Publications by authors named "Rene S Hendriksen"

110 Publications

Extended-spectrum ß-lactamase-producing among humans, chickens and poultry environments in Abuja, Nigeria.

One Health Outlook 2020 27;2. Epub 2020 May 27.

Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina USA.

Background: Globally, chicken is known to be a reservoir for the spread of antimicrobial resistance genes to humans. In Nigeria, antimicrobial drugs are readily accessible for use in poultry production, either for preventive or therapeutic purposes. Extended-spectrum beta-lactamase-producing (ESBL-EC) are transmissible to humans because of their zoonotic potentials. People working very closely with chickens either on farms or markets are at greater risk. The aim of this study was to investigate the prevalence and zoonotic transmission of ESBL-EC among poultry-workers, chickens, and poultry environments in Abuja, Nigeria.

Methods: We conducted a cross-sectional study among workers, chickens and poultry environment in selected farms/chicken markets in Abuja. Stool, faecal, and environmental samples were collected from apparently healthy workers, chickens, and farm/market environments from December 2018 to April 2019. Data were collected electronically using an open data kit (ODK) installed on a Smartphone. Antimicrobial resistance was determined using broth micro-dilution methods against a panel of 14 antimicrobial agents. We carried out the phenotypic and genotypic characterization of the isolates. Data were analyzed by computing frequencies, proportions and spearman's correlation (ρ).

Results: Of 429 samples, 26.8% ( = 115) were positive for . Of the 115 isolates, 32.2% ( = 37) were confirmed ESBL producers by phenotypic characterization. Prevalence of ESBL-EC was highest among both poultry-workers (37.8%;  = 14) and chickens (37.8%; n = 14) followed by the environment (24.3%;  = 9). Both human and chicken isolates showed similar patterns of multidrug resistance to tested antimicrobials with a positive correlation (ρ = 0.91). Among ESBL producers, we observed the dissemination of CTX-M (10.8%;  = 4) genes. The coexistence of CTX-M-15 and TEM-1 genes was observed in 8.1% ( = 3) of the isolates, out of which (66.7%;  = 2) were chicken isolates from the farm, while a single human isolate was from the chicken market.

Conclusions: ESBL-EC isolates were prevalent amongst apparently healthy individuals, chickens and the poultry farm/market environment in Abuja. It is important to educate healthcare workers that people in proximity with poultry are a high-risk group for faecal carriage of ESBL-EC, hence pose a higher risk to the general population for the spread of antimicrobial resistance.
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http://dx.doi.org/10.1186/s42522-020-00014-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7993457PMC
May 2020

Genetic relatedness of multidrug resistant Escherichia coli isolated from humans, chickens and poultry environments.

Antimicrob Resist Infect Control 2021 Mar 23;10(1):58. Epub 2021 Mar 23.

Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA.

Background: Inappropriate use of antimicrobial agents in animal production has led to the development of antimicrobial resistance (AMR) in foodborne pathogens. Transmission of AMR foodborne pathogens from reservoirs, particularly chickens to the human population does occur. Recently, we reported that occupational exposure was a risk factor for multidrug-resistant (MDR) Escherichia coli (E. coli) among poultry-workers. Here we determined the prevalence and genetic relatedness among MDR E. coli isolated from poultry-workers, chickens, and poultry environments in Abuja, Nigeria. This study was conducted to address the gaps identified by the Nigerian AMR situation analysis.

Methods: We conducted a cross-sectional study among poultry-workers, chickens, and poultry farm/live bird market (LBM) environments. The isolates were tested phenotypically for their antimicrobial susceptibility profiles, genotypically characterized using whole-genome sequencing (WGS) and in silico multilocus sequence types (MLST). We conducted a phylogenetic single nucleotide polymorphism (SNPs) analysis to determine relatedness and clonality among the isolates.

Results: A total of 115 (26.8%) out of 429 samples were positive for E. coli. Of these, 110 isolates were viable for phenotypic and genotypic characterization. The selection comprised 47 (42.7%) isolates from poultry-workers, 36 (32.7%) from chickens, and 27 (24.5%) from poultry-farm or LBM environments. Overall, 101 (91.8%) of the isolates were MDR conferring resistance to at least three drug classes. High frequency of resistance was observed for tetracycline (n = 102; 92.7%), trimethoprim/sulfamethoxazole (n = 93; 84.5%), streptomycin (n = 87; 79.1%) and ampicillin (n = 88; 80%). Two plasmid-mediated colistin genes-mcr-1.1 harboured on IncX4 plasmids were detected in environmental isolates. The most prevalent sequence types (ST) were ST-155 (n = 8), ST-48 (n = 8) and ST-10 (n = 6). Two isolates of human and environmental sources with a SNPs difference of 6161 originating from the same farm shared a novel ST. The isolates had similar AMR genes and plasmid replicons.

Conclusion: MDR E.coli isolates were prevalent amongst poultry-workers, poultry, and the poultry farm/LBM environment. The emergence of MDR E. coli with novel ST in two isolates may be plasmid-mediated. Competent authorities should enforce AMR regulations to ensure prudent use of antimicrobials to limit the risk of transmission along the food chain.
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http://dx.doi.org/10.1186/s13756-021-00930-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7988975PMC
March 2021

New Brucella variant isolated from Croatian cattle.

BMC Vet Res 2021 Mar 20;17(1):126. Epub 2021 Mar 20.

Department of Bacteriology and Parasitology, Laboratory for Bacterial Zoonosis and Molecular Diagnostics of Bacterial Diseases, Croatian Veterinary Institute, Savska street 143, Zagreb, Croatia.

Background: A novel Brucella strain closely related to Brucella (B.) melitensis biovar (bv) 3 was found in Croatian cattle during testing within a brucellosis eradication programme.

