Acinetobacter isolates were phylogenetically identified (16S rRNA gene and rpoB sequence analyses) and 14 different phylotypes were detected. Fiftytwo isolates represented A. baumannii which were cultured from raw and digested manure of different biogas plants, and most stages of the rural WWTP (no hospital wastewater receiving) and the two studied urban WWTPs receiving veterinarian and human hospital wastewater. Multi-locus sequence typing (Pasteur_MLST) identified 23 novel and 12 known STs of A. baumannii. Most novel STs (18/23) were cultured from livestock samples and the rural WWTP. A. baumannii isolates from livestock and the rural WWTP were susceptible to carbapenems, colistin, ciprofloxacin, ceftazidime, and piperacillin. In contrast, A. baumannii isolates from the two urban WWTPs showed clinical linkage with respect to MLST and were multi-drug resistant (MDR). The presence of viable A. baumannii in digested manure and sewage sludge confirmed the survival of the strict aerobic bacteria during anoxic conditions. The study indicated the spread of diverse Acinetobacter from anthropogenic sources into the environment with a strong linkage of clinial associated MDR A. baumannii strains to the inflow of hospital wastewater to WWTPs. A more frequent detection of Acinetobacter in sewage sludge than effluent waters indicated that particle-attachment of Acinetobacter must be considered by the risk assessment of these bacteria.
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Affiliation(s)
- Dipen Pulami
- Institut for Applied Microbiology, Justus-Liebig-University Giessen, Germany
| | - Peter Kämpfer
- Institut for Applied Microbiology, Justus-Liebig-University Giessen, Germany
| | - Stefanie P Glaeser
- Institut for Applied Microbiology, Justus-Liebig-University Giessen, Germany.
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8
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Wunderlich A, Xanthopoulou K, Wille J, Wohlfarth E, Gerson S, Kaase M, Seifert H, Higgins PG. Carbapenem resistance in Acinetobacter pittii isolates mediated by metallo-β-lactamases. J Antimicrob Chemother 2023; 78:488-496. [PMID: 36537203 DOI: 10.1093/jac/dkac418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 11/20/2022] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVES To characterize the genetic environment of metallo-β-lactamases (MBL) in carbapenem-resistant clinical Acinetobacter pittii isolates. METHODS Seventeen carbapenem-resistant A. pittii isolates harbouring an MBL were collected between 2010 and 2015 in Germany. Antimicrobial susceptibility testing was performed using agar dilution. Presence of MBLs was confirmed by PCR and their genetic location determined by S1-pulsed-field gel electrophoresis followed by Southern blot hybridization. Whole-genome sequencing was performed using the Miseq and MinION platforms. Isolates were typed using an ad hoc core genome MLST scheme. Conjugation into A. baumannii was tested by broth mating. RESULTS In 10 isolates the MBL was plasmid-encoded and in seven isolates chromosomally encoded. blaGIM-1 and blaVIM-2 were plasmid-encoded, blaVIM-4 was chromosomally encoded, while blaNDM-1 was chromosomally encoded in four and plasmid-encoded in three isolates. Seven of ten plasmids were conjugative into A. baumannii. Although most isolates were unrelated, the backbones of the MBL-encoding plasmid showed >99% similarity and only differed in the MBL-encoding area. blaNDM-1-harbouring plasmids were highly similar to other plasmids from Acinetobacter isolates worldwide while the blaVIM-2- and blaGIM-1-encoding plasmids have not been described. CONCLUSIONS These data show the existence of a promiscuous plasmid circulating in A. pittii isolates in Germany that differs only in the MBL-encoding region. Its plasmid backbone has been found globally among multiple Acinetobacter spp. These data should raise awareness of an epidemic conjugative plasmid that has independently acquired MBLs. We should also consider that future comparative plasmid analysis will look beyond solely the resistome and include the mobile elements carrying the resistance genes.
