1
|
Machado RAR, Malan AP, Boss A, Claasen NJ, Bhat AH, Abolafia J. Photorhabdus africana sp. nov. isolated from Heterorhabditis entomopathogenic nematodes. Curr Microbiol 2024; 81:240. [PMID: 38910178 PMCID: PMC11194217 DOI: 10.1007/s00284-024-03744-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 05/20/2024] [Indexed: 06/25/2024]
Abstract
One Gram-negative, rod-shaped bacterial strain, isolated from an undescribed Heterorhabditis entomopathogenic nematode species was characterized to determine its taxonomic position. The 16S rRNA gene sequences indicate that it belongs to the class Gammaproteobacteria, to the family Morganellaceae, to the genus Photorhabdus, and likely represents a novel bacterial species. This strain, designated here as CRI-LCT, was therefore molecularly, biochemically, and morphologically characterized to describe the novel bacterial species. Phylogenetic reconstructions using 16S rRNA gene sequences show that CRI-LCT is closely related to P. laumondii subsp. laumondii TT01T and to P. laumondii subsp. clarkei BOJ-47T. The 16rRNA gene sequences between CRI-LCT and P. laumondii subsp. laumondii TT01T are 99.1% identical, and between CRI-LCT and P. laumondii subsp. clarkei BOJ-47T are 99.2% identical. Phylogenetic reconstructions using whole genome sequences show that CRI-LCT is closely related to P. laumondii subsp. laumondii TT01T and to P. laumondii subsp. clarkei BOJ-47T. Moreover, digital DNA-DNA hybridization (dDDH) values between CRI-LCT and its two relative species P. laumondii subsp. laumondii TT01T and P. laumondii subsp. clarkei BOJ-47T are 65% and 63%, respectively. In addition, we observed that average nucleotide identity (ANI) values between CRI-LCT and its two relative species P. laumondii subsp. laumondii TT01T and P. laumondii subsp. clarkei BOJ-47T are 95.8% and 95.5%, respectively. These values are below the 70% dDDH and the 95-96% ANI divergence thresholds that delimits prokaryotic species. Based on these genomic divergence values, and the phylogenomic separation, we conclude that CRI-LCT represents a novel bacterial species, for which we propose the name Photorhabdus africana sp. nov. with CRI-LCT (= CCM 9390T = CCOS 2112T) as the type strain. The following biochemical tests allow to differentiate P. africana sp. nov. CRI-LCT from other species of the genus, including its more closely related taxa: β-Galactosidase, citrate utilization, urease and tryptophan deaminase activities, indole and acetoin production, and glucose and inositol oxidation. Our study contributes to a better understanding of the taxonomy and biodiversity of this important bacterial group with great biotechnological and agricultural potential.
Collapse
Affiliation(s)
- Ricardo A R Machado
- Experimental Biology Research Group, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland.
| | - Antoinette P Malan
- Department of Conservation Ecology and Entomology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Anja Boss
- Experimental Biology Research Group, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland
| | - Nicholle J Claasen
- Department of Conservation Ecology and Entomology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Aashaq Hussain Bhat
- Department of Biosciences and University Center for Research and Development, Chandigarh University, Gharuan, Mohali, Punjab, 140413, India
- Department of Biomaterials, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, 600077, India
| | - Joaquín Abolafia
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Campus 'Las Lagunillas', Jaén, Spain
| |
Collapse
|
2
|
Quek ZBR, Ng SH. Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology. Pathogens 2024; 13:275. [PMID: 38668230 PMCID: PMC11054155 DOI: 10.3390/pathogens13040275] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/11/2024] [Accepted: 03/18/2024] [Indexed: 04/29/2024] Open
Abstract
High-throughput sequencing (HTS) has revolutionised the field of pathogen genomics, enabling the direct recovery of pathogen genomes from clinical and environmental samples. However, pathogen nucleic acids are often overwhelmed by those of the host, requiring deep metagenomic sequencing to recover sufficient sequences for downstream analyses (e.g., identification and genome characterisation). To circumvent this, hybrid-capture target enrichment (HC) is able to enrich pathogen nucleic acids across multiple scales of divergences and taxa, depending on the panel used. In this review, we outline the applications of HC in human pathogens-bacteria, fungi, parasites and viruses-including identification, genomic epidemiology, antimicrobial resistance genotyping, and evolution. Importantly, we explored the applicability of HC to clinical metagenomics, which ultimately requires more work before it is a reliable and accurate tool for clinical diagnosis. Relatedly, the utility of HC was exemplified by COVID-19, which was used as a case study to illustrate the maturity of HC for recovering pathogen sequences. As we unravel the origins of COVID-19, zoonoses remain more relevant than ever. Therefore, the role of HC in biosurveillance studies is also highlighted in this review, which is critical in preparing us for the next pandemic. We also found that while HC is a popular tool to study viruses, it remains underutilised in parasites and fungi and, to a lesser extent, bacteria. Finally, weevaluated the future of HC with respect to bait design in the eukaryotic groups and the prospect of combining HC with long-read HTS.
Collapse
Affiliation(s)
- Z. B. Randolph Quek
- Defence Medical & Environmental Research Institute, DSO National Laboratories, Singapore 117510, Singapore
| | | |
Collapse
|
3
|
Álvarez Narváez S, Beaudry MS, Norris CG, Bartlett PB, Glenn TC, Sanchez S. Improved Equine Fecal Microbiome Characterization Using Target Enrichment by Hybridization Capture. Animals (Basel) 2024; 14:445. [PMID: 38338088 PMCID: PMC10854943 DOI: 10.3390/ani14030445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/18/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
GITDs are among the most common causes of death in adult and young horses in the United States (US). Previous studies have indicated a connection between GITDs and the equine gut microbiome. However, the low taxonomic resolution of the current microbiome sequencing methods has hampered the identification of specific bacterial changes associated with GITDs in horses. Here, we have compared TEHC, a new approach for 16S rRNA gene selection and sequencing, with conventional 16S rRNA gene amplicon sequencing for the characterization of the equine fecal microbiome. Both sequencing approaches were used to determine the fecal microbiome of four adult horses and one commercial mock microbiome. Our results show that TEHC yielded significantly more operational taxonomic units (OTUs) than conventional 16S amplicon sequencing when the same number of reads were used in the analysis. This translated into a deeper and more accurate characterization of the fecal microbiome when the samples were sequenced with TEHC according to the relative abundance analysis. Alpha and beta diversity metrics corroborated these findings and demonstrated that the microbiome of the fecal samples was significantly richer when sequenced with TEHC compared to 16S amplicon sequencing. Altogether, our study suggests that the TEHC strategy provides a more extensive characterization of the fecal microbiome of horses than the current alternative based on the PCR amplification of a portion of the 16S rRNA gene.
Collapse
Affiliation(s)
- Sonsiray Álvarez Narváez
- Department of Infectious Disease, College of Veterinary Medicine, The University of Georgia, Athens, GA 30602, USA; (C.G.N.); (P.B.B.)
| | - Megan S. Beaudry
- Department of Environmental Health Science, College of Public Health, The University of Georgia, Athens, GA 30602, USA; (M.S.B.); (T.C.G.)
| | - Connor G. Norris
- Department of Infectious Disease, College of Veterinary Medicine, The University of Georgia, Athens, GA 30602, USA; (C.G.N.); (P.B.B.)
| | - Paula B. Bartlett
- Department of Infectious Disease, College of Veterinary Medicine, The University of Georgia, Athens, GA 30602, USA; (C.G.N.); (P.B.B.)
| | - Travis C. Glenn
- Department of Environmental Health Science, College of Public Health, The University of Georgia, Athens, GA 30602, USA; (M.S.B.); (T.C.G.)
| | - Susan Sanchez
- Department of Infectious Disease, College of Veterinary Medicine, The University of Georgia, Athens, GA 30602, USA; (C.G.N.); (P.B.B.)
| |
Collapse
|
4
|
Cooper AL, Low A, Wong A, Tamber S, Blais BW, Carrillo CD. Modeling the limits of detection for antimicrobial resistance genes in agri-food samples: a comparative analysis of bioinformatics tools. BMC Microbiol 2024; 24:31. [PMID: 38245666 PMCID: PMC10799530 DOI: 10.1186/s12866-023-03148-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 12/07/2023] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Although the spread of antimicrobial resistance (AMR) through food and its production poses a significant concern, there is limited research on the prevalence of AMR bacteria in various agri-food products. Sequencing technologies are increasingly being used to track the spread of AMR genes (ARGs) in bacteria, and metagenomics has the potential to bypass some of the limitations of single isolate characterization by allowing simultaneous analysis of the agri-food product microbiome and associated resistome. However, metagenomics may still be hindered by methodological biases, presence of eukaryotic DNA, and difficulties in detecting low abundance targets within an attainable sequence coverage. The goal of this study was to assess whether limits of detection of ARGs in agri-food metagenomes were influenced by sample type and bioinformatic approaches. RESULTS We simulated metagenomes containing different proportions of AMR pathogens and analysed them for taxonomic composition and ARGs using several common bioinformatic tools. Kraken2/Bracken estimates of species abundance were closest to expected values. However, analysis by both Kraken2/Bracken indicated presence of organisms not included in the synthetic metagenomes. Metaphlan3/Metaphlan4 analysis of community composition was more specific but with lower sensitivity than the Kraken2/Bracken analysis. Accurate detection of ARGs dropped drastically below 5X isolate genome coverage. However, it was sometimes possible to detect ARGs and closely related alleles at lower coverage levels if using a lower ARG-target coverage cutoff (< 80%). While KMA and CARD-RGI only predicted presence of expected ARG-targets or closely related gene-alleles, SRST2 (which allows read to map to multiple targets) falsely reported presence of distantly related ARGs at all isolate genome coverage levels. The presence of background microbiota in metagenomes influenced the accuracy of ARG detection by KMA, resulting in mcr-1 detection at 0.1X isolate coverage in the lettuce but not in the beef metagenome. CONCLUSIONS This study demonstrates accurate detection of ARGs in synthetic metagenomes using various bioinformatic methods, provided that reads from the ARG-encoding organism exceed approximately 5X isolate coverage (i.e. 0.4% of a 40 million read metagenome). While lowering thresholds for target gene detection improved sensitivity, this led to the identification of alternative ARG-alleles, potentially confounding the identification of critical ARGs in the resistome. Further advancements in sequencing technologies providing increased coverage depth or extended read lengths may improve ARG detection in agri-food metagenomic samples, enabling use of this approach for tracking clinically important ARGs in agri-food samples.
