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Göpel L, Prenger-Berninghoff E, Wolf SA, Semmler T, Bauerfeind R, Ewers C. Repeated Occurrence of Mobile Colistin Resistance Gene-Carrying Plasmids in Pathogenic Escherichia coli from German Pig Farms. Microorganisms 2024; 12:729. [PMID: 38674671 PMCID: PMC11052496 DOI: 10.3390/microorganisms12040729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 03/26/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
The global spread of plasmid-mediated mobile colistin resistance (mcr) genes threatens the vital role of colistin as a drug of last resort. We investigated whether the recurrent occurrence of specific E. coli pathotypes and plasmids in individual pig farms resulted from the continued presence or repeated reintroduction of distinct E. coli strains. E. coli isolates (n = 154) obtained from three pig farms with at least four consecutive years of mcr detection positive for virulence-associated genes (VAGs) predicting an intestinal pathogenic pathotype via polymerase chain reaction were analyzed. Detailed investigation of VAGs, antimicrobial resistance genes and plasmid Inc types was conducted using whole genome sequencing for 87 selected isolates. Sixty-one E. coli isolates harbored mcr-1, and one isolate carried mcr-4. On Farm 1, mcr-positive isolates were either edema disease E. coli (EDEC; 77.3%) or enterotoxigenic E. coli (ETEC; 22.7%). On Farm 2, all mcr-positive strains were ETEC, while mcr-positive isolates from Farm 3 showed a wider range of pathotypes. The mcr-1.1 gene was located on IncHI2 (Farm 1), IncX4 (Farm 2) or IncX4 and IncI2 plasmids (Farm 3). These findings suggest that various pathogenic E. coli strains play an important role in maintaining plasmid-encoded colistin resistance genes in the pig environment over time.
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Affiliation(s)
- Lisa Göpel
- Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, 35392 Giessen, Germany;
- Department of Infectious Diseases and Microbiology, University of Luebeck, 23538 Luebeck, Germany
| | - Ellen Prenger-Berninghoff
- Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, 35392 Giessen, Germany;
| | - Silver A. Wolf
- Microbial Genomics, Robert Koch Institute, 13353 Berlin, Germany
| | - Torsten Semmler
- Microbial Genomics, Robert Koch Institute, 13353 Berlin, Germany
| | - Rolf Bauerfeind
- Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, 35392 Giessen, Germany;
| | - Christa Ewers
- Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, 35392 Giessen, Germany;
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2
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Ulrich JU, Epping L, Pilz T, Walther B, Stingl K, Semmler T, Renard BY. Nanopore adaptive sampling effectively enriches bacterial plasmids. mSystems 2024; 9:e0094523. [PMID: 38376263 PMCID: PMC10949517 DOI: 10.1128/msystems.00945-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 01/23/2024] [Indexed: 02/21/2024] Open
Abstract
Bacterial plasmids play a major role in the spread of antibiotic resistance genes. However, their characterization via DNA sequencing suffers from the low abundance of plasmid DNA in those samples. Although sample preparation methods can enrich the proportion of plasmid DNA before sequencing, these methods are expensive and laborious, and they might introduce a bias by enriching only for specific plasmid DNA sequences. Nanopore adaptive sampling could overcome these issues by rejecting uninteresting DNA molecules during the sequencing process. In this study, we assess the application of adaptive sampling for the enrichment of low-abundant plasmids in known bacterial isolates using two different adaptive sampling tools. We show that a significant enrichment can be achieved even on expired flow cells. By applying adaptive sampling, we also improve the quality of de novo plasmid assemblies and reduce the sequencing time. However, our experiments also highlight issues with adaptive sampling if target and non-target sequences span similar regions. IMPORTANCE Antimicrobial resistance causes millions of deaths every year. Mobile genetic elements like bacterial plasmids are key drivers for the dissemination of antimicrobial resistance genes. This makes the characterization of plasmids via DNA sequencing an important tool for clinical microbiologists. Since plasmids are often underrepresented in bacterial samples, plasmid sequencing can be challenging and laborious. To accelerate the sequencing process, we evaluate nanopore adaptive sampling as an in silico method for the enrichment of low-abundant plasmids. Our results show the potential of this cost-efficient method for future plasmid research but also indicate issues that arise from using reference sequences.
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Affiliation(s)
- Jens-Uwe Ulrich
- Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam, Germany
- Department of Mathematics and Computer Science, Free University of Berlin, Berlin, Germany
- Phylogenomics Unit, Center for Artificial Intelligence in Public Health Research, Robert Koch Institute, Wildau, Germany
| | - Lennard Epping
- Genome Sequencing and Genomic Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Tanja Pilz
- Genome Sequencing and Genomic Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Birgit Walther
- Advanced Light and Electron Microscopy, Robert Koch Institute, Berlin, Germany
| | - Kerstin Stingl
- National Reference Laboratory for Campylobacter, Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Torsten Semmler
- Genome Sequencing and Genomic Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Bernhard Y. Renard
- Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam, Germany
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3
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Saini P, Bandsode V, Singh A, Mendem SK, Semmler T, Alam M, Ahmed N. Genomic insights into virulence, antimicrobial resistance, and adaptation acumen of Escherichia coli isolated from an urban environment. mBio 2024; 15:e0354523. [PMID: 38376265 PMCID: PMC10936179 DOI: 10.1128/mbio.03545-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 01/23/2024] [Indexed: 02/21/2024] Open
Abstract
Populations of common commensal bacteria such as Escherichia coli undergo genetic changes by the acquisition of certain virulence and antimicrobial resistance (AMR) encoding genetic elements leading to the emergence of pathogenic strains capable of surviving in the previously uninhabited or protected niches. These bacteria are also reported to be prevalent in the environment where they survive by adopting various recombination strategies to counter microflora of the soil and water, under constant selection pressure(s). In this study, we performed molecular characterization, phenotypic AMR analysis, and whole genome sequencing (WGS) of E. coli (n = 37) isolated from soil and surface water representing the urban and peri-urban areas. The primary aim of this study was to understand the genetic architecture and pathogenic acumen exhibited by environmental E. coli. WGS-based analysis entailing resistome and virulome profiling indicated the presence of various virulence (adherence, iron uptake, and toxins) and AMR encoding genes, including blaNDM-5 in the environmental isolates. A majority of our isolates belonged to phylogroup B1 (73%). A few isolates in our collection were of sequence type(s) (ST) 58 and 224 that could have emerged recently as clonal lineages and might pose risk of infection/transmission. Mobile genetic elements (MGEs) such as plasmids (predominantly) of the IncF family, prophages, pipolins, and insertion elements such as IS1 and IS5 were also observed to exist, which may presumably aid in the propagation of genes encoding resistance against antimicrobial drugs. The observed high prevalence of MGEs associated with multidrug resistance in pathogenic E. coli isolates belonging to the phylogroup B1 underscores the need for extended surveillance to keep track of and prevent the transmission of the bacterium to certain vulnerable human and animal populations. IMPORTANCE Evolutionary patterns of E. coli bacteria convey that they evolve into highly pathogenic forms by acquiring fitness advantages, such as AMR, and various virulence factors through the horizontal gene transfer (HGT)-mediated acquisition of MGEs. However, limited research on the genetic profiles of environmental E. coli, particularly from India, hinders our understanding of their transition to pathogenic forms and impedes the adoption of a comprehensive approach to address the connection between environmentally dwelling E. coli populations and human and veterinary public health. This study focuses on high-resolution genomic analysis of the environmental E. coli isolates aiming to understand the genetic similarities and differences among isolates from different environmental niches and uncover the survival strategies employed by these bacteria to thrive in their surroundings. Our approach involved molecular characterization of environmental samples using PCR-based DNA fingerprinting and subsequent WGS analysis. This multidisciplinary approach is likely to provide valuable insights into the understanding of any potential spill-over to human and animal populations and locales. Investigating these environmental isolates has significant potential for developing epidemiological strategies against transmission and understanding niche-specific evolutionary patterns.
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Affiliation(s)
- Poorvi Saini
- Department of Biotechnology and Bioinformatics, Pathogen Biology Laboratory, University of Hyderabad, Hyderabad, Telangana State, India
| | - Viraj Bandsode
- Department of Biotechnology and Bioinformatics, Pathogen Biology Laboratory, University of Hyderabad, Hyderabad, Telangana State, India
| | - Anuradha Singh
- Department of Biotechnology and Bioinformatics, Pathogen Biology Laboratory, University of Hyderabad, Hyderabad, Telangana State, India
| | - Suresh Kumar Mendem
- Department of Biotechnology and Bioinformatics, Pathogen Biology Laboratory, University of Hyderabad, Hyderabad, Telangana State, India
| | | | - Munirul Alam
- International Centre for Diarrheal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Niyaz Ahmed
- Department of Biotechnology and Bioinformatics, Pathogen Biology Laboratory, University of Hyderabad, Hyderabad, Telangana State, India
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Wagner H, Heller M, Fawzy A, Schnee C, Nesseler A, Kaim U, Ewers C, Semmler T, Spergser J, Schultze T, Eisenberg T. Mycoplasma mycoides subspecies capri, an uncommon mastitis and respiratory pathogen isolated in a German flock of goats. Vet Microbiol 2024; 290:109996. [PMID: 38295490 DOI: 10.1016/j.vetmic.2024.109996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 12/27/2023] [Accepted: 01/11/2024] [Indexed: 02/02/2024]
Abstract
Mycoplasma mycoides ssp. capri (Mmc) is one of the etiological microorganisms of contagious agalactia, which is among the diseases causing the highest economical losses in small ruminants. We report a disease outbreak in a German flock that led to significant suffering of goats characterized by mastitis, arthritis, pleuropneumonia and sudden deaths. Mmc was persistently isolated from many animals both from milk, and from a number of different swab and tissue samples. A number of closely related Mycoplasma spp. have to be taken into consideration to rule out important animal epizootics listed by European Animal Health Law and the World Organisation for Animal Health (WOAH). Some goats developed cross-reacting antibodies against Mycoplasma mycoides ssp. mycoides. Although Mmc is believed to be an uncommon microorganism in Germany, this study highlights that veterinarians should consider this pathogen in their work during herd health monitoring in Central Europe. Although eradication was not fully achieved, autogenous vaccination significantly seemed to improve animal health and welfare.
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Affiliation(s)
- Henrik Wagner
- Veterinary Clinic for Reproductive Medicine and Neonatology, Justus-Liebig-University Giessen, Giessen 35392, Germany
| | - Martin Heller
- Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis (IMP), Jena 07743, Germany
| | - Ahmad Fawzy
- Cairo University, Faculty of Veterinary Medicine, Department of Medicine and Infectious Diseases, Cairo, Egypt; Hessian State Laboratory (LHL), Schubertstr. 60, Giessen 35392, Germany
| | - Christiane Schnee
- Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis (IMP), Jena 07743, Germany
| | - Anne Nesseler
- Hessian State Laboratory (LHL), Schubertstr. 60, Giessen 35392, Germany
| | - Ute Kaim
- Hessian State Laboratory (LHL), Schubertstr. 60, Giessen 35392, Germany
| | - Christa Ewers
- Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Giessen 35392, Germany
| | - Torsten Semmler
- NG1 Microbial Genomics, Robert Koch Institute, Berlin, Germany
| | - Joachim Spergser
- Institute of Microbiology, University of Veterinary Medicine, Vienna 1210, Austria
| | - Tilman Schultze
- Hessian State Laboratory (LHL), Schubertstr. 60, Giessen 35392, Germany
| | - Tobias Eisenberg
- Hessian State Laboratory (LHL), Schubertstr. 60, Giessen 35392, Germany; Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Giessen 35392, Germany.
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Schotte U, Ehlers J, Nieter J, Rakotozandrindrainy R, Wolf SA, Semmler T, Frickmann H, Poppert S, Ewers C. ESBL-Type and AmpC-Type Beta-Lactamases in Third Generation Cephalosporin-Resistant Enterobacterales Isolated from Animal Feces in Madagascar. Animals (Basel) 2024; 14:741. [PMID: 38473126 DOI: 10.3390/ani14050741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/23/2024] [Accepted: 02/24/2024] [Indexed: 03/14/2024] Open
Abstract
Third generation cephalosporin-resistant (3GCR) Enterobacterales are known to be prevalent in Madagascar, with high colonization or infection rates in particular in Madagascan patients. Extended spectrum beta-lactamases (ESBLs) have been reported to be the predominant underlying resistance mechanism in human isolates. So far, little is known on antimicrobial resistance and its molecular determinants in Enterobacterales and other bacteria causing enteric colonization of Madagascan wild animals. To address this topic, swabs from 49 animal stool droppings were collected in the Madagascan Tsimanapesotsa National Park and assessed by cultural growth of bacterial microorganisms on elective media. In addition to 7 Acinetobacter spp., a total of 31 Enterobacterales growing on elective agar for Enterobacterales could be isolated and subjected to whole genome sequencing. Enterobacter spp. was the most frequently isolated genus, and AmpC-type beta-lactamases were the quantitatively dominating molecular resistance mechanism. In contrast, the blaCTX-M-15 gene, which has repeatedly been associated with 3GC-resistance in Madagascan Enterobacterales from humans, was detected in a single Escherichia coli isolate only. The identification of the fosfomycin-resistance gene fosA in a high proportion of isolates is concerning, as fosfomycin is increasingly used to treat infections caused by multidrug-resistant bacteria. In conclusion, the proof-of-principle assessment indicated a high colonization rate of resistant bacteria in stool droppings of Madagascan wild animals with a particular focus on 3GCR Enterobacterales. Future studies should confirm these preliminary results in a more systematic way and assess the molecular relationship of animal and human isolates to identify potential routes of transmission.
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Affiliation(s)
- Ulrich Schotte
- Department A-Veterinary Medicine, Central Institute of the Bundeswehr Medical Service Kiel, 24119 Kronshagen, Germany
| | - Julian Ehlers
- Bernhard Nocht Institute for Tropical Medicine Hamburg, 20359 Hamburg, Germany
| | - Johanna Nieter
- Department A-Veterinary Medicine, Central Institute of the Bundeswehr Medical Service Kiel, 24119 Kronshagen, Germany
| | | | - Silver A Wolf
- Genome Competence Centre, Robert Koch Institute, 13353 Berlin, Germany
| | - Torsten Semmler
- Genome Competence Centre, Robert Koch Institute, 13353 Berlin, Germany
| | - Hagen Frickmann
- Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg, 20359 Hamburg, Germany
- Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, 18057 Rostock, Germany
| | - Sven Poppert
- Bernhard Nocht Institute for Tropical Medicine Hamburg, 20359 Hamburg, Germany
| | - Christa Ewers
- Institute for Hygiene and Infectious Diseases of Animals, University of Giessen, 35392 Giessen, Germany
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Singh A, Lankapalli AK, Mendem SK, Semmler T, Ahmed N. Unraveling the evolutionary dynamics of toxin-antitoxin systems in diverse genetic lineages of Escherichia coli including the high-risk clonal complexes. mBio 2024; 15:e0302323. [PMID: 38117088 PMCID: PMC10790755 DOI: 10.1128/mbio.03023-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 12/21/2023] Open
Abstract
IMPORTANCE Large-scale genomic studies of E. coli provide an invaluable opportunity to understand how genomic fine-tuning contributes to the transition of bacterial lifestyle from being commensals to mutualists or pathogens. Within this context, through machine learning-based studies, it appears that TA systems play an important role in the classification of high-risk clonal lineages and could be attributed to their epidemiological success. Due to these profound indications and assumptions, we attempted to provide unique insights into the ordered world of TA systems at the population level by investigating the diversity and evolutionary patterns of TA genes across 19 different STs of E. coli. Further in-depth analysis of ST-specific TA structures and associated genetic coordinates holds the potential to elucidate the functional implications of TA systems in bacterial cell survival and persistence, by and large.
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Affiliation(s)
- Anuradha Singh
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, Telangana State, India
| | - Aditya Kumar Lankapalli
- Department of Biology and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, United Kingdom
| | - Suresh Kumar Mendem
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, Telangana State, India
| | | | - Niyaz Ahmed
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, Telangana State, India
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Aurich S, Wolf SA, Prenger-Berninghoff E, Thrukonda L, Semmler T, Ewers C. Genotypic Characterization of Uropathogenic Escherichia coli from Companion Animals: Predominance of ST372 in Dogs and Human-Related ST73 in Cats. Antibiotics (Basel) 2023; 13:38. [PMID: 38247597 PMCID: PMC10812829 DOI: 10.3390/antibiotics13010038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/13/2023] [Accepted: 12/26/2023] [Indexed: 01/23/2024] Open
Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) account for over 80% and 60% of bacterial urinary tract infections (UTIs) in humans and animals, respectively. As shared uropathogenic E. coli (UPEC) strains have been previously reported among humans and pets, our study aimed to characterize E. coli lineages among UTI isolates from dogs and cats and to assess their overlaps with human UPEC lineages. We analysed 315 non-duplicate E. coli isolates from the UT of dogs (198) and cats (117) collected in central Germany in 2019 and 2020 utilizing whole genome sequencing and in silico methods. Phylogroup B2 (77.8%), dog-associated sequence type (ST) 372 (18.1%), and human-associated ST73 (16.6%), were predominant. Other STs included ST12 (8.6%), ST141 (5.1%), ST127 (4.8%), and ST131 (3.5%). Among these, 58.4% were assigned to the ExPEC group and 51.1% to the UPEC group based on their virulence associated gene (VAG) profile (ExPEC, presence of ≥VAGs: papAH and/or papC, sfa/focG, afaD/draBC, kpsMTII, and iutA; UPEC, additionally cnf1 or hlyD). Extended-spectrum cephalosporin (ESC) resistance mediated by extended-spectrum β-lactamases (ESBL) and AmpC-β-lactamase was identified in 1.9% of the isolates, along with one carbapenemase-producing isolate and one isolate carrying a mcr gene. Low occurrence of ESC-resistant or multidrug-resistant (MDR) isolates (2.9%) in the two most frequently detected STs implies that E. coli isolated from UTIs of companion animals are to a lesser extent associated with resistance, but possess virulence-associated genes enabling efficient UT colonization and carriage. Detection of human-related pandemic lineages suggests interspecies transmission and underscores the importance of monitoring companion animals.
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Affiliation(s)
- Sophie Aurich
- Institute of Hygiene and Infectious Diseases of Animals, Faculty of Veterinary Medicine, Justus Liebig University Giessen, 35392 Giessen, Germany; (E.P.-B.); (C.E.)
| | - Silver Anthony Wolf
- Genome Competence Centre, Robert Koch Institute, 13353 Berlin, Germany (L.T.)
| | - Ellen Prenger-Berninghoff
- Institute of Hygiene and Infectious Diseases of Animals, Faculty of Veterinary Medicine, Justus Liebig University Giessen, 35392 Giessen, Germany; (E.P.-B.); (C.E.)
| | | | - Torsten Semmler
- Genome Competence Centre, Robert Koch Institute, 13353 Berlin, Germany (L.T.)
| | - Christa Ewers
- Institute of Hygiene and Infectious Diseases of Animals, Faculty of Veterinary Medicine, Justus Liebig University Giessen, 35392 Giessen, Germany; (E.P.-B.); (C.E.)
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Saathoff M, Kosol S, Semmler T, Tedin K, Dimos N, Kupke J, Seidel M, Ghazisaeedi F, Jonske MC, Wolf SA, Kuropka B, Czyszczoń W, Ghilarov D, Grätz S, Heddle JG, Loll B, Süssmuth RD, Fulde M. Gene amplifications cause high-level resistance against albicidin in gram-negative bacteria. PLoS Biol 2023; 21:e3002186. [PMID: 37561817 PMCID: PMC10414762 DOI: 10.1371/journal.pbio.3002186] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 06/07/2023] [Indexed: 08/12/2023] Open
Abstract
Antibiotic resistance is a continuously increasing concern for public healthcare. Understanding resistance mechanisms and their emergence is crucial for the development of new antibiotics and their effective use. The peptide antibiotic albicidin is such a promising candidate that, as a gyrase poison, shows bactericidal activity against a wide range of gram-positive and gram-negative bacteria. Here, we report the discovery of a gene amplification-based mechanism that imparts an up to 1000-fold increase in resistance levels against albicidin. RNA sequencing and proteomics data show that this novel mechanism protects Salmonella Typhimurium and Escherichia coli by increasing the copy number of STM3175 (YgiV), a transcription regulator with a GyrI-like small molecule binding domain that traps albicidin with high affinity. X-ray crystallography and molecular docking reveal a new conserved motif in the binding groove of the GyrI-like domain that can interact with aromatic building blocks of albicidin. Phylogenetic studies suggest that this resistance mechanism is ubiquitous in gram-negative bacteria, and our experiments confirm that STM3175 homologs can confer resistance in pathogens such as Vibrio vulnificus and Pseudomonas aeruginosa.