Case Presentation: Standardised serological, brucellin skin test, bacteriological and molecular diagnostic screening for Brucella infection led to positive detection in one dairy cattle herd. Three isolates from that herd were identified to species level using the Bruce ladder method. Initially, two strains were typed as B. melitensis and one as B. abortus, but multiplex PCR based on IS711 and the Suis ladder showed that all of them to belong to B. melitensis, and the combination of whole-genome and multi-locus sequencing as well as Multi-Locus Variable numbers of tandem repeats Analysis (MLVA) highlighted a strong proximity within the phylogenetic branch of B. melitensis strains previously isolated from Croatia, Albania, Kosovo and Bosnia and Herzegovina. Two isolates were determined to be B. melitensis bv. 3, while the third showed a unique phylogenetic profile, growth profile on dyes and bacteriophage typing results. This isolate contained the 609-bp omp31 sequence, but not the 723-bp omp31 sequence present in the two isolates of B. melitensis bv. 3.

Conclusions: Identification of a novel Brucella variant in this geographic region is predictable given the historic endemicity of brucellosis. The emergence of a new variant may reflect a combination of high prevalence among domestic ruminants and humans as well as weak eradication strategies. The zoonotic potential, reservoirs and transmission pathways of this and other Brucella variants should be explored.
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http://dx.doi.org/10.1186/s12917-021-02833-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7981855PMC
March 2021

Salmonella enterica serovar Typhi H58 clone has been endemic in Zimbabwe from 2012 to 2019.

J Antimicrob Chemother 2021 Apr;76(5):1160-1167

Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa.

Background: Typhoid fever, caused by S. enterica ser. Typhi, continues to be a substantial health burden in developing countries. Little is known of the genotypic diversity of S. enterica ser. Typhi in Zimbabwe, but this is key for understanding the emergence and spread of this pathogen and devising interventions for its control.

Objectives: To report the molecular epidemiology of S. enterica ser. Typhi outbreak strains circulating from 2012 to 2019 in Zimbabwe, using comparative genomics.

Methods: A review of typhoid cases records from 2012 to 2019 in Zimbabwe was performed. The phylogenetic relationship of outbreak isolates from 2012 to 2019 and emergence of antibiotic resistance was investigated by whole-genome sequence analysis.

Results: A total 22 479 suspected typhoid cases, 760 confirmed cases were reported from 2012 to 2019 and 29 isolates were sequenced. The majority of the sequenced isolates were predicted to confer resistance to aminoglycosides, β-lactams, phenicols, sulphonamides, tetracycline and fluoroquinolones (including qnrS detection). The qnrS1 gene was associated with an IncN (subtype PST3) plasmid in 79% of the isolates. Whole-genome SNP analysis, SNP-based haplotyping and resistance determinant analysis showed that 93% of the isolates belonged to a single clade represented by multidrug-resistant H58 lineage I (4.3.1.1), with a maximum pair-wise distance of 22 SNPs.

Conclusions: This study has provided detailed genotypic characterization of the outbreak strain, identified as S. Typhi 4.3.1.1 (H58). The strain has reduced susceptibility to ciprofloxacin due to qnrS carried by an IncN (subtype PST3) plasmid resulting from ongoing evolution to full resistance.
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http://dx.doi.org/10.1093/jac/dkaa519DOI Listing
April 2021

A metagenomic glimpse into the gut of wild and domestic animals: Quantification of antimicrobial resistance and more.

PLoS One 2020 3;15(12):e0242987. Epub 2020 Dec 3.

Department of Microbiology, National Veterinary Research Institute, Puławy, Poland.

Antimicrobial resistance (AMR) in bacteria is a complex subject, why one need to look at this phenomenon from a wider and holistic perspective. The extensive use of the same antimicrobial classes in human and veterinary medicine as well as horticulture is one of the main drivers for the AMR selection. Here, we applied shotgun metagenomics to investigate the AMR epidemiology in several animal species including farm animals, which are often exposed to antimicrobial treatment opposed to an unique set of wild animals that seems not to be subjected to antimicrobial pressure. The comparison of the domestic and wild animals allowed to investigate the possible anthropogenic impact on AMR spread. Inclusion of animals with different feeding behaviors (carnivores, omnivores) enabled to further assess which AMR genes that thrives within the food chain. We tested fecal samples not only of intensively produced chickens, turkeys, and pigs, but also of wild animals such as wild boars, red foxes, and rodents. A multi-directional approach mapping obtained sequences to several databases provided insight into the occurrence of the different AMR genes. The method applied enabled also analysis of other factors that may influence AMR of intestinal microbiome such as diet. Our findings confirmed higher levels of AMR in farm animals than in wildlife. The results also revealed the potential of wildlife in the AMR dissemination. Particularly in red foxes, we found evidence of several AMR genes conferring resistance to critically important antimicrobials like quinolones and cephalosporins. In contrast, the lowest abundance of AMR was observed in rodents originating from natural environment with presumed limited exposure to antimicrobials. Shotgun metagenomics enabled us to demonstrate that discrepancies between AMR profiles found in the intestinal microbiome of various animals probably resulted from the different antimicrobial exposure, habitats, and behavior of the tested animal species.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0242987PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7714112PMC
February 2021

Metagenomics-Based Proficiency Test of Smoked Salmon Spiked with a Mock Community.

Microorganisms 2020 Nov 25;8(12). Epub 2020 Nov 25.

Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra 50, 40064 Ozzano dell'Emilia, Italy.

An inter-laboratory proficiency test was organized to assess the ability of participants to perform shotgun metagenomic sequencing of cold smoked salmon, experimentally spiked with a mock community composed of six bacteria, one parasite, one yeast, one DNA, and two RNA viruses. Each participant applied its in-house wet-lab workflow(s) to obtain the metagenomic dataset(s), which were then collected and analyzed using MG-RAST. A total of 27 datasets were analyzed. Sample pre-processing, DNA extraction protocol, library preparation kit, and sequencing platform, influenced the abundance of specific microorganisms of the mock community. Our results highlight that despite differences in wet-lab protocols, the reads corresponding to the mock community members spiked in the cold smoked salmon, were both detected and quantified in terms of relative abundance, in the metagenomic datasets, proving the suitability of shotgun metagenomic sequencing as a genomic tool to detect microorganisms belonging to different domains in the same food matrix. The implementation of standardized wet-lab protocols would highly facilitate the comparability of shotgun metagenomic sequencing dataset across laboratories and sectors. Moreover, there is a need for clearly defining a sequencing reads threshold, to consider pathogens as detected or undetected in a food sample.
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http://dx.doi.org/10.3390/microorganisms8121861DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7760972PMC
November 2020

Proficiency Testing of Metagenomics-Based Detection of Food-Borne Pathogens Using a Complex Artificial Sequencing Dataset.