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Affiliation(s)
- Alexander Wunderlich
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Kyriaki Xanthopoulou
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Julia Wille
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | | | - Stefanie Gerson
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Martin Kaase
- Institute for Medical Microbiology, Ruhr-University Bochum, Bochum, Germany
| | - Harald Seifert
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Paul G Higgins
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
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9
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Bigge R, Bunk B, Rudolph WW, Gunzer F, Coldewey SM, Riedel T, Schröttner P. Comparative Study of Different Diagnostic Routine Methods for the Identification of Acinetobacter radioresistens. Microorganisms 2022; 10:microorganisms10091767. [PMID: 36144369 PMCID: PMC9503985 DOI: 10.3390/microorganisms10091767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/19/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022] Open
Abstract
Recent publications indicate that A. radioresistens can cause infections in humans, even though it is rarely reported in routine diagnostics. However, the fact that it is infrequently detected may be explained by the misidentification of the species by conventional methods. It is also likely that A. radioresistens is not considered clinically relevant and therefore not consistently included in diagnostic results. To elucidate the medical significance of this probably clinically underestimated bacterial species, we created a well-documented reference strain collection of 21 strains collected in routine diagnostics. For further analysis of A. radioresistens, it is essential to know which methods can be used to achieve a trustworthy identification. We, therefore, compared three methods widely used in routine diagnostics (MALDI-TOF MS, VITEK 2, and sequencing of housekeeping genes) in terms of secure and reliable identification of A. radioresistens. As reference methods, whole genome-based approaches were applied. VITEK 2 led to misidentification for four strains. However, MALDI-TOF MS and sequencing of housekeeping genes led to reliable and robust identifications.
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Affiliation(s)
- Richard Bigge
- Institute for Microbiology and Virology, University Hospital Carl Gustav Carus, 01307 Dresden, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany
| | - Wolfram W. Rudolph
- Department of Hospital Infection Control, University Hospital Carl Gustav Carus, 01307 Dresden, Germany
| | - Florian Gunzer
- Department of Hospital Infection Control, University Hospital Carl Gustav Carus, 01307 Dresden, Germany
| | - Sina M. Coldewey
- Department of Anesthesiology and Intensive Care Medicine, Jena University Hospital, 07745 Jena, Germany
- Septomics Research Center, Jena University Hospital, 07747 Jena, Germany
- Center for Sepsis Control and Care, Jena University Hospital, 07747 Jena, Germany
| | - Thomas Riedel
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Percy Schröttner
- Institute for Microbiology and Virology, University Hospital Carl Gustav Carus, 01307 Dresden, Germany
- Correspondence: ; Tel.: +49-(351)-458-16585
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10
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A Variant Carbapenem Inactivation Method (CIM) for Acinetobacter baumannii Group with Shortened Time-to-Result: rCIM-A. Pathogens 2022; 11:pathogens11040482. [PMID: 35456157 PMCID: PMC9024794 DOI: 10.3390/pathogens11040482] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/10/2022] [Accepted: 04/13/2022] [Indexed: 02/01/2023] Open
Abstract
Carbapenem-resistant Acinetobacter baumannii group organisms (CRAB) are challenging because the choice between targeted, new antibiotic drug options and hygiene measures should be guided by a timely identification of resistance mechanisms. In CRAB, acquired class-D carbapenemases (CHDLs) are active against meropenem and imipenem. If PCR methods are not the first choice, phenotypic methods have to be implemented. While promising, the carbapenemase inactivation method (CIM) using meropenem-hydrolysis is, however, hampered by poor performance or overly long time-to-result. We developed a rapid CIM (rCIM-A) with good performance using ertapenem, imipenem, and meropenem disks, 2-h permeabilization and incubation with the test strain in trypticase soy broth, and a read-out of residual carbapenem activity after 6 h, and optionally after 16–18 h. Using clinical isolates and type-strains of Acinetobacter (n = 67) not harboring carbapenemases (n = 28) or harboring acquired carbapenemases (n = 39), the sensitivity of detection was 97.4% with the imipenem disk after 6 h at a specificity of 92.9%. If the inhibition zone around the ertapenem disk at 6 h was 6 or ≤26 mm at 16–18 h, or ≤25.5 mm for meropenem, the specificity was 100%. Because of the high negative predictive value, the rCIM-A seems particularly appropriate in areas of lower CRAB-frequency.