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Affiliation(s)
- Mareike Saathoff
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Simone Kosol
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Torsten Semmler
- Robert Koch-Institute (RKI), MF2—Genome Sequencing and Genomic Epidemiology, Berlin, Germany
| | - Karsten Tedin
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Nicole Dimos
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Johannes Kupke
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Maria Seidel
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | | | - Micela Condor Jonske
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Silver A. Wolf
- Robert Koch-Institute (RKI), MF2—Genome Sequencing and Genomic Epidemiology, Berlin, Germany
| | - Benno Kuropka
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Wojciech Czyszczoń
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Dmitry Ghilarov
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Stefan Grätz
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Jonathan G. Heddle
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Bernhard Loll
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | | | - Marcus Fulde
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
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Salzberger B, Mellmann A, Bludau A, Ciesek S, Corman V, Dilthey A, Donker T, Eckmanns T, Egelkamp R, Gatermann SG, Grundmann H, Häcker G, Kaase M, Lange B, Mielke M, Pletz MW, Semmler T, Thürmer A, Wieler LH, Wolff T, Widmer AF, Scheithauer S. An appeal for strengthening genomic pathogen surveillance to improve pandemic preparedness and infection prevention: the German perspective. Infection 2023:10.1007/s15010-023-02040-9. [PMID: 37129842 PMCID: PMC10152431 DOI: 10.1007/s15010-023-02040-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/13/2023] [Indexed: 05/03/2023]
Abstract
The SARS-CoV-2 pandemic has highlighted the importance of viable infection surveillance and the relevant infrastructure. From a German perspective, an integral part of this infrastructure, genomic pathogen sequencing, was at best fragmentary and stretched to its limits due to the lack or inefficient use of equipment, human resources, data management and coordination. The experience in other countries has shown that the rate of sequenced positive samples and linkage of genomic and epidemiological data (person, place, time) represent important factors for a successful application of genomic pathogen surveillance. Planning, establishing and consistently supporting adequate structures for genomic pathogen surveillance will be crucial to identify and combat future pandemics as well as other challenges in infectious diseases such as multi-drug resistant bacteria and healthcare-associated infections. Therefore, the authors propose a multifaceted and coordinated process for the definition of procedural, legal and technical standards for comprehensive genomic pathogen surveillance in Germany, covering the areas of genomic sequencing, data collection and data linkage, as well as target pathogens. A comparative analysis of the structures established in Germany and in other countries is applied. This proposal aims to better tackle epi- and pandemics to come and take action from the "lessons learned" from the SARS-CoV-2 pandemic.
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Affiliation(s)
- Bernd Salzberger
- Department for Infection Control and Infectious Diseases, University Hospital Regensburg, Franz-Josef-Strauß-Allee 11, 93053, Regensburg, Germany.
| | - Alexander Mellmann
- Institute for Hygiene, University Hospital Münster, Robert-Koch-Straße 41, 48149, Münster, Germany.
| | - Anna Bludau
- Department for Infection Control and Infectious Diseases, University Medical Center (UMG), Georg-August University Göttingen, Robert-Koch-Straße 40, 37075, Göttingen, Germany
| | - Sandra Ciesek
- Institute of Medical Virology, University Hospital Frankfurt, Goethe University, Frankfurt Am Main, Germany
| | - Victor Corman
- Institute of Virology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Alexander Dilthey
- Institute of Medical Microbiology and Hospital Hygiene, University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Tjibbe Donker
- Institute for Infection Prevention and Hospital Epidemiology, University Medical Center Freiburg, Freiburg, Germany
| | | | - Richard Egelkamp
- Next Generation Sequencing, Public Health Agency of Lower Saxony, Hanover, Germany
| | - Sören G Gatermann
- Department of Medical Microbiology, Ruhr University Bochum, Bochum, Germany
| | - Hajo Grundmann
- Institute for Infection Prevention and Hospital Epidemiology, University Medical Center Freiburg, Freiburg, Germany
| | - Georg Häcker
- Faculty of Medicine, Institute of Medical Microbiology and Hygiene, Medical Centre University of Freiburg, Freiburg, Germany
| | - Martin Kaase
- Department for Infection Control and Infectious Diseases, University Medical Center (UMG), Georg-August University Göttingen, Robert-Koch-Straße 40, 37075, Göttingen, Germany
| | - Berit Lange
- Department of Epidemiology, Helmholtz Centre for Infection Research, Brunswick, Germany
| | | | - Mathias W Pletz
- Institute of Infectious Diseases and Infection Control, University Hospital, Jena, Germany
| | | | | | | | | | - Andreas F Widmer
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Simone Scheithauer
- Department for Infection Control and Infectious Diseases, University Medical Center (UMG), Georg-August University Göttingen, Robert-Koch-Straße 40, 37075, Göttingen, Germany.
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10
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Tiwari SK, van der Putten BCL, Fuchs TM, Vinh TN, Bootsma M, Oldenkamp R, La Ragione R, Matamoros S, Hoa NT, Berens C, Leng J, Álvarez J, Ferrandis-Vila M, Ritchie JM, Fruth A, Schwarz S, Domínguez L, Ugarte-Ruiz M, Bethe A, Huber C, Johanns V, Stamm I, Wieler LH, Ewers C, Fivian-Hughes A, Schmidt H, Menge C, Semmler T, Schultsz C. Genome-wide association reveals host-specific genomic traits in Escherichia coli. BMC Biol 2023; 21:76. [PMID: 37038177 PMCID: PMC10088187 DOI: 10.1186/s12915-023-01562-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/10/2023] [Indexed: 04/12/2023] Open
Abstract
BACKGROUND Escherichia coli is an opportunistic pathogen which colonizes various host species. However, to what extent genetic lineages of E. coli are adapted or restricted to specific hosts and the genomic determinants of such adaptation or restriction is poorly understood. RESULTS We randomly sampled E. coli isolates from four countries (Germany, UK, Spain, and Vietnam), obtained from five host species (human, pig, cattle, chicken, and wild boar) over 16 years, from both healthy and diseased hosts, to construct a collection of 1198 whole-genome sequenced E. coli isolates. We identified associations between specific E. coli lineages and the host from which they were isolated. A genome-wide association study (GWAS) identified several E. coli genes that were associated with human, cattle, or chicken hosts, whereas no genes associated with the pig host could be found. In silico characterization of nine contiguous genes (collectively designated as nan-9) associated with the human host indicated that these genes are involved in the metabolism of sialic acids (Sia). In contrast, the previously described sialic acid regulon known as sialoregulon (i.e. nanRATEK-yhcH, nanXY, and nanCMS) was not associated with any host species. In vitro growth experiments with a Δnan-9 E. coli mutant strain, using the sialic acids 5-N-acetylneuraminic acid (Neu5Ac) and N-glycolylneuraminic acid (Neu5Gc) as sole carbon source, showed impaired growth behaviour compared to the wild-type. CONCLUSIONS This study provides an extensive analysis of genetic determinants which may contribute to host specificity in E. coli. Our findings should inform risk analysis and epidemiological monitoring of (antimicrobial resistant) E. coli.
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Affiliation(s)
- Sumeet K Tiwari
- Robert Koch Institute, Genome Sequencing and Genomic Epidemiology, Berlin, Germany
- Quadram Institute Bioscience, Gut Microbes and Health Institute Strategic Program, Norwich Research Park, Norwich, UK
| | - Boas C L van der Putten
- Department of Global Health, Amsterdam Institute for Global Health and Development, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Thilo M Fuchs
- Friedrich-Loeffler-Institut, Institute of Molecular Pathogenesis, Jena, Germany
| | - Trung N Vinh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Faculty of Veterinary Medicine, College of Agriculture, Can Tho University, Can Tho, Vietnam
| | | | - Rik Oldenkamp
- Department of Global Health, Amsterdam Institute for Global Health and Development, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Life and Environment, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Roberto La Ragione
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, UK
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, UK
| | - Sebastien Matamoros
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Ngo T Hoa
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Tropical medicine and global health, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
- Microbiology- Parasitology Unit, Biomedical Research Center and Microbiology Department, Pham Ngoc Thach University of Medicine, Ho Chi Minh City, Vietnam
| | - Christian Berens
- Friedrich-Loeffler-Institut, Institute of Molecular Pathogenesis, Jena, Germany
| | - Joy Leng
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, UK
| | - Julio Álvarez
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
- Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, Madrid, Spain
| | | | - Jenny M Ritchie
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, UK
| | - Angelika Fruth
- Robert Koch Institute, Enteropathogenic Bacteria and Legionella, Wernigerode, Germany
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - Lucas Domínguez
- Tropical medicine and global health, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
- Microbiology- Parasitology Unit, Biomedical Research Center and Microbiology Department, Pham Ngoc Thach University of Medicine, Ho Chi Minh City, Vietnam
| | - María Ugarte-Ruiz
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
| | - Astrid Bethe
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - Charlotte Huber
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Vanessa Johanns
- Robert Koch Institute, Advanced Light and Electron Microscopy, Berlin, Germany
| | - Ivonne Stamm
- Vet Med Labor GmbH, Division of IDEXX Laboratories, Kornwestheim, Germany
| | | | - Christa Ewers
- Institute of Hygiene and Infectious Diseases of Animals, Giessen, Germany
| | - Amanda Fivian-Hughes
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, UK
| | - Herbert Schmidt
- Institute of Food Science and Biotechnology, Department of Food Microbiology and Hygiene, University of Hohenheim, Stuttgart, Germany
| | - Christian Menge
- Friedrich-Loeffler-Institut, Institute of Molecular Pathogenesis, Jena, Germany
| | - Torsten Semmler
- Robert Koch Institute, Genome Sequencing and Genomic Epidemiology, Berlin, Germany.
| | - Constance Schultsz
- Department of Global Health, Amsterdam Institute for Global Health and Development, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.
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11
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Scheithauer S, Dilthey A, Bludau A, Ciesek S, Corman V, Donker T, Eckmanns T, Egelkamp R, Grundmann H, Häcker G, Kaase M, Lange B, Mellmann A, Mielke M, Pletz M, Salzberger B, Thürmer A, Widmer A, Wieler LH, Wolff T, Gatermann S, Semmler T. [Establishment of genomic pathogen surveillance to strengthen pandemic preparedness and infection prevention in Germany]. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2023; 66:443-449. [PMID: 36811648 PMCID: PMC9945818 DOI: 10.1007/s00103-023-03680-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
The SARS-CoV‑2 pandemic has shown a deficit of essential epidemiological infrastructure, especially with regard to genomic pathogen surveillance in Germany. In order to prepare for future pandemics, the authors consider it urgently necessary to remedy this existing deficit by establishing an efficient infrastructure for genomic pathogen surveillance. Such a network can build on structures, processes, and interactions that have already been initiated regionally and further optimize them. It will be able to respond to current and future challenges with a high degree of adaptability.The aim of this paper is to address the urgency and to outline proposed measures for establishing an efficient, adaptable, and responsive genomic pathogen surveillance network, taking into account external framework conditions and internal standards. The proposed measures are based on global and country-specific best practices and strategy papers. Specific next steps to achieve an integrated genomic pathogen surveillance include linking epidemiological data with pathogen genomic data; sharing and coordinating existing resources; making surveillance data available to relevant decision-makers, the public health service, and the scientific community; and engaging all stakeholders. The establishment of a genomic pathogen surveillance network is essential for the continuous, stable, active surveillance of the infection situation in Germany, both during pandemic phases and beyond.
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Affiliation(s)
- Simone Scheithauer
- Institut für Krankenhaushygiene und Infektiologie, Universitätsmedizin Göttingen (UMG), Georg-August Universität Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Deutschland.
| | - Alexander Dilthey
- Medizinische Mikrobiologie und Krankenhaushygiene, Universitätsklinikum Düsseldorf, Düsseldorf, Deutschland
| | - Anna Bludau
- Institut für Krankenhaushygiene und Infektiologie, Universitätsmedizin Göttingen (UMG), Georg-August Universität Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Deutschland
| | - Sandra Ciesek
- Institut für Medizinische Virologie, Universitätsklinikum Frankfurt, Frankfurt am Main, Deutschland
| | - Victor Corman
- Institut für Virologie, Charité Universitätsmedizin Berlin, Berlin, Deutschland
| | - Tjibbe Donker
- Institut für Infektionsprävention und Krankenhaushygiene, Universitätsklinikum Freiburg, Freiburg, Deutschland
| | | | - Richard Egelkamp
- Next Generation Sequencing, Niedersächsisches Landesgesundheitsamt, Hannover, Deutschland
| | - Hajo Grundmann
- Institut für Infektionsprävention und Krankenhaushygiene, Universitätsklinikum Freiburg, Freiburg, Deutschland
| | - Georg Häcker
- Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Freiburg, Freiburg, Deutschland
| | - Martin Kaase
- Institut für Krankenhaushygiene und Infektiologie, Universitätsmedizin Göttingen (UMG), Georg-August Universität Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Deutschland
| | - Berit Lange
- Abteilung Epidemiologie, Helmholtz-Zentrum für Infektionsforschung, Braunschweig, Deutschland
| | - Alexander Mellmann
- Institut für Hygiene, Universitätsklinikum Münster, Münster, Deutschland
| | | | - Mathias Pletz
- Institut für Infektionsmedizin und Krankenhaushygiene, Universitätsklinikum Jena, Jena, Deutschland
| | - Bernd Salzberger
- Infektiologie, Abteilung für Krankenhaushygiene und Infektiologie, Universitätsklinikum Regensburg, Regensburg, Deutschland
| | | | - Andreas Widmer
- Abteilung für Infektiologie und Spitalhygiene, Universitätsspital Basel, Basel, Schweiz
| | | | | | - Sören Gatermann
- Institut für Hygiene und Mikrobiologie, Ruhr-Universität Bochum, Bochum, Deutschland
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12
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Rotinsulu DA, Ewers C, Kerner K, Amrozi A, Soejoedono RD, Semmler T, Bauerfeind R. Molecular Features and Antimicrobial Susceptibilities of Streptococcus equi ssp. equi Isolates from Strangles Cases in Indonesia. Vet Sci 2023; 10:vetsci10010049. [PMID: 36669050 PMCID: PMC9867300 DOI: 10.3390/vetsci10010049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 12/30/2022] [Accepted: 01/03/2023] [Indexed: 01/12/2023] Open
Abstract
Strangles, caused by Streptococcus equi ssp. equi (S. equi equi), is a highly infectious and frequent disease of equines worldwide. No data are available regarding the molecular epidemiology of strangles in Indonesia. This study aimed to characterize S. equi equi isolates obtained from suspected strangles cases in Indonesia in 2018. Isolates originated from seven diseased horses on four different farms located in three provinces of Indonesia. Whole genome sequences of these isolates were determined and used for seM typing, multilocus sequence typing (MLST), and core genome MLS typing (cgMLST). Genomes were also screened for known antimicrobial resistance genes and genes encoding for the recombinant antigens used in the commercial Strangvac® subunit vaccine. All seven S. equi equi isolates from Indonesia belonged to ST179 and carried seM allele 166. Isolates differed from each other by only 2 to 14 cgSNPs and built an exclusive sub-cluster within the Bayesian Analysis of Population Structure (BAPS) cluster 2 (BAPS-2) of the S. equi equi cgMLST scheme. All isolates revealed predicted amino acid sequence identity to seven and high similarity to one of the eight antigen fragments contained in Strangvac®. Furthermore, all isolates were susceptible to beta-lactam antibiotics penicillin G, ampicillin, and ceftiofur. Our data suggest that the horses from this study were affected by strains of the same novel sublineage within globally distributed BAPS-2 of S. equi equi. Nevertheless, penicillin G can be used as a first-choice antibiotic against these strains and Strangvac® may also be protective against Indonesian strains.
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Affiliation(s)
- Dordia Anindita Rotinsulu
- Institute for Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, 35392 Giessen, Germany
- School of Veterinary Medicine and Biomedical Sciences, IPB University, Bogor 16680, Indonesia
- Correspondence: or
| | - Christa Ewers
- Institute for Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Katharina Kerner
- Institute for Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Amrozi Amrozi
- School of Veterinary Medicine and Biomedical Sciences, IPB University, Bogor 16680, Indonesia
| | | | - Torsten Semmler
- NG-1 Microbial Genomics, Robert Koch Institute, 13353 Berlin, Germany
| | - Rolf Bauerfeind
- Institute for Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, 35392 Giessen, Germany
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13
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Soundararajan M, Marincola G, Liong O, Marciniak T, Wencker FDR, Hofmann F, Schollenbruch H, Kobusch I, Linnemann S, Wolf SA, Helal M, Semmler T, Walther B, Schoen C, Nyasinga J, Revathi G, Boelhauve M, Ziebuhr W. Farming Practice Influences Antimicrobial Resistance Burden of Non-Aureus Staphylococci in Pig Husbandries. Microorganisms 2022; 11:microorganisms11010031. [PMID: 36677324 PMCID: PMC9865537 DOI: 10.3390/microorganisms11010031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/15/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Non-aureus staphylococci (NAS) are ubiquitous bacteria in livestock-associated environments where they may act as reservoirs of antimicrobial resistance (AMR) genes for pathogens such as Staphylococcus aureus. Here, we tested whether housing conditions in pig farms could influence the overall AMR-NAS burden. Two hundred and forty porcine commensal and environmental NAS isolates from three different farm types (conventional, alternative, and organic) were tested for phenotypic antimicrobial susceptibility and subjected to whole genome sequencing. Genomic data were analysed regarding species identity and AMR gene carriage. Seventeen different NAS species were identified across all farm types. In contrast to conventional farms, no AMR genes were detectable towards methicillin, aminoglycosides, and phenicols in organic farms. Additionally, AMR genes to macrolides and tetracycline were rare among NAS in organic farms, while such genes were common in conventional husbandries. No differences in AMR detection existed between farm types regarding fosfomycin, lincosamides, fusidic acid, and heavy metal resistance gene presence. The combined data show that husbandry conditions influence the occurrence of resistant and multidrug-resistant bacteria in livestock, suggesting that changing husbandry practices may be an appropriate means of limiting the spread of AMR bacteria on farms.