Front Microbiol 2020 4;11:575377. Epub 2020 Nov 4.

Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany.

Metagenomics-based high-throughput sequencing (HTS) enables comprehensive detection of all species comprised in a sample with a single assay and is becoming a standard method for outbreak investigation. However, unlike real-time PCR or serological assays, HTS datasets generated for pathogen detection do not easily provide yes/no answers. Rather, results of the taxonomic read assignment need to be assessed by trained personnel to gain information thereof. Proficiency tests are important instruments of validation, harmonization, and standardization. Within the European Union funded project COMPARE [COllaborative Management Platform for detection and Analyses of (Re-) emerging and foodborne outbreaks in Europe], we conducted a proficiency test to scrutinize the ability to assess diagnostic metagenomics data. An artificial dataset resembling shotgun sequencing of RNA from a sample of contaminated trout was provided to 12 participants with the request to provide a table with per-read taxonomic assignments at species level and a report with a summary and assessment of their findings, considering different categories like pathogen, background, or contaminations. Analysis of the read assignment tables showed that the software used reliably classified the reads taxonomically overall. However, usage of incomplete reference databases or inappropriate data pre-processing caused difficulties. From the combination of the participants' reports with their read assignments, we conclude that, although most species were detected, a number of important taxa were not or not correctly categorized. This implies that knowledge of and awareness for potentially dangerous species and contaminations need to be improved, hence, capacity building for the interpretation of diagnostic metagenomics datasets is necessary.
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http://dx.doi.org/10.3389/fmicb.2020.575377DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7672002PMC
November 2020

Quantitative Microbial Risk Assessment Based on Whole Genome Sequencing Data: Case of .

Microorganisms 2020 Nov 11;8(11). Epub 2020 Nov 11.

Research Group for Genomic Epidemiology, Division for Global Surveillance, National Food Institute, Technical University of Denmark, 2800 Lyngby, Denmark.

The application of high-throughput DNA sequencing technologies (WGS) data remain an increasingly discussed but vastly unexplored resource in the public health domain of quantitative microbial risk assessment (QMRA). This is due to challenges including high dimensionality of WGS data and heterogeneity of microbial growth phenotype data. This study provides an innovative approach for modeling the impact of population heterogeneity in microbial phenotypic stress response and integrates this into predictive models inputting a high-dimensional WGS data for increased precision exposure assessment using an example of . Finite mixture models were used to distinguish the number of sub-populations for each of the stress phenotypes, acid, cold, salt and desiccation. Machine learning predictive models were selected from six algorithms by inputting WGS data to predict the sub-population membership of new strains with unknown stress response data. An example QMRA was conducted for cultured milk products using the strains of unknown stress phenotype to illustrate the significance of the findings of this study. Increased resistance to stress conditions leads to increased growth, the likelihood of higher exposure and probability of illness. Neglecting within-species genetic and phenotypic heterogeneity in microbial stress response may over or underestimate microbial exposure and eventual risk during QMRA.
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http://dx.doi.org/10.3390/microorganisms8111772DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7698238PMC
November 2020

Molecular Characteristics and Zoonotic Potential of Weltevreden From Cultured Shrimp and Tilapia in Vietnam and China.

Front Microbiol 2020 25;11:1985. Epub 2020 Aug 25.

Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.

Weltevreden is increasingly reported from aquatic environments, seafood, and patients in several Southeast Asian countries. Using genome-wide analysis, we characterized . Weltevreden isolated from cultured shrimp and tilapia from Vietnam and China to study their genetic characteristics and relatedness to clinical isolates of . Weltevreden ST-365. The phylogenetic analysis revealed up to 312 single-nucleotide polymorphism (SNP) difference between tilapia isolates, whereas isolates from shrimp were genetically more closely related. Epidemiologically unrelated isolates from Vietnam were closely related to isolates from China, e.g., 20 SNPs differences between strains 28V and 75C. In comparison with strains from other parts of the world, our environmental isolates predominantly clustered within the continental South Asia lineage, constituted mostly of strains from human stool with as low as seven SNPs difference, e.g., 30V versus Cont_ERR495254. All sequenced isolates were MLST type ST-365 and contained the major virulence-related genes encoded by the Pathogenicity Islands 1-5. Ten of the isolates harbored the FII(S) plasmid similar to the virulence genes-mediated plasmid pSPCV of Paratyphi C, and one isolate had the Q1 plasmid on the same contig with A/B, 2, and A resistance genes similar to the Q1 type, pNUC of Typhimurium. A pangenomic analysis yielded 7891 genes including a core genome of 4892 genes, with a closely related accessory genome content between clinical and environmental isolates (Benjamini > 0.05). In a search for differences that could explain the higher prevalence of . Weltevreden in aquatic samples, genomes were compared with those of other serovars. Weltevreden revealed specific regions harboring X (Fructose-1;6-bisphosphatase; class II), C (dTDP-4-dehydrorhamnose 3;5-epimerase), and B (PTS Mannitol-specific cryptic phosphotransferase enzyme IIA component) involved in carbohydrate biosynthesis pathways. Our study builds grounds for future experiments to determine genes or pathways that are essential when Weltevreden are in aquatic environments and microbial interactions providing survival advantages to Weltevreden in such environments.
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http://dx.doi.org/10.3389/fmicb.2020.01985DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7477899PMC
August 2020

Understanding and predicting ciprofloxacin minimum inhibitory concentration in Escherichia coli with machine learning.

Sci Rep 2020 09 14;10(1):15026. Epub 2020 Sep 14.

Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.