Collapse
Affiliation(s)
- Ashley L Cooper
- Research and Development, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON, Canada
- Department of Biology, Carleton University, Ottawa, ON, Canada
| | - Andrew Low
- Research and Development, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Alex Wong
- Department of Biology, Carleton University, Ottawa, ON, Canada
| | - Sandeep Tamber
- Microbiology Research Division, Bureau of Microbial Hazards, Health Canada, Ottawa, ON, Canada
| | - Burton W Blais
- Research and Development, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON, Canada
- Department of Biology, Carleton University, Ottawa, ON, Canada
| | - Catherine D Carrillo
- Research and Development, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON, Canada.
- Department of Biology, Carleton University, Ottawa, ON, Canada.
| |
Collapse
|
5
|
Kyono Y, Magboo JD, Daley EA, Flowers SA. Antipsychotic quetiapine alters the mouse fecal resistome by impacting antibiotic efflux, cell membrane, and cell wall synthesis genes. Microbiol Spectr 2024; 12:e0380423. [PMID: 38099619 PMCID: PMC10782992 DOI: 10.1128/spectrum.03804-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 11/16/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE This study significantly contributes to our understanding of how certain medications can unintentionally contribute to a major global health issue, i.e., antibiotic resistance. Quetiapine, a widely used antipsychotic medication, was found to increase key resistance mechanisms of gut bacteria to antibiotics in mice. Specifically, these data suggest that quetiapine may target elements of the bacterial cell membrane. If similar effects are found in humans, this medicine could unexpectedly make it harder to treat certain infections. This research emphasizes the importance of being mindful about not just antibiotics themselves, but also about other medications that could inadvertently contribute to this problem. Ultimately, these findings underline the necessity for more in-depth research on the broader impact of pharmaceuticals.
Collapse
Affiliation(s)
- Yasuhiro Kyono
- Department of Pharmacy Practice, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Jonathan D. Magboo
- Department of Pharmacy Practice, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Elizabeth A. Daley
- Department of Pharmacy Practice, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Stephanie A. Flowers
- Department of Pharmacy Practice, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois, USA
| |
Collapse
|
6
|
Walsh LH, Coakley M, Walsh AM, O'Toole PW, Cotter PD. Bioinformatic approaches for studying the microbiome of fermented food. Crit Rev Microbiol 2023; 49:693-725. [PMID: 36287644 DOI: 10.1080/1040841x.2022.2132850] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/11/2022] [Accepted: 09/28/2022] [Indexed: 11/03/2022]
Abstract
High-throughput DNA sequencing-based approaches continue to revolutionise our understanding of microbial ecosystems, including those associated with fermented foods. Metagenomic and metatranscriptomic approaches are state-of-the-art biological profiling methods and are employed to investigate a wide variety of characteristics of microbial communities, such as taxonomic membership, gene content and the range and level at which these genes are expressed. Individual groups and consortia of researchers are utilising these approaches to produce increasingly large and complex datasets, representing vast populations of microorganisms. There is a corresponding requirement for the development and application of appropriate bioinformatic tools and pipelines to interpret this data. This review critically analyses the tools and pipelines that have been used or that could be applied to the analysis of metagenomic and metatranscriptomic data from fermented foods. In addition, we critically analyse a number of studies of fermented foods in which these tools have previously been applied, to highlight the insights that these approaches can provide.
Collapse
Affiliation(s)
- Liam H Walsh
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- School of Microbiology, University College Cork, Ireland
| | - Mairéad Coakley
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Aaron M Walsh
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Paul W O'Toole
- School of Microbiology, University College Cork, Ireland
- APC Microbiome Ireland, University College Cork, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Ireland
- VistaMilk SFI Research Centre, Teagasc, Moorepark, Fermoy, Cork, Ireland
| |
Collapse
|
7
|
Hershko Y, Levytskyi K, Rannon E, Assous MV, Ken-Dror S, Amit S, Ben-Zvi H, Sagi O, Schwartz O, Sorek N, Szwarcwort M, Barkan D, Burstein D, Adler A. Phenotypic and genotypic analysis of antimicrobial resistance in Nocardia species. J Antimicrob Chemother 2023; 78:2306-2314. [PMID: 37527397 DOI: 10.1093/jac/dkad236] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 07/19/2023] [Indexed: 08/03/2023] Open
Abstract
BACKGROUND Antimicrobial resistance is common in Nocardia species but data regarding the molecular mechanisms beyond their resistance traits are limited. Our study aimed to determine the species distribution, the antimicrobial susceptibility profiles, and investigate the associations between the resistance traits and their genotypic determinants. METHODS The study included 138 clinical strains of Nocardia from nine Israeli microbiology laboratories. MIC values of 12 antimicrobial agents were determined using broth microdilution. WGS was performed on 129 isolates of the eight predominant species. Bioinformatic analysis included phylogeny and determination of antimicrobial resistance genes and mutations. RESULTS Among the isolates, Nocardia cyriacigeorgica was the most common species (36%), followed by Nocardia farcinica (16%), Nocardia wallacei (13%), Nocardia abscessus (9%) and Nocardia brasiliensis (8%). Linezolid was active against all isolates, followed by trimethoprim/sulfamethoxazole (93%) and amikacin (91%). Resistance to other antibiotics was species-specific, often associated with the presence of resistance genes or mutations: (1) aph(2″) in N. farcinica and N. wallacei (resistance to tobramycin); (ii) blaAST-1 in N. cyriacigeorgica and Nocardia neocaledoniensis (resistance to amoxicillin/clavulanate); (iii) blaFAR-1 in N. farcinica (resistance to ceftriaxone); (iv) Ser83Ala substitution in the gyrA gene in four species (resistance to ciprofloxacin); and (v) the 16S rRNA m1A1408 methyltransferase in N. wallacei isolates (correlating with amikacin resistance). CONCLUSIONS Our study provides a comprehensive understanding of Nocardia species diversity, antibiotic resistance patterns, and the molecular basis of antimicrobial resistance. Resistance appears to follow species-related patterns, suggesting a lesser role for de novo evolution or transmission of antimicrobial resistance.
Collapse
Affiliation(s)
- Yizhak Hershko
- Koret School of Veterinary Medicine, Robert H. Smith Faculty for Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
- Clinical Microbiology Laboratory, Tel-Aviv Sourasky Medical Center, Tel-Aviv University, Tel-Aviv, Israel
| | - Katia Levytskyi
- Koret School of Veterinary Medicine, Robert H. Smith Faculty for Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Ella Rannon
- The Shmunis School of Biomedicine and Cancer Research, Faculty of Life Science, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Marc V Assous
- Clinical Microbiology Laboratory, Shaare Zedek Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shifra Ken-Dror
- Clalit Health Services, Haifa and Western Galilee District, Israel
| | - Sharon Amit
- Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Haim Ben-Zvi
- Microbiology Laboratory, Rabin Medical Center, Beilinson Hospital, Petah Tikva, Israel
| | - Orli Sagi
- Clinical Microbiology Laboratory, Soroka University Medical Center, Beer-Sheva 84105, Israel
| | | | - Nadav Sorek
- Assuta Ashdod University Hospital, Ashdod, Israel
| | - Moran Szwarcwort
- Clinical Microbiology Laboratories, Laboratories Division, Rambam Health Care Campus, Haifa, Israel
| | - Daniel Barkan
- Koret School of Veterinary Medicine, Robert H. Smith Faculty for Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - David Burstein
- The Shmunis School of Biomedicine and Cancer Research, Faculty of Life Science, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Amos Adler
- Clinical Microbiology Laboratory, Tel-Aviv Sourasky Medical Center, Tel-Aviv University, Tel-Aviv, Israel
| |
Collapse
|
8
|
Machado RAR, Bhat AH, Castaneda-Alvarez C, Askary TH, Půža V, Pagès S, Abolafia J. Xenorhabdus aichiensis sp. nov., Xenorhabdus anantnagensis sp. nov., and Xenorhabdus yunnanensis sp. nov., Isolated from Steinernema Entomopathogenic Nematodes. Curr Microbiol 2023; 80:300. [PMID: 37493817 PMCID: PMC10371910 DOI: 10.1007/s00284-023-03373-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/12/2023] [Indexed: 07/27/2023]
Abstract
Three bacterial strains, XENO-2T, XENO-7T, and XENO-10T, isolated from Steinernema entomopathogenic nematodes, were found to represent novel Xenorhabdus species. In this study, we describe these new species by whole-genome and whole-proteome phylogenomic reconstructions, by calculating sequence identity scores using core genome sequences, and by phenotypic characterization. Phylogenomic reconstructions using ribosomal and house-keeping genes, and whole-genome and whole-proteome sequences show that XENO-2T and XENO-10T are closely related to Xenorhabdus japonica DSM 16522T and that XENO-7T is closely related to Xenorhabdus bovienii subsp. africana XENO-1T and to X. bovienii subsp. bovienii T228T. The dDDH values between XENO-2T and XENO-10T and between XENO-2T and X. japonica DSM 16522T are 56.4 and 51.8%, respectively. The dDDH value between XENO-10T and X. japonica DSM 16522T is 53.4%. The dDDH values between XENO-7T and X. bovienii subsp. africana XENO-1T and between XENO-7T and X. bovienii subsp. bovienii T228T are 63.6 and 69.4%, respectively. These dDDH values are below the 70% divergence threshold for prokaryotic species delineation. The newly described species are highly pathogenic to G. mellonella larvae, grow at pH between 5 and 9 (optimum 5-7), at salt concentrations of 1-3% (optimum 1-2%), and temperatures between 20 and 37 °C (optimum 28-30 °C). Biochemical tests such as lysine decarboxylase, ornithine decarboxylase, urease, gelatinase, citrate utilization, indole and acetoin production, and cytochrome oxidase tests allow to differentiate the novel species from their more closely related species. Considering these genetic and phenotypic divergencies, we propose the following new species: Xenorhabdus aichiensis sp. nov. with XENO-7T (= CCM 9233T = CCOS 2024T) as the type strain, Xenorhabdus anantnagensis sp. nov., with XENO-2T (= CCM 9237T = CCOS 2023T) as the type strain, and Xenorhabdus yunnanensis sp. nov., with XENO-10T (= CCM 9322T = CCOS 2071T) as the type strain. Our study contributes to a better understanding of the biodiversity and phylogenetic relationships of entomopathogenic bacteria associated with insect parasitic nematodes.