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Affiliation(s)
| | - Gabriella Marincola
- Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Olivia Liong
- Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Tessa Marciniak
- Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Freya D. R. Wencker
- Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Franka Hofmann
- Department of Agriculture; South Westphalia University of Applied Sciences, 59494 Soest, Germany
| | - Hannah Schollenbruch
- Department of Agriculture; South Westphalia University of Applied Sciences, 59494 Soest, Germany
| | - Iris Kobusch
- Department of Agriculture; South Westphalia University of Applied Sciences, 59494 Soest, Germany
| | - Sabrina Linnemann
- Department of Agriculture; South Westphalia University of Applied Sciences, 59494 Soest, Germany
| | - Silver A. Wolf
- Genome Sequencing and Genomic Epidemiology, Robert Koch Institute, 13353 Berlin, Germany
| | - Mustafa Helal
- Genome Sequencing and Genomic Epidemiology, Robert Koch Institute, 13353 Berlin, Germany
| | - Torsten Semmler
- Genome Sequencing and Genomic Epidemiology, Robert Koch Institute, 13353 Berlin, Germany
| | - Birgit Walther
- Advanced Light and Electron Microscopy (ZBS4), Robert Koch Institute, 13353 Berlin, Germany
| | - Christoph Schoen
- Institute of Hygiene and Microbiology, University of Würzburg, 97080 Würzburg, Germany
| | - Justin Nyasinga
- Department of Pathology, Aga-Khan-University Hospital Nairobi, Nairobi, Kenya
- Department of Biomedical Sciences and Technology, The Technical University of Kenya, Nairobi, Kenya
| | - Gunturu Revathi
- Department of Pathology, Aga-Khan-University Hospital Nairobi, Nairobi, Kenya
| | - Marc Boelhauve
- Department of Agriculture; South Westphalia University of Applied Sciences, 59494 Soest, Germany
| | - Wilma Ziebuhr
- Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
- Correspondence: ; Tel.: +49-(0)931-31-2578
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14
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Oh DY, Hölzer M, Paraskevopoulou S, Trofimova M, Hartkopf F, Budt M, Wedde M, Richard H, Haldemann B, Domaszewska T, Reiche J, Keeren K, Radonić A, Calderón JPR, Smith MR, Brinkmann A, Trappe K, Drechsel O, Klaper K, Hein S, Hildt E, Haas W, Calvignac-Spencer S, Semmler T, Dürrwald R, Thürmer A, Drosten C, Fuchs S, von Kleist M, Kröger S, Wolff T. 1358. Establishing Genomic SARS-CoV-2 Surveillance at the National Level: Germany, 2021. Open Forum Infect Dis 2022. [PMCID: PMC9752442 DOI: 10.1093/ofid/ofac492.1187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Background The COVID-19 pandemic has demonstrated the importance of pathogen genomic surveillance. At RKI, the German National Institute of Public Health, we established the Integrated Molecular Surveillance for SARS-CoV-2 (IMS-SC2) network to perform SARS-CoV-2 genomic surveillance. Methods SARS-CoV-2 positive samples from laboratories distributed across Germany regularly undergo whole-genome sequencing at RKI. This surveillance instrument enables (i) almost-real-time monitoring of SARS-CoV-2 genomic diversity and evolution, (ii) in vitro assessment of vaccine coverage against emerging variants and (iii) genome-based estimates of SARS-CoV-2-incidences. Results We report the results of our analyses of 3623 SARS-CoV-2 genomes collected between 12/1/2020 and 12/31/2021. All variants of concern were identified, at ratios equivalent to those in the 100-fold larger German GISAID sequence dataset from the same time period. Lineage distributions fluctuated over time, covering the rise of the Alpha and Delta, as well as the emergence of Omicron. Phylogenetic analysis confirmed variant assignments. Multiple mutations of concern emerged during the observation period. To model vaccine effectiveness in vitro, we employed authentic-virus neutralization assays, confirming that both the Beta and Zeta variants are capable of immune evasion. The IMS-SC2 sequence dataset facilitated an estimate of the SARS-CoV-2 incidence based on genetic evolution rates. Together with modelled vaccine efficacies, Delta-specific incidence estimation indicated that the German vaccination campaign contributed substantially to a deceleration of the nascent German Delta wave. Conclusion This example illustrates that pathogen genomics enables a proactive approach to controlling a pandemic as the virus evolves. Molecular and genomic SARS-CoV-2 surveillance will be crucial during the post-pandemic future, informing public health policies including vaccination strategies. Of note, the IMS-SC2 infrastructure can be adapted to many other pathogens, serving as a blueprint for future efforts to increase genomic pathogen surveillance. Disclosures All Authors: No reported disclosures.
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Affiliation(s)
- Djin-Ye Oh
- Robert Koch Institute (RKI), Berlin, Berlin, Germany
| | - Martin Hölzer
- Robert Koch Institute (RKI), Berlin, Berlin, Germany
| | | | | | | | - Matthias Budt
- Robert Koch Institute (RKI), Berlin, Berlin, Germany
| | | | | | | | | | - Janine Reiche
- Robert Koch Institute (RKI), Berlin, Berlin, Germany
| | | | | | | | | | | | | | | | | | - Sascha Hein
- Paul Ehrlich Institute, Berlin, Berlin, Germany
| | | | - Walter Haas
- Robert Koch Institute (RKI), Berlin, Berlin, Germany
| | | | | | - Ralf Dürrwald
- Robert Koch Institute (RKI), Berlin, Berlin, Germany
| | | | - Christian Drosten
- Institute of Virology, Charité-University Medicine Berlin, Berlin, Berlin, Germany
| | - Stephan Fuchs
- Robert Koch Institute (RKI), Berlin, Berlin, Germany
| | | | - Stefan Kröger
- Robert Koch Institute (RKI), Berlin, Berlin, Germany
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15
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Ewers C, Göpel L, Prenger-Berninghoff E, Semmler T, Kerner K, Bauerfeind R. Occurrence of mcr-1 and mcr-2 colistin resistance genes in porcine Escherichia coli isolates (2010-2020) and genomic characterization of mcr-2-positive E. coli. Front Microbiol 2022; 13:1076315. [PMID: 36569100 PMCID: PMC9780603 DOI: 10.3389/fmicb.2022.1076315] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022] Open
Abstract
Introduction The global emergence of plasmid-mediated colistin resistance is threatening the efficacy of colistin as one of the last treatment options against multi-drug resistant Gram-negative bacteria. To date, ten mcr-genes (mcr-1 to mcr-10) were reported. While mcr-1 has disseminated globally, the occurrence of mcr-2 was reported scarcely. Methods and results We determined the occurrence of mcr-1 and mcr-2 genes among Escherichia coli isolates from swine and performed detailed genomic characterization of mcr-2-positive strains. In the years 2010-2017, 7,614 porcine E. coli isolates were obtained from fecal swine samples in Europe and isolates carrying at least one of the virulence associated genes predicting Shiga toxin producing E. coli (STEC), enterotoxigenic E. coli (ETEC) or enteropathogenic E. coli (EPEC) were stored. 793 (10.4%) of these isolates carried the mcr-1 gene. Of 1,477 additional E. coli isolates obtained from sheep blood agar containing 4 mg/L colistin between 2018 and 2020, 36 (2.4%) isolates were mcr-1-positive. In contrast to mcr-1, the mcr-2 gene occurred at a very low frequency (0.13%) among the overall 9,091 isolates. Most mcr-2-positive isolates originated from Belgium (n = 9), one from Spain and two from Germany. They were obtained from six different farms and revealed multilocus sequence types ST10, ST29, ST93, ST100, ST3057 and ST5786. While the originally described mcr-2.1 was predominant, we also detected a new mcr-2 variant in two isolates from Belgium, which was termed mcr-2.8. MCR-2 isolates were mostly classified as ETEC or ETEC-like, while one isolate from Spain represented an atypical enteropathogenic E. coli (aEPEC; eae+). The ST29-aEPEC isolate carried mcr-2 on the chromosome. Another eight isolates carried their mcr-2 gene on IncX4 plasmids that resembled the pKP37-BE MCR-2 plasmid originally described in Belgium in 2015. Three ST100 E. coli isolates from a single farm in Belgium carried the mcr-2.1 gene on a 47-kb self-transmissible IncP type plasmid of a new IncP-1 clade. Discussion This is the first report of mcr-2 genes in E. coli isolates from Germany. The detection of a new mcr-2 allele and a novel plasmid backbone suggests the presence of so far undetected mcr-2 variants and mobilizable vehicles.
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Affiliation(s)
- Christa Ewers
- Faculty of Veterinary Medicine, Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Giessen, Germany,*Correspondence: Christa Ewers,
| | - Lisa Göpel
- Faculty of Veterinary Medicine, Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Giessen, Germany
| | - Ellen Prenger-Berninghoff
- Faculty of Veterinary Medicine, Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Giessen, Germany
| | - Torsten Semmler
- NG1 Microbial Genomics, Robert Koch Institute, Berlin, Germany
| | - Katharina Kerner
- Faculty of Veterinary Medicine, Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Giessen, Germany
| | - Rolf Bauerfeind
- Faculty of Veterinary Medicine, Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Giessen, Germany
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16
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Huber C, Wolf SA, Ziebuhr W, Holmes MA, Assmann J, Lübke-Becker A, Thürmer A, Semmler T, Brombach J, Bethe A, Bischoff M, Wieler LH, Epping L, Walther B. How to survive pig farming: Mechanism of SCC mec element deletion and metabolic stress adaptation in livestock-associated MRSA. Front Microbiol 2022; 13:969961. [PMID: 36504815 PMCID: PMC9728531 DOI: 10.3389/fmicb.2022.969961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 10/04/2022] [Indexed: 11/24/2022] Open
Abstract
Previous research on methicillin susceptible Staphylococcus aureus (MSSA) belonging to livestock-associated (LA-) sequence type (ST) 398, isolated from pigs and their local surroundings, indicated that differences between these MSSA and their methicillin resistant predecessors (MRSA) are often limited to the absence of the staphylococcal cassette chromosome mec (SCCmec) and few single nucleotide polymorphisms. So far, our understanding on how LA-MRSA endure the environmental conditions associated with pig-farming as well as the putative impact of this particular environment on the mobilisation of SCCmec elements is limited. Thus, we performed in-depth genomic and transcriptomic analyses using the LA-MRSA ST398 strain IMT38951 and its methicillin susceptible descendant. We identified a mosaic-structured SCCmec region including a putative replicative SCCmecVc which is absent from the MSSA chromosome through homologous recombination. Based on our data, such events occur between short repetitive sequences identified within and adjacent to two distinct alleles of the large cassette recombinase genes C (ccrC). We further evaluated the global transcriptomic response of MRSA ST398 to particular pig-farm associated conditions, i.e., contact with host proteins (porcine serum) and a high ammonia concentration. Differential expression of global regulators involved in stress response control were identified, i.e., ammonia-induced alternative sigma factor B-depending activation of genes for the alkaline shock protein 23, the heat shock response and the accessory gene regulator (agr)-controlled transcription of virulence factors. Exposure to serum transiently induced the transcription of distinct virulence factor encoding genes. Transcription of genes reported for mediating the loss of methicillin resistance, especially ccrC, was not significantly different compared to the unchallenged controls. We concluded that, from an evolutionary perspective, bacteria may save energy by incidentally dismissing a fully replicative SCCmec element in contrast to the induction of ccr genes on a population scale. Since the genomic SCCmec integration site is a hot-spot of recombination, occasional losses of elements of 16 kb size may restore capacities for the uptake of foreign genetic material. Subsequent spread of resistance, on the other hand, might depend on the autonomous replication machinery of the deleted SCCmec elements that probably enhance chances for reintegration of SCCmec into susceptible genomes by mere multiplication.
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Affiliation(s)
- Charlotte Huber
- Advanced Light and Electron Microscopy (ZBS4), Robert Koch Institute, Berlin, Germany
| | - Silver A. Wolf
- Genome Sequencing and Genomic Epidemiology (MF2), Robert Koch Institute, Berlin, Germany
| | - Wilma Ziebuhr
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Mark A. Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Julia Assmann
- Advanced Light and Electron Microscopy (ZBS4), Robert Koch Institute, Berlin, Germany
| | - Antina Lübke-Becker
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Andrea Thürmer
- Genome Sequencing and Genomic Epidemiology (MF2), Robert Koch Institute, Berlin, Germany
| | - Torsten Semmler
- Genome Sequencing and Genomic Epidemiology (MF2), Robert Koch Institute, Berlin, Germany
| | - Julian Brombach
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Astrid Bethe
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Markus Bischoff
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
| | - Lothar H. Wieler
- Methodology and Research Infrastructure, Robert Koch Institute, Berlin, Germany
| | - Lennard Epping
- Genome Sequencing and Genomic Epidemiology (MF2), Robert Koch Institute, Berlin, Germany
| | - Birgit Walther
- Advanced Light and Electron Microscopy (ZBS4), Robert Koch Institute, Berlin, Germany,*Correspondence: Birgit Walther,
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17
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Reichelt B, Szott V, Epping L, Semmler T, Merle R, Roesler U, Friese A. Transmission pathways of campylobacter spp. at broiler farms and their environment in Brandenburg, Germany. Front Microbiol 2022; 13:982693. [PMID: 36312983 PMCID: PMC9598865 DOI: 10.3389/fmicb.2022.982693] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/20/2022] [Indexed: 09/08/2023] Open
Abstract
Broiler meat is widely known as an important source of foodborne Campylobacter jejuni and Campylobacter coli infections in humans. In this study, we thoroughly investigated transmission pathways that may contribute to possible Campylobacter contamination inside and outside broiler houses. For this purpose we carried out a comprehensive longitudinal sampling approach, using a semi-quantitative cultivation method to identify and quantify transmissions and reservoirs of Campylobacter spp.. Three german broiler farms in Brandenburg and their surrounding areas were intensively sampled, from April 2018 until September 2020. Consecutive fattening cycles and intervening downtimes after cleaning and disinfection were systematically sampled in summer and winter. To display the potential phylogeny of barn and environmental isolates, whole genome sequencing (WGS) and bioinformatic analyses were performed. Results obtained in this study showed very high Campylobacter prevalence in 51/76 pooled feces (67.1%) and 49/76 boot swabs (64.5%). Average counts between 6.4 to 8.36 log10MPN/g were detected in pooled feces. In addition, levels of 4.7 and 4.1 log10MPN/g were detected in boot swabs and litter, respectively. Samples from the barn interior showed mean Campyloacter values in swabs from drinkers 2.6 log10MPN/g, walls 2.0 log10MPN/g, troughs 1.7 log10MPN/g, boards 1.6 log10MPN/g, ventilations 0.9 log10MPN/g and 0.7 log10MPN/g for air samples. However, Campylobacter was detected only in 7/456 (1.5%) of the environmental samples (water bodies, puddles or water-filled wheel tracks; average of 0.6 log10MPN/g). Furthermore, WGS showed recurring Campylobacter genotypes over several consecutive fattening periods, indicating that Campylobacter genotypes persist in the environment during downtime periods. However, after cleaning and disinfection of the barns, we were unable to identify potential sources in the broiler houses. Interestingly, alternating Campylobacter genotypes were observed after each fattening period, also indicating sources of contamination from the wider environment outside the farm. Therefore, the results of this study suggest that a potential risk of Campylobacter transmission may originate from present environmental sources (litter and water reservoirs). However, the sources of Campylobacter transmission may vary depending on the operation and farm environmental conditions.
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Affiliation(s)
- Benjamin Reichelt
- Department of Veterinary Medicine, Institute for Animal Hygiene and Environmental Health, Freie Universität Berlin, Berlin, Germany
| | - Vanessa Szott
- Department of Veterinary Medicine, Institute for Animal Hygiene and Environmental Health, Freie Universität Berlin, Berlin, Germany
| | - Lennard Epping
- Genome Sequencing and Genomic Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Torsten Semmler
- Genome Sequencing and Genomic Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Roswitha Merle
- Department of Veterinary Medicine, Institute for Veterinary Epidemiology and Biostatistics, Freie Universität Berlin, Berlin, Germany
| | - Uwe Roesler
- Department of Veterinary Medicine, Institute for Animal Hygiene and Environmental Health, Freie Universität Berlin, Berlin, Germany
| | - Anika Friese
- Department of Veterinary Medicine, Institute for Animal Hygiene and Environmental Health, Freie Universität Berlin, Berlin, Germany
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18
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Eisenberg T, Mühldorfer K, Erhard M, Fawzy A, Kehm S, Ewers C, Semmler T, Blom J, Lipski A, Rau J, Kämpfer P, Glaeser SP. Erysipelothrix anatis sp. nov., Erysipelothrix aquatica sp. nov. and Erysipelothrix urinaevulpis sp. nov., three novel species of the genus, and emended description of Erysipelothrix. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005454] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Seven genotypically distinct strains assigned to the genus
Erysipelothrix
were isolated in different laboratories from several animal sources. Strain D17_0559-3-2-1T and three further strains were isolated from samples of duck, pig and goose. The strains had >99 % 16S rRNA gene sequence similarity to each other and to strain VA92-K48T and two further strains isolated from samples of medical leech and a turtle. The closest related type strains to the seven strains were those of
Erysipelothrix inopinata
(96.74 %) and
Erysipelothrix rhusiopathiae
(95.93 %). Average nucleotide identity, amino acid identity and in silico DNA–DNA hybridization results showed that the strains represented two separate novel species. One further phylogenetically distinct strain (165301687T) was isolated from fox urine. The strain had highest 16S rRNA gene sequence similarity to the type strains of
Erysipelothrix tonsillarum
(95.67 %), followed by
Erysipelothrix piscisicarius
(95.58 %) and
Erysipelothrix larvae
(94.22 %) and represented a further novel species. Chemotaxonomic and physiological data of the novel strains were assessed, but failed to unequivocally differentiate the novel species from existing members of the genus. MALDI-TOF MS data proved the discrimination of at least strain 165301687T from all currently described species. Based on the presented phylogenomic and physiological data, we propose three novel species, Erysipelothrix anatis sp. nov. with strain D17_0559-3-2-1T (=DSM 111258T= CIP 111884T=CCM 9044T) as type strain, Erysipelothrix aquatica sp. nov. with strain VA92-K48T (=DSM 106012T=LMG 30351T=CIP 111492T) as type strain and Erysipelothrix urinaevulpis sp. nov. with strain 165301687T (=DSM 106013T= LMG 30352T= CIP 111494T) as type strain.
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Affiliation(s)
- Tobias Eisenberg
- Department of Veterinary Medicine, Hessian State Laboratory (LHL), Giessen, Germany
- Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Giessen, Germany
| | - Kristin Mühldorfer
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | | | - Ahmad Fawzy
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
- Department of Veterinary Medicine, Hessian State Laboratory (LHL), Giessen, Germany
| | - Sabine Kehm
- LHL, Border Control Post, Frankfurt, Germany
| | - Christa Ewers
- Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Giessen, Germany
| | - Torsten Semmler
- NG1 Microbial Genomics, Robert Koch Institute, Berlin, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University, Giessen, Germany
| | - André Lipski
- Institut für Ernährungs- und Lebensmittelwissenschaften, Friedrich-Wilhelms-Universität, Bonn, Germany
| | - Jörg Rau
- Chemisches und Veterinäruntersuchungsamt Stuttgart, Fellbach, Germany
| | - Peter Kämpfer
- Institut für angewandte Mikrobiologie, Justus Liebig University, Giessen, Germany
| | - Stefanie P. Glaeser
- Institut für angewandte Mikrobiologie, Justus Liebig University, Giessen, Germany
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19
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Oh DY, Hölzer M, Paraskevopoulou S, Trofimova M, Hartkopf F, Budt M, Wedde M, Richard H, Haldemann B, Domaszewska T, Reiche J, Keeren K, Radonić A, Ramos Calderón JP, Smith MR, Brinkmann A, Trappe K, Drechsel O, Klaper K, Hein S, Hildt E, Haas W, Calvignac-Spencer S, Semmler T, Dürrwald R, Thürmer A, Drosten C, Fuchs S, Kröger S, von Kleist M, Wolff T. Advancing Precision Vaccinology by Molecular and Genomic Surveillance of Severe Acute Respiratory Syndrome Coronavirus 2 in Germany, 2021. Clin Infect Dis 2022; 75:S110-S120. [PMID: 35749674 PMCID: PMC9278222 DOI: 10.1093/cid/ciac399] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Comprehensive pathogen genomic surveillance represents a powerful tool to complement and advance precision vaccinology. The emergence of the Alpha variant in December 2020 and the resulting efforts to track the spread of this and other severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern led to an expansion of genomic sequencing activities in Germany. METHODS At Robert Koch Institute (RKI), the German National Institute of Public Health, we established the Integrated Molecular Surveillance for SARS-CoV-2 (IMS-SC2) network to perform SARS-CoV-2 genomic surveillance at the national scale, SARS-CoV-2-positive samples from laboratories distributed across Germany regularly undergo whole-genome sequencing at RKI. RESULTS We report analyses of 3623 SARS-CoV-2 genomes collected between December 2020 and December 2021, of which 3282 were randomly sampled. All variants of concern were identified in the sequenced sample set, at ratios equivalent to those in the 100-fold larger German GISAID sequence dataset from the same time period. Phylogenetic analysis confirmed variant assignments. Multiple mutations of concern emerged during the observation period. To model vaccine effectiveness in vitro, we employed authentic-virus neutralization assays, confirming that both the Beta and Zeta variants are capable of immune evasion. The IMS-SC2 sequence dataset facilitated an estimate of the SARS-CoV-2 incidence based on genetic evolution rates. Together with modeled vaccine efficacies, Delta-specific incidence estimation indicated that the German vaccination campaign contributed substantially to a deceleration of the nascent German Delta wave. CONCLUSIONS SARS-CoV-2 molecular and genomic surveillance may inform public health policies including vaccination strategies and enable a proactive approach to controlling coronavirus disease 2019 spread as the virus evolves.