It is important that antibiotics prescriptions are based on antimicrobial susceptibility data to ensure effective treatment outcomes. The increasing availability of next-generation sequencing, bacterial whole genome sequencing (WGS) can facilitate a more reliable and faster alternative to traditional phenotyping for the detection and surveillance of AMR. This work proposes a machine learning approach that can predict the minimum inhibitory concentration (MIC) for a given antibiotic, here ciprofloxacin, on the basis of both genome-wide mutation profiles and profiles of acquired antimicrobial resistance genes. We analysed 704 Escherichia coli genomes combined with their respective MIC measurements for ciprofloxacin originating from different countries. The four most important predictors found by the model, mutations in gyrA residues Ser83 and Asp87, a mutation in parC residue Ser80 and presence of the qnrS1 gene, have been experimentally validated before. Using only these four predictors in a linear regression model, 65% and 93% of the test samples' MIC were correctly predicted within a two- and a four-fold dilution range, respectively. The presented work does not treat machine learning as a black box model concept, but also identifies the genomic features that determine susceptibility. The recent progress in WGS technology in combination with machine learning analysis approaches indicates that in the near future WGS of bacteria might become cheaper and faster than a MIC measurement.
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http://dx.doi.org/10.1038/s41598-020-71693-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7490380PMC
September 2020

Molecular epidemiology of Infantis in Europe: insights into the success of the bacterial host and its parasitic pESI-like megaplasmid.

Microb Genom 2020 05 9;6(5). Epub 2020 Apr 9.

Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", Rome, Italy.

Infantis is one of the five serovars most frequently causing human salmonellosis in Europe, mainly associated with poultry. A clone harbouring a conjugative plasmid of emerging . Infantis (pESI)-like megaplasmid, carrying multidrug resistant (MDR) and extended-spectrum beta-lactamases (ESBL) genes, has spread in the Italian broiler chicken industry also causing human illness. This work is aimed at elucidating the molecular epidemiology of . Infantis and pESI-like in Europe using whole-genome sequencing and bioinformatics analysis, and to investigate the genetic relatedness of . Infantis clones and pESI-like from animals, meat, feed and humans provided by institutions of nine European countries. Two genotyping approaches were used: chromosome or plasmid SNP-based analysis and the minimum spanning tree (MST) algorithm based on core-genome multilocus sequence typing (cgMLST). The European . Infantis population appeared heterogeneous, with different genetic clusters defined at core-genome level. However, pESI-like variants present in 64.1 % of the isolates were more genetically homogeneous and capable of infecting different clonal lineages in most of the countries. Two different pESI-like with ESBL genes (=82) were observed: -positive in European isolates and -positive in American isolates (study outgroup). Both variants had toxin-antitoxin systems, resistance genes towards tetracyclines, trimethoprim, sulphonamides and aminoglycosides, heavy metals (A) and disinfectants (EΔ). Worryingly, 66 % of the total isolates studied presented different A chromosomal point mutations associated with (fluoro)quinolone resistance (MIC range 0.125-0.5 mg/L), while 18 % displayed transferable macrolide resistance mediated by , and (B) genes. Proper intervention strategies are needed to prevent further dissemination/transmission of MDR . Infantis and pESI-like along the food chain in Europe.
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http://dx.doi.org/10.1099/mgen.0.000365DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7371121PMC
May 2020

Accelerating surveillance and research of antimicrobial resistance - an online repository for sharing of antimicrobial susceptibility data associated with whole-genome sequences.

Microb Genom 2020 05 30;6(5). Epub 2020 Mar 30.

See the full list of the COMPARE ML-AMR group members, in acknowledgements.

Antimicrobial resistance (AMR) is an emerging threat to modern medicine. Improved diagnostics and surveillance of resistant bacteria require the development of next-generation analysis tools and collaboration between international partners. Here, we present the 'AMR Data Hub', an online infrastructure for storage and sharing of structured phenotypic AMR data linked to bacterial whole-genome sequences. Leveraging infrastructure built by the European COMPARE Consortium and structured around the European Nucleotide Archive (ENA), the AMR Data Hub already provides an extensive data collection of more than 2500 isolates with linked genome and AMR data. Representing these data in standardized formats, we provide tools for the validation and submission of new data and services supporting search, browse and retrieval. The current collection was created through a collaboration by several partners from the European COMPARE Consortium, demonstrating the capacities and utility of the AMR Data Hub and its associated tools. We anticipate growth of content and offer the hub as a basis for future research into methods to explore and predict AMR.
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http://dx.doi.org/10.1099/mgen.0.000342DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7371118PMC
May 2020

Metaphylogenetic analysis of global sewage reveals that bacterial strains associated with human disease show less degree of geographic clustering.

Sci Rep 2020 02 20;10(1):3033. Epub 2020 Feb 20.

DTU Food. Technical University of Denmark, Kongens Lyngby, Denmark, 2800, Danmark.

Knowledge about the difference in the global distribution of pathogens and non-pathogens is limited. Here, we investigate it using a multi-sample metagenomics phylogeny approach based on short-read metagenomic sequencing of sewage from 79 sites around the world. For each metagenomic sample, bacterial template genomes were identified in a non-redundant database of whole genome sequences. Reads were mapped to the templates identified in each sample. Phylogenetic trees were constructed for each template identified in multiple samples. The countries from which the samples were taken were grouped according to different definitions of world regions. For each tree, the tendency for regional clustering was determined. Phylogenetic trees representing 95 unique bacterial templates were created covering 4 to 71 samples. Varying degrees of regional clustering could be observed. The clustering was most pronounced for environmental bacterial species and human commensals, and less for colonizing opportunistic pathogens, opportunistic pathogens and pathogens. No pattern of significant difference in clustering between any of the organism classifications and country groupings according to income were observed. Our study suggests that while the same bacterial species might be found globally, there is a geographical regional selection or barrier to spread for individual clones of environmental and human commensal bacteria, whereas this is to a lesser degree the case for strains and clones of human pathogens and opportunistic pathogens.
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http://dx.doi.org/10.1038/s41598-020-59292-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7033184PMC
February 2020

Corrigendum: Surveillance and Genomics of Toxigenic O1 From Fish, Phytoplankton and Water in Lake Victoria, Tanzania.