Collapse
Affiliation(s)
- Ricardo A R Machado
- Experimental Biology Research Group, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland.
| | - Aashaq Hussain Bhat
- Experimental Biology Research Group, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland
- Department of Biosciences, University Center for Research and Development, Chandigarh University, Mohali, Punjab, India
| | - Carlos Castaneda-Alvarez
- Experimental Biology Research Group, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland
- Departamento de Sanidad Vegetal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile
| | - Tarique Hassan Askary
- Division of Entomology, Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences and Technology, Wadura Campus, Jammu, Jammu and Kashmir, India
| | - Vladimir Půža
- Biology Centre CAS, Institute of Entomology, České Budějovice, Czech Republic
| | - Sylvie Pagès
- INRAe, Université de Montpellier, Montpellier, France
| | - Joaquín Abolafia
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Campus 'Las Lagunillas', Jaén, Spain
| |
Collapse
|
9
|
Flint A, Cooper A, Rao M, Weedmark K, Carrillo C, Tamber S. Targeted metagenomics using bait-capture to detect antibiotic resistance genes in retail meat and seafood. Front Microbiol 2023; 14:1188872. [PMID: 37520363 PMCID: PMC10373929 DOI: 10.3389/fmicb.2023.1188872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/28/2023] [Indexed: 08/01/2023] Open
Abstract
Metagenomics analysis of foods has the potential to provide comprehensive data on the presence and prevalence of antimicrobial resistance (AMR) genes in the microbiome of foods. However, AMR genes are generally present in low abundance compared to other bacterial genes in the food microbiome and consequently require multiple rounds of in-depth sequencing for detection. Here, a metagenomics approach, using bait-capture probes targeting antimicrobial resistance and plasmid genes, is used to characterize the resistome and plasmidome of retail beef, chicken, oyster, shrimp, and veal enrichment cultures (n = 15). Compared to total shotgun metagenomics, bait-capture required approximately 40-fold fewer sequence reads to detect twice the number of AMR gene classes, AMR gene families, and plasmid genes across all sample types. For the detection of critically important extended spectrum beta-lactamase (ESBL) genes the bait capture method had a higher overall positivity rate (44%) compared to shotgun metagenomics (26%), and a culture-based method (29%). Overall, the results support the use of bait-capture for the identification of low abundance genes such as AMR genes from food samples.
Collapse
Affiliation(s)
- Annika Flint
- Bureau of Microbial Hazards, Health Canada, Sir Frederick Banting Driveway, Ottawa, ON, Canada
| | - Ashley Cooper
- Research and Development, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Mary Rao
- Bureau of Microbial Hazards, Health Canada, Sir Frederick Banting Driveway, Ottawa, ON, Canada
| | - Kelly Weedmark
- Bureau of Microbial Hazards, Health Canada, Sir Frederick Banting Driveway, Ottawa, ON, Canada
| | - Catherine Carrillo
- Research and Development, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Sandeep Tamber
- Bureau of Microbial Hazards, Health Canada, Sir Frederick Banting Driveway, Ottawa, ON, Canada
| |
Collapse
|
10
|
Machado RAR, Bhat AH, Castaneda-Alvarez C, Půža V, San-Blas E. Photorhabdus aballayi sp. nov. and Photorhabdus luminescens subsp. venezuelensis subsp. nov., isolated from Heterorhabditis amazonensis entomopathogenic nematodes. Int J Syst Evol Microbiol 2023; 73. [PMID: 37171451 DOI: 10.1099/ijsem.0.005872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Abstract
Six Gram-negative, rod-shaped bacterial strains isolated from Heterorhabditis amazonensis entomopathogenic nematodes were characterized to determine their taxonomic position. 16S rRNA and gyrB gene sequences indicate that they belong to the class Gammaproteobacteria, family Morganellaceae and genus Photorhabdus, and that some of them are conspecifics. Two of them, APURET and JART, were selected for further molecular characterization using whole genome- and whole-proteome-based phylogenetic reconstructions and sequence comparisons. Phylogenetic reconstructions using whole genome and whole proteome sequences show that strains APURET and JART are closely related to Photorhabdus luminescens subsp. luminescens ATCC 29999T and to P. luminescens subsp. mexicana MEX47-22T. Moreover, digital DNA-DNA hybridization (dDDH) values between APURET and P. luminescens subsp. luminescens ATCC 29999T, APURET and P. luminescens subsp. mexicana MEX47-22T, and APURET and JART are 61.6, 61.2 and 64.1 %, respectively. These values are below the 70 % divergence threshold that delimits prokaryotic species. dDDH scores between JART and P. luminescens subsp. luminescens ATCC 29999T and between JART and P. luminescens subsp. mexicana MEX47-22T are 71.9 and 74.8 %, respectively. These values are within the 70 and 79 % divergence thresholds that delimit prokaryotic subspecies. Based on these genomic divergence values, APURET and JART represent two different taxa, for which we propose the names: Photorhabdus aballayi sp. nov. with APURET (=CCM 9236T =CCOS 2019T) as type strain and Photorhabdus luminescens subsp. venezuelensis subsp. nov. with JART (=CCM 9235T =CCOS 2021T) as type strain. Our study contributes to a better understanding of the biodiversity of an important bacterial group with enormous biotechnological and agricultural potential.
Collapse
Affiliation(s)
- Ricardo A R Machado
- Experimental Biology Research Group, Institute of Biology. University of Neuchâtel, Neuchâtel, Switzerland
| | - Aashaq Hussain Bhat
- Experimental Biology Research Group, Institute of Biology. University of Neuchâtel, Neuchâtel, Switzerland
- Department of Biosciences, University Center for Research and Development, Chandigarh University, Gharuan, Mohali, 140413, Punjab, India
| | - Carlos Castaneda-Alvarez
- Experimental Biology Research Group, Institute of Biology. University of Neuchâtel, Neuchâtel, Switzerland
- Departamento de Sanidad Vegetal, Facultad de Ciencias Agronómicas. Universidad de Chile, Santiago, Chile
| | - Vladimir Půža
- Biology Centre CAS, Institute of Entomology, Branišovská 1160/31, 370 05 České Budějovice, Czech Republic
| | - Ernesto San-Blas
- Instituto de Ciencias Agroalimentarias, Animales y Ambientales (ICA3), Universidad de O'Higgins, San Fernando, Chile
| |
Collapse
|
11
|
Shay JA, Haniford LSE, Cooper A, Carrillo CD, Blais BW, Lau CHF. Exploiting a targeted resistome sequencing approach in assessing antimicrobial resistance in retail foods. ENVIRONMENTAL MICROBIOME 2023; 18:25. [PMID: 36991496 PMCID: PMC10052294 DOI: 10.1186/s40793-023-00482-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 03/15/2023] [Indexed: 06/16/2023]
Abstract
BACKGROUND With the escalating risk of antimicrobial resistance (AMR), there are limited analytical options available that can comprehensively assess the burden of AMR carried by clinical/environmental samples. Food can be a potential source of AMR bacteria for humans, but its significance in driving the clinical spread of AMR remains unclear, largely due to the lack of holistic-yet-sensitive tools for surveillance and evaluation. Metagenomics is a culture-independent approach well suited for uncovering genetic determinants of defined microbial traits, such as AMR, present within unknown bacterial communities. Despite its popularity, the conventional approach of non-selectively sequencing a sample's metagenome (namely, shotgun-metagenomics) has several technical drawbacks that lead to uncertainty about its effectiveness for AMR assessment; for instance, the low discovery rate of resistance-associated genes due to their naturally small genomic footprint within the vast metagenome. Here, we describe the development of a targeted resistome sequencing method and demonstrate its application in the characterization of the AMR gene profile of bacteria associated with several retail foods. RESULT A targeted-metagenomic sequencing workflow using a customized bait-capture system targeting over 4,000 referenced AMR genes and 263 plasmid replicon sequences was validated against both mock and sample-derived bacterial community preparations. Compared to shotgun-metagenomics, the targeted method consistently provided for improved recovery of resistance gene targets with a much-improved target detection efficiency (> 300-fold). Targeted resistome analyses conducted on 36 retail-acquired food samples (fresh sprouts, n = 10; ground meat, n = 26) and their corresponding bacterial enrichment cultures (n = 36) reveals in-depth features regarding the identity and diversity of AMR genes, most of which were otherwise undetected by the whole-metagenome shotgun sequencing method. Furthermore, our findings suggest that foodborne Gammaproteobacteria could be the major reservoir of food-associated AMR genetic determinants, and that the resistome structure of the selected high-risk food commodities are, to a large extent, dictated by microbiome composition. CONCLUSIONS For metagenomic sequencing-based surveillance of AMR, the target-capture method presented herein represents a more sensitive and efficient approach to evaluate the resistome profile of complex food or environmental samples. This study also further implicates retail foods as carriers of diverse resistance-conferring genes indicating a potential impact on the dissemination of AMR.
Collapse
Affiliation(s)
- Julie A Shay
- Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Laura S E Haniford
- Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Ashley Cooper
- Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Catherine D Carrillo
- Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Burton W Blais
- Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Calvin Ho-Fung Lau
- Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON, Canada.
| |
Collapse
|
12
|
A case for investment in clinical metagenomics in low-income and middle-income countries. THE LANCET. MICROBE 2023; 4:e192-e199. [PMID: 36563703 DOI: 10.1016/s2666-5247(22)00328-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 12/24/2022]
Abstract
Clinical metagenomics is the diagnostic approach with the broadest capacity to detect both known and novel pathogens. Clinical metagenomics is costly to run and requires infrastructure, but the use of next-generation sequencing for SARS-CoV-2 molecular epidemiology in low-income and middle-income countries (LMICs) offers an opportunity to direct this infrastructure to the establishment of clinical metagenomics programmes. Local implementation of clinical metagenomics is important to create relevant systems and evaluate cost-effective methodologies for its use, as well as to ensure that reference databases and result interpretation tools are appropriate to local epidemiology. Rational implementation, based on the needs of LMICs and the available resources, could ultimately improve individual patient care in instances in which available diagnostics are inadequate and supplement emerging infectious disease surveillance systems to ensure the next pandemic pathogen is quickly identified.