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11
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Precise Species Identification for Acinetobacter: a Genome-Based Study with Description of Two Novel Acinetobacter Species. mSystems 2021; 6:e0023721. [PMID: 34061620 PMCID: PMC8269215 DOI: 10.1128/msystems.00237-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The genus Acinetobacter comprises species with ecological significance and opportunistic pathogens and has a complicated taxonomy. Precise species identification is a foundation for understanding bacteria. In this study, we found and characterized two novel Acinetobacter species, namely, Acinetobacter tianfuensis sp. nov. and Acinetobacter rongchengensis sp. nov., based on phenotype examinations and genome analyses of the two strains WCHAc060012T and WCHAc060115T. The two strains had ≤89.69% (mean, 79.28% or 79.72%) average nucleotide identity (ANI) and ≤36.4% (mean, 20.89% or 22.19%) in silico DNA-DNA hybridization (isDDH) values compared with each other and all known Acinetobacter species. Both species can be differentiated from all hitherto known Acinetobacter species by a combination of phenotypic characteristics. We found that Acinetobacter pullorum B301T and Acinetobacter portensis AC 877T are actually the same species with 98.59% ANI and 90.4% isDDH values. We then applied the updated taxonomy to curate 3,956 Acinetobacter genomes in GenBank and found that 6% of Acinetobacter genomes (n = 234) are required to be corrected or updated. We identified 56 novel tentative Acinetobacter species, extending the number of Acinetobacter species to 144, including 68 with species names and 76 unnamed taxa. We also found that ANI and the average amino acid identity (AAI) values among type or reference strains of all Acinetobacter species and taxa are ≥76.97% and ≥66.5%, respectively, which are higher than the proposed cutoffs to define the genus boundary. This study highlights the complex taxonomy of Acinetobacter as a single genus and the paramount importance of precise species identification. The newly identified unnamed taxa warrant further studies. IMPORTANCEAcinetobacter species are widely distributed in nature and are of important ecological significance and clinical relevance. In this study, first, we significantly update the taxonomy of Acinetobacter by reporting two novel Acinetobacter species, namely, Acinetobacter tianfuensis and Acinetobacter rongchengensis, and by identifying Acinetobacter portensis as a synonym of Acinetobacter pullorum. Second, we curated Acinetobacter genome sequences deposited in GenBank (n = 3,956) using the updated taxonomy by correcting species assignations for 6% (n = 234) genomes and by assigning 94 (2.4%) to 56 previously unknown tentative species (taxa). Therefore, after curation, we further update the genus Acinetobacter to comprise 144 species, including 68 with species names and 76 unnamed taxa. Third, we addressed the question of whether such a large number of species should be divided in different genera and found that Acinetobacter is indeed a single genus. Our study significantly advanced the taxonomy of Acinetobacter, an important genus with science and health implications.