Front Microbiol 2019;10:2974. Epub 2019 Dec 20.

Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.

[This corrects the article DOI: 10.3389/fmicb.2019.00901.].
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http://dx.doi.org/10.3389/fmicb.2019.02974DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6934033PMC
December 2019

Genomic insights into Vibrio cholerae O1 responsible for cholera epidemics in Tanzania between 1993 and 2017.

PLoS Negl Trop Dis 2019 12 23;13(12):e0007934. Epub 2019 Dec 23.

Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark.

Background: Tanzania is one of seven countries with the highest disease burden caused by cholera in Africa. We studied the evolution of Vibrio cholerae O1 isolated in Tanzania during the past three decades.

Methodology/principal Findings: Genome-wide analysis was performed to characterize V. cholerae O1 responsible for the Tanzanian 2015-2017 outbreak along with strains causing outbreaks in the country for the past three decades. The genomes were further analyzed in a global context of 590 strains of the seventh cholera pandemic (7PET), as well as environmental isolates from Lake Victoria. All Tanzanian cholera outbreaks were caused by the 7PET lineage. The T5 sub-lineage (ctxB3) dominated outbreaks until 1997, followed by the T10 atypical El Tor (ctxB1) up to 2015, which were replaced by the T13 atypical El Tor of the current third wave (ctxB7) causing most cholera outbreaks until 2017 with T13 being phylogenetically related to strains from East African countries, Yemen and Lake Victoria. The strains were less drug resistant with approximate 10-kb deletions found in the SXT element, which encodes resistance to sulfamethoxazole and trimethoprim. Nucleotide deletions were observed in the CTX prophage of some strains, which warrants further virulence studies. Outbreak strains share 90% of core genes with V. cholerae O1 from Lake Victoria with as low as three SNPs difference and a significantly similar accessory genome, composed of genomic islands namely the CTX prophage, Vibrio Pathogenicity Islands; toxin co-regulated pilus biosynthesis proteins and the SXT-ICE element.

Conclusion/significance: Characterization of V. cholerae O1 from Tanzania reveals genetic diversity of the 7PET lineage composed of T5, T10 and T13 sub-lineages with introductions of new sequence types from neighboring countries. The presence of these sub-lineages in environmental isolates suggests that the African Great Lakes may serve as aquatic reservoirs for survival of V. cholerae O1 favoring continuous human exposure.
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http://dx.doi.org/10.1371/journal.pntd.0007934DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6927581PMC
December 2019

Corrigendum: Occurrence and Characterization of -Positive Isolated From Food-Producing Animals in Poland, 2011-2016.

Front Microbiol 2019;10:2816. Epub 2019 Dec 4.

Department of Microbiology, National Veterinary Research Institute, Puławy, Poland.

[This corrects the article DOI: 10.3389/fmicb.2019.01753.].
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http://dx.doi.org/10.3389/fmicb.2019.02816DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6904549PMC
December 2019

Pathogen surveillance in the informal settlement, Kibera, Kenya, using a metagenomics approach.

PLoS One 2019 10;14(10):e0222531. Epub 2019 Oct 10.

National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Foodborne Pathogens and Genomics and European Union Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark, Kgs. Lyngby, Denmark.

Background: Worldwide, the number of emerging and re-emerging infectious diseases is increasing, highlighting the importance of global disease pathogen surveillance. Traditional population-based methods may fail to capture important events, particularly in settings with limited access to health care, such as urban informal settlements. In such environments, a mixture of surface water runoff and human feces containing pathogenic microorganisms could be used as a surveillance surrogate.

Method: We conducted a temporal metagenomic analysis of urban sewage from Kibera, an urban informal settlement in Nairobi, Kenya, to detect and quantify bacterial and associated antimicrobial resistance (AMR) determinants, viral and parasitic pathogens. Data were examined in conjunction with data from ongoing clinical infectious disease surveillance.

Results: A large variation of read abundances related to bacteria, viruses, and parasites of medical importance, as well as bacterial associated antimicrobial resistance genes over time were detected. Significant increased abundances were observed for a number of bacterial pathogens coinciding with higher abundances of AMR genes. Vibrio cholerae as well as rotavirus A, among other virus peaked in several weeks during the study period whereas Cryptosporidium spp. and Giardia spp, varied more over time.

Conclusion: The metagenomic surveillance approach for monitoring circulating pathogens in sewage was able to detect putative pathogen and resistance loads in an urban informal settlement. Thus, valuable if generated in real time to serve as a comprehensive infectious disease agent surveillance system with the potential to guide disease prevention and treatment. The approach may lead to a paradigm shift in conducting real-time global genomics-based surveillance in settings with limited access to health care.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0222531PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6786639PMC
March 2020

Using Genomics to Track Global Antimicrobial Resistance.

Front Public Health 2019 4;7:242. Epub 2019 Sep 4.

Center for Veterinary Medicine, Office of Research, United States Food and Drug Administration, Laurel, MD, United States.

The recent advancements in rapid and affordable DNA sequencing technologies have revolutionized diagnostic microbiology and microbial surveillance. The availability of bioinformatics tools and online accessible databases has been a prerequisite for this. We conducted a scientific literature review and here we present a description of examples of available tools and databases for antimicrobial resistance (AMR) detection and provide future perspectives and recommendations. At least 47 freely accessible bioinformatics resources for detection of AMR determinants in DNA or amino acid sequence data have been developed to date. These include, among others but not limited to, ARG-ANNOT, CARD, SRST2, MEGARes, Genefinder, ARIBA, KmerResistance, AMRFinder, and ResFinder. Bioinformatics resources differ for several parameters including type of accepted input data, presence/absence of software for search within a database of AMR determinants that can be specific to a tool or cloned from other resources, and for the search approach employed, which can be based on mapping or on alignment. As a consequence, each tool has strengths and limitations in sensitivity and specificity of detection of AMR determinants and in application, which for some of the tools have been highlighted in benchmarking exercises and scientific articles. The identified tools are either available at public genome data centers, from GitHub or can be run locally. NCBI and European Nucleotide Archive (ENA) provide possibilities for online submission of both sequencing and accompanying phenotypic antimicrobial susceptibility data, allowing for other researchers to further analyze data, and develop and test new tools. The advancement in whole genome sequencing and the application of online tools for real-time detection of AMR determinants are essential to identify control and prevention strategies to combat the increasing threat of AMR. Accessible tools and DNA sequence data are expanding, which will allow establishing global pathogen surveillance and AMR tracking based on genomics. There is however, a need for standardization of pipelines and databases as well as phenotypic predictions based on the data.
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http://dx.doi.org/10.3389/fpubh.2019.00242DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6737581PMC
September 2019

Occurrence and Characterization of -Positive Isolated From Food-Producing Animals in Poland, 2011-2016.