Collapse
|
13
|
Abstract
Shopping malls offer various niches for microbial populations, potentially serving as sources and reservoirs for the spread of microorganisms of public health concern. However, knowledge about the microbiome and the distribution of human pathogens in malls is largely unknown. Here, we examine the microbial community dynamics and genotypes of potential pathogens from floor and escalator surfaces in shopping malls and adjacent road dusts and greenbelt soils. The distribution pattern of microbial communities is driven primarily by habitats and seasons. A significant enrichment of human-associated microbiota in the indoor environment indicates that human interactions with surfaces might be another strong driver for mall microbiomes. Neutral community models suggest that the microbial community assembly is strongly driven by stochastic processes. Distinct performances of microbial taxonomic signatures for environmental classifications indicate the consistent differences of microbial communities of different seasons/habitats and the strong anthropogenic effect on homogenizing microbial communities of shopping malls. Indoor environments harbored higher concentrations of human pathogens than outdoor samples, also carrying a high proportion of antimicrobial resistance-associated multidrug efflux genes and virulence genes. These findings enhanced the understanding of the microbiome in the built environment and the interactions between humans and the built environment, providing a basis for tracking biothreats and communicable diseases and developing sophisticated early warning systems. IMPORTANCE Shopping malls are distinct microbial environments which can facilitate a constant transmission of microorganisms of public health concern between humans and the built environment or between human and human. Despite extensive investigation of the natural environmental microbiome, no comprehensive profile of microbial ecology has been reported in malls. Characterizing microbial distribution, potential pathogens, and antimicrobial resistance will enhance our understanding of how these microbial communities are formed, maintained, and transferred and help establish a baseline for biosurveillance of potential public health threats in malls.
Collapse
|
14
|
Validation and Application of Long-Read Whole-Genome Sequencing for Antimicrobial Resistance Gene Detection and Antimicrobial Susceptibility Testing. Antimicrob Agents Chemother 2023; 67:e0107222. [PMID: 36533931 PMCID: PMC9872642 DOI: 10.1128/aac.01072-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Next-generation sequencing applications are increasingly used for detection and characterization of antimicrobial-resistant pathogens in clinical settings. Oxford Nanopore Technologies (ONT) sequencing offers advantages for clinical use compared with other sequencing methodologies because it enables real-time basecalling, produces long sequencing reads that increase the ability to correctly assemble DNA fragments, provides short turnaround times, and requires relatively uncomplicated sample preparation. A drawback of ONT sequencing, however, is its lower per-read accuracy than short-read sequencing. We sought to identify best practices in ONT sequencing protocols. As some variability in sequencing results may be introduced by the DNA extraction methodology, we tested three DNA extraction kits across three independent laboratories using a representative set of six bacterial isolates to investigate accuracy and reproducibility of ONT technology. All DNA extraction techniques showed comparable performance; however, the DNeasy PowerSoil Pro kit had the highest sequencing yield. This kit was subsequently applied to 42 sequentially collected bacterial isolates from blood cultures to assess Ares Genetics's pipelines for predictive whole-genome sequencing antimicrobial susceptibility testing (WGS-AST) performance compared to phenotypic triplicate broth microdilution results. WGS-AST results ranged across the organisms and resulted in an overall categorical agreement of 95% for penicillins, 82.4% for cephalosporins, 76.7% for carbapenems, 86.9% for fluoroquinolones, and 96.2% for aminoglycosides. Very major errors/major errors were 0%/16.7% (penicillins), 11.7%/3.6% (cephalosporins), 0%/24.4% (carbapenems), 2.5%/7.7% (fluoroquinolones), and 0%/4.1% (aminoglycosides), respectively. This work showed that, although additional refinements are necessary, ONT sequencing demonstrates potential as a method to perform WGS-AST on cultured isolates for patient care.
Collapse
|
15
|
Li Y, Shi X, Zuo Y, Li T, Liu L, Shen Z, Shen J, Zhang R, Wang S. Multiplexed Target Enrichment Enables Efficient and In-Depth Analysis of Antimicrobial Resistome in Metagenomes. Microbiol Spectr 2022; 10:e0229722. [PMID: 36287061 PMCID: PMC9769626 DOI: 10.1128/spectrum.02297-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 10/04/2022] [Indexed: 01/06/2023] Open
Abstract
Antibiotic resistance genes (ARGs) pose a serious threat to public health and ecological security in the 21st century. However, the resistome only accounts for a tiny fraction of metagenomic content, which makes it difficult to investigate low-abundance ARGs in various environmental settings. Thus, a highly sensitive, accurate, and comprehensive method is needed to describe ARG profiles in complex metagenomic samples. In this study, we established a high-throughput sequencing method based on targeted amplification, which could simultaneously detect ARGs (n = 251), mobile genetic element genes (n = 8), and metal resistance genes (n = 19) in metagenomes. The performance of amplicon sequencing was compared with traditional metagenomic shotgun sequencing (MetaSeq). A total of 1421 primer pairs were designed, achieving extremely high coverage of target genes. The amplicon sequencing significantly improved the recovery of target ARGs (~9 × 104-fold), with higher sensitivity and diversity, less cost, and computation burden. Furthermore, targeted enrichment allows deep scanning of single nucleotide polymorphisms (SNPs), and elevated SNPs detection was shown in this study. We further performed this approach for 48 environmental samples (37 feces, 20 soils, and 7 sewage) and 16 clinical samples. All samples tested in this study showed high diversity and recovery of targeted genes. Our results demonstrated that the approach could be applied to various metagenomic samples and served as an efficient tool in the surveillance and evolution assessment of ARGs. Access to the resistome using the enrichment method validated in this study enabled the capture of low-abundance resistomes while being less costly and time-consuming, which can greatly advance our understanding of local and global resistome dynamics. IMPORTANCE ARGs, an increasing global threat to human health, can be transferred into health-related microorganisms in the environment by horizontal gene transfer, posing a serious threat to public health. Advancing profiling methods are needed for monitoring and predicting the potential risks of ARGs in metagenomes. Our study described a customized amplicon sequencing assay that could enable a high-throughput, targeted, in-depth analysis of ARGs and detect a low-abundance portion of resistomes. This method could serve as an efficient tool to assess the variation and evolution of specific ARGs in the clinical and natural environment.
Collapse
Affiliation(s)
- Yiming Li
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Xiaomin Shi
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Yang Zuo
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Tian Li
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Lu Liu
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Zhangqi Shen
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Jianzhong Shen
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Rong Zhang
- The Second Affiliated Hospital of Zhejiang University, Zhejiang University, Hangzhou, China
| | - Shaolin Wang
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| |
Collapse
|
16
|
Harrington A, Vo V, Papp K, Tillett RL, Chang CL, Baker H, Shen S, Amei A, Lockett C, Gerrity D, Oh EC. Urban monitoring of antimicrobial resistance during a COVID-19 surge through wastewater surveillance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 853:158577. [PMID: 36087661 PMCID: PMC9450474 DOI: 10.1016/j.scitotenv.2022.158577] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/25/2022] [Accepted: 09/03/2022] [Indexed: 05/31/2023]
Abstract
During the early phase of the COVID-19 pandemic, infected patients presented with symptoms similar to bacterial pneumonias and were treated with antibiotics before confirmation of a bacterial or fungal co-infection. We reasoned that wastewater surveillance could reveal potential relationships between reduced antimicrobial stewardship, specifically misprescribing antibiotics to treat viral infections, and the occurrence of antimicrobial resistance (AMR) in an urban community. Here, we analyzed microbial communities and AMR profiles in sewage samples from a wastewater treatment plant (WWTP) and a community shelter in Las Vegas, Nevada during a COVID-19 surge in December 2020. Using a respiratory pathogen and AMR enrichment next-generation sequencing panel, we identified four major phyla in the wastewater, including Actinobacteria, Firmicutes, Bacteroidetes and Proteobacteria. Consistent with antibiotics that were reportedly used to treat COVID-19 infections (e.g., fluoroquinolones and beta-lactams), we also measured a significant spike in corresponding AMR genes in the wastewater samples. AMR genes associated with colistin resistance (mcr genes) were also identified exclusively at the WWTP, suggesting that multidrug resistant bacterial infections were being treated during this time. We next compared the Las Vegas sewage data to local 2018-2019 antibiograms, which are antimicrobial susceptibility profile reports about common clinical pathogens. Similar to the discovery of higher levels of beta-lactamase resistance genes in sewage during 2020, beta-lactam antibiotics accounted for 51 ± 3 % of reported antibiotics used in antimicrobial susceptibility tests of 2018-2019 clinical isolates. Our data highlight how wastewater-based epidemiology (WBE) can be leveraged to complement more traditional surveillance efforts by providing community-level data to help identify current and emerging AMR threats.