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12
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Almeida OGGD, Furlan JPR, Stehling EG, De Martinis ECP. Comparative phylo-pangenomics reveals generalist lifestyles in representative Acinetobacter species and proposes candidate gene markers for species identification. Gene 2021; 791:145707. [PMID: 33979679 DOI: 10.1016/j.gene.2021.145707] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 04/09/2021] [Accepted: 05/06/2021] [Indexed: 02/05/2023]
Abstract
Acinetobacter species have the potential to invade and colonize immunocompromised patients, therefore being well-known as opportunistic pathogens. Among these bacteria, the species of the Acinetobacter calcoaceticus-Acinetobacter baumannii "complex" (Acb members) emerge as the main often isolated bacteria in clinical specimens. The unequivocal taxonomy is crucial to correctly identify these species and associated with comparative genomic analyses aids to understand their life-styles as well. In this study, all publicly available Acinetobacter species at the date of this study preparation were analyzed. The results revealed that the Acb members are in fact a complex when phenotypic methods are confronted, while for comparative and phylogenomics analyses this term is misleading, since they composed a monophyletic group instead. Nine best gene markers (response regulator, recJ, recG, phosphomannomutase, pepSY, monovalent cation/H + antiporter subunit D, mnmE, glnE, and bamA) were selected for identification of Acinetobacter species. Moreover, representative strains of each species were split according their isolation sources in the categories: environmental, human, insect and non-human vertebrate. Neither niche-specific genome signature nor niche-associated functional and pathogenic potential were associated with their isolation source, meaning it is not the main force acting on Acinetobacter adaptation in a given niche and corroborating that their ubiquitous distribution is a reflex of their generalist life-styles.
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Affiliation(s)
| | | | - Eliana Guedes Stehling
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Brazil
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13
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Munson E, Carroll KC. Summary of Novel Bacterial Isolates Derived from Human Clinical Specimens and Nomenclature Revisions Published in 2018 and 2019. J Clin Microbiol 2021; 59:e01309-20. [PMID: 32967902 PMCID: PMC8111135 DOI: 10.1128/jcm.01309-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Knowledge of novel prokaryotic taxon discovery and nomenclature revisions is of importance to clinical microbiology laboratory practice, infectious disease epidemiology, and studies of microbial pathogenesis. Relative to bacterial isolates derived from human clinical specimens, we present an in-depth summary of novel taxonomic designations and revisions to prokaryotic taxonomy that were published in 2018 and 2019. Included are several changes pertinent to former designations of or within Propionibacterium spp., Corynebacterium spp., Clostridium spp., Mycoplasma spp., Methylobacterium spp., and Enterobacteriaceae Future efforts to ascertain clinical relevance for many of these changes may be augmented by a document development committee that has been appointed by the Clinical and Laboratory Standards Institute.
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Affiliation(s)
- Erik Munson
- College of Health Sciences, Marquette University, Milwaukee, Wisconsin, USA
| | - Karen C Carroll
- Division of Medical Microbiology, Department of Pathology, the Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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14
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Carvalheira A, Silva J, Teixeira P. Acinetobacter spp. in food and drinking water - A review. Food Microbiol 2020; 95:103675. [PMID: 33397609 DOI: 10.1016/j.fm.2020.103675] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 01/01/2023]
Abstract
Acinetobacter spp. has emerged as a pathogen of major public health concern due to their increased resistance to antibiotics and their association with a wide range of nosocomial infections, community-acquired infections and war and natural disaster-related infections. It is recognized as a ubiquitous organism however, information about the prevalence of different pathogenic species of this genus in food sources and drinking water is scarce. Since the implementation of molecular techniques, the role of foods as a source of several species, including the Acinetobacter baumannii group, has been elucidated. Multidrug resistance was also detected among Acinetobacter spp. isolated from food products. This highlights the importance of foods as potential sources of dissemination of Acinetobacter spp. between the community and clinical environments and reinforces the need for further investigations on the potential health risks of Acinetobacter spp. as foodborne pathogens. The aim of this review was to summarize the published data on the occurrence of Acinetobacter spp. in different food sources and drinking water. This information should be taken into consideration by those responsible for infection control in hospitals and other healthcare facilities.
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Affiliation(s)
- Ana Carvalheira
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal
| | - Joana Silva
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal
| | - Paula Teixeira
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal.