Front Microbiol 2019 8;10:1753. Epub 2019 Aug 8.

Department of Microbiology, National Veterinary Research Institute, Puławy, Poland.

The emergence of plasmid-mediated colistin resistance ( genes) threatens the effectiveness of polymyxins, which are last-resort drugs to treat infections by multidrug- and carbapenem-resistant Gram-negative bacteria. Based on the occurrence of colistin resistance the aims of the study were to determine possible resistance mechanisms and then characterize the -positive . The research used material from the Polish national and EU harmonized antimicrobial resistance (AMR) monitoring programs. A total of 5,878 commensal from fecal samples of turkeys, chickens, pigs, and cattle collected in 2011-2016 were screened by minimum inhibitory concentration (MIC) determination for the presence of resistance to colistin (R) defined as > 2 mg/L. Strains with MIC = 2 mg/L isolated in 2014-2016 were also included. A total of 128 isolates were obtained, and most (66.3%) had colistin MIC of 2 mg/L. PCR revealed in 80 (62.5%) isolates recovered from 61 turkeys, 11 broilers, 2 laying hens, 1 pig, and 1 bovine. No other -type genes (including to -) were detected. Whole-genome sequencing (WGS) of the -positive isolates showed high diversity in the multi-locus sequence types (MLST) of , plasmid replicons, and AMR and virulence genes. Generally was detected on the same contig as the IncX4 (76.3%) and IncHI2 (6.3%) replicons. One isolate harbored . on the chromosome. Various extended-spectrum beta-lactamase (, , , , , and ) and quinolone resistance genes (, , and chromosomal , and mutations) were present in the .-positive . A total of 49 sequence types (ST) were identified, ST354, ST359, ST48, and ST617 predominating. One isolate, identified as ST189, belonged to atypical enteropathogenic Our findings show that . has spread widely among production animals in Poland, particularly in turkeys and appears to be transferable mainly by IncX4 and IncHI2 plasmids spread across diverse lineages. Interestingly, most of these -positive would remain undetected using phenotypic methods with the current epidemiological cut-off value (ECOFF). The appearance and spread of among various animals, but notably in turkeys, might be considered a food chain, and public health hazard.
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http://dx.doi.org/10.3389/fmicb.2019.01753DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6694793PMC
August 2019

Worldwide human mitochondrial haplogroup distribution from urban sewage.

Sci Rep 2019 08 12;9(1):11624. Epub 2019 Aug 12.

Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány P. s. 1A, Budapest, 1117, Hungary.

Community level genetic information can be essential to direct health measures and study demographic tendencies but is subject to considerable ethical and legal challenges. These concerns become less pronounced when analyzing urban sewage samples, which are ab ovo anonymous by their pooled nature. We were able to detect traces of the human mitochondrial DNA (mtDNA) in urban sewage samples and to estimate the distribution of human mtDNA haplogroups. An expectation maximization approach was used to determine mtDNA haplogroup mixture proportions for samples collected at each different geographic location. Our results show reasonable agreement with both previous studies of ancient evolution or migration and current US census data; and are also readily reproducible and highly robust. Our approach presents a promising alternative for sample collection in studies focusing on the ethnic and genetic composition of populations or diseases associated with different mtDNA haplogroups and genotypes.
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http://dx.doi.org/10.1038/s41598-019-48093-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6690936PMC
August 2019

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage.

Nat Microbiol 2019 10 8;4(10):1727-1736. Epub 2019 Jul 8.

National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark.

Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.
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http://dx.doi.org/10.1038/s41564-019-0494-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7440971PMC
October 2019

Proficiency Testing of Virus Diagnostics Based on Bioinformatics Analysis of Simulated High-Throughput Sequencing Data Sets.

J Clin Microbiol 2019 08 26;57(8). Epub 2019 Jul 26.

Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany.

Quality management and independent assessment of high-throughput sequencing-based virus diagnostics have not yet been established as a mandatory approach for ensuring comparable results. The sensitivity and specificity of viral high-throughput sequence data analysis are highly affected by bioinformatics processing using publicly available and custom tools and databases and thus differ widely between individuals and institutions. Here we present the results of the COMPARE [llaborative anagement latform for Detection and nalyses of (e-)emerging and Foodborne Outbreaks in urope] virus proficiency test. An artificial, simulated data set of Illumina HiSeq sequences was provided to 13 different European institutes for bioinformatics analysis to identify viral pathogens in high-throughput sequence data. Comparison of the participants' analyses shows that the use of different tools, programs, and databases for bioinformatics analyses can impact the correct identification of viral sequences from a simple data set. The identification of slightly mutated and highly divergent virus genomes has been shown to be most challenging. Furthermore, the interpretation of the results, together with a fictitious case report, by the participants showed that in addition to the bioinformatics analysis, the virological evaluation of the results can be important in clinical settings. External quality assessment and proficiency testing should become an important part of validating high-throughput sequencing-based virus diagnostics and could improve the harmonization, comparability, and reproducibility of results. There is a need for the establishment of international proficiency testing, like that established for conventional laboratory tests such as PCR, for bioinformatics pipelines and the interpretation of such results.
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http://dx.doi.org/10.1128/JCM.00466-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6663916PMC
August 2019

Surveillance and Genomics of Toxigenic O1 From Fish, Phytoplankton and Water in Lake Victoria, Tanzania.

Front Microbiol 2019 30;10:901. Epub 2019 Apr 30.

Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.