Collapse
Affiliation(s)
- Anthony Harrington
- Laboratory of Neurogenetics and Precision Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Van Vo
- Laboratory of Neurogenetics and Precision Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA; Nevada Institute of Personalized Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Katerina Papp
- Southern Nevada Water Authority, P.O. Box 99954, Las Vegas, NV 89193, USA
| | - Richard L Tillett
- Nevada Institute of Personalized Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Ching-Lan Chang
- Laboratory of Neurogenetics and Precision Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Hayley Baker
- Laboratory of Neurogenetics and Precision Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Shirley Shen
- Nevada Institute of Personalized Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Amei Amei
- Department of Mathematical Sciences, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | | | - Daniel Gerrity
- Southern Nevada Water Authority, P.O. Box 99954, Las Vegas, NV 89193, USA
| | - Edwin C Oh
- Laboratory of Neurogenetics and Precision Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA; Nevada Institute of Personalized Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA; Department of Internal Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA.
| |
Collapse
|
17
|
Slizovskiy IB, Oliva M, Settle JK, Zyskina LV, Prosperi M, Boucher C, Noyes NR. Target-enriched long-read sequencing (TELSeq) contextualizes antimicrobial resistance genes in metagenomes. MICROBIOME 2022; 10:185. [PMID: 36324140 PMCID: PMC9628182 DOI: 10.1186/s40168-022-01368-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Metagenomic data can be used to profile high-importance genes within microbiomes. However, current metagenomic workflows produce data that suffer from low sensitivity and an inability to accurately reconstruct partial or full genomes, particularly those in low abundance. These limitations preclude colocalization analysis, i.e., characterizing the genomic context of genes and functions within a metagenomic sample. Genomic context is especially crucial for functions associated with horizontal gene transfer (HGT) via mobile genetic elements (MGEs), for example antimicrobial resistance (AMR). To overcome this current limitation of metagenomics, we present a method for comprehensive and accurate reconstruction of antimicrobial resistance genes (ARGs) and MGEs from metagenomic DNA, termed target-enriched long-read sequencing (TELSeq). RESULTS Using technical replicates of diverse sample types, we compared TELSeq performance to that of non-enriched PacBio and short-read Illumina sequencing. TELSeq achieved much higher ARG recovery (>1,000-fold) and sensitivity than the other methods across diverse metagenomes, revealing an extensive resistome profile comprising many low-abundance ARGs, including some with public health importance. Using the long reads generated by TELSeq, we identified numerous MGEs and cargo genes flanking the low-abundance ARGs, indicating that these ARGs could be transferred across bacterial taxa via HGT. CONCLUSIONS TELSeq can provide a nuanced view of the genomic context of microbial resistomes and thus has wide-ranging applications in public, animal, and human health, as well as environmental surveillance and monitoring of AMR. Thus, this technique represents a fundamental advancement for microbiome research and application. Video abstract.
Collapse
Affiliation(s)
- Ilya B Slizovskiy
- Food-Centric Corridor, Infectious Disease Laboratory, Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - Marco Oliva
- Department of Computer and Information Science and Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, USA
| | - Jonathen K Settle
- Department of Computer and Information Science and Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, USA
| | - Lidiya V Zyskina
- Program in Human-Computer Interaction, College of Information Studies, University of Maryland, College Park, MD, USA
| | - Mattia Prosperi
- Data Intelligence Systems Lab, Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, FL, USA
| | - Christina Boucher
- Department of Computer and Information Science and Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, USA
| | - Noelle R Noyes
- Food-Centric Corridor, Infectious Disease Laboratory, Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA.
| |
Collapse
|
18
|
Alcock BP, Huynh W, Chalil R, Smith KW, Raphenya A, Wlodarski MA, Edalatmand A, Petkau A, Syed SA, Tsang KK, Baker SJC, Dave M, McCarthy M, Mukiri KM, Nasir JA, Golbon B, Imtiaz H, Jiang X, Kaur K, Kwong M, Liang ZC, Niu KC, Shan P, Yang JYJ, Gray K, Hoad GR, Jia B, Bhando T, Carfrae L, Farha M, French S, Gordzevich R, Rachwalski K, Tu M, Bordeleau E, Dooley D, Griffiths E, Zubyk HL, Brown ED, Maguire F, Beiko R, Hsiao WWL, Brinkman FSL, Van Domselaar G, McArthur AG. CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database. Nucleic Acids Res 2022; 51:D690-D699. [PMID: 36263822 PMCID: PMC9825576 DOI: 10.1093/nar/gkac920] [Citation(s) in RCA: 229] [Impact Index Per Article: 114.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/03/2022] [Accepted: 10/11/2022] [Indexed: 01/30/2023] Open
Abstract
The Comprehensive Antibiotic Resistance Database (CARD; card.mcmaster.ca) combines the Antibiotic Resistance Ontology (ARO) with curated AMR gene (ARG) sequences and resistance-conferring mutations to provide an informatics framework for annotation and interpretation of resistomes. As of version 3.2.4, CARD encompasses 6627 ontology terms, 5010 reference sequences, 1933 mutations, 3004 publications, and 5057 AMR detection models that can be used by the accompanying Resistance Gene Identifier (RGI) software to annotate genomic or metagenomic sequences. Focused curation enhancements since 2020 include expanded β-lactamase curation, incorporation of likelihood-based AMR mutations for Mycobacterium tuberculosis, addition of disinfectants and antiseptics plus their associated ARGs, and systematic curation of resistance-modifying agents. This expanded curation includes 180 new AMR gene families, 15 new drug classes, 1 new resistance mechanism, and two new ontological relationships: evolutionary_variant_of and is_small_molecule_inhibitor. In silico prediction of resistomes and prevalence statistics of ARGs has been expanded to 377 pathogens, 21,079 chromosomes, 2,662 genomic islands, 41,828 plasmids and 155,606 whole-genome shotgun assemblies, resulting in collation of 322,710 unique ARG allele sequences. New features include the CARD:Live collection of community submitted isolate resistome data and the introduction of standardized 15 character CARD Short Names for ARGs to support machine learning efforts.
Collapse
Affiliation(s)
- Brian P Alcock
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - William Huynh
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Romeo Chalil
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Keaton W Smith
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Amogelang R Raphenya
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Mateusz A Wlodarski
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Arman Edalatmand
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Aaron Petkau
- Department of Computer Science, University of Manitoba, Winnipeg, Manitoba, Canada,National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Sohaib A Syed
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Kara K Tsang
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Sheridan J C Baker
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Mugdha Dave
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Madeline C McCarthy
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Karyn M Mukiri
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Jalees A Nasir
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Bahar Golbon
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Hamna Imtiaz
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Xingjian Jiang
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Komal Kaur
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Megan Kwong
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Zi Cheng Liang
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Keyu C Niu
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Prabakar Shan
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Jasmine Y J Yang
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Kristen L Gray
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Gemma R Hoad
- Research Computing Group, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Baofeng Jia
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Timsy Bhando
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Lindsey A Carfrae
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Maya A Farha
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Shawn French
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Rodion Gordzevich
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Kenneth Rachwalski
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Megan M Tu
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Emily Bordeleau
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Damion Dooley
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Emma Griffiths
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Haley L Zubyk
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Eric D Brown
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Finlay Maguire
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada,Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada,Department of Community Health & Epidemiology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Robert G Beiko
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada,Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - William W L Hsiao
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada,Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Fiona S L Brinkman
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Gary Van Domselaar
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada,Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Andrew G McArthur
- To whom correspondence should be addressed. Tel: +1 905 525 9140 (Ext 21663);
| |
Collapse
|
19
|
Castaneda-Alvarez C, Machado RAR, Morales-Montero P, Boss A, Muller A, Prodan S, Zamorano A, San-Blas E, Půža V, Aballay E. Photorhabdus antumapuensis sp. nov., a novel symbiotic bacterial species associated with Heterorhabditis atacamensis entomopathogenic nematodes. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
One motile, Gram-negative, non-spore-forming and rod-shaped symbiotic bacterium, strain UCH-936T, was isolated from Heterorhabditis atacamensis nematodes. Results of biochemical, physiological, molecular and genomic analyses suggest that it represents a new species, which we propose to name Photorhabdus antumapuensis sp. nov. Digital DNA–DNA hybridization shows that strain UCH-936T is more closely related to
Photorhabdus kleinii
DSM 23513T, but shares solely 50.5 % similarity, which is below the 70% cut-off value that delimits species boundaries in bacteria. Phylogenetic reconstructions using whole-genome sequences show that strain UCH-936T forms a unique clade, suggesting its novel and distinct taxonomic status again. Similarly, comparative genomic analyses shows that the virulence factor flagella-related gene fleR, the type IV pili-related gene pilL and the vibriobactin-related gene vibE are present in the genome of strain UCH-936T but absent in the genomes of its closest relatives. Biochemically and physiologically, UCH-936T differs also from all closely related
Photorhabdus
species. Therefore, Photorhabdus antumapuensis sp. nov. is proposed as a new species with the type strain UCH-936T (CCCT 21.06T=CCM 9188T=CCOS 1991T).
Collapse
Affiliation(s)
- Carlos Castaneda-Alvarez
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur Universidad de Chile, Santa Rosa 11315, La Pintana, Santiago, CP 8820808, Chile
- Departamento de Sanidad Vegetal, Facultad de Ciencias Agronómicas, Universidad de Chile, P.O. Box 1004, Santiago, Chile
| | - Ricardo A. R. Machado
- Experimental Biology Research Group, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Patricia Morales-Montero
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Macul, Santiago, Chile
- Experimental Biology Research Group, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Anja Boss
- Experimental Biology Research Group, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Arthur Muller
- Experimental Biology Research Group, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Simona Prodan
- Departamento de Sanidad Vegetal, Facultad de Ciencias Agronómicas, Universidad de Chile, P.O. Box 1004, Santiago, Chile
| | - Alan Zamorano
- Departamento de Sanidad Vegetal, Facultad de Ciencias Agronómicas, Universidad de Chile, P.O. Box 1004, Santiago, Chile
| | - Ernesto San-Blas
- Instituto de Ciencias Agroalimentarias, Animales y Ambientales (ICA3), Universidad de O'Higgins, San Pedro, San José Province, Chile
| | - Vladimír Půža
- Laboratory of Entomopathogenic Nematodes, Institute of Entomology, Biology Centre CAS, Branišovská 31, České Budějovice, 370 05, Czechia
| | - Erwin Aballay
- Departamento de Sanidad Vegetal, Facultad de Ciencias Agronómicas, Universidad de Chile, P.O. Box 1004, Santiago, Chile
| |
Collapse
|
20
|
Cui G, Liu Z, Xu W, Gao Y, Yang S, Grossart HP, Li M, Luo Z. Metagenomic exploration of antibiotic resistance genes and their hosts in aquaculture waters of the semi-closed Dongshan Bay (China). THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:155784. [PMID: 35537512 DOI: 10.1016/j.scitotenv.2022.155784] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/30/2022] [Accepted: 05/04/2022] [Indexed: 06/14/2023]
Abstract
In marine environments, increasing occurrence and numbers of microbial Antibiotic Resistance Gene (ARG) subtypes, especially of new beta-lactamases, have received lots of attention in recent years. Updated databases with novel developed tools provide new opportunities to obtain more comprehensive ARG profiles as well as ARG-carrying hosts. Yet, ARGs in human-associated marine aquaculture environments, e.g. in China, remains largely unknown. Using metagenomic data, we revealed high numbers of Multi-drug Resistance, beta-lactamase and aminoglycoside genes throughout the year. Thereby, Alpha- and Gamma-proteobacteria were assigned to the majority of beta-lactamase-carrying hosts. From Metagenome-assembled genomes, three blaF-like beta-lactamases (91.7-94.7% identity with beta-lactamase from Mycobacterium fortuitum (blaF)) were exclusively observed in an unclassified Mycobacterium genus. Notably, other new beta-lactamases, VMB-1-like (n = 3) (58.5-67.4% identity to Vibrio metallo-beta-lactamase 1 (VMB-1)), were found in Gammaproteobacteria. Additionally, 175 Multi-drug Resistant Organisms possessed at least 3 ARG subtypes, and seven of the potentially pathogenic genera (n = 17) were assigned to Gammaproteobacteria. These results, together with high-risk ARGs (e.g. tetM, dfrA14 and dfrA17), provide hosts and new beta-lactamases of ARGs in Chinese coastal aquaculture.