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15
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Carvalheira A, Gonzales-Siles L, Salvà-Serra F, Lindgren Å, Svensson-Stadler L, Thorell K, Piñeiro-Iglesias B, Karlsson R, Silva J, Teixeira P, Moore ERB. Acinetobacter portensis sp. nov. and Acinetobacter guerrae sp. nov., isolated from raw meat. Int J Syst Evol Microbiol 2020; 70:4544-4554. [PMID: 32618559 DOI: 10.1099/ijsem.0.004311] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic status of six strains of Acinetobacter obtained from meat samples, collected from supermarkets in Porto, Portugal, was investigated using polyphasic analysis. Partial rpoB sequence similarities lower than 95 % to other Acinetobacter species with validly published names led to the hypothesis that these strains represented novel species. This was confirmed based on comparative multilocus sequence analysis, which included the gyrB, recA and 16S rRNA genes, revealing that these strains represented two coherent lineages that were distinct from each other and from all known species. The names Acinetobacter portensis sp. nov. (comprising four strains) and Acinetobacter guerrae sp. nov. (comprising two strains) are proposed for these novel species. The species status of these two groups was confirmed by low (below 95 %) whole-genome sequence average nucleotide identity values and low (below 70 %) digital DNA-DNA hybridization similarities between the whole-genome sequences of the proposed type strains of each novel species and the representatives of the known Acinetobacter species. Phylogenomic treeing from core genome analysis supported these results. The coherence of each new species lineage was supported by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry differentiation of the species at the protein level, by cellular fatty acid profiles, and by unique and differential combinations of metabolic and physiological properties shared by each novel species. The type strain of A. portensis sp. nov. is AC 877T (=CCUG 68672T=CCM 8789T) and the type strain of A. guerrae sp. nov. is AC 1271T (=CCUG 68674T=CCM 8791T).
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Affiliation(s)
- Ana Carvalheira
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Porto, Portugal
| | - Lucia Gonzales-Siles
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden.,Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
| | - Francisco Salvà-Serra
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden.,Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain.,Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden.,Culture Collection University of Gothenburg (CCUG), Department of Clinical Microbiology, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
| | - Åsa Lindgren
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
| | - Liselott Svensson-Stadler
- Culture Collection University of Gothenburg (CCUG), Department of Clinical Microbiology, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden.,Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
| | - Kaisa Thorell
- Center for Translational Microbiome Research, Department of Microbiology, Cell and Tumor biology, Karolinska Institutet, Stockholm, Sweden.,Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
| | - Beatriz Piñeiro-Iglesias
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
| | - Roger Karlsson
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden.,Nanoxis Consulting AB, Gothenburg, Sweden.,Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
| | - Joana Silva
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Porto, Portugal
| | - Paula Teixeira
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Porto, Portugal
| | - Edward R B Moore
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden.,Culture Collection University of Gothenburg (CCUG), Department of Clinical Microbiology, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
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16
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Casanovas Moreno-Torres MI, Rodríguez-Campos F, Gutiérrez-Soto M, Navarro-Marí JM, Gutiérrez-Fernández J. [Urinary tract infection by Acinetobacter dijkshoorniae and good clinical response to treatment]. REVISTA ESPANOLA DE QUIMIOTERAPIA 2020; 33:281-282. [PMID: 32466628 PMCID: PMC7374032 DOI: 10.37201/req/011.2020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
| | | | | | | | - J Gutiérrez-Fernández
- José Gutiérrez-Fernández. Laboratorio de Microbiología. Hospital Universitario Virgen de las Nieves. Avenida de las Fuerzas Armadas, 2. E-18012 Granada, Spain.