The occurrence of toxigenic O1 during a non- outbreak period in Lake Victoria was studied and genetic characteristics for environmental persistence and relatedness to pandemic strains were assessed. We analyzed 360 samples of carps, phytoplankton and water collected in 2017 during dry and rainy seasons in the Tanzanian basin of Lake Victoria. Samples were tested using PCR (W and A) with DNA extracted from bacterial isolates and samples enriched in alkaline peptone water. Isolates were screened with polyvalent antiserum O1 followed by antimicrobial susceptibility testing. Whole genome sequencing and bioinformatics tools were employed to investigate the genomic characteristics of the isolates. More positive samples were recovered by PCR when DNA was obtained from enriched samples than from isolates (69.0% vs. 21.3%, < 0.05), irrespectively of season. We identified ten O1 among 22 A-positive isolates. Further studies are needed to serotype the remaining A-positive non-O1 strains. Sequenced strains belonged to El Tor atypical biotype of O1 of MLST ST69 harboring the seventh pandemic gene. Major virulence genes, and pathogenicity islands VPI-1, VPI-2, VSP-1, and VSP-2 were found in all strains. The strains contained polysaccharide biosynthesis enzymes, the gene and two-component response regulator proteins involved in stress response and autoinducers for quorum sensing and biofilm formation. They carried the SXT integrative conjugative element with phenotypic and genotypic resistance to aminoglycoside, sulfamethoxazole, trimethoprim, phenicol, and quinolones. Strains contained a multidrug efflux pump component and were resistant to toxic compounds with copper homeostasis and cobalt-zinc-cadmium resistance proteins. The environmental strains belonged to the third wave of the seventh pandemic and most are genetically closely related to recent outbreak strains from Tanzania, Kenya, and Uganda with as low as three SNPs difference. Some strains have persisted longer in the environment and were more related to older outbreak strains in the region. O1 of outbreak potential seem to persist in Lake Victoria through interactions with fish and phytoplankton supported by the optimum water parameters and intrinsic genetic features enhancing survival in the aquatic environment.
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http://dx.doi.org/10.3389/fmicb.2019.00901DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6503148PMC
April 2019

Global phylogenomics of multidrug-resistant Salmonella enterica serotype Kentucky ST198.

Microb Genom 2019 07 20;5(7). Epub 2019 May 20.

Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella , World Health Organization Collaborative Centre for the Typing and Antibiotic Resistance of Salmonella , Institut Pasteur, 75015 Paris, France.

Salmonella enterica serotype Kentucky can be a common causative agent of salmonellosis, usually associated with consumption of contaminated poultry. Antimicrobial resistance (AMR) to multiple drugs, including ciprofloxacin, is an emerging problem within this serotype. We used whole-genome sequencing (WGS) to investigate the phylogenetic structure and AMR content of 121 S.enterica serotype Kentucky sequence type 198 isolates from five continents. Population structure was inferred using phylogenomic analysis and whole genomes were compared to investigate changes in gene content, with a focus on acquired AMR genes. Our analysis showed that multidrug-resistant (MDR) S.enterica serotype Kentucky isolates belonged to a single lineage, which we estimate emerged circa 1989 following the acquisition of the AMR-associated Salmonella genomic island (SGI) 1 (variant SGI1-K) conferring resistance to ampicillin, streptomycin, gentamicin, sulfamethoxazole and tetracycline. Phylogeographical analysis indicates this clone emerged in Egypt before disseminating into Northern, Southern and Western Africa, then to the Middle East, Asia and the European Union. The MDR clone has since accumulated various substitution mutations in the quinolone-resistance-determining regions (QRDRs) of DNA gyrase (gyrA) and DNA topoisomerase IV (parC), such that most strains carry three QRDR mutations which together confer resistance to ciprofloxacin. The majority of AMR genes in the S. enterica serotype Kentucky genomes were carried either on plasmids or SGI structures. Remarkably, each genome of the MDR clone carried a different SGI1-K derivative structure; this variation could be attributed to IS26-mediated insertions and deletions, which appear to have hampered previous attempts to trace the clone's evolution using sub-WGS resolution approaches. Several different AMR plasmids were also identified, encoding resistance to chloramphenicol, third-generation cephalosporins, carbapenems and/or azithromycin. These results indicate that most MDR S. enterica serotype Kentucky circulating globally result from the clonal expansion of a single lineage that acquired chromosomal AMR genes 30 years ago, and has continued to diversify and accumulate additional resistances to last-line oral antimicrobials. This article contains data hosted by Microreact.
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http://dx.doi.org/10.1099/mgen.0.000269DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6700661PMC
July 2019

Whole-Genome Sequencing Analysis of Nontyphoidal of Chicken Meat and Human Origin Under Surveillance in Sri Lanka.

Foodborne Pathog Dis 2019 07 21;16(7):531-537. Epub 2019 May 21.

1 School of Chemical and Biomedical Engineering, Nanyang Technological University (NTU), Singapore, Singapore.

A total of 73 nontyphoidal isolates, 33 from raw chicken meat and 40 from routine clinical specimens, were collected between 2015 and 2017 from eight cities in Sri Lanka for a pilot study of whole-genome sequencing for surveillance. The isolates were characterized by conventional serotyping and whole-genome sequencing. The raw sequenced data were assembled and analyzed to predict serotypes, determine sequence type (ST) profiles of genome and plasmid, and identify plasmid replicon sequences and antimicrobial resistance (AMR) genes. The most common serovar isolated from chicken meat was serovar Agona of ST13 ( = 16), in contrast to serovar Enteritidis of ST11 ( = 21) in human. serovar Corvallis is the only serovar that was overlapping between human and chicken meat. The level of agreement between serotyping and serotype prediction results was 100%. Among the 33 chicken isolates, multidrug resistance (MDR) was observed in five isolates, including two serovar Kentucky ST314, which harbored six different classes of AMR determinants. Among the 40 human isolates, MDR was detected in two serovar Chester (ST2063) isolates containing five different antibiotic classes of AMR determinants. Out of 73 isolates, the only human serovar Typhimurium strain of ST36 was found to possess extended-spectrum beta-lactamase (ESBL) gene, bla, and it was positive for ESBL production. In summary, this study identified . serovars that were dominating in chicken meat and human and showed the genomic differences among the chicken meat and human strains. It should be noted that the limited number of isolates and sampling at a different time period means that thorough source attribution is not possible. To the best of our knowledge, this is the first report on the use of whole-genome sequencing analysis of nontyphoidal . isolated from chicken meat and human in Sri Lanka.
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http://dx.doi.org/10.1089/fpd.2018.2604DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6653781PMC
July 2019

IncI1 ST3 and IncI1 ST7 plasmids from CTX-M-1-producing Escherichia coli obtained from patients with bloodstream infections are closely related to plasmids from E. coli of animal origin.