Collapse
Affiliation(s)
- Guojie Cui
- College of Civil and Transportation Engineering, Shenzhen University, Shenzhen 518060, China; Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Zongbao Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Wei Xu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Yuanhao Gao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Shuai Yang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Hans-Peter Grossart
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Stechlin 16775, Germany; Institute of Biochemistry and Biology, Postdam University, Potsdam 14469, Germany
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China.
| | - Zhuhua Luo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China; School of Marine Sciences, Nanjing University of Information Science and Technology, Nanjing 210044, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China.
| |
Collapse
|
21
|
Lindstedt K, Buczek D, Pedersen T, Hjerde E, Raffelsberger N, Suzuki Y, Brisse S, Holt K, Samuelsen Ø, Sundsfjord A. Detection of Klebsiella pneumoniae human gut carriage: a comparison of culture, qPCR, and whole metagenomic sequencing methods. Gut Microbes 2022; 14:2118500. [PMID: 36045603 PMCID: PMC9450895 DOI: 10.1080/19490976.2022.2118500] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Klebsiella pneumoniae is an important opportunistic healthcare-associated pathogen and major contributor to the global spread of antimicrobial resistance. Gastrointestinal colonization with K. pneumoniae is a major predisposing risk factor for infection and forms an important hub for the dispersal of resistance. Current culture-based detection methods are time consuming, give limited intra-sample abundance and strain diversity information, and have uncertain sensitivity. Here we investigated the presence and abundance of K. pneumoniae at the species and strain level within fecal samples from 103 community-based adults by qPCR and whole metagenomic sequencing (WMS) compared to culture-based detection. qPCR demonstrated the highest sensitivity, detecting K. pneumoniae in 61.2% and 75.8% of direct-fecal and culture-enriched sweep samples, respectively, including 52/52 culture-positive samples. WMS displayed lower sensitivity, detecting K. pneumoniae in 71.2% of culture-positive fecal samples at a 0.01% abundance cutoff, and was inclined to false positives in proportion to the relative abundance of other Enterobacterales present. qPCR accurately quantified K. pneumoniae to 16 genome copies/reaction while WMS could estimate relative abundance to at least 0.01%. Quantification by both methods correlated strongly with each other (Spearman's rho = 0.91). WMS also supported accurate intra-sample K. pneumoniae sequence type (ST)-level diversity detection from fecal microbiomes to 0.1% relative abundance, agreeing with the culture-based detected ST in 16/19 samples. Our results show that qPCR and WMS are sensitive and reliable tools for detection, quantification, and strain analysis of K. pneumoniae from fecal samples with potential to support infection control and enhance insights in K. pneumoniae gastrointestinal ecology.
Collapse
Affiliation(s)
- Kenneth Lindstedt
- Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway,CONTACT Kenneth Lindstedt
| | - Dorota Buczek
- Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway
| | - Torunn Pedersen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Erik Hjerde
- Department of Chemistry, UiT the Arctic University of Norway, Tromsø, Norway
| | - Niclas Raffelsberger
- Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway,Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, The University of Tokyo, Tokyo, Japan
| | - Sylvain Brisse
- Biodiversity and Epidemiology of Bacterial Pathogens Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - Kathryn Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia,Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Ørjan Samuelsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway,Department of Pharmacy, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway
| | - Arnfinn Sundsfjord
- Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway,Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway,Arnfinn Sundsfjord Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, 9038, Norway
| |
Collapse
|
22
|
Guitor AK, Yousuf EI, Raphenya AR, Hutton EK, Morrison KM, McArthur AG, Wright GD, Stearns JC. Capturing the antibiotic resistome of preterm infants reveals new benefits of probiotic supplementation. MICROBIOME 2022; 10:136. [PMID: 36008821 PMCID: PMC9414150 DOI: 10.1186/s40168-022-01327-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/14/2022] [Indexed: 05/28/2023]
Abstract
BACKGROUND Probiotic use in preterm infants can mitigate the impact of antibiotic exposure and reduce rates of certain illnesses; however, the benefit on the gut resistome, the collection of antibiotic resistance genes, requires further investigation. We hypothesized that probiotic supplementation of early preterm infants (born < 32-week gestation) while in hospital reduces the prevalence of antibiotic resistance genes associated with pathogenic bacteria in the gut. We used a targeted capture approach to compare the resistome from stool samples collected at the term corrected age of 40 weeks for two groups of preterm infants (those that routinely received a multi-strain probiotic during hospitalization and those that did not) with samples from full-term infants at 10 days of age to identify if preterm birth or probiotic supplementation impacted the resistome. We also compared the two groups of preterm infants up to 5 months of age to identify persistent antibiotic resistance genes. RESULTS At the term corrected age, or 10 days of age for the full-term infants, we found over 80 antibiotic resistance genes in the preterm infants that did not receive probiotics that were not identified in either the full-term or probiotic-supplemented preterm infants. More genes associated with antibiotic inactivation mechanisms were identified in preterm infants unexposed to probiotics at this collection time-point compared to the other infants. We further linked these genes to mobile genetic elements and Enterobacteriaceae, which were also abundant in their gut microbiomes. Various genes associated with aminoglycoside and beta-lactam resistance, commonly found in pathogenic bacteria, were retained for up to 5 months in the preterm infants that did not receive probiotics. CONCLUSIONS This pilot survey of preterm infants shows that probiotics administered after preterm birth during hospitalization reduced the diversity and prevented persistence of antibiotic resistance genes in the gut microbiome. The benefits of probiotic use on the microbiome and the resistome should be further explored in larger groups of infants. Due to its high sensitivity and lower sequencing cost, our targeted capture approach can facilitate these surveys to further address the implications of resistance genes persisting into infancy without the need for large-scale metagenomic sequencing. Video Abstract.
Collapse
Affiliation(s)
- Allison K Guitor
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Canada
| | - Efrah I Yousuf
- Department of Pediatrics, McMaster University, Hamilton, Canada
| | - Amogelang R Raphenya
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Canada
| | - Eileen K Hutton
- Department of Obstetrics & Gynecology, McMaster University, Hamilton, Canada
- The Baby & Mi and the Baby & Pre-Mi Cohort Studies, Hamilton, Canada
| | - Katherine M Morrison
- Department of Pediatrics, McMaster University, Hamilton, Canada
- The Baby & Mi and the Baby & Pre-Mi Cohort Studies, Hamilton, Canada
| | - Andrew G McArthur
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Canada
| | - Gerard D Wright
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Canada
| | - Jennifer C Stearns
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada.
- The Baby & Mi and the Baby & Pre-Mi Cohort Studies, Hamilton, Canada.
- Department of Medicine, McMaster University, Hamilton, Canada.
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Canada.
| |
Collapse
|
23
|
Pailhoriès H, Herrmann JL, Velo-Suarez L, Lamoureux C, Beauruelle C, Burgel PR, Héry-Arnaud G. Antibiotic resistance in chronic respiratory diseases: from susceptibility testing to the resistome. Eur Respir Rev 2022; 31:31/164/210259. [PMID: 35613743 DOI: 10.1183/16000617.0259-2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 03/02/2022] [Indexed: 12/28/2022] Open
Abstract
The development of resistome analysis, i.e. the comprehensive analysis of antibiotic-resistance genes (ARGs), is enabling a better understanding of the mechanisms of antibiotic-resistance emergence. The respiratory microbiome is a dynamic and interactive network of bacteria, with a set of ARGs that could influence the response to antibiotics. Viruses such as bacteriophages, potential carriers of ARGs, may also form part of this respiratory resistome. Chronic respiratory diseases (CRDs) such as cystic fibrosis, severe asthma, chronic obstructive pulmonary disease and bronchiectasis, managed with long-term antibiotic therapies, lead to multidrug resistance. Antibiotic susceptibility testing provides a partial view of the bacterial response to antibiotics in the complex lung environment. Assessing the ARG network would allow personalised, targeted therapeutic strategies and suitable antibiotic stewardship in CRDs, depending on individual resistome and microbiome signatures. This review summarises the influence of pulmonary antibiotic protocols on the respiratory microbiome, detailing the variable consequences according to antibiotic class and duration of treatment. The different resistome-profiling methods are explained to clarify their respective place in antibiotic-resistance analysis in the lungs. Finally, this review details current knowledge on the respiratory resistome related to therapeutic strategies and provides insight into the application of resistome analysis to counter the emergence of multidrug-resistant respiratory pathogens.