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17
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Qin J, Feng Y, Lü X, Zong Z. Characterization of Acinetobacter chengduensis sp. nov., isolated from hospital sewage and capable of acquisition of carbapenem resistance genes. Syst Appl Microbiol 2020; 43:126092. [PMID: 32690195 DOI: 10.1016/j.syapm.2020.126092] [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: 12/11/2019] [Revised: 04/01/2020] [Accepted: 05/08/2020] [Indexed: 02/05/2023]
Abstract
Two strains of the genus Acinetobacter, WCHAc060005T and WCHAc060007, were isolated from hospital sewage in China. The two strains showed different patterns of resistance to clinically important antibiotics and their taxonomic positions were investigated. Cells are Gram-negative, obligate aerobic, non-motile, catalase-positive and oxidase-negative coccobacilli. A preliminary analysis based on the 16S rRNA gene sequences indicated that the two strains had the highest similarity to Acinetobacter cumulans WCHAc060092T (99.02%). Whole-genome sequencing of the two strains and genus-wide phylogeny reconstruction based on a set of 107 Acinetobacter core genes indicated that they formed a separate and internally cohesive clade within the genus. The average nucleotide identity based on BLAST and in silico DNA-DNA hybridization values between the two new genomes were 99.77% and 98.7% respectively, whereas those between the two genomes and the known Acinetobacter species were <88.93% and <34.0%, respectively. A total of 7 different genes were found in the two genome sequences which encode resistance to five classes of antimicrobial agents, including clinically important carbapenems, oxyimino-cephalosporins, and quinolones. In addition, the combination of their ability to assimilate gentisate, but not l-glutamate and d,l-lactate could distinguish the two strains from all known Acinetobacter species. Based on these combined data, we concluded that the two strains represent a novel species of the genus Acinetobacter, for which the name Acinetobacter chengduensis sp. nov. is proposed. The type strain is WCHAc060005T (CCTCC AB 2019139=GDMCC 1.1622=JCM 33509).
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Affiliation(s)
- Jiayuan Qin
- Center of Infectious Diseases, West China Hospital, Sichuan University, Guoxuexiang 37, Chengdu 610041, Sichuan, China; Division of Infectious Diseases, State Key Laboratory of Biotherapy, Guoxuexiang 37, Chengdu 610041, Sichuan, China
| | - Yu Feng
- Center of Infectious Diseases, West China Hospital, Sichuan University, Guoxuexiang 37, Chengdu 610041, Sichuan, China; Division of Infectious Diseases, State Key Laboratory of Biotherapy, Guoxuexiang 37, Chengdu 610041, Sichuan, China; Center for Pathogen Research, West China Hospital, Sichuan University, Guoxuexiang 37, Chengdu 610041, Sichuan, China
| | - Xiaoju Lü
- Center of Infectious Diseases, West China Hospital, Sichuan University, Guoxuexiang 37, Chengdu 610041, Sichuan, China; Division of Infectious Diseases, State Key Laboratory of Biotherapy, Guoxuexiang 37, Chengdu 610041, Sichuan, China
| | - Zhiyong Zong
- Center of Infectious Diseases, West China Hospital, Sichuan University, Guoxuexiang 37, Chengdu 610041, Sichuan, China; Division of Infectious Diseases, State Key Laboratory of Biotherapy, Guoxuexiang 37, Chengdu 610041, Sichuan, China; Center for Pathogen Research, West China Hospital, Sichuan University, Guoxuexiang 37, Chengdu 610041, Sichuan, China; Department of Infection Control, West China Hospital, Sichuan University, Guoxuexiang 37, Chengdu 610041, Sichuan, China.