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Affiliation(s)
- Djin Ye Oh
- Correspondence: D.-Y. Oh Robert Koch Institute, Dept. of Infectious Diseases, Seestr. 10, 13353 Berlin, Germany ()
| | | | - Sofia Paraskevopoulou
- Methodology and Research Infrastructure, Bioinformatics and Systems Biology (MF1), Robert Koch Institute, Berlin, Germany
| | - Maria Trofimova
- Systems Medicine of Infectious Disease (P5), Robert Koch Institute, Berlin, Germany
| | - Felix Hartkopf
- Methodology and Research Infrastructure, Genome Sequencing and Genomic Epidemiology (MF2), Robert Koch Institute, Berlin, Germany
| | - Matthias Budt
- Influenza and Other Respiratory Viruses (FG17), Robert Koch Institute, Berlin, Germany
| | - Marianne Wedde
- Influenza and Other Respiratory Viruses (FG17), Robert Koch Institute, Berlin, Germany
| | - Hugues Richard
- Methodology and Research Infrastructure, Bioinformatics and Systems Biology (MF1), Robert Koch Institute, Berlin, Germany
| | - Berit Haldemann
- Methodology and Research Infrastructure, Bioinformatics and Systems Biology (MF1), Robert Koch Institute, Berlin, Germany
| | | | - Janine Reiche
- Influenza and Other Respiratory Viruses (FG17), Robert Koch Institute, Berlin, Germany
| | - Kathrin Keeren
- Gastroenteritis and Hepatitis Pathogens and Enteroviruses (FG15), Robert Koch Institute, Berlin, Germany
| | - Aleksandar Radonić
- Methodology and Research Infrastructure, Genome Sequencing and Genomic Epidemiology (MF2), Robert Koch Institute, Berlin, Germany
| | | | | | - Annika Brinkmann
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS1), Robert Koch Institute, Berlin, Germany
| | - Kathrin Trappe
- Methodology and Research Infrastructure, Bioinformatics and Systems Biology (MF1), Robert Koch Institute, Berlin, Germany
| | - Oliver Drechsel
- Methodology and Research Infrastructure, Bioinformatics and Systems Biology (MF1), Robert Koch Institute, Berlin, Germany
| | - Kathleen Klaper
- Methodology and Research Infrastructure, Genome Sequencing and Genomic Epidemiology (MF2), Robert Koch Institute, Berlin, Germany,Sexually Transmitted Bacterial Pathogens and HIV (FG18), Robert Koch Institute, Berlin, Germany
| | - Sascha Hein
- Division of Virology, Paul Ehrlich Institute, Langen, Germany
| | - Eberhardt Hildt
- Division of Virology, Paul Ehrlich Institute, Langen, Germany
| | - Walter Haas
- Gastroenteritis and Hepatitis Pathogens and Enteroviruses (FG15), Robert Koch Institute, Berlin, Germany
| | - Sébastien Calvignac-Spencer
- Epidemiology of Highly Pathogenic Microorganisms (P3), Viral Evolution, Robert Koch Institute, Berlin, Germany
| | - Torsten Semmler
- Methodology and Research Infrastructure, Genome Sequencing and Genomic Epidemiology (MF2), Robert Koch Institute, Berlin, Germany
| | - Ralf Dürrwald
- Influenza and Other Respiratory Viruses (FG17), Robert Koch Institute, Berlin, Germany
| | - Andrea Thürmer
- Methodology and Research Infrastructure, Genome Sequencing and Genomic Epidemiology (MF2), Robert Koch Institute, Berlin, Germany
| | - Christian Drosten
- Institute of Virology, Charité-University Medicine Berlin, Berlin, Germany
| | - Stephan Fuchs
- Methodology and Research Infrastructure, Bioinformatics and Systems Biology (MF1), Robert Koch Institute, Berlin, Germany
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20
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Ferrandis-Vila M, Tiwari SK, Mamerow S, Semmler T, Menge C, Berens C. Using unique ORFan genes as strain-specific identifiers for Escherichia coli. BMC Microbiol 2022; 22:135. [PMID: 35585491 PMCID: PMC9118744 DOI: 10.1186/s12866-022-02508-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 03/30/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bacterial identification at the strain level is a much-needed, but arduous and challenging task. This study aimed to develop a method for identifying and differentiating individual strains among multiple strains of the same bacterial species. The set used for testing the method consisted of 17 Escherichia coli strains picked from a collection of strains isolated in Germany, Spain, the United Kingdom and Vietnam from humans, cattle, swine, wild boars, and chickens. We targeted unique or rare ORFan genes to address the problem of selective and specific strain identification. These ORFan genes, exclusive to each strain, served as templates for developing strain-specific primers. RESULTS Most of the experimental strains (14 out of 17) possessed unique ORFan genes that were used to develop strain-specific primers. The remaining three strains were identified by combining a PCR for a rare gene with a selection step for isolating the experimental strains. Multiplex PCR allowed the successful identification of the strains both in vitro in spiked faecal material in addition to in vivo after experimental infections of pigs and recovery of bacteria from faecal material. In addition, primers for qPCR were also developed and quantitative readout from faecal samples after experimental infection was also possible. CONCLUSIONS The method described in this manuscript using strain-specific unique genes to identify single strains in a mixture of strains proved itself efficient and reliable in detecting and following individual strains both in vitro and in vivo, representing a fast and inexpensive alternative to more costly methods.
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Affiliation(s)
- Marta Ferrandis-Vila
- Friedrich-Loeffler-Institut - Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Naumburger Straße 96a, 07743, Jena, Germany
| | | | - Svenja Mamerow
- Friedrich-Loeffler-Institut - Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Naumburger Straße 96a, 07743, Jena, Germany
| | | | | | - Christian Menge
- Friedrich-Loeffler-Institut - Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Naumburger Straße 96a, 07743, Jena, Germany
| | - Christian Berens
- Friedrich-Loeffler-Institut - Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Naumburger Straße 96a, 07743, Jena, Germany.
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21
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Wu J, Danko D, Afshinnekoo E, Bezdan D, Bhattacharyya M, Castro-Nallar E, Chmielarczyk A, Hazrin-Chong NH, Deng Y, Dias-Neto E, Frolova A, Mason-Buck G, Iraola G, Jang S, Łabaj P, Lee PKH, Nieto-Caballero M, Osuolale OO, Ouzounis CA, Perlin MH, Prithiviraj B, Rascovan N, Różańska A, Schriml LM, Semmler T, Suzuki H, Ugalde JA, Young B, Werner J, Zambrano MM, Zhao Y, Mason C, Shi T. Annotating unknown species of urban microorganisms on a global scale unveils novel functional diversity and local environment association. Environ Res 2022; 207:112183. [PMID: 34637759 DOI: 10.1016/j.envres.2021.112183] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 06/13/2023]
Abstract
In urban ecosystems, microbes play a key role in maintaining major ecological functions that directly support human health and city life. However, the knowledge about the species composition and functions involved in urban environments is still limited, which is largely due to the lack of reference genomes in metagenomic studies comprises more than half of unclassified reads. Here we uncovered 732 novel bacterial species from 4728 samples collected from various common surface with the matching materials in the mass transit system across 60 cities by the MetaSUB Consortium. The number of novel species is significantly and positively correlated with the city population, and more novel species can be identified in the skin-associated samples. The in-depth analysis of the new gene catalog showed that the functional terms have a significant geographical distinguishability. Moreover, we revealed that more biosynthetic gene clusters (BGCs) can be found in novel species. The co-occurrence relationship between BGCs and genera and the geographical specificity of BGCs can also provide us more information for the synthesis pathways of natural products. Expanded the known urban microbiome diversity and suggested additional mechanisms for taxonomic and functional characterization of the urban microbiome. Considering the great impact of urban microbiomes on human life, our study can also facilitate the microbial interaction analysis between human and urban environment.
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Affiliation(s)
- Jun Wu
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - David Danko
- Weill Cornell Medicine, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, USA
| | - Ebrahim Afshinnekoo
- Weill Cornell Medicine, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, USA
| | - Daniela Bezdan
- Weill Cornell Medicine, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, USA
| | - Malay Bhattacharyya
- Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India; Centre for Artificial Intelligence and Machine Learning, Indian Statistical Institute, Kolkata, India
| | - Eduardo Castro-Nallar
- Universidad Andrés Bello, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Argentina
| | | | - Nur Hazlin Hazrin-Chong
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor, Malaysia
| | - Youping Deng
- University of Hawaii, John A. Burns School of Mecidine, USA
| | - Emmanuel Dias-Neto
- Medical Genomics Group, A.C. Camargo Cancer Center and LIM-27 Faculdade de Medicina, USP, São Paulo, Brazil
| | - Alina Frolova
- Institute of Molecular Biology and Genetics of National Academy of Science of Ukraine, Ukraine
| | - Gabriella Mason-Buck
- Department of Analytical, Environmental and Forensic Sciences, King's College London, UK
| | - Gregorio Iraola
- Microbial Genomics Laboratory, Institut Pasteur de Montevideo, Uruguay; Center for Integrative Biology, Universidad Mayor, Santiago de Chile, Chile; Wellcome Sanger Institute, Hinxton, United Kingdom
| | | | - Paweł Łabaj
- Małopolska Centre of Biotechnology, Jagiellonian University, Poland
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Marina Nieto-Caballero
- University of Colorado at Boulder, Civil, Environmental and Architectural Department, Boulder, 80303, USA
| | - Olayinka O Osuolale
- Applied Environmental Metagenomics and Infectious Diseases Research (AEMIDR), Department of Biological Sciences, Elizade University, Nigeria
| | - Christos A Ouzounis
- BCPL-CPERI, Centre for Research & Technology Hellas, Thessalonica, GR, 57001, Greece
| | - Michael H Perlin
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY, 40292, USA
| | - Bharath Prithiviraj
- Reckitt Health, Montvale, NJ, USA; Dept. of Biology, City University of New York, Brooklyn, 11210, NY, USA
| | - Nicolás Rascovan
- Aix-Marseille Université, IRD, AP-HM, IHU Méditerranée Infection, France
| | - Anna Różańska
- Jagiellonian University, Faculty of Medicine, Department of Microbiology, Poland
| | - Lynn M Schriml
- University of Maryland School of Medicine, Institute for Genome Sciences, USA
| | | | - Haruo Suzuki
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa, Japan
| | - Juan A Ugalde
- Millennium Initiative for Collaborative Research on Bacterial Resistance, Germany
| | - Ben Young
- Weill Cornell Medicine, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, USA
| | - Johannes Werner
- High Performance and Cloud Computing Group, Zentrum für Datenverarbeitung (ZDV), Eberhard Karls University of Tübingen, Wächterstraße 76, 72074, Tübingen, Germany
| | | | - Yongxiang Zhao
- Biological Targeting Diagnosis and Therapy Research Center, Guangxi Medical University, Nanning, 530021, China
| | - Christopher Mason
- Weill Cornell Medicine, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, USA
| | - Tieliu Shi
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China; Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University & Capital Medical University, Beijing, 100083, China.
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22
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Unger F, Eisenberg T, Prenger-Berninghoff E, Leidner U, Semmler T, Ewers C. Imported Pet Reptiles and Their “Blind Passengers”—In-Depth Characterization of 80 Acinetobacter Species Isolates. Microorganisms 2022; 10:microorganisms10050893. [PMID: 35630338 PMCID: PMC9144363 DOI: 10.3390/microorganisms10050893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 04/19/2022] [Accepted: 04/21/2022] [Indexed: 11/16/2022] Open
Abstract
Reptiles are popular pet animals and important food sources, but the trade of this vertebrate class is—besides welfare and conservation—under debate due to zoonotic microbiota. Ninety-two shipments of live reptiles were sampled during border inspections at Europe’s most relevant transshipment point for the live animal trade. Acinetobacter spp. represented one significant fraction of potentially MDR bacteria that were further analyzed following non-selective isolation or selective enrichment from feces, urinate, or skin samples. Taxonomic positions of respective isolates were confirmed by MALDI-TOF MS and whole-genome sequencing analysis (GBDP, dDDH, ANIb, and rMLST). The majority of the 80 isolates represented established species; however, a proportion of potentially novel taxa was found. Antimicrobial properties and genome-resistance gene screening revealed novel and existing resistance mechanisms. Acinetobacter spp. strains were most often resistant to 6–10 substance groups (n = 63) in vitro. Resistance to fluorchinolones (n = 4) and colistin (n = 7), but not to carbapenems, was noted, and novel oxacillinase variants (n = 39) were detected among other genes. Phylogenetic analysis (MLST) assigned few isolates to the known STs (25, 46, 49, 220, and 249) and to a number of novel STs. No correlation was found to indicate that MDR Acinetobacter spp. in reptiles were associated with harvesting mode, e.g., captive-bred, wild-caught, or farmed in natural ecosystems. The community of Acinetobacter spp. in healthy reptiles turned out to be highly variable, with many isolates displaying a MDR phenotype or genotype.
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Affiliation(s)
- Franziska Unger
- Institute of Hygiene and Infectious Diseases of Animals, Faculty of Veterinary Medicine, Justus-Liebig University Giessen, 35392 Giessen, Germany; (F.U.); (E.P.-B.); (U.L.)
| | | | - Ellen Prenger-Berninghoff
- Institute of Hygiene and Infectious Diseases of Animals, Faculty of Veterinary Medicine, Justus-Liebig University Giessen, 35392 Giessen, Germany; (F.U.); (E.P.-B.); (U.L.)
| | - Ursula Leidner
- Institute of Hygiene and Infectious Diseases of Animals, Faculty of Veterinary Medicine, Justus-Liebig University Giessen, 35392 Giessen, Germany; (F.U.); (E.P.-B.); (U.L.)
| | - Torsten Semmler
- NG1 Microbial Genomics, Robert Koch Institute, 13353 Berlin, Germany;
| | - Christa Ewers
- Institute of Hygiene and Infectious Diseases of Animals, Faculty of Veterinary Medicine, Justus-Liebig University Giessen, 35392 Giessen, Germany; (F.U.); (E.P.-B.); (U.L.)
- Correspondence: ; Tel.: +49-641-9938300
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23
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Schink AK, Hanke D, Semmler T, Brombach J, Bethe A, Lübke-Becker A, Teske K, Müller KE, Schwarz S. Novel multiresistance-mediating integrative and conjugative elements carrying unusual antimicrobial resistance genes in Mannheimia haemolytica and Pasteurella multocida. J Antimicrob Chemother 2022; 77:2033-2035. [DOI: 10.1093/jac/dkac116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Anne-Kathrin Schink
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - Dennis Hanke
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - Torsten Semmler
- NG1-Microbial Genomics, Robert Koch Institute, Berlin, Germany
| | - Julian Brombach
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - Astrid Bethe
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - Antina Lübke-Becker
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - Kinga Teske
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
- Institute of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Kerstin Elisabeth Müller
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
- Clinic for Ruminants and Swine, Freie Universität Berlin, Berlin, Germany
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
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24
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Smith DM, Eade R, Andrews MB, Ayres H, Clark A, Chripko S, Deser C, Dunstone NJ, García-Serrano J, Gastineau G, Graff LS, Hardiman SC, He B, Hermanson L, Jung T, Knight J, Levine X, Magnusdottir G, Manzini E, Matei D, Mori M, Msadek R, Ortega P, Peings Y, Scaife AA, Screen JA, Seabrook M, Semmler T, Sigmond M, Streffing J, Sun L, Walsh A. Robust but weak winter atmospheric circulation response to future Arctic sea ice loss. Nat Commun 2022; 13:727. [PMID: 35132058 PMCID: PMC8821642 DOI: 10.1038/s41467-022-28283-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 01/17/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractThe possibility that Arctic sea ice loss weakens mid-latitude westerlies, promoting more severe cold winters, has sparked more than a decade of scientific debate, with apparent support from observations but inconclusive modelling evidence. Here we show that sixteen models contributing to the Polar Amplification Model Intercomparison Project simulate a weakening of mid-latitude westerlies in response to projected Arctic sea ice loss. We develop an emergent constraint based on eddy feedback, which is 1.2 to 3 times too weak in the models, suggesting that the real-world weakening lies towards the higher end of the model simulations. Still, the modelled response to Arctic sea ice loss is weak: the North Atlantic Oscillation response is similar in magnitude and offsets the projected response to increased greenhouse gases, but would only account for around 10% of variations in individual years. We further find that relationships between Arctic sea ice and atmospheric circulation have weakened recently in observations and are no longer inconsistent with those in models.
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25
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Lynch CT, Buttimer C, Epping L, O'Connor J, Walsh N, McCarthy C, O'Brien D, Vaughan C, Semmler T, Bolton D, Coffey A, Lucey B. Phenotypic and genetic analyses of two Campylobacter fetus isolates from a patient with relapsed prosthetic valve endocarditis. Pathog Dis 2021; 79:6486444. [PMID: 34962980 DOI: 10.1093/femspd/ftab055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 12/24/2021] [Indexed: 11/12/2022] Open
Abstract
Campylobacter fetus can cause intestinal and systemic disease in humans and are well established veterinary and economic pathogens. We report the complete genomic sequences of two C. fetus subsp. fetus (Cff) isolates recovered in 2017 (CITCf01) and 2018 (CITCf02) from a case of recurrent prosthetic valve endocarditis. Both were capable of growth aerobically. Their genomes were found to be highly conserved and syntenic with 99.97% average nucleotide identity (ANI) while differences in their respective sap loci defined the temporal separation of their genomes. Based on core genome phylogeny and ANI of 83 Cff genomes belonging to the previously described human-associated Cff lineage, CITCf01 and CITCf02 grouped in a clade of eleven sequence type (ST)3 Cff (including the Cff type strain NCTC 10842T). CITCf01 and CITCf02 were marked for their lack of unique genomic features when compared to isolates within the subspecies and the type strain in particular. We identified point mutations in oxidative stress response genes, among others, that may contribute to aerobiosis. We report a case of Cff causing relapsed prosthetic valve endocarditis and we highlight the sap island as a polymorphic site within the genetically stable ST3 lineage, central to pathogenicity.