Collapse
Affiliation(s)
- Hélène Pailhoriès
- Laboratoire de Bactériologie, Institut de Biologie en Santé - PBH, CHU Angers, Angers, France.,HIFIH Laboratory UPRES EA3859, SFR ICAT 4208, Angers University, Angers, France
| | - Jean-Louis Herrmann
- Université Paris-Saclay, UVSQ, INSERM, Infection and Inflammation, Montigny-le-Bretonneux, France.,AP-HP, Groupe Hospitalo-Universitaire Paris-Saclay, Hôpital Raymond Poincaré, Garches, France
| | - Lourdes Velo-Suarez
- Brest Center for Microbiota Analysis (CBAM), Brest University Hospital, Brest, France
| | - Claudie Lamoureux
- Dept of Bacteriology, Virology, Hospital Hygiene, and Parasitology-Mycology, Brest University Hospital, Brest, France.,Université de Brest, INSERM, EFS, UMR 1078, GGB, Brest, France
| | - Clémence Beauruelle
- Dept of Bacteriology, Virology, Hospital Hygiene, and Parasitology-Mycology, Brest University Hospital, Brest, France.,Université de Brest, INSERM, EFS, UMR 1078, GGB, Brest, France
| | - Pierre-Régis Burgel
- Respiratory Medicine and National Cystic Fibrosis Reference Center, Cochin Hospital, Assistance Publique-Hôpitaux de Paris, Université de Paris, Institut Cochin, INSERM U1016, Paris, France
| | - Geneviève Héry-Arnaud
- Brest Center for Microbiota Analysis (CBAM), Brest University Hospital, Brest, France .,Dept of Bacteriology, Virology, Hospital Hygiene, and Parasitology-Mycology, Brest University Hospital, Brest, France.,Université de Brest, INSERM, EFS, UMR 1078, GGB, Brest, France
| |
Collapse
|
24
|
Harnessing Rare Actinomycete Interactions and Intrinsic Antimicrobial Resistance Enables Discovery of an Unusual Metabolic Inhibitor. mBio 2022; 13:e0039322. [PMID: 35608300 PMCID: PMC9239090 DOI: 10.1128/mbio.00393-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Bacterial natural products have historically been a deep source of new medicines, but their slowed discovery in recent decades has put a premium on developing strategies that enhance the likelihood of capturing novel compounds. Here, we used a straightforward approach that capitalizes on the interactive ecology of “rare” actinomycetes. Specifically, we screened for interactions that triggered the production of antimicrobials that inhibited the growth of a bacterial strain with exceptionally diverse natural antimicrobial resistance. This strategy led to the discovery of a family of antimicrobials we term the dynaplanins. Heterologous expression enabled identification of the dynaplanin biosynthetic gene cluster, which was missed by typical algorithms for natural product gene cluster detection. Genome sequencing of partially resistant mutants revealed a 2-oxo acid dehydrogenase E2 subunit as the likely molecular target of the dynaplanins, and this finding was supported by computational modeling of the dynaplanin scaffold within the active site of this enzyme. Thus, this simple strategy, which leverages microbial interactions and natural antibiotic resistance, can enable discovery of molecules with unique antimicrobial activity. In addition, these results indicate that primary metabolism may be a direct target for inhibition via chemical interference in competitive microbial interactions.
Collapse
|
25
|
Performance Characteristics of Next-Generation Sequencing for the Detection of Antimicrobial Resistance Determinants in Escherichia coli Genomes and Metagenomes. mSystems 2022; 7:e0002222. [PMID: 35642524 PMCID: PMC9238399 DOI: 10.1128/msystems.00022-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Short-read sequencing can provide detection of multiple genomic determinants of antimicrobial resistance from single bacterial genomes and metagenomic samples. Despite its increasing application in human, animal, and environmental microbiology, including human clinical trials, the performance of short-read Illumina sequencing for antimicrobial resistance gene (ARG) detection, including resistance-conferring single nucleotide polymorphisms (SNPs), has not been systematically characterized. Using paired-end 2 × 150 bp (base pair) Illumina sequencing and an assembly-based method for ARG prediction, we determined sensitivity, positive predictive value (PPV), and sequencing depths required for ARG detection in an Escherichia coli isolate of sequence type (ST) 38 spiked into a synthetic microbial community at varying abundances. Approximately 300,000 reads or 15× genome coverage was sufficient to detect ARGs in E. coli ST38, with comparable sensitivity and PPV to ~100× genome coverage. Using metagenome assembly of mixed microbial communities, ARG detection at E. coli relative abundances of 1% would require assembly of approximately 30 million reads to achieve 15× target coverage. The minimum sequencing depths were validated using public data sets of 948 E. coli genomes and 10 metagenomic rectal swab samples. A read-based approach using k-mer alignment (KMA) for ARG prediction did not substantially improve minimum sequencing depths for ARG detection compared to assembly of the E. coli ST38 genome or the combined metagenomic samples. Analysis of sequencing depths from recent studies assessing ARG content in metagenomic samples demonstrated that sequencing depths had a median estimated detection frequency of 84% (interquartile range: 30%-92%) for a relative abundance of 1%. IMPORTANCE Systematically determining Illumina sequencing performance characteristics for detection of ARGs in metagenomic samples is essential to inform study design and appraisal of human, animal, and environmental metagenomic antimicrobial resistance studies. In this study, we quantified the performance characteristics of ARG detection in E. coli genomes and metagenomes and established a benchmark of ~15× coverage for ARG detection for E. coli in metagenomes. We demonstrate that for low relative abundances, sequencing depths of ~30 million reads or more may be required for adequate sensitivity for many applications.
Collapse
|
26
|
Alanko JN, Slizovskiy IB, Lokshtanov D, Gagie T, Noyes NR, Boucher C. Syotti: scalable bait design for DNA enrichment. Bioinformatics 2022; 38:i177-i184. [PMID: 35758776 PMCID: PMC9235489 DOI: 10.1093/bioinformatics/btac226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Bait enrichment is a protocol that is becoming increasingly ubiquitous as it has been shown to successfully amplify regions of interest in metagenomic samples. In this method, a set of synthetic probes ('baits') are designed, manufactured and applied to fragmented metagenomic DNA. The probes bind to the fragmented DNA and any unbound DNA is rinsed away, leaving the bound fragments to be amplified for sequencing. Metsky et al. demonstrated that bait-enrichment is capable of detecting a large number of human viral pathogens within metagenomic samples. RESULTS We formalize the problem of designing baits by defining the Minimum Bait Cover problem, show that the problem is NP-hard even under very restrictive assumptions, and design an efficient heuristic that takes advantage of succinct data structures. We refer to our method as Syotti. The running time of Syotti shows linear scaling in practice, running at least an order of magnitude faster than state-of-the-art methods, including the method of Metsky et al. At the same time, our method produces bait sets that are smaller than the ones produced by the competing methods, while also leaving fewer positions uncovered. Lastly, we show that Syotti requires only 25 min to design baits for a dataset comprised of 3 billion nucleotides from 1000 related bacterial substrains, whereas the method of Metsky et al. shows clearly super-linear running time and fails to process even a subset of 17% of the data in 72 h. AVAILABILITY AND IMPLEMENTATION https://github.com/jnalanko/syotti. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Jarno N Alanko
- Department of Computer Science, University of Helsinki, Helsinki, Finland
- Faculty of Computer Science, Dalhousie University, Halifax, Canada
| | - Ilya B Slizovskiy
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN, USA
| | - Daniel Lokshtanov
- Department of Computer Science, University of California, Santa Barbara, CA, USA
| | - Travis Gagie
- Faculty of Computer Science, Dalhousie University, Halifax, Canada
| | - Noelle R Noyes
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN, USA
| | - Christina Boucher
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL, USA
| |
Collapse
|
27
|
Dias D, Fonseca C, Caetano T, Mendo S. Oh, deer! How worried should we be about the diversity and abundance of the faecal resistome of red deer? THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 825:153831. [PMID: 35151727 DOI: 10.1016/j.scitotenv.2022.153831] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
The emergence of antimicrobial resistance (AMR) is a global threat to public health. Antimicrobials are used in animal production and human medicine, which contribute to the circulation of antibiotic resistance genes (ARGs) in the environment. Wildlife can be reservoirs of pathogens and resistant bacteria. Furthermore, anthropogenic pressure can influence their resistome. This work aimed to study the AMR of the faecal microbiome of red deer, one of the most important game species in Europe. To this end, a high-throughput qPCR approach was employed to screen a high number of ARGs and the antimicrobial susceptibility of indicator bacteria was determined. Several genes that confer resistance to different classes of antibiotics were identified, with the most abundant being tetracycline ARGs. Other genes were also present that are considered current and future threats to human health, and some of these were relatively abundant. Multidrug-resistant E. coli and Enterococcus spp. were isolated, although the overall level of antibiotic resistance was low. These results highlight the pressing need to know the origin and transmission of AMR in wildlife. Thus, and considering the One Health concept, studies such as this one shows the need for surveillance programs to prevent the spread of drug-resistant strains and ARGs.
Collapse
Affiliation(s)
- Diana Dias
- CESAM and Department of Biology, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Carlos Fonseca
- CESAM and Department of Biology, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal; ForestWISE - Collaborative Laboratory for Integrated Forest & Fire Management, Quinta de Prados, 5001-801 Vila Real, Portugal
| | - Tânia Caetano
- CESAM and Department of Biology, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Sónia Mendo
- CESAM and Department of Biology, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal.
| |
Collapse
|
28
|
Diversity of Antibiotic Resistance genes and Transfer Elements-Quantitative Monitoring (DARTE-QM): a method for detection of antimicrobial resistance in environmental samples. Commun Biol 2022; 5:216. [PMID: 35301418 PMCID: PMC8931014 DOI: 10.1038/s42003-022-03155-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 02/02/2022] [Indexed: 12/01/2022] Open
Abstract
Effective monitoring of antibiotic resistance genes and their dissemination in environmental ecosystems has been hindered by the cost and efficiency of methods available for the task. We developed the Diversity of Antibiotic Resistance genes and Transfer Elements-Quantitative Monitoring (DARTE-QM), a method implementing TruSeq high-throughput sequencing to simultaneously sequence thousands of antibiotic resistant gene targets representing a full-spectrum of antibiotic resistance classes common to environmental systems. In this study, we demonstrated DARTE-QM by screening 662 antibiotic resistance genes within complex environmental samples originated from manure, soil, and livestock feces, in addition to a mock-community reference to assess sensitivity and specificity. DARTE-QM offers a new approach to studying antibiotic resistance in environmental microbiomes, showing advantages in efficiency and the ability to scale for many samples. This method provides a means of data acquisition that will alleviate some of the obstacles that many researchers in this area currently face. Smith et al. present DARTE-QM, a highthroughput sequencing method for screening environmental DNA samples for antibiotic resistance genes on a broad scale. This method is demonstrated as effective on soil, manure and livestock fecal samples, as well as a synthetic mock-community reference.