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18
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Wang X, Li J, Cao X, Wang W, Luo Y. Isolation, identification and characterisation of an emerging fish pathogen, Acinetobacter pittii, from diseased loach (Misgurnus anguillicaudatus) in China. Antonie van Leeuwenhoek 2019; 113:21-32. [PMID: 31432291 DOI: 10.1007/s10482-019-01312-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 07/31/2019] [Indexed: 11/29/2022]
Abstract
Although members of the genus Acinetobacter have emerged as important nosocomial pathogens causing severe human infections, there are few reports about their occurrence as fish pathogens. In this study, five bacterial strains were isolated from diseased loach (Misgurnus anguillicaudatus) cultured in a farm in China. The diseased loach displayed shedding of skin mucus and many petechial haemorrhages all over the body. Based on sequence analyses of 16S rRNA and rpoB genes, the isolates were identified as Acinetobacter pittii. An experimental infection assay confirmed their pathogenicity to loach. The results of artificial infection in zebrafish (Barchydanio rerio) and nematode (Caenorhabditis elegans) suggested that, as well as loach, these A. pittii isolates are pathogenic and highly virulent to these organisms. Multilocus sequence typing analysis revealed that all the isolates belong to sequence type (ST) 839, which may be the dominant clone causing fish disease and exhibits a close phylogenetic relationship with ST396 from human clinical samples in Korea or Taiwan China. This is the first report demonstrating that A. pittii is an emerging causal agent of mass mortality in loach and poses significant risks to fish culturing besides causing human clinical infection worldwide.
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Affiliation(s)
- Xu Wang
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Jie Li
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Xiaojuan Cao
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Weimin Wang
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Yi Luo
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China. .,State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China.
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Villalón P, Ortega M, Sáez-Nieto JA, Carrasco G, Medina-Pascual MJ, Garrido N, Valdezate S. Dynamics of a Sporadic Nosocomial Acinetobacter calcoaceticus - Acinetobacter baumannii Complex Population. Front Microbiol 2019; 10:593. [PMID: 30967856 PMCID: PMC6440288 DOI: 10.3389/fmicb.2019.00593] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 03/08/2019] [Indexed: 12/27/2022] Open
Abstract
Our objective was to improve current knowledge of sporadic (Spo) nosocomial Acinetobactercalcoaceticus-Acinetobacter baumannii (Acb) complex populations, and thus better understand the epidemiology of Spo and endemoepidemic (EE) strains. Between 1999 and 2010, 133 isolates of Spo Acb complex were obtained from a single hospital. Species were identified by gyrB-PCR, and via gyrB- and rpoB-sequencing. Clonal analysis was undertaken using pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing. Susceptibility to antimicrobial agents was determined by microdilution and E-tests. Carbapenemase genes were detected by PCR. One hundred and one PFGE types were detected. A. baumannii was the most common (67/101 PFGE types), followed by Acinetobacter pittii (22/101), Acinetobacter lactucae (6/101), and Acinetobacter calcoaceticus (2/101). gyrB, rpoB1, and rpoB2 sequencing returned 49, 13, and 16 novel sequences, respectively. Sixty-three sequence types (STs) (38 new STs and 66 new alleles) were detected; the most common were ST2 (29/133 isolates) and ST132 (14/133). Twenty-six OXA-51 allelic variants were detected, nine of which were novel. The PFGE types were generally susceptible (88/101) to all the tested antimicrobials; 3/101 were carbapenem-resistant due to the presence of the genetic structure ISAba2-blaOXA-58-like-ISAba3, and 2/101 were multidrug-resistant. It can be concluded that the examined Spo Acb complex population was mainly composed of A. baumannii. Many different clones were detected (with ST2 clearly dominant), all largely susceptible to antimicrobials; multidrug resistance was rare. In contrast, a previously examined EE Acb population was composed of just four expanding, multidrug-resistant A. baumannii clones -ST2, ST3, ST15, and ST80-.