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Affiliation(s)
- Caoimhe T Lynch
- Department of Biological Sciences, Munster Technological University, Rossa Ave, Bishopstown, Cork, Ireland
| | - Colin Buttimer
- APC Microbiome Ireland, University College Cork, College Road, Cork, Ireland
| | - Lennard Epping
- Genome Sequencing and Genomic Epidemiology, Robert Koch Institute, Nordufer 20, Berlin, Germany
| | - James O'Connor
- Department of Microbiology, Grenville Place, Mercy University Hospital, Cork, Ireland
| | - Niamh Walsh
- Department of Biological Sciences, Munster Technological University, Rossa Ave, Bishopstown, Cork, Ireland
| | - Conor McCarthy
- Department of Biological Sciences, Munster Technological University, Rossa Ave, Bishopstown, Cork, Ireland
| | - Deirdre O'Brien
- Department of Microbiology, Grenville Place, Mercy University Hospital, Cork, Ireland
| | - Carl Vaughan
- Department of Cardiology, Grenville Place, Mercy University Hospital, Cork, Ireland
| | - Torsten Semmler
- Genome Sequencing and Genomic Epidemiology, Robert Koch Institute, Nordufer 20, Berlin, Germany
| | - Declan Bolton
- Food Safety Department, Teagasc Ashtown Food Research Centre, Ashtown, Dublin 15, Ireland
| | - Aidan Coffey
- Department of Biological Sciences, Munster Technological University, Rossa Ave, Bishopstown, Cork, Ireland.,APC Microbiome Ireland, University College Cork, College Road, Cork, Ireland
| | - Brigid Lucey
- Department of Biological Sciences, Munster Technological University, Rossa Ave, Bishopstown, Cork, Ireland
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26
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Thomas P, Abdel-Glil MY, Eichhorn I, Semmler T, Werckenthin C, Baumbach C, Murmann W, Bodenthin-Drauschke A, Zimmermann P, Schotte U, Galante D, Slavic D, Wagner M, Wieler LH, Neubauer H, Seyboldt C. Genome Sequence Analysis of Clostridium chauvoei Strains of European Origin and Evaluation of Typing Options for Outbreak Investigations. Front Microbiol 2021; 12:732106. [PMID: 34659160 PMCID: PMC8513740 DOI: 10.3389/fmicb.2021.732106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/31/2021] [Indexed: 01/08/2023] Open
Abstract
Black quarter caused by Clostridium (C.) chauvoei is an important bacterial disease that affects cattle and sheep with high mortality. A comparative genomics analysis of 64 C. chauvoei strains, most of European origin and a few of non-European and unknown origin, was performed. The pangenome analysis showed limited new gene acquisition for the species. The accessory genome involved prophages and genomic islands, with variations in gene composition observed in a few strains. This limited accessory genome may indicate that the species replicates only in the host or that an active CRISPR/Cas system provides immunity to foreign genetic elements. All strains contained a CRISPR type I-B system and it was confirmed that the unique spacer sequences therein can be used to differentiate strains. Homologous recombination events, which may have contributed to the evolution of this pathogen, were less frequent compared to other related species from the genus. Pangenome single nucleotide polymorphism (SNP) based phylogeny and clustering indicate diverse clusters related to geographical origin. Interestingly the identified SNPs were mostly non-synonymous. The study demonstrates the possibility of the existence of polymorphic populations in one host, based on strain variability observed for strains from the same animal and strains from different animals of one outbreak. The study also demonstrates that new outbreak strains are mostly related to earlier outbreak strains from the same farm/region. This indicates the last common ancestor strain from one farm can be crucial to understand the genetic changes and epidemiology occurring at farm level. Known virulence factors for the species were highly conserved among the strains. Genetic elements involved in Nicotinamide adenine dinucleotide (NAD) precursor synthesis (via nadA, nadB, and nadC metabolic pathway) which are known as potential anti-virulence loci are completely absent in C. chauvoei compared to the partial inactivation in C. septicum. A novel core-genome MLST based typing method was compared to sequence typing based on CRISPR spacers to evaluate the usefulness of the methods for outbreak investigations.
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Affiliation(s)
- Prasad Thomas
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Mostafa Y Abdel-Glil
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Inga Eichhorn
- Department of Veterinary Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | | | - Christiane Werckenthin
- Lower Saxony State Office for Consumer Protection and Food Safety (LAVES), Food and Veterinary Institute Oldenburg, Oldenburg, Germany
| | - Christina Baumbach
- State Office for Agriculture, Food Safety and Fisheries Mecklenburg-Western Pomerania, Rostock, Germany
| | - Wybke Murmann
- Chemical and Veterinary Investigations Office, Freiburg, Germany
| | | | - Pia Zimmermann
- Bavarian Health and Food Safety Authority (LGL), Laboratory of Food Microbiology, Oberschleißheim, Germany
| | - Ulrich Schotte
- Department A-Veterinary Medicine, Central Institute of the Bundeswehr Medical Service Kiel, Kronshagen, Germany
| | - Domenico Galante
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Durda Slavic
- Animal Health Laboratory, Laboratory Services Division, University of Guelph, Guelph, ON, Canada
| | - Martin Wagner
- Unit for Food Microbiology, Institute for Food Safety, Technology and Veterinary Public Health, University for Veterinary Medicine, Vienna, Austria
| | | | - Heinrich Neubauer
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Christian Seyboldt
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
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27
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Saidenberg ABS, Stegger M, Semmler T, Rocha VGP, Cunha MPV, Souza VAF, Cristina Menão M, Milanelo L, Petri BSS, Knöbl T. Salmonella Newport outbreak in Brazilian parrots: confiscated birds from the illegal pet trade as possible zoonotic sources. Environ Microbiol Rep 2021; 13:702-707. [PMID: 34169662 DOI: 10.1111/1758-2229.12984] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 06/08/2021] [Indexed: 06/13/2023]
Abstract
Salmonella has long been linked to zoonotic risks, including exotic pets. Parrots are popular pets, and we here describe a salmonellosis outbreak involving Blue-fronted Amazon parrots (Amazona aestiva) confiscated from the illegal pet trade in Brazil. High mortality was observed during the rehabilitation for which the causative agent was identified by cultures, and VITEK®2 GN identification card as Salmonella enterica. Genome sequencing of two isolates revealed serovar Newport ST45. The isolates were resistant to aminoglycosides and fluoroquinolones, and genomic analyses detected characteristic Salmonella Pathogenicity Islands (SPIs) and virulence factors. A phylogenetic analysis with other 275 S. Newport ST45 from different international sources showed clustering with poultry and vegetables isolates and closely related clades of intermingled animal, human, food/environmental isolates from different countries (Tables S1 and S2). The virulent profiles and phylogenetic connection to multiple sources bring the attention to the non-host specificity of these strains highlighting the zoonotic potential in the illegal wildlife trade for companion animals.
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Affiliation(s)
- André B S Saidenberg
- Faculty of Veterinary Sciences and Animal Health, University of Sao Paulo, São Paulo, Brazil
- Department of Bacteria, Parasite and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Marc Stegger
- Department of Bacteria, Parasite and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | | | - Victória G P Rocha
- Faculty of Veterinary Sciences and Animal Health, University of Sao Paulo, São Paulo, Brazil
| | - Marcos P V Cunha
- Faculty of Veterinary Sciences and Animal Health, University of Sao Paulo, São Paulo, Brazil
| | - Vanessa A F Souza
- Centro Universitário das Faculdades Metropolitanas Unidas, R. Ministro Nelson Hungria, São Paulo, Brazil
| | - Márcia Cristina Menão
- Centro Universitário das Faculdades Metropolitanas Unidas, R. Ministro Nelson Hungria, São Paulo, Brazil
| | - Liliane Milanelo
- Centro de Recuperação de Animais Selvagens do Parque Ecológico do Tietê, R. Guira Acangatara 70, São Paulo, Brazil
| | - Bruno S S Petri
- Centro de Recuperação de Animais Selvagens do Parque Ecológico do Tietê, R. Guira Acangatara 70, São Paulo, Brazil
| | - Terezinha Knöbl
- Faculty of Veterinary Sciences and Animal Health, University of Sao Paulo, São Paulo, Brazil
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28
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Lewin A, Kamal E, Semmler T, Winter K, Kaiser S, Schäfer H, Mao L, Eschenhagen P, Grehn C, Bender J, Schwarz C. Genetic diversification of persistent Mycobacterium abscessus within cystic fibrosis patients. Virulence 2021; 12:2415-2429. [PMID: 34546836 PMCID: PMC8526041 DOI: 10.1080/21505594.2021.1959808] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Mycobacterium (M.) abscessus infections in Cystic Fibrosis (CF) patients cause a deterioration of lung function. Treatment of these multidrug-resistant pathogens is associated with severe side-effects, while frequently unsuccessful. Insight on M. abscessus genomic evolvement during chronic lung infection would be beneficial for improving treatment strategies. A longitudinal study enrolling 42 CF patients was performed at a CF center in Berlin, Germany, to elaborate phylogeny and genomic diversification of in-patient M. abscessus. Eleven of the 42 CF patients were infected with M. abscessus. Five of these 11 patients were infected with global human-transmissible M. abscessus cluster strains. Phylogenetic analysis of 88 genomes from isolates of the 11 patients excluded occurrence of M. abscessus transmission among members of the study group. Genome sequencing and variant analysis of 30 isolates from 11 serial respiratory samples collected over 4.5 years from a chronically infected patient demonstrated accumulation of gene mutations. In total, 53 genes exhibiting non-synonymous variations were identified. Enrichment analysis emphasized genes involved in synthesis of glycopeptidolipids, genes from the embABC (arabinosyltransferase) operon, betA (glucose-methanol-choline oxidoreductase) and choD (cholesterol oxidase). Genetic diversity evolved in a variety of virulence- and resistance-associated genes. The strategy of M. abscessus populations in chronic lung infection is not clonal expansion of dominant variants, but to sustain simultaneously a wide range of genetic variants facilitating adaptation of the population to changing living conditions in the lung. Genomic diversification during chronic infection requires increased attention when new control strategies against M. abscessus infections are explored.
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Affiliation(s)
- Astrid Lewin
- Unit 16 Mycotic and Parasitic Agents and Mycobacteria, Robert Koch Institute, Berlin, Germany
| | - Elisabeth Kamal
- Unit 16 Mycotic and Parasitic Agents and Mycobacteria, Robert Koch Institute, Berlin, Germany
| | - Torsten Semmler
- Unit NG 1 Microbial Genomics, Robert Koch Institute, Berlin, Germany
| | - Katja Winter
- Unit MF1 Bioinformatics, Robert Koch Institute, Berlin, Germany
| | - Sandra Kaiser
- Unit MF1 Bioinformatics, Robert Koch Institute, Berlin, Germany
| | - Hubert Schäfer
- Unit 16 Mycotic and Parasitic Agents and Mycobacteria, Robert Koch Institute, Berlin, Germany
| | - Lei Mao
- Unit 16 Mycotic and Parasitic Agents and Mycobacteria, Robert Koch Institute, Berlin, Germany.,Unit 31 Infectious Disease Data Science Unit, Robert Koch Institute, Berlin, Germany
| | - Patience Eschenhagen
- Klinikum Westbrandenburg, Campus Potsdam, Cystic Fibrosis Section, Potsdam, Germany.,Pediatric Respiratory Medicine, Immunology and Intensive Care Medicine, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Claudia Grehn
- Department of Pediatrics, Division of Pulmonology, Immunology and Intensive Care Medicine, Division of Cystic Fibrosis, Charité - Universitätsmedizin, Berlin, Germany
| | - Jennifer Bender
- Unit 13 Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode, Germany.,ECDC Fellowship Programme, Public Health Microbiology Path (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Solna, Sweden
| | - Carsten Schwarz
- Klinikum Westbrandenburg, Campus Potsdam, Cystic Fibrosis Section, Potsdam, Germany.,Pediatric Respiratory Medicine, Immunology and Intensive Care Medicine, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
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29
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Kutzer P, Szentiks CA, Bock S, Fritsch G, Magyar T, Schulze C, Semmler T, Ewers C. Re-Emergence and Spread of Haemorrhagic Septicaemia in Germany: The Wolf as a Vector? Microorganisms 2021; 9:microorganisms9091999. [PMID: 34576894 PMCID: PMC8465458 DOI: 10.3390/microorganisms9091999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/15/2021] [Accepted: 09/17/2021] [Indexed: 11/16/2022] Open
Abstract
Since 2010, outbreaks of haemorrhagic septicaemia (HS) caused by Pasteurella (P.) multocida capsular type B (PmB) emerged in Germany. In 2017, we noticed a close spatiotemporal relationship between HS outbreak sites and wolf (Canis lupus) territories. Thus, the main objectives of our study were to investigate the molecular epidemiology of German PmB-HS-isolates and to assess the role of wolves as putative vectors of this pathogen. We collected 83 PmB isolates from HS outbreaks that occurred between 2010 and 2019 and sampled 150 wolves, which were found dead in the years 2017 to 2019, revealing another three PmB isolates. A maximum-likelihood-based phylogeny of the core genomes of 65 PmB-HS-isolates and the three PmB-wolf-isolates showed high relatedness. Furthermore, all belonged to capsular:LPS:MLST genotype B:L2:ST122RIRDC and showed highly similar virulence gene profiles, but clustered separately from 35 global ST122RIRDC strains. Our data revealed that German HS outbreaks were caused by a distinct genomic lineage of PmB-ST122 strains, hinting towards an independent, ongoing epidemiologic event. We demonstrated for the first time, that carnivores, i.e., wolves, might harbour PmB as a part of their oropharyngeal microbiota. Furthermore, the results of our study imply that wolves can carry the pathogen over long distances, indicating a major role of that animal species in the ongoing epidemiological event of HS in Germany.
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Affiliation(s)
- Peter Kutzer
- Landeslabor Berlin-Brandenburg, 15236 Frankfurt (Oder), Germany; (S.B.); (C.S.)
- Correspondence: ; Tel.: +49-335-5217-2118
| | - Claudia A. Szentiks
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, 10315 Berlin, Germany;
| | - Sabine Bock
- Landeslabor Berlin-Brandenburg, 15236 Frankfurt (Oder), Germany; (S.B.); (C.S.)
| | - Guido Fritsch
- Department of Reproduction Management, Leibniz Institute for Zoo and Wildlife Research, 10315 Berlin, Germany;
| | - Tibor Magyar
- Veterinary Medical Research Institute, Eötvös Lóránd Research Network (ELKH), 1143 Budapest, Hungary;
| | - Christoph Schulze
- Landeslabor Berlin-Brandenburg, 15236 Frankfurt (Oder), Germany; (S.B.); (C.S.)
| | - Torsten Semmler
- Microbial Genomics, Robert Koch Institute, 13353 Berlin, Germany;
| | - Christa Ewers
- Faculty of Veterinary Medicine, Institute for Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, 35392 Giessen, Germany;
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30
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Kürekci C, Sakin F, Epping L, Knüver MT, Semmler T, Stingl K. Characterization of Campylobacter spp. Strains Isolated From Wild Birds in Turkey. Front Microbiol 2021; 12:712106. [PMID: 34489902 PMCID: PMC8416542 DOI: 10.3389/fmicb.2021.712106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
Turkey is an important stopover site for many migrating birds between Europe, Asia and Africa. Campylobacter spp. are frequently found in wildlife, in particular waterfowl, and distinct strains are disseminated within this reservoir. In this study, 183 wild birds of hunting areas in Turkey were collected and thermophilic Campylobacter spp. from cloacal swabs were isolated at a prevalence of 5.2% from song thrushes (6/116) and 93% from Eurasian coots (41/44). After PCR species differentiation and flaA restriction profiles determination, C. jejuni and C. coli strains were further investigated by whole genome sequencing. PCR target amplification of the ceuE gene, commonly used for C. coli species-identification was inefficient and even hampered in one isolate. A close look on the ceuE sequence revealed that various mismatches in the ceuE oligo annealing sites caused less efficient diagnostic detection. All C. coli isolates belonged to the environmental clade II and clade III, for which thirty-six novel MLST types were identified. Further single nucleotide polymorphism (SNP) analysis showed a high genomic divergence between the C. coli isolates. High variability was also implicated for putative plasmid-located genes detected in 51% of the C. coli isolates. Distinct gene variants in clades II and III C. coli were identified by a k-mer analysis. After substracting k-mers in common with C. coli clade I database, 11 and 35 distinct genes were identified in clades II and III isolates, mainly involved in surface structures and modifications as well as signal transduction, suggesting niche adaptation of C. coli strains in wild birds. All strains were susceptible against (fluoro-)quinolones, erythromycin, tetracycline, gentamicin and only one isolate was resistant against streptomycin, suggesting that the sensitive phenotype was due to absence of selective pressure and niche separation in wild birds in Turkey. We conclude that Campylobacter spp. isolates from wildlife and environmental sources are still scarce in the databases and that there is a need for more studies on thermophilic Campylobacter spp. from different places all over the world in order to complement our understanding on dissemination and adaptation to distinct niches of this global food-borne pathogen.
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Affiliation(s)
- Cemil Kürekci
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, Hatay Mustafa Kemal University, Hatay, Turkey
| | - Fatih Sakin
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Hatay Mustafa Kemal University, Hatay, Turkey
| | - Lennard Epping
- Robert Koch Institute, Genome Sequencing and Genomic Epidemiology, Berlin, Germany
| | - Marie-Theres Knüver
- German Federal Institute for Risk Assessment, Department of Biological Safety, National Reference Laboratory for Campylobacter, Berlin, Germany
| | - Torsten Semmler
- Robert Koch Institute, Genome Sequencing and Genomic Epidemiology, Berlin, Germany
| | - Kerstin Stingl
- German Federal Institute for Risk Assessment, Department of Biological Safety, National Reference Laboratory for Campylobacter, Berlin, Germany
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31
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Calvignac-Spencer S, Budt M, Huska M, Richard H, Leipold L, Grabenhenrich L, Semmler T, von Kleist M, Kröger S, Wolff T, Hölzer M. Rise and Fall of SARS-CoV-2 Lineage A.27 in Germany. Viruses 2021; 13:1491. [PMID: 34452356 PMCID: PMC8402818 DOI: 10.3390/v13081491] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 07/23/2021] [Accepted: 07/24/2021] [Indexed: 01/01/2023] Open
Abstract
Here, we report on the increasing frequency of the SARS-CoV-2 lineage A.27 in Germany during the first months of 2021. Genomic surveillance identified 710 A.27 genomes in Germany as of 2 May 2021, with a vast majority identified in laboratories from a single German state (Baden-Wuerttemberg, n = 572; 80.5%). Baden-Wuerttemberg is located near the border with France, from where most A.27 sequences were entered into public databases until May 2021. The first appearance of this lineage based on sequencing in a laboratory in Baden-Wuerttemberg can be dated to early January '21. From then on, the relative abundance of A.27 increased until the end of February but has since declined-meanwhile, the abundance of B.1.1.7 increased in the region. The A.27 lineage shows a mutational pattern typical of VOIs/VOCs, including an accumulation of amino acid substitutions in the Spike glycoprotein. Among those, L18F, L452R and N501Y are located in the epitope regions of the N-terminal- (NTD) or receptor binding domain (RBD) and have been suggested to result in immune escape and higher transmissibility. In addition, A.27 does not show the D614G mutation typical for all VOIs/VOCs from the B lineage. Overall, A.27 should continue to be monitored nationally and internationally, even though the observed trend in Germany was initially displaced by B.1.1.7 (Alpha), while now B.1.617.2 (Delta) is on the rise.
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Affiliation(s)
| | - Matthias Budt
- Influenza and other Respiratory Viruses, Robert Koch Institute, 13353 Berlin, Germany; (M.B.); (T.W.)
| | - Matthew Huska
- Methodology and Research Infrastructure, Bioinformatics, Robert Koch Institute, 13353 Berlin, Germany; (M.H.); (H.R.)
| | - Hugues Richard
- Methodology and Research Infrastructure, Bioinformatics, Robert Koch Institute, 13353 Berlin, Germany; (M.H.); (H.R.)
| | - Luca Leipold
- Methodology and Research Infrastructure, Information and Research Data Management, Robert Koch Institute, 13353 Berlin, Germany; (L.L.); (L.G.)
| | - Linus Grabenhenrich
- Methodology and Research Infrastructure, Information and Research Data Management, Robert Koch Institute, 13353 Berlin, Germany; (L.L.); (L.G.)
| | - Torsten Semmler
- Methodology and Research Infrastructure, Genome Sequencing and Genomic Epidemiology, Robert Koch Institute, 13353 Berlin, Germany;
| | - Max von Kleist
- Systems Medicine of Infectious Disease, Robert Koch Institute, 13353 Berlin, Germany;
| | - Stefan Kröger
- Infectious Disease Epidemiology, Robert Koch Institute, 13353 Berlin, Germany;
| | - Thorsten Wolff
- Influenza and other Respiratory Viruses, Robert Koch Institute, 13353 Berlin, Germany; (M.B.); (T.W.)
| | - Martin Hölzer
- Methodology and Research Infrastructure, Bioinformatics, Robert Koch Institute, 13353 Berlin, Germany; (M.H.); (H.R.)