J Antimicrob Chemother 2019 08;74(8):2171-2175

Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark.

Objectives: Fully sequenced IncI1 plasmids obtained from CTX-M-1-producing Escherichia coli of human and animal origin were compared.

Methods: Twelve E. coli isolates sharing identical ESBL genes and plasmid multilocus STs sequenced on Illumina and MinION platforms were obtained from the Danish antimicrobial resistance surveillance programme, DANMAP. After de novo assembly, the sequences of plasmids harbouring blaCTX-M-1 were manually curated and ORFs annotated. Within-group comparisons were performed separately for the IncI1 ST3 plasmid type and the IncI1 ST7 plasmid type. The IncI1 ST3 plasmid group was obtained from 10 E. coli isolates (2 from patients with bloodstream infections, 6 from food and 2 from animals). The IncI1 ST7 plasmids originated from E. coli isolates obtained from a patient with bloodstream infection and from a pig. Sequences of IncI1 ST3 and IncI1 ST7 plasmids harbouring blaCTX-M-1 with determined origin were retrieved from GenBank and used for comparison within the respective group.

Results: The 10 IncI1 ST3 blaCTX-M-1 plasmids were highly similar in structure and organization with only minor plasmid rearrangements and differences in the variable region. The IncI1 ST7 blaCTX-M-1 plasmids also showed high similarity in structure and organization. The high level of similarity was also observed when including plasmids from E. coli of animal origin from Australia, Switzerland, the Netherlands and France.

Conclusions: This study shows broad spread of a very successful CTX-M-1-producing IncI1 type plasmid among E. coli of both human and animal origin.
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http://dx.doi.org/10.1093/jac/dkz199DOI Listing
August 2019

Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage.

Nat Commun 2019 03 8;10(1):1124. Epub 2019 Mar 8.

Usher Institute, University of Edinburgh, Edinburgh, EH8 9AG, UK.

Antimicrobial resistance (AMR) is a serious threat to global public health, but obtaining representative data on AMR for healthy human populations is difficult. Here, we use metagenomic analysis of untreated sewage to characterize the bacterial resistome from 79 sites in 60 countries. We find systematic differences in abundance and diversity of AMR genes between Europe/North-America/Oceania and Africa/Asia/South-America. Antimicrobial use data and bacterial taxonomy only explains a minor part of the AMR variation that we observe. We find no evidence for cross-selection between antimicrobial classes, or for effect of air travel between sites. However, AMR gene abundance strongly correlates with socio-economic, health and environmental factors, which we use to predict AMR gene abundances in all countries in the world. Our findings suggest that global AMR gene diversity and abundance vary by region, and that improving sanitation and health could potentially limit the global burden of AMR. We propose metagenomic analysis of sewage as an ethically acceptable and economically feasible approach for continuous global surveillance and prediction of AMR.
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http://dx.doi.org/10.1038/s41467-019-08853-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6408512PMC
March 2019

Cross-Border Transmission of Choleraesuis var. Kunzendorf in European Pigs and Wild Boar: Infection, Genetics, and Evolution.

Front Microbiol 2019 6;10:179. Epub 2019 Feb 6.

European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Center for Antimicrobial Resistance in Food Borne Pathogens and Genomics, Research Group for Genomic Epidemiology, National Food Institute, Kongens Lyngby, Denmark.

subspecies serotype Choleraesuis is a swine adapted serovar. Choleraesuis variant Kunzendorf is responsible for the majority of outbreaks among pigs. Choleraesuis is rare in Europe, although there have been serious outbreaks in pigs including two outbreaks in Denmark in 1999-2000 and 2012-2013. Here, we elucidate the epidemiology, possible transmission routes and sources, and clonality of European . Choleraesuis isolates including the Danish outbreak isolates. A total of 102 . Choleraesuis isolates from different European countries and the United States, covering available isolates from the last two decades were selected for whole genome sequencing. We applied a temporally structured sequence analysis within a Bayesian framework to reconstruct a temporal and spatial phylogenetic tree. MLST type, resistance genes, plasmid replicons, and accessory genes were identified using bioinformatics tools. Fifty-eight isolates including 11 out of 12 strains from wild boars were pan-susceptible. The remaining isolates carried multiple resistance genes. Eleven different plasmid replicons in eight plasmids were determined among the isolates. Accessory genes were associated to the identified resistance genes and plasmids. The European . Choleraesuis was estimated to have emerged in ∼1837 (95% credible interval, 1733-1983) with the mutation rate of 1.02 SNPs/genome/year. The isolates were clustered according to countries and neighbor countries. There were transmission events between strains from the United States and European countries. Wild boar and pig isolates were genetically linked suggesting cross-border transmission and transmission due to a wildlife reservoir. The phylogenetic tree shows that multiple introductions were responsible for the outbreak of 2012-2013 in Denmark, and suggests that poorly disinfected vehicles crossing the border into Denmark were potentially the source of the outbreak. Low levels of single nucleotide polymorphisms (SNPs) differences (0-4 SNPs) can be observed between clonal strains isolated from different organs of the same animal. Proper disinfection of livestock vehicles and improved quality control of livestock feed could help to prevent future spread of . Choleraesuis or other more serious infectious diseases such as African swine fever (ASF) in the European pig production system.
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http://dx.doi.org/10.3389/fmicb.2019.00179DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6373457PMC
February 2019