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Affiliation(s)
- Pilar Villalón
- Laboratorio de Referencia e Investigación en Taxonomía, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Montserrat Ortega
- Laboratorio de Referencia e Investigación en Taxonomía, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Juan A Sáez-Nieto
- Laboratorio de Referencia e Investigación en Taxonomía, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Gema Carrasco
- Laboratorio de Referencia e Investigación en Taxonomía, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - María J Medina-Pascual
- Laboratorio de Referencia e Investigación en Taxonomía, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Noelia Garrido
- Laboratorio de Referencia e Investigación en Taxonomía, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Sylvia Valdezate
- Laboratorio de Referencia e Investigación en Taxonomía, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
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Püntener-Simmen S, Zurfluh K, Schmitt S, Stephan R, Nüesch-Inderbinen M. Phenotypic and Genotypic Characterization of Clinical Isolates Belonging to the Acinetobacter calcoaceticus-Acinetobacter baumannii (ACB) Complex Isolated From Animals Treated at a Veterinary Hospital in Switzerland. Front Vet Sci 2019; 6:17. [PMID: 30805352 PMCID: PMC6370676 DOI: 10.3389/fvets.2019.00017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 01/17/2019] [Indexed: 11/25/2022] Open
Abstract
Objectives: We investigated a collection of strains belonging to the Acinetobacter calcoaceticus-Acinetobacter baumannii (ACB) complex obtained from a veterinary clinic with regard to their genetic relatedness, presence of antibiotic resistance genes and antimicrobial susceptibility profiles. Methods: Fifty-eight ACB-complex strains from animals treated at a veterinary clinic between 2006 and 2017, and seven strains collected from the hospital environment during 2012 were analyzed. Assignment to sequence types (ST) and international complexes (IC) was done by multilocus sequence typing (MLST) according to the Pasteur scheme. Genes encoding carbapenemases, aminoglycoside-modifying enzymes, macrolide-, quinolone- and co-trimoxazole resistance genes, the ISAba1 element, virulence associated intI1 genes and plasmid associated toxin-antitoxin markers were identified by microarray. Genes encoding blaOXA−51-like carbapenemases were amplified by PCR and sequenced. Susceptibility profiles were determined by disc diffusion or by broth microdilution. Results: Among 50 A. baumannii isolates from animals, two predominant clones were observed linked to CC1 (n = 27/54% of the isolates) and CC25 (n = 14/28%), respectively. Strains of IC I harbored blaOXA−69, aac(3′)-la, aadA1, sul1, intI1, and splA/T genes. Isolates belonging to CC25 possessed blaOXA−64. Six (12%) isolates belonging to CC2 and carrying blaOXA−66 were also noted. One isolate belonged to CC10 (blaOXA−68), one to CC149 (blaOXA−104), the remaining isolate was assigned to ST1220 and possessed blaOXA−116. Of six environmental A. baumannii, four (66.7%) belonged to CC25 (blaOXA−64), one (16.7%) to CC2 (blaOXA−66) and one to CC3 (blaOXA−71). Nine isolates (eight from animals and one environmental strain) were non-baumannii strains and did not harbor blaOXA−51-like genes. None of the isolates carried blaOXA−23, blaOXA−48, or blaOXA−58, and none were resistant to carbapenems. Conclusions: Clonal lineages of the veterinary A. baumannii isolates in our collection are identical to those globally emerging in humans but do not harbor blaOXA−23. A. baumannii CC25 may be specific for this particular veterinary clinic environment.
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Affiliation(s)
- Sabrina Püntener-Simmen
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Katrin Zurfluh
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Sarah Schmitt
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Roger Stephan
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
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Acinetobacter as a potentially important producer of urocanic acid in chub mackerel, a histidine metabolite of emerging health concern. Eur Food Res Technol 2019. [DOI: 10.1007/s00217-018-3217-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Proposed nomenclature or classification changes for bacteria of medical importance: Taxonomic Update 4. Diagn Microbiol Infect Dis 2018; 94:205-208. [PMID: 30683468 DOI: 10.1016/j.diagmicrobio.2018.12.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 12/18/2018] [Accepted: 12/21/2018] [Indexed: 11/22/2022]
Abstract
A key aspect of medical, public health, and diagnostic microbiology laboratories is the accurate identification and rapid reporting and communication to medical staff regarding patients with infectious agents of clinical importance. Microbial taxonomy continues to change at a very rapid rate in the era of molecular diagnostics including whole genome sequencing. This update focuses on taxonomic changes and proposals that may be of medical importance for years 2017 and 2018.
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