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32
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Lerche N, Holtfreter S, Walther B, Semmler T, Al'Sholui F, Dancer SJ, Daeschlein G, Hübner NO, Bröker BM, Papke R, Kohlmann T, Baguhl R, Seifert U, Kramer A. Staphylococcus aureus nasal colonization among dental health care workers in Northern Germany (StaphDent study). Int J Med Microbiol 2021; 311:151524. [PMID: 34371345 DOI: 10.1016/j.ijmm.2021.151524] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 06/10/2021] [Accepted: 07/16/2021] [Indexed: 10/20/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) can colonize dental patients and students, however, studies on the prevalence of MRSA and methicillin-susceptible S. aureus (MSSA) among dental health care workers (DHCW) including use of personal protective equipment (PPE) are scarce. We conducted an observational study (StaphDent study) to (I) determine the prevalence of MRSA and MSSA colonization in DHCW in the region of Mecklenburg Western-Pomerania, Germany, (II) resolve the S. aureus population structure to gain hints on possible transmission events between co-workers, and (III) clarify use of PPE. Nasal swabs were obtained from dentists (n = 149), dental assistants (n = 297) and other dental practice staff (n = 38). Clonal relatedness of MSSA isolates was investigated using spa typing and, in some cases, whole genome sequencing (WGS). PPE use was assessed by questionnaire. While 22.3% (108/485) of the participants were colonized with MSSA, MRSA was not detected. MSSA prevalence was not associated with size of dental practices, gender, age, or duration of employment. The identified 61 spa types grouped into 17 clonal complexes and four sequence types. Most spa types (n = 47) were identified only once. In ten dental practices one spa type occurred twice. WGS data analysis confirmed a close clonal relationship for 4/10 isolate pairs. PPE was regularly used by most dentists and assistants. To conclude, the failure to recover MRSA from DHCW reflects the low MRSA prevalence in this region. Widespread PPE use suggests adherence to routine hygiene protocols. Compared to other regional HCW MRSA rates the consequent usage of PPE seems to be protective.
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Affiliation(s)
- Nadine Lerche
- Institute of Hygiene and Environmental Medicine, University Medicine Greifswald, Ferdinand-Sauerbruch-Straße, DE-17475, Greifswald, Germany.
| | - Silva Holtfreter
- Institute of Immunology, University Medicine Greifswald, Ferdinand-Sauerbruch-Straße, DE-17475, Greifswald, Germany.
| | - Birgit Walther
- ZBS 4, Advanced Light and Electron Microscopy, Robert Koch Institute, Seestraße 10, DE-13353, Berlin, Germany.
| | - Torsten Semmler
- Microbial Genomics (NG1), Robert Koch Institute, Nordufer 20, 13353, Berlin, Germany.
| | - Fawaz Al'Sholui
- Institute of Immunology, University Medicine Greifswald, Ferdinand-Sauerbruch-Straße, DE-17475, Greifswald, Germany.
| | - Stephanie J Dancer
- Department of Microbiology, Hairmyres Hospital, NHS Lanarkshire, G75 8RG, UK; School of Applied Sciences, Edinburgh Napier University, Edinburgh, EH11 4BN, UK.
| | - Georg Daeschlein
- Department of Dermatology, University Medicine Greifswald, Ferdinand-Sauerbruch-Straße, DE-17475, Greifswald, Germany.
| | - Nils-Olaf Hübner
- Institute of Hygiene and Environmental Medicine, University Medicine Greifswald, Ferdinand-Sauerbruch-Straße, DE-17475, Greifswald, Germany; Central Unit for Infection Prevention and Control, University Medicine Greifswald, 17475, Greifswald, Germany.
| | - Barbara M Bröker
- Institute of Immunology, University Medicine Greifswald, Ferdinand-Sauerbruch-Straße, DE-17475, Greifswald, Germany.
| | - Roald Papke
- Institute of Hygiene and Environmental Medicine, University Medicine Greifswald, Ferdinand-Sauerbruch-Straße, DE-17475, Greifswald, Germany.
| | - Thomas Kohlmann
- Institute for Community Medicine, Methodical Subdivision, University Medicine Greifswald, Walther-Rathenau-Str. 48, DE-17475, Greifswald, Germany.
| | - Romy Baguhl
- Institute of Hygiene and Environmental Medicine, University Medicine Greifswald, Ferdinand-Sauerbruch-Straße, DE-17475, Greifswald, Germany.
| | - Ulrike Seifert
- Friedrich Loeffler Institute of Medical Microbiology, University Medicine Greifswald, Ferdinand-Sauerbruch-Straße, DE-17475, Greifswald, Germany.
| | - Axel Kramer
- Institute of Hygiene and Environmental Medicine, University Medicine Greifswald, Ferdinand-Sauerbruch-Straße, DE-17475, Greifswald, Germany.
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Danko D, Bezdan D, Afshin EE, Ahsanuddin S, Bhattacharya C, Butler DJ, Chng KR, Donnellan D, Hecht J, Jackson K, Kuchin K, Karasikov M, Lyons A, Mak L, Meleshko D, Mustafa H, Mutai B, Neches RY, Ng A, Nikolayeva O, Nikolayeva T, Png E, Ryon KA, Sanchez JL, Shaaban H, Sierra MA, Thomas D, Young B, Abudayyeh OO, Alicea J, Bhattacharyya M, Blekhman R, Castro-Nallar E, Cañas AM, Chatziefthimiou AD, Crawford RW, De Filippis F, Deng Y, Desnues C, Dias-Neto E, Dybwad M, Elhaik E, Ercolini D, Frolova A, Gankin D, Gootenberg JS, Graf AB, Green DC, Hajirasouliha I, Hastings JJA, Hernandez M, Iraola G, Jang S, Kahles A, Kelly FJ, Knights K, Kyrpides NC, Łabaj PP, Lee PKH, Leung MHY, Ljungdahl PO, Mason-Buck G, McGrath K, Meydan C, Mongodin EF, Moraes MO, Nagarajan N, Nieto-Caballero M, Noushmehr H, Oliveira M, Ossowski S, Osuolale OO, Özcan O, Paez-Espino D, Rascovan N, Richard H, Rätsch G, Schriml LM, Semmler T, Sezerman OU, Shi L, Shi T, Siam R, Song LH, Suzuki H, Court DS, Tighe SW, Tong X, Udekwu KI, Ugalde JA, Valentine B, Vassilev DI, Vayndorf EM, Velavan TP, Wu J, Zambrano MM, Zhu J, Zhu S, Mason CE. A global metagenomic map of urban microbiomes and antimicrobial resistance. Cell 2021; 184:3376-3393.e17. [PMID: 34043940 PMCID: PMC8238498 DOI: 10.1016/j.cell.2021.05.002] [Citation(s) in RCA: 129] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/05/2021] [Accepted: 04/29/2021] [Indexed: 01/14/2023]
Abstract
We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.
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Affiliation(s)
- David Danko
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Daniela Bezdan
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA; Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany; NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, Germany
| | - Evan E Afshin
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | | | - Chandrima Bhattacharya
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Daniel J Butler
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Kern Rei Chng
- Genome Institute of Singapore, A(∗)STAR, Singapore, Singapore
| | - Daisy Donnellan
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Jochen Hecht
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Katelyn Jackson
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Katerina Kuchin
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Mikhail Karasikov
- ETH Zurich, Department of Computer Science, Biomedical Informatics Group, Zurich, Switzerland; University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Abigail Lyons
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Lauren Mak
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Dmitry Meleshko
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Harun Mustafa
- ETH Zurich, Department of Computer Science, Biomedical Informatics Group, Zurich, Switzerland; University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Beth Mutai
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Kenya Medical Research Institute - Kisumu, Kisumu, Kenya
| | - Russell Y Neches
- Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Amanda Ng
- Genome Institute of Singapore, A(∗)STAR, Singapore, Singapore
| | | | | | - Eileen Png
- Genome Institute of Singapore, A(∗)STAR, Singapore, Singapore
| | - Krista A Ryon
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Jorge L Sanchez
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Heba Shaaban
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Maria A Sierra
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Dominique Thomas
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Ben Young
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Omar O Abudayyeh
- Massachusetts Institute of Technology, McGovern Institute for Brain Research, Cambridge, MA, USA
| | - Josue Alicea
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Malay Bhattacharyya
- Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India; Centre for Artificial Intelligence and Machine Learning, Indian Statistical Institute, Kolkata, India
| | | | - Eduardo Castro-Nallar
- Universidad Andres Bello, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Santiago, Chile
| | - Ana M Cañas
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Aspassia D Chatziefthimiou
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | | | - Francesca De Filippis
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Naples, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Youping Deng
- University of Hawaii John A. Burns School of Medicine, Honolulu, HI, USA
| | - Christelle Desnues
- Aix-Marseille Université, Mediterranean Institute of Oceanology, Université de Toulon, CNRS, IRD, UM 110, Marseille, France
| | - Emmanuel Dias-Neto
- Medical Genomics group, A.C.Camargo Cancer Center, São Paulo - SP, Brazil
| | - Marius Dybwad
- Norwegian Defence Research Establishment FFI, Kjeller, Norway
| | - Eran Elhaik
- Department of Biology, Lund University, Lund, Sweden
| | - Danilo Ercolini
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Naples, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Alina Frolova
- Institute of Molecular Biology and Genetics of National Academy of Sciences of Ukraine, Kyiv, Ukraine; Kyiv Academic University, Kyiv, Ukraine
| | - Dennis Gankin
- Massachusetts Institute of Technology, McGovern Institute for Brain Research, Cambridge, MA, USA
| | - Jonathan S Gootenberg
- Massachusetts Institute of Technology, McGovern Institute for Brain Research, Cambridge, MA, USA
| | | | - David C Green
- Department of Analytical, Environmental and Forensic Sciences, King's College London, London, UK
| | - Iman Hajirasouliha
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Jaden J A Hastings
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | | | - Gregorio Iraola
- Microbial Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay; Center for Integrative Biology, Universidad Mayor, Santiago de Chile, Santiago, Chile; Wellcome Sanger Institute, Hinxton, UK
| | | | - Andre Kahles
- ETH Zurich, Department of Computer Science, Biomedical Informatics Group, Zurich, Switzerland; Kyiv Academic University, Kyiv, Ukraine; C+, Research Center in Technologies for Society, School of Engineering, Universidad del Desarrollo, Santiago, Chile
| | - Frank J Kelly
- Department of Analytical, Environmental and Forensic Sciences, King's College London, London, UK
| | - Kaymisha Knights
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Nikos C Kyrpides
- Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Paweł P Łabaj
- State Key Laboratory of Genetic Engineering (SKLGE) and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China; Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland; Boku University Viennna, Vienna, Austria
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Marcus H Y Leung
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Per O Ljungdahl
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Gabriella Mason-Buck
- Department of Analytical, Environmental and Forensic Sciences, King's College London, London, UK
| | - Ken McGrath
- Microba, 388 Queen St, Brisbane City, QLD 4000, Australia
| | - Cem Meydan
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Emmanuel F Mongodin
- University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, USA
| | | | | | | | - Houtan Noushmehr
- University of São Paulo, Ribeirão Preto Medical School, Ribeirão Preto - SP, Brazil
| | - Manuela Oliveira
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
| | - Stephan Ossowski
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany; NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, Germany
| | - Olayinka O Osuolale
- Applied Environmental Metagenomics and Infectious Diseases Research (AEMIDR), Department of Biological Sciences, Elizade University, Ilara-Mokin, Nigeria
| | - Orhan Özcan
- Acibadem Mehmet Ali Aydınlar University, Istanbul, Turkey
| | - David Paez-Espino
- Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nicolás Rascovan
- Microbial Paleogenomics Unit, Institut Pasteur, CNRS UMR2000, Paris 75015, France
| | - Hugues Richard
- Sorbonne University, Faculty of Science, Institute of Biology Paris-Seine, Laboratory of Computational and Quantitative Biology, Paris, France; Robert Koch Institute, Berlin, Germany
| | - Gunnar Rätsch
- ETH Zurich, Department of Computer Science, Biomedical Informatics Group, Zurich, Switzerland; University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Lynn M Schriml
- University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, USA
| | | | | | - Leming Shi
- Center for Pharmacogenomics, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China; State Key Laboratory of Genetic Engineering (SKLGE) and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China
| | - Tieliu Shi
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Rania Siam
- University of Medicine and Health Sciences, St. Kitts, West Indies and American University in Cairo, Cairo, Egypt
| | - Le Huu Song
- 108 Military Central Hospital, Hanoi, Vietnam; Vietnamese-German Center for Medical Research (VG-CARE), Hanoi, Vietnam
| | | | - Denise Syndercombe Court
- Department of Analytical, Environmental and Forensic Sciences, King's College London, London, UK
| | | | - Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Klas I Udekwu
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden; SciLife EVP, Department of Aquatic Sciences Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Juan A Ugalde
- Millennium Initiative for Collaborative Research on Bacterial Resistance, Santiago, Chile; C+, Research Center in Technologies for Society, School of Engineering, Universidad del Desarrollo, Santiago, Chile
| | - Brandon Valentine
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Dimitar I Vassilev
- Faculty of Mathematics and Informatics, Sofia University "St. Kliment Ohridski," Sofia, Bulgaria
| | - Elena M Vayndorf
- Institute of Arctic Biology, University of Alaska, Fairbanks, Fairbanks, AK, USA
| | - Thirumalaisamy P Velavan
- Institute of Tropical Medicine, Univeristätsklinikum Tübingen, Tübingen, Germany; Faculty of Medicine, Duy Tan University, Da Nang, Vietnam
| | - Jun Wu
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | | | - Jifeng Zhu
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Sibo Zhu
- State Key Laboratory of Genetic Engineering (SKLGE) and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China; Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
| | - Christopher E Mason
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA; The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
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Jacobmeyer L, Stamm I, Semmler T, Ewers C. First report of NDM-1 in an Acinetobacter baumannii strain from a pet animal in Europe. J Glob Antimicrob Resist 2021; 26:128-129. [PMID: 34044179 DOI: 10.1016/j.jgar.2021.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/15/2021] [Accepted: 05/16/2021] [Indexed: 11/24/2022] Open
Affiliation(s)
- Lisa Jacobmeyer
- Institute of Hygiene and Infectious Diseases of Animals (IHIT), Giessen, Germany
| | | | | | - Christa Ewers
- Institute of Hygiene and Infectious Diseases of Animals (IHIT), Giessen, Germany.
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Wolf SA, Epping L, Andreotti S, Reinert K, Semmler T. SCORE: Smart Consensus Of RNA Expression-a consensus tool for detecting differentially expressed genes in bacteria. Bioinformatics 2021; 37:426-428. [PMID: 32717040 DOI: 10.1093/bioinformatics/btaa681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/11/2020] [Accepted: 07/24/2020] [Indexed: 11/13/2022] Open
Abstract
SUMMARY RNA-sequencing (RNA-Seq) is the current method of choice for studying bacterial transcriptomes. To date, many computational pipelines have been developed to predict differentially expressed genes from RNA-Seq data, but no gold-standard has been widely accepted. We present the Snakemake-based tool Smart Consensus Of RNA Expression (SCORE) which uses a consensus approach founded on a selection of well-established tools for differential gene expression analysis. This allows SCORE to increase the overall prediction accuracy and to merge varying results into a single, human-readable output. SCORE performs all steps for the analysis of bacterial RNA-Seq data, from read preprocessing to the overrepresentation analysis of significantly associated ontologies. Development of consensus approaches like SCORE will help to streamline future RNA-Seq workflows and will fundamentally contribute to the creation of new gold-standards for the analysis of these types of data. AVAILABILITY AND IMPLEMENTATION https://github.com/SiWolf/SCORE. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Silver A Wolf
- Microbial Genomics, Robert Koch Institute, Berlin 13353, Germany
| | - Lennard Epping
- Microbial Genomics, Robert Koch Institute, Berlin 13353, Germany
| | - Sandro Andreotti
- Department of Mathematics and Computer Science, Freie Universität, Berlin 14195, Germany
| | - Knut Reinert
- Department of Mathematics and Computer Science, Freie Universität, Berlin 14195, Germany
| | - Torsten Semmler
- Microbial Genomics, Robert Koch Institute, Berlin 13353, Germany
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Kauter A, Epping L, Ghazisaeedi F, Lübke-Becker A, Wolf SA, Kannapin D, Stoeckle SD, Semmler T, Günther S, Gehlen H, Walther B. Frequency, Local Dynamics, and Genomic Characteristics of ESBL-Producing Escherichia coli Isolated From Specimens of Hospitalized Horses. Front Microbiol 2021; 12:671676. [PMID: 33936023 PMCID: PMC8085565 DOI: 10.3389/fmicb.2021.671676] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 03/23/2021] [Indexed: 12/04/2022] Open
Abstract
Previous research identified veterinary clinics as hotspots with respect to accumulation and spread of multidrug resistant extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (EC). Therefore, promoting the prudent use of antibiotics to decrease selective pressure in that particular clinical environment is preferable to enhance biosecurity for animal patients and hospital staff. Accordingly, this study comparatively investigated the impact of two distinct perioperative antibiotic prophylaxis (PAP) regimens (short-term versus prolonged) on ESBL-EC carriage of horses subjected to colic surgery. While all horses received a combination of penicillin/gentamicin (P/G) as PAP, they were assigned to either the “single-shot group” (SSG) or the conventional “5-day group” (5DG). Fecal samples collected on arrival (t0), on the 3rd (t1) and on the 10th day after surgery (t2) were screened for ESBL-EC. All isolates were further investigated using whole genome sequences. In total, 81 of 98 horses met the inclusion criteria for this study. ESBL-EC identified in samples available at t0, t1 and t2 were 4.8% (SSG) and 9.7% (5DG), 37% (SSG) and 47.2% (5DG) as well as 55.6% (SSG) and 56.8% (5DG), respectively. Regardless of the P/G PAP regimen, horses were 9.12 times (95% CI 2.79–29.7) more likely to carry ESBL-EC at t1 compared to t0 (p < 0.001) and 15.64 times (95% CI 4.57–53.55) more likely to carry ESBL-EC at t2 compared to t0 (p < 0.001). ESBL-EC belonging to sequence type (ST) 10, ST86, ST641, and ST410 were the most prevalent lineages, with blaCTX–M–1 (60%) being the dominant ESBL gene. A close spatio-temporal relationship between isolates sharing a particular ST was revealed by genome analysis, strongly indicating local spread. Consequently, hospitalization itself has a strong impact on ESBL-EC isolation rates in horses, possibly masking differences between distinct PAP regimens. The results of this study reveal accumulation and spread of multi-drug resistant ESBL-EC among horses subjected to colic surgery with different P/G PAP regimens, challenging the local hygiene management system and work-place safety of veterinary staff. Moreover, the predominance of particular ESBL-EC lineages in clinics providing health care for horses needs further investigation.
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Affiliation(s)
- Anne Kauter
- Advanced Light and Electron Microscopy (ZBS-4), Robert Koch Institute, Berlin, Germany
| | - Lennard Epping
- Genome Sequencing and Genomic Epidemiology (MF2), Robert Koch Institute, Berlin, Germany
| | - Fereshteh Ghazisaeedi
- Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Antina Lübke-Becker
- Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Silver A Wolf
- Genome Sequencing and Genomic Epidemiology (MF2), Robert Koch Institute, Berlin, Germany
| | - Dania Kannapin
- Equine Clinic, Surgery and Radiology, Freie Universität Berlin, Berlin, Germany
| | - Sabita D Stoeckle
- Equine Clinic, Surgery and Radiology, Freie Universität Berlin, Berlin, Germany
| | - Torsten Semmler
- Genome Sequencing and Genomic Epidemiology (MF2), Robert Koch Institute, Berlin, Germany
| | | | - Heidrun Gehlen
- Equine Clinic, Surgery and Radiology, Freie Universität Berlin, Berlin, Germany
| | - Birgit Walther
- Advanced Light and Electron Microscopy (ZBS-4), Robert Koch Institute, Berlin, Germany
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Ewers C, de Jong A, Prenger-Berninghoff E, El Garch F, Leidner U, Tiwari SK, Semmler T. Genomic Diversity and Virulence Potential of ESBL- and AmpC-β-Lactamase-Producing Escherichia coli Strains From Healthy Food Animals Across Europe. Front Microbiol 2021; 12:626774. [PMID: 33868190 PMCID: PMC8047082 DOI: 10.3389/fmicb.2021.626774] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 03/02/2021] [Indexed: 01/07/2023] Open
Abstract
The role of livestock animals as a putative source of ESBL/pAmpC E. coli for humans is a central issue of research. In a large-scale pan-European surveillance, 2,993 commensal Escherichia spp. isolates were recovered from randomly collected fecal samples of healthy cattle, pigs and chickens in various abattoirs. One-hundred Escherichia spp. isolates (0.5% from cattle, 1.3% pigs, 8.0% chickens) fulfilled the criteria for cefotaxime and ceftazidime non-wildtype (EUCAST). In silico screening of WGS data of 99 isolates (98 E. coli and 1 E. fergusonii) revealed blaSHV–12 (32.3%), blaCTX–M–1 (24.2%), and blaCMY–2 (22.2%) as predominant ESBL/pAmpC types. Other types were blaSHV–2 (1.0%), blaCTX–M–2/–14/–15 (1.0/6.1/1.0%), and blaTEM–52 (5.1%). Six isolates revealed AmpC-promoter mutations (position −42 (C > T) and one carried mcr-1. The majority (91.3%) of ESBL/pAmpC genes were located on plasmids. SHV-12 was mainly (50%) encoded on IncI1α plasmids (pST-3/-26/-95), followed by IncX3 (12.5%) and IncK2 (3.1%). The blaTEM–52 genes were located on IncI1α-pST-36 (60%) and IncX1 plasmids (20%). The dominant plasmid lineage among CTX-M-1 isolates was IncI1α (pST-3/-295/-317) (87.5%), followed by IncN-pST-1 (8.3%). CMY-2 was mostly identified on IncI1α (pST-12/-2) (54.5%) and IncK2 (31.8%) plasmids. Several plasmids revealed high similarity to published plasmids from human and animal Enterobacteriaceae. The isolates were assigned to phylogroups A/C (34.7/7.1%), B1 (27.6%), B2 (3.1%), D/F (9.2/10.2%), E (5.1%), and to E. clades (3.0%). With 51 known and 2 novel MLST types, a wide variety of STs was found, including STs previously observed in human isolates (ST10/38/117/131/648). ESBL/AmpC types or STs were rarely correlated with the geographic origin of the isolates or animal species. Virulence gene typing identified extraintestinal pathogenic E. coli (ExPEC; 2.0%), avian pathogenic E. coli (APEC; 51.5%), and atypical enteropathogenic E. coli (EPEC; 6.1%). In conclusion, the high diversity of STs and phylogenetic groups provides hardly any hint for clonal spread of single lineages but hints toward the dissemination of cephalosporin resistance genes in livestock via distinct, globally successful plasmid lineages. Even though a number of isolates could not be assigned to a distinct pathotype, our finding of combined multidrug-resistance and virulence in this facultative pathogen should be considered an additional threat to public health.
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Affiliation(s)
- Christa Ewers
- Department of Veterinary Medicine, Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Giessen, Germany
| | - Anno de Jong
- European Antimicrobial Susceptibility Surveillance in Animals (EASSA) Study Group, Executive Animal Health Study Center (CEESA), Brussels, Belgium
| | - Ellen Prenger-Berninghoff
- Department of Veterinary Medicine, Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Giessen, Germany
| | - Farid El Garch
- European Antimicrobial Susceptibility Surveillance in Animals (EASSA) Study Group, Executive Animal Health Study Center (CEESA), Brussels, Belgium
| | - Ursula Leidner
- Department of Veterinary Medicine, Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Giessen, Germany
| | - Sumeet K Tiwari
- NG1 Microbial Genomics, Robert Koch Institute, Berlin, Germany
| | - Torsten Semmler
- NG1 Microbial Genomics, Robert Koch Institute, Berlin, Germany
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Abstract
The zoonotic pathogen Campylobacter is the leading cause for bacterial foodborne infections in humans. Campylobacters are most commonly transmitted via the consumption of undercooked poultry meat or raw milk products. The decreasing costs of whole genome sequencing enabled large genome-based analyses of the evolution and population structure of this pathogen, as well as the development of novel high-throughput molecular typing methods. Here, we review the evolutionary development and the population diversity of the two most clinically relevant Campylobacter species; C. jejuni and C. coli. The state-of-the-art phylogenetic studies showed clustering of C. jejuni lineages into host specialists and generalists with coexisting lifestyles in chicken and livestock-associated hosts, as well as the separation of C. coli isolates of riparian origin (waterfowl, water) from C. coli isolated from clinical and farm-related samples. We will give an overview of recombination between both species and the potential impact of horizontal gene transfer on host adaptation in Campylobacter. Additionally, this review briefly places the current knowledge of the population structure of other Campylobacter species such as C. lari, C. concisus and C. upsaliensis into perspective. We also provide an overview of how molecular typing methods such as multilocus sequence typing (MLST) and whole genome MLST have been used to detect and trace Campylobacter outbreaks along the food chain.
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Affiliation(s)
- Lennard Epping
- Microbial Genomics, Robert Koch Institute, Nordufer 20, 13353, Berlin, Germany
| | | | - Torsten Semmler
- Microbial Genomics, Robert Koch Institute, Nordufer 20, 13353, Berlin, Germany.
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Johanns VC, Epping L, Semmler T, Ghazisaeedi F, Lübke-Becker A, Pfeifer Y, Eichhorn I, Merle R, Bethe A, Walther B, Wieler LH. High-Zinc Supplementation of Weaned Piglets Affects Frequencies of Virulence and Bacteriocin Associated Genes Among Intestinal Escherichia coli Populations. Front Vet Sci 2020; 7:614513. [PMID: 33392299 PMCID: PMC7772137 DOI: 10.3389/fvets.2020.614513] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 11/20/2020] [Indexed: 12/22/2022] Open
Abstract
To prevent economic losses due to post-weaning diarrhea (PWD) in industrial pig production, zinc (Zn) feed additives have been widely used, especially since awareness has risen that the regular application of antibiotics promotes buildup of antimicrobial resistance in both commensal and pathogenic bacteria. In a previous study on 179 Escherichia coli collected from piglets sacrificed at the end of a Zn feeding trial, including isolates obtained from animals of a high-zinc fed group (HZG) and a corresponding control group (CG), we found that the isolate collection exhibited three different levels of tolerance toward zinc, i.e., the minimal inhibitory concentration (MIC) detected was 128, followed by 256 and 512 μg/ml ZnCl2. We further provided evidence that enhanced zinc tolerance in porcine intestinal E. coli populations is clearly linked to excessive zinc feeding. Here we provide insights about the genomic make-up and phylogenetic background of these 179 E. coli genomes. Bayesian analysis of the population structure (BAPS) revealed a lack of association between the actual zinc tolerance level and a particular phylogenetic E. coli cluster or even branch for both, isolates belonging to the HZG and CG. In addition, detection rates for genes and operons associated with virulence (VAG) and bacteriocins (BAG) were lower in isolates originating from the HZG (41 vs. 65% and 22 vs. 35%, p < 0.001 and p = 0.002, resp.). Strikingly, E. coli harboring genes defining distinct pathotypes associated with intestinal disease, i.e., enterotoxigenic, enteropathogenic, and Shiga toxin-producing E. coli (ETEC, EPEC, and STEC) constituted 1% of the isolates belonging to the HZG but 14% of those from the CG. Notably, these pathotypes were positively associated with enhanced zinc tolerance (512 μg/ml ZnCl2 MIC, p < 0.001). Taken together, zinc excess seems to influence carriage rates of VAGs and BAGs in porcine intestinal E. coli populations, and high-zinc feeding is negatively correlated with enteral pathotype occurrences, which might explain earlier observations concerning the relative increase of Enterobacterales considering the overall intestinal microbiota of piglets during zinc feeding trials while PWD rates have decreased.
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Affiliation(s)
- Vanessa C. Johanns
- Advanced Light and Electron Microscopy (ZBS-4), Robert Koch Institute, Berlin, Germany
| | - Lennard Epping
- Microbial Genomics (NG1), Robert Koch Institute, Berlin, Germany
| | - Torsten Semmler
- Microbial Genomics (NG1), Robert Koch Institute, Berlin, Germany
| | - Fereshteh Ghazisaeedi
- Center for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Antina Lübke-Becker
- Center for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Yvonne Pfeifer
- Nosocomial Pathogens and Antibiotic Resistance (FG13), Robert Koch Institute, Wernigerode, Germany
| | - Inga Eichhorn
- Center for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Roswitha Merle
- Institute for Veterinary Epidemiology and Biostatistics, Freie Universität Berlin, Berlin, Germany
| | - Astrid Bethe
- Center for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Birgit Walther
- Advanced Light and Electron Microscopy (ZBS-4), Robert Koch Institute, Berlin, Germany
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Mühldorfer K, Szentiks CA, Wibbelt G, van der Linden M, Ewers C, Semmler T, Akimkin V, Blom J, Rau J, Eisenberg T. Streptococcus catagoni sp. nov., isolated from the respiratory tract of diseased Chacoan peccaries ( Catagonus wagneri). Int J Syst Evol Microbiol 2020; 70:5734-5739. [PMID: 32941130 DOI: 10.1099/ijsem.0.004471] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Novel catalase-negative, Gram-stain-positive, beta-haemolytic, coccus-shaped organisms were isolated from Chacoan peccaries that died from respiratory disease. The initial API 20 Strep profiles suggested Streptococcus agalactiae with acceptable identification scores, but the 16S rRNA gene similarity (1548 bp) to available sequences of streptococci was below 98 %. Next taxa of the genus Streptococcus, displaying highest similarities to the strains from this study, were S. bovimastitidis NZ1587T (97.5 %), S. iniae ATCC 29178T (97.5 %), S. hongkongensis HKU30T (97.4 %), S. parauberis DSM 6631T (97.1 %), S. penaeicida CAIM 1838T (97.1 %), S. pseudoporcinus DSM 18513T (97.0 %), S. didelphis DSM 15616T (96.6 %), S. ictaluri 707-05T (96.6 %), S. uberis JCM 5709T (96.5 %) and S. porcinus NCTC 10999T (96.4 %). All other Streptococcus species had sequence similarities of below 96.4 %. A sodA gene as well as whole genome-based core genome phylogeny of three representative strains and 145 available Streptococcus genomes confirmed the unique taxonomic position. Interstrain average nucleotide identity (ANI) and amino acid identity (AAI) values were high (ANI >96 %; AAI 100%), but for other streptococci clearly below the proposed species boundary of 95-96 % (ANI <75 %; AAI <83 %). Results were confirmed by genome-to-genome distance calculations. Pairwise digital DNA-DNA hybridization estimates were high (>90 %) between the novel strains, but well below the species boundary of 70 % for closely related Streptococcus type strains (23.5-19.7 %). Phenotypic properties as obtained from extended biochemical profiles and MALDI-TOF mass spectrometry supported the outstanding rank. Based on the presented molecular and physiological data of the six strains, we propose a novel taxon for which we suggest the name Streptococcus catagoni sp. nov. with the type strain 99-1/2017T (=DSM 110457T=CCUG 74072T) and five reference strains.
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Affiliation(s)
- Kristin Mühldorfer
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Claudia A Szentiks
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Gudrun Wibbelt
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Mark van der Linden
- German National Reference Center for Streptococci, Department of Medical Microbiology, University Hospital RWTH Aachen, Aachen, Germany
| | - Christa Ewers
- Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Giessen, Germany
| | - Torsten Semmler
- NG1 Microbial Genomics, Robert Koch Institute, Berlin, Germany
| | - Valerij Akimkin
- Chemical and Veterinary Analysis Agency Stuttgart, Fellbach, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Jörg Rau
- Chemical and Veterinary Analysis Agency Stuttgart, Fellbach, Germany
| | - Tobias Eisenberg
- Hessian State Laboratory, Giessen, Germany.,Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Giessen, Germany
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Neumann B, Bender JK, Maier BF, Wittig A, Fuchs S, Brockmann D, Semmler T, Einsele H, Kraus S, Wieler LH, Vogel U, Werner G. Comprehensive integrated NGS-based surveillance and contact-network modeling unravels transmission dynamics of vancomycin-resistant enterococci in a high-risk population within a tertiary care hospital. PLoS One 2020; 15:e0235160. [PMID: 32579600 PMCID: PMC7314025 DOI: 10.1371/journal.pone.0235160] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 06/09/2020] [Indexed: 02/07/2023] Open
Abstract
Vancomycin-resistant E. faecium (VRE) are an important cause of nosocomial infections, which are rapidly transmitted in hospitals. To identify possible transmission routes, we applied combined genomics and contact-network modeling to retrospectively evaluate routine VRE screening data generated by the infection control program of a hemato-oncology unit. Over 1 year, a total of 111 VRE isolates from 111 patients were collected by anal swabs in a tertiary care hospital in Southern Germany. All isolated VRE were whole-genome sequenced, followed by different in-depth bioinformatics analyses including genotyping and determination of phylogenetic relations, aiming to evaluate a standardized workflow. Patient movement data were used to overlay sequencing data to infer transmission events and strain dynamics over time. A predominant clone harboring vanB and exhibiting genotype ST117/CT469 (n = 67) was identified. Our comprehensive combined analyses suggested intra-hospital spread, especially of clone ST117/CT469, despite of extensive screening, single room placement, and contact isolation. A new interactive tool to visualize these complex data was designed. Furthermore, a patient-contact network-modeling approach was developed, which indicates both the periodic import of the clone into the hospital and its spread within the hospital due to patient movements. The analyzed spread of VRE was most likely due to placement of patients in the same room prior to positivity of screening. We successfully demonstrated the added value for this combined strategy to extract well-founded knowledge from interdisciplinary data sources. The combination of patient-contact modeling and high-resolution typing unraveled the transmission dynamics within the hospital department and, additionally, a constant VRE influx over time.
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Affiliation(s)
- Bernd Neumann
- Division of Nosocomial Pathogens and Antibiotic Resistance, Robert Koch Institute, Wernigerode, Germany
- * E-mail:
| | - Jennifer K. Bender
- Division of Nosocomial Pathogens and Antibiotic Resistance, Robert Koch Institute, Wernigerode, Germany
| | - Benjamin F. Maier
- Computational Epidemiology, Robert Koch Institute, Berlin, Germany
- Department of Physics, Humboldt University of Berlin, Berlin, Germany
| | - Alice Wittig
- Computational Epidemiology, Robert Koch Institute, Berlin, Germany
- Institute for Theoretical Biology, Humboldt University of Berlin, Berlin, Germany
| | - Stephan Fuchs
- Division of Nosocomial Pathogens and Antibiotic Resistance, Robert Koch Institute, Wernigerode, Germany
| | - Dirk Brockmann
- Computational Epidemiology, Robert Koch Institute, Berlin, Germany
- Institute for Theoretical Biology, Humboldt University of Berlin, Berlin, Germany
| | | | - Hermann Einsele
- Department of Internal Medicine II, University Hospital Würzburg, Wüzburg, Germany
| | - Sabrina Kraus
- Department of Internal Medicine II, University Hospital Würzburg, Wüzburg, Germany
| | | | - Ulrich Vogel
- Institute for Hygiene and Microbiology, Julius-Maximilians University Würzburg, Würzburg, Germany
| | - Guido Werner
- Division of Nosocomial Pathogens and Antibiotic Resistance, Robert Koch Institute, Wernigerode, Germany
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Palmer R, Fleming GTA, Glaeser S, Semmler T, Flamm A, Ewers C, Kämpfer P, Budich O, Berrow S, O'Brien J, Siebert U, Collins E, Ruttledge M, Eisenberg T. Marine mammals are natural hosts of Oceanivirga salmonicida, a bacterial pathogen of Atlantic salmon. Dis Aquat Organ 2020; 139:161-174. [PMID: 32406871 DOI: 10.3354/dao03478] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
During 1992 and 1993, a bacterial disease occurred in a seawater Atlantic salmon Salmo salar farm, causing serious mortalities. The causative agent was subsequently named as Oceanivirga salmonicida, a member of the Leptotrichiaceae. Searches of 16S rRNA gene sequence databases have shown sequence similarities between O. salmonicida and uncultured bacterial clones from the digestive tracts of marine mammals. In the current study, oral samples were taken from stranded dolphins (common dolphin Delphinus delphis, striped dolphin Stenella coeruleoalba) and healthy harbour seals Phoca vitulina. A bacterium with growth characteristics consistent with O. salmonicida was isolated from a common dolphin. The isolate was confirmed as O. salmonicida, by comparisons to the type strain, using 16S rRNA gene, gyrB, groEL, and recA sequence analyses, average nucleotide identity analysis, and MALDI-TOF mass spectrometry. Metagenomic analysis indicated that the genus Oceanivirga represented a significant component of the oral bacterial microbiomes of the dolphins and seals. However, sequences consistent with O. salmonicida were only found in the dolphin samples. Analyses of marine mammal microbiome studies in the NCBI databases showed sequences consistent with O. salmonicida from the common dolphin, striped dolphin, bottlenose dolphin Tursiops truncatus, humpback whale Megaptera novaeangliae, and harbour seal. Sequences from marine environmental studies in the NCBI databases showed no sequences consistent with O. salmonicida. The findings suggest that several species of marine mammals are natural hosts of O. salmonicida.
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Affiliation(s)
- Roy Palmer
- Discipline of Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway H91TK33, Ireland
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Eisenberg T, Heydel C, Prenger-Berninghoff E, Fawzy A, Kling U, Akimkin V, Semmler T, Mühldorfer K, Kämpfer P, Blom J, Ewers C. Streptobacillus canis sp. nov. isolated from a dog. Int J Syst Evol Microbiol 2020; 70:2648-2656. [PMID: 32209168 DOI: 10.1099/ijsem.0.004086] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
From a phlegmon in a dog an aerobic and facultatively anaerobic, indole-, oxidase- and catalase-negative, non-motile bacterium was isolated in 2019 in Germany that stained Gram-negative and showed a pleomorphic, rod-shaped, non-spore-forming appearance. Based on the results of 16S rRNA gene sequence analyses, strain IHIT1603-19T was assigned to the genus Streptobacillus with sequence similarities of 98.6, 98.0, 97.9, 97.1 and 94.4 % to the type strains of Streptobacillus felis, Streptobacillus notomytis, Streptobacillus ratti, Streptobacillus moniliformis and Streptobacillus hongkongensis, respectively. Strain IHIT1603-19T could also clearly be differentiated from other Streptobacillus species by rpoB, groEL and recA gene, nucleotide and amino acid sequence analyses as well as by core genome phylogeny. Regarding DNA-DNA relatedness, strain IHIT1603-19T demonstrated an average nucleotide identity of 83.00 and 82.28 % compared to S. felis 131000547T and S. moniliformis DSM 12112T, respectively. Chemotaxonomic and physiological data of strain IHIT1603-19T were in congruence with other closely related members of the family Leptotrichiaceae, represented by highly similar enzyme profiles and fatty acid patterns. MALDI-TOF MS analysis also proved suitable in unequivocally discriminating strain IHIT1603-19T from all currently described taxa of the genus Streptobacillus. On the basis of these data, we propose the novel species Streptobacillus canis sp. nov. with the type strain IHIT1603-19T (=DSM 110501T=CCUG 74118T=CIP 111795T). The G+C content of the DNA of the type strain is 26.6 mol%, genome size is 1.60 Mbp.
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Affiliation(s)
- Tobias Eisenberg
- Institute of Hygiene and Infectious Diseases of Animals, Justus-Liebig-University Giessen, 35392 Giessen, Germany.,Hessian State Laboratory, 35392 Giessen, Germany
| | - Carsten Heydel
- Institute of Hygiene and Infectious Diseases of Animals, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Ellen Prenger-Berninghoff
- Institute of Hygiene and Infectious Diseases of Animals, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Ahmad Fawzy
- Cairo University, Faculty of Veterinary Medicine, Department of Medicine and Infectious Diseases, Giza Square 12211, Egypt.,Hessian State Laboratory, 35392 Giessen, Germany
| | - Ulrike Kling
- Hessian State Laboratory, 35392 Giessen, Germany
| | - Valerij Akimkin
- Chemical and Veterinary Investigatory Office Stuttgart, 70702 Fellbach, Germany
| | - Torsten Semmler
- Robert Koch Institute, Microbial Genomics, 13353 Berlin, Germany
| | - Kristin Mühldorfer
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, 10315 Berlin, Germany
| | - Peter Kämpfer
- Institute of Applied Microbiology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Christa Ewers
- Institute of Hygiene and Infectious Diseases of Animals, Justus-Liebig-University Giessen, 35392 Giessen, Germany
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Golz JC, Epping L, Knüver MT, Borowiak M, Hartkopf F, Deneke C, Malorny B, Semmler T, Stingl K. Whole genome sequencing reveals extended natural transformation in Campylobacter impacting diagnostics and the pathogens adaptive potential. Sci Rep 2020; 10:3686. [PMID: 32111893 PMCID: PMC7048796 DOI: 10.1038/s41598-020-60320-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 02/05/2020] [Indexed: 11/09/2022] Open
Abstract
Campylobacter is the major bacterial agent of human gastroenteritis worldwide and represents a crucial global public health burden. Species differentiation of C. jejuni and C. coli and phylogenetic analysis is challenged by inter-species horizontal gene transfer. Routine real-time PCR on more than 4000 C. jejuni and C. coli field strains identified isolates with ambiguous PCR results for species differentiation, in particular, from the isolation source eggs. K-mer analysis of whole genome sequencing data indicated the presence of C. coli hybrid strains with huge amounts of C. jejuni introgression. Recombination events were distributed over the whole chromosome. MLST typing was impaired, since C. jejuni sequences were also found in six of the seven housekeeping genes. cgMLST suggested that the strains were phylogenetically unrelated. Intriguingly, the strains shared a stress response set of C. jejuni variant genes, with proposed roles in oxidative, osmotic and general stress defence, chromosome maintenance and repair, membrane transport, cell wall and capsular biosynthesis and chemotaxis. The results have practical impact on routine typing and on the understanding of the functional adaption to harsh environments, enabling successful spreading and persistence of Campylobacter.
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Affiliation(s)
- Julia C Golz
- German Federal Institute for Risk Assessment, Department of Biological Safety, National Reference Laboratory for Campylobacter, Berlin, Germany
| | - Lennard Epping
- Robert Koch Institute, Microbial Genomics, Berlin, Germany
| | - Marie-Theres Knüver
- German Federal Institute for Risk Assessment, Department of Biological Safety, National Reference Laboratory for Campylobacter, Berlin, Germany
| | - Maria Borowiak
- German Federal Institute for Risk Assessment, Department of Biological Safety, Study Centre for Genome Sequencing and Analysis, Berlin, Germany
| | - Felix Hartkopf
- Robert Koch Institute, Microbial Genomics, Berlin, Germany
| | - Carlus Deneke
- German Federal Institute for Risk Assessment, Department of Biological Safety, Study Centre for Genome Sequencing and Analysis, Berlin, Germany
| | - Burkhard Malorny
- German Federal Institute for Risk Assessment, Department of Biological Safety, Study Centre for Genome Sequencing and Analysis, Berlin, Germany
| | | | - Kerstin Stingl
- German Federal Institute for Risk Assessment, Department of Biological Safety, National Reference Laboratory for Campylobacter, Berlin, Germany.
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Epping L, Golz JC, Knüver MT, Huber C, Thürmer A, Wieler LH, Stingl K, Semmler T. Comparison of different technologies for the decipherment of the whole genome sequence of Campylobacter jejuni BfR-CA-14430. Gut Pathog 2019; 11:59. [PMID: 31890037 PMCID: PMC6913002 DOI: 10.1186/s13099-019-0340-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 12/05/2019] [Indexed: 01/31/2023] Open
Abstract
Background Campylobacter jejuni is a zoonotic pathogen that infects the human gut through the food chain mainly by consumption of undercooked chicken meat, raw chicken cross-contaminated ready-to-eat food or by raw milk. In the last decades, C. jejuni has increasingly become the most common bacterial cause for food-born infections in high income countries, costing public health systems billions of euros each year. Currently, different whole genome sequencing techniques such as short-read bridge amplification and long-read single molecule real-time sequencing techniques are applied for in-depth analysis of bacterial species, in particular, Illumina MiSeq, PacBio and MinION. Results In this study, we analyzed a recently isolated C. jejuni strain from chicken meat by short- and long-read data from Illumina, PacBio and MinION sequencing technologies. For comparability, this strain is used in the German PAC-CAMPY research consortium in several studies, including phenotypic analysis of biofilm formation, natural transformation and in vivo colonization models. The complete assembled genome sequence most likely consists of a chromosome of 1,645,980 bp covering 1665 coding sequences as well as a plasmid sequence with 41,772 bp that encodes for 46 genes. Multilocus sequence typing revealed that the strain belongs to the clonal complex CC-21 (ST-44) which is known to be involved in C. jejuni human infections, including outbreaks. Furthermore, we discovered resistance determinants and a point mutation in the DNA gyrase (gyrA) that render the bacterium resistant against ampicillin, tetracycline and (fluoro-)quinolones. Conclusion The comparison of Illumina MiSeq, PacBio and MinION sequencing and analyses with different assembly tools enabled us to reconstruct a complete chromosome as well as a circular plasmid sequence of the C. jejuni strain BfR-CA-14430. Illumina short-read sequencing in combination with either PacBio or MinION can substantially improve the quality of the complete chromosome and epichromosomal elements on the level of mismatches and insertions/deletions, depending on the assembly program used.
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Affiliation(s)
- Lennard Epping
- 1NG1-Microbial Genomics, Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany
| | - Julia C Golz
- 2National Reference Laboratory for Campylobacter, Department of Biological Safety, Federal Institute for Risk Assessment, Berlin, Germany
| | - Marie-Theres Knüver
- 2National Reference Laboratory for Campylobacter, Department of Biological Safety, Federal Institute for Risk Assessment, Berlin, Germany
| | - Charlotte Huber
- 3Advanced Light and Electron Microscopy, Robert Koch Institute, Berlin, Germany
| | - Andrea Thürmer
- 4Methodology and Research Infrastructure, Robert Koch Institute, Berlin, Germany
| | - Lothar H Wieler
- 4Methodology and Research Infrastructure, Robert Koch Institute, Berlin, Germany
| | - Kerstin Stingl
- 2National Reference Laboratory for Campylobacter, Department of Biological Safety, Federal Institute for Risk Assessment, Berlin, Germany
| | - Torsten Semmler
- 1NG1-Microbial Genomics, Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany
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Hussain A, Shaik S, Ranjan A, Suresh A, Sarker N, Semmler T, Wieler LH, Alam M, Watanabe H, Chakravortty D, Ahmed N. Genomic and Functional Characterization of Poultry Escherichia coli From India Revealed Diverse Extended-Spectrum β-Lactamase-Producing Lineages With Shared Virulence Profiles. Front Microbiol 2019; 10:2766. [PMID: 31849903 PMCID: PMC6901389 DOI: 10.3389/fmicb.2019.02766] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 11/13/2019] [Indexed: 01/16/2023] Open
Abstract
Extended-spectrum β-lactamases (ESBLs) form the most important resistance determinants prevalent worldwide. Data on ESBL-producing Escherichia coli from poultry and livestock are scarce in India. We present data on the functional and genomic characterization of ESBL-producing E. coli obtained from poultry in India. The whole genome sequences of 28 ESBL-producing E. coli were analyzed comprising of 12 broiler chicken E. coli isolates, 11 free-range chicken E. coli isolates, and 5 human extraintestinal pathogenic E. coli. All of the 28 ESBL-producing E. coli isolates were tested for antibiotic susceptibilities, in vitro conjugation, and virulence-associated phenotypic characteristics. A total of 13 sequence types were identified from the poultry E. coli, which included globally successful sequence types such as ST117 (9%), ST131 (4.3%), and ST10 (4.3%). The most common ESBL gene detected in poultry E. coli genomes was blaCTX-M-15 (17%). Also, FIB (73%) and FII (73%) were the most common plasmid replicons identified. Conjugation experiments demonstrated 54 (7/13), 30 (3/10), and 40% (2/5) of broiler, free-range, and human ExPEC E. coli to be able to transfer their ESBL genes, respectively. The in vitro virulence-associated phenotypic tests revealed the broiler, free-range, and human ExPEC isolates to be comparable in biofilm formation, resistance to serum bactericidal activity, adherence, and invasion capabilities. Our overall results showed prevalence of virulence phenotypes among the diverse ESBL-producing E. coli from poultry; while certain E. coli clones from broiler-poultry may indeed have the potential to cause infection in humans.
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Affiliation(s)
- Arif Hussain
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India.,International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Sabiha Shaik
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, India
| | - Amit Ranjan
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, India
| | - Arya Suresh
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, India
| | - Nishat Sarker
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Torsten Semmler
- Methodology and Research Infrastructure, Robert Koch Institute, Berlin, Germany
| | - Lothar H Wieler
- Methodology and Research Infrastructure, Robert Koch Institute, Berlin, Germany
| | - Munirul Alam
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Haruo Watanabe
- International University of Health and Welfare, Tokyo, Japan
| | - Dipshikha Chakravortty
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Niyaz Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh.,Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, India
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47
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Johanns VC, Ghazisaeedi F, Epping L, Semmler T, Lübke-Becker A, Pfeifer Y, Bethe A, Eichhorn I, Merle R, Walther B, Wieler LH. Effects of a Four-Week High-Dosage Zinc Oxide Supplemented Diet on Commensal Escherichia coli of Weaned Pigs. Front Microbiol 2019; 10:2734. [PMID: 31849886 PMCID: PMC6892955 DOI: 10.3389/fmicb.2019.02734] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 11/11/2019] [Indexed: 12/11/2022] Open
Abstract
Strategies to reduce economic losses associated with post-weaning diarrhea in pig farming include high-level dietary zinc oxide supplementation. However, excessive usage of zinc oxide in the pig production sector was found to be associated with accumulation of multidrug resistant bacteria in these animals, presenting an environmental burden through contaminated manure. Here we report on zinc tolerance among a random selection of intestinal Escherichia coli comprising of different antibiotic resistance phenotypes and sampling sites isolated during a controlled feeding trial from 16 weaned piglets: In total, 179 isolates from "pigs fed with high zinc concentrations" (high zinc group, [HZG]: n = 99) and a corresponding "control group" ([CG]: n = 80) were investigated with regard to zinc tolerance, antimicrobial- and biocide susceptibilities by determining minimum inhibitory concentrations (MICs). In addition, in silico whole genome screening (WGSc) for antibiotic resistance genes (ARGs) as well as biocide- and heavy metal tolerance genes was performed using an in-house BLAST-based pipeline. Overall, porcine E. coli isolates showed three different ZnCl2 MICs: 128 μg/ml (HZG, 2%; CG, 6%), 256 μg/ml (HZG, 64%; CG, 91%) and 512 μg/ml ZnCl2 (HZG, 34%, CG, 3%), a unimodal distribution most likely reflecting natural differences in zinc tolerance associated with different genetic lineages. However, a selective impact of the zinc-rich supplemented diet seems to be reasonable, since the linear mixed regression model revealed a statistically significant association between "higher" ZnCl2 MICs and isolates representing the HZG as well as "lower ZnCl2 MICs" with isolates of the CG (p = 0.005). None of the zinc chloride MICs was associated with a particular antibiotic-, heavy metal- or biocide- tolerance/resistance phenotype. Isolates expressing the 512 μg/ml MIC were either positive for ARGs conferring resistance to aminoglycosides, tetracycline and sulfamethoxazole-trimethoprim, or harbored no ARGs at all. Moreover, WGSc revealed a ubiquitous presence of zinc homeostasis and - detoxification genes, including zitB, zntA, and pit. In conclusion, we provide evidence that zinc-rich supplementation of pig feed selects for more zinc tolerant E. coli, including isolates harboring ARGs and biocide- and heavy metal tolerance genes - a putative selective advantage considering substances and antibiotics currently used in industrial pork production systems.
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Affiliation(s)
- Vanessa C Johanns
- Advanced Light and Electron Microscopy (ZBS-4), Robert Koch Institute, Berlin, Germany
| | - Fereshteh Ghazisaeedi
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Freie Universität Berlin, Berlin, Germany
| | - Lennard Epping
- Microbial Genomics (NG1), Robert Koch Institute, Berlin, Germany
| | - Torsten Semmler
- Microbial Genomics (NG1), Robert Koch Institute, Berlin, Germany
| | - Antina Lübke-Becker
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Freie Universität Berlin, Berlin, Germany
| | - Yvonne Pfeifer
- Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode, Germany
| | - Astrid Bethe
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Freie Universität Berlin, Berlin, Germany
| | - Inga Eichhorn
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Freie Universität Berlin, Berlin, Germany
| | - Roswitha Merle
- Institute for Veterinary Epidemiology and Biostatistics, Freie Universität Berlin, Berlin, Germany
| | - Birgit Walther
- Advanced Light and Electron Microscopy (ZBS-4), Robert Koch Institute, Berlin, Germany
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48
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Kauter A, Epping L, Semmler T, Antao EM, Kannapin D, Stoeckle SD, Gehlen H, Lübke-Becker A, Günther S, Wieler LH, Walther B. The gut microbiome of horses: current research on equine enteral microbiota and future perspectives. Anim Microbiome 2019; 1:14. [PMID: 33499951 PMCID: PMC7807895 DOI: 10.1186/s42523-019-0013-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 09/09/2019] [Indexed: 12/26/2022] Open
Abstract
Understanding the complex interactions of microbial communities including bacteria, archaea, parasites, viruses and fungi of the gastrointestinal tract (GIT) associated with states of either health or disease is still an expanding research field in both, human and veterinary medicine. GIT disorders and their consequences are among the most important diseases of domesticated Equidae, but current gaps of knowledge hinder adequate progress with respect to disease prevention and microbiome-based interventions. Current literature on enteral microbiomes mirrors a vast data and knowledge imbalance, with only few studies tackling archaea, viruses and eukaryotes compared with those addressing the bacterial components.Until recently, culture-dependent methods were used for the identification and description of compositional changes of enteral microorganisms, limiting the outcome to cultivatable bacteria only. Today, next generation sequencing technologies provide access to the entirety of genes (microbiome) associated with the microorganisms of the equine GIT including the mass of uncultured microbiota, or "microbial dark matter".This review illustrates methods commonly used for enteral microbiome analysis in horses and summarizes key findings reached for bacteria, viruses and fungi so far. Moreover, reasonable possibilities to combine different explorative techniques are described. As a future perspective, knowledge expansion concerning beneficial compositions of microorganisms within the equine GIT creates novel possibilities for early disorder diagnostics as well as innovative therapeutic approaches. In addition, analysis of shotgun metagenomic data enables tracking of certain microorganisms beyond species barriers: transmission events of bacteria including pathogens and opportunists harboring antibiotic resistance factors between different horses but also between humans and horses will reach new levels of depth concerning strain-level distinctions.
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Affiliation(s)
- Anne Kauter
- Advanced Light and Electron Microscopy (ZBS-4), Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Lennard Epping
- Microbial Genomics (NG1), Robert Koch Institute, Berlin, Germany
| | - Torsten Semmler
- Microbial Genomics (NG1), Robert Koch Institute, Berlin, Germany
| | | | - Dania Kannapin
- Equine Clinic, Surgery and Radiology, Freie Universität Berlin, Berlin, Germany
| | - Sabita D Stoeckle
- Equine Clinic, Surgery and Radiology, Freie Universität Berlin, Berlin, Germany
| | - Heidrun Gehlen
- Equine Clinic, Surgery and Radiology, Freie Universität Berlin, Berlin, Germany
| | - Antina Lübke-Becker
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Freie Universität Berlin, Berlin, Germany
| | - Sebastian Günther
- Pharmaceutical Biology Institute of Pharmacy, Universität Greifswald, Greifswald, Germany
| | | | - Birgit Walther
- Advanced Light and Electron Microscopy (ZBS-4), Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany.
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49
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Ruangkiattikul N, Rys D, Abdissa K, Rohde M, Semmler T, Tegtmeyer PK, Kalinke U, Schwarz C, Lewin A, Goethe R. Type I interferon induced by TLR2-TLR4-MyD88-TRIF-IRF3 controls Mycobacterium abscessus subsp. abscessus persistence in murine macrophages via nitric oxide. Int J Med Microbiol 2019; 309:307-318. [PMID: 31178418 DOI: 10.1016/j.ijmm.2019.05.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 04/08/2019] [Accepted: 05/31/2019] [Indexed: 12/15/2022] Open
Abstract
Mycobacterium abscessus (MAB) is an emerging, rapidly growing non-tuberculous Mycobacterium causing therapy-resistant pulmonary disease especially in patients with cystic fibrosis (CF). Smooth and rough colony type MAB can be isolated from infected patients whereby rough colony type MAB are more often associated with severe disease. Disease severity is also associated with an alternated type I interferon (IFN-I) response of the MAB-infected patients. However the relevance of this response for the outcome of MAB infection is still unknown. In this study, we analyzed the IFNβ expression of murine macrophages infected with a MAB rough colony strain (MAB-R) isolated from a patient with progressive CF and compared it to macrophages infected with the MAB smooth colony type reference strain (MAB-S). We found that MAB-R infected macrophages expressed significantly more IFNβ mRNA and protein than MAB-S infected macrophages. Higher IFNβ induction by MAB-R was associated with higher TNF expression and intracellular killing while low IFNβ induction was associated with lower TNF expression and persistence of MAB-S. IFNβ induction was independent of the intracellular cGAS-STING recognition pathway. MAB appeared to be recognized extracellularly and induced IFNβ expression via TLR2-TLR4-MyD88-TRIF-IRF3 dependent pathways. By using macrophages lacking the IFN-I receptor we demonstrate that MAB induced IFN-I response essentially contributed to restricting MAB-R and MAB-S infections by activating macrophage Nos2 expression and nitric oxide production. Thus IFN-I seem to influence the intrinsic ability of macrophages to control MAB infections. As MAB persists over long time periods in susceptible patients, our findings suggest that virulence of MAB strains is promoted by an insufficient IFN-I response of the host.
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Affiliation(s)
| | - Doris Rys
- Institute for Microbiology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Ketema Abdissa
- Institute for Microbiology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Torsten Semmler
- NG1 Microbial Genomics, Robert Koch Institute, Berlin, Germany
| | - Pia-K Tegtmeyer
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, A Joint Venture Between The Helmholtz Centre for Infection Research, Braunschweig, and The Hannover Medical School, Hannover, Germany
| | - Ulrich Kalinke
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, A Joint Venture Between The Helmholtz Centre for Infection Research, Braunschweig, and The Hannover Medical School, Hannover, Germany
| | - Carsten Schwarz
- Department of Pediatric Pneumonology and Immunology, Division of Cystic Fibrosis, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Astrid Lewin
- FG16 Mycotic and Parasitic Agents and Mycobacteria, Robert Koch Institute, Berlin, Germany
| | - Ralph Goethe
- Institute for Microbiology, University of Veterinary Medicine Hannover, Hannover, Germany.
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50
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Klotz P, Jacobmeyer L, Stamm I, Leidner U, Pfeifer Y, Semmler T, Prenger-Berninghoff E, Ewers C. Carbapenem-resistant Acinetobacter baumannii ST294 harbouring the OXA-72 carbapenemase from a captive grey parrot. J Antimicrob Chemother 2019; 73:1098-1100. [PMID: 29309610 DOI: 10.1093/jac/dkx490] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Peter Klotz
- Institute of Hygiene and Infectious Diseases of Animals, Justus-Liebig-University Giessen, Giessen, Germany
| | - Lisa Jacobmeyer
- Institute of Hygiene and Infectious Diseases of Animals, Justus-Liebig-University Giessen, Giessen, Germany
| | - Ivonne Stamm
- Vet Med Labor GmbH, Division of IDEXX Laboratories, Ludwigsburg, Germany
| | - Ursula Leidner
- Institute of Hygiene and Infectious Diseases of Animals, Justus-Liebig-University Giessen, Giessen, Germany
| | - Yvonne Pfeifer
- FG13 Nosocomial Pathogens and Antibiotic Resistance, Robert Koch Institute, Wernigerode, Germany
| | - Torsten Semmler
- NG1 Microbial Genomics, Robert Koch Institute, Berlin, Germany
| | - Ellen Prenger-Berninghoff
- Institute of Hygiene and Infectious Diseases of Animals, Justus-Liebig-University Giessen, Giessen, Germany
| | - Christa Ewers
- Institute of Hygiene and Infectious Diseases of Animals, Justus-Liebig-University Giessen, Giessen, Germany
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