Collapse
|
29
|
Impact of long-term dietary habits on the human gut resistome in the Dutch population. Sci Rep 2022; 12:1892. [PMID: 35115599 PMCID: PMC8814023 DOI: 10.1038/s41598-022-05817-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 01/11/2022] [Indexed: 11/08/2022] Open
Abstract
The human gut microbiome plays a central role in health and disease. Environmental factors, such as lifestyle and diet, are known to shape the gut microbiome as well as the reservoir of resistance genes that these microbes harbour; the resistome. In this study we assessed whether long-term dietary habits within a single geographical region (the Netherlands) impact the human gut resistome. Faecal samples from Dutch omnivores, pescatarians, vegetarians and vegans were analysed by metagenomic shotgun sequencing (MSS) (n = 149) and resistome capture sequencing approach (ResCap) (n = 64). Among all diet groups, 119 and 145 unique antibiotic resistance genes (ARGs) were detected by MSS or ResCap, respectively. Five or fifteen ARGs were shared between all diet groups, based on MSS and ResCap, respectively. The total number of detected ARGs by MSS or ResCap was not significantly different between the groups. MSS also revealed that vegans have a distinct microbiome composition, compared to other diet groups. Vegans had a lower abundance of Streptococcus thermophilus and Lactococcus lactis compared to pescatarians and a lower abundance of S. thermophilus when compared to omnivores. In summary, our study showed that long-term dietary habits are not associated with a specific resistome signature.
Collapse
|
30
|
Aslam B, Khurshid M, Arshad MI, Muzammil S, Rasool M, Yasmeen N, Shah T, Chaudhry TH, Rasool MH, Shahid A, Xueshan X, Baloch Z. Antibiotic Resistance: One Health One World Outlook. Front Cell Infect Microbiol 2021; 11:771510. [PMID: 34900756 PMCID: PMC8656695 DOI: 10.3389/fcimb.2021.771510] [Citation(s) in RCA: 161] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 10/29/2021] [Indexed: 01/07/2023] Open
Abstract
Antibiotic resistance (ABR) is a growing public health concern worldwide, and it is now regarded as a critical One Health issue. One Health’s interconnected domains contribute to the emergence, evolution, and spread of antibiotic-resistant microorganisms on a local and global scale, which is a significant risk factor for global health. The persistence and spread of resistant microbial species, and the association of determinants at the human-animal-environment interface can alter microbial genomes, resulting in resistant superbugs in various niches. ABR is motivated by a well-established link between three domains: human, animal, and environmental health. As a result, addressing ABR through the One Health approach makes sense. Several countries have implemented national action plans based on the One Health approach to combat antibiotic-resistant microbes, following the Tripartite’s Commitment Food and Agriculture Organization (FAO)-World Organization for Animal Health (OIE)-World Health Organization (WHO) guidelines. The ABR has been identified as a global health concern, and efforts are being made to mitigate this global health threat. To summarize, global interdisciplinary and unified approaches based on One Health principles are required to limit the ABR dissemination cycle, raise awareness and education about antibiotic use, and promote policy, advocacy, and antimicrobial stewardship.
Collapse
Affiliation(s)
- Bilal Aslam
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Mohsin Khurshid
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | | | - Saima Muzammil
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Maria Rasool
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Nafeesa Yasmeen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Taif Shah
- Faculty of Life Science and Technology, Kunming University of Life Science and Technology, Kunming, China
| | - Tamoor Hamid Chaudhry
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan.,Public Health Laboratories Division, National Institute of Health, Islamabad, Pakistan
| | | | - Aqsa Shahid
- Faculty of Rehabilitation and Allied Health Sciences, Riphah International University, Faisalabad, Pakistan
| | - Xia Xueshan
- Faculty of Life Science and Technology, Kunming University of Life Science and Technology, Kunming, China
| | - Zulqarnain Baloch
- Faculty of Life Science and Technology, Kunming University of Life Science and Technology, Kunming, China
| |
Collapse
|
31
|
Dickson ZW, Hackenberger D, Kuch M, Marzok A, Banerjee A, Rossi L, Klowak JA, Fox-Robichaud A, Mossmann K, Miller MS, Surette MG, Golding GB, Poinar H. Probe design for simultaneous, targeted capture of diverse metagenomic targets. CELL REPORTS METHODS 2021; 1:100069. [PMID: 35474894 PMCID: PMC9017208 DOI: 10.1016/j.crmeth.2021.100069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 06/10/2021] [Accepted: 08/05/2021] [Indexed: 11/20/2022]
Abstract
The compounding challenges of low signal, high background, and uncertain targets plague many metagenomic sequencing efforts. One solution has been DNA capture, wherein probes are designed to hybridize with target sequences, enriching them in relation to their background. However, balancing probe depth with breadth of capture is challenging for diverse targets. To find this balance, we have developed the HUBDesign pipeline, which makes use of sequence homology to design probes at multiple taxonomic levels. This creates an efficient probe set capable of simultaneously and specifically capturing known and related sequences. We validated HUBDesign by generating probe sets targeting the breadth of coronavirus diversity, as well as a suite of bacterial pathogens often underlying sepsis. In separate experiments demonstrating significant, simultaneous enrichment, we captured SARS-CoV-2 and HCoV-NL63 in a human RNA background and seven bacterial strains in human blood. HUBDesign (https://github.com/zacherydickson/HUBDesign) has broad applicability wherever there are multiple organisms of interest.
Collapse
Affiliation(s)
- Zachery W. Dickson
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Dirk Hackenberger
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Melanie Kuch
- McMaster aDNA Center, Department of Anthropology, McMaster University, Hamilton, ON L8S 4L9, Canada
| | - Art Marzok
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada
- McMaster Immunology Research Center, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Arinjay Banerjee
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada
- McMaster Immunology Research Center, McMaster University, Hamilton, ON L8S 4K1, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
- Vaccine and Infectious Disease Organization, Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | - Laura Rossi
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada
| | | | | | - Karen Mossmann
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada
- McMaster Immunology Research Center, McMaster University, Hamilton, ON L8S 4K1, Canada
- Department of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Matthew S. Miller
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada
- McMaster Immunology Research Center, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Michael G. Surette
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada
- Department of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
| | | | - Hendrik Poinar
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada
- McMaster aDNA Center, Department of Anthropology, McMaster University, Hamilton, ON L8S 4L9, Canada
| |
Collapse
|
32
|
Comparative Evaluation of Assays for Broad Detection of Molecular Resistance Mechanisms in Enterobacterales Isolates. J Clin Microbiol 2021; 59:e0103321. [PMID: 34406800 DOI: 10.1128/jcm.01033-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Rapid detection of antimicrobial resistance in both surveillance and diagnostic settings is still a major challenge for the clinical lab, compounded by the rapid evolution of antibiotic resistance mechanisms. This study compares four methods for the broad detection of antibiotic resistance genes in Enterobacterales isolates: two multiplex PCR assays (the Streck ARM-D beta-lactamase kit and the OpGen Acuitas AMR Gene Panel u5.47 (research use only [RUO]) and one microarray assay (the Check-MDR CT103XL assay), with whole-genome sequencing as a reference standard. A total of 65 Gram-negative bacterial isolates, from 56 patients, classified by phenotypic antimicrobial susceptibility testing (AST) as showing resistance to beta-lactam antimicrobials (extended-spectrum beta-lactamase [ESBL] positive or resistance to third-generation cephalosporins or carbapenems) were included in the study. Overall concordance between the molecular assays and sequencing was high. While all three assays had similar performance, the OpGen Acuitas AMR assay had the highest overall percent concordance with sequencing results. The primary differences between the assays tested were the number and diversity of targets, ranging from 9 for Streck to 34 for OpGen. This study shows that commercially available PCR-based assays can provide accurate identification of antimicrobial resistance loci in clinically significant Gram-negative bacteria. Further studies are needed to determine the clinical diagnostic role and potential benefit of such methods.
Collapse
|
33
|
Schwan CL, Lomonaco S, Bastos LM, Cook PW, Maher J, Trinetta V, Bhullar M, Phebus RK, Gragg S, Kastner J, Vipham JL. Genotypic and Phenotypic Characterization of Antimicrobial Resistance Profiles in Non-typhoidal Salmonella enterica Strains Isolated From Cambodian Informal Markets. Front Microbiol 2021; 12:711472. [PMID: 34603240 PMCID: PMC8481621 DOI: 10.3389/fmicb.2021.711472] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/26/2021] [Indexed: 12/03/2022] Open
Abstract
Non-typhoidal Salmonella enterica is a pathogen of global importance, particularly in low and middle-income countries (LMICs). The presence of antimicrobial resistant (AMR) strains in market environments poses a serious health threat to consumers. In this study we identified and characterized the genotypic and phenotypic AMR profiles of 81 environmental S. enterica strains isolated from samples from informal markets in Cambodia in 2018–2019. AMR genotypes were retrieved from the NCBI Pathogen Detection website (https://www.ncbi.nlm.nih.gov/pathogens/) and using ResFinder (https://cge.cbs.dtu.dk/services/) Salmonella pathogenicity islands (SPIs) were identified with SPIFinder (https://cge.cbs.dtu.dk/services/). Susceptibility testing was performed by broth microdilution according to the Clinical and Laboratory Standards Institute (CLSI) standard guidelines M100-S22 using the National Antimicrobial Resistance Monitoring System (NARMS) Sensititre Gram Negative plate. A total of 17 unique AMR genes were detected in 53% (43/81) of the isolates, including those encoding tetracycline, beta-lactam, sulfonamide, quinolone, aminoglycoside, phenicol, and trimethoprim resistance. A total of 10 SPIs (SPI-1, 3–5, 8, 9, 12–14, and centisome 63 [C63PI]) were detected in 59 isolates. C63PI, an iron transport system in SPI-1, was observed in 56% of the isolates (n = 46). SPI-1, SPI-4, and SPI-9 were present in 13, 2, and 5% of the isolates, respectively. The most common phenotypic resistances were observed to tetracycline (47%; n = 38), ampicillin (37%; n = 30), streptomycin (20%; n = 16), chloramphenicol (17%; n = 14), and trimethoprim-sulfamethoxazole (16%; n = 13). This study contributes to understanding the AMR genes present in S. enterica isolates from informal markets in Cambodia, as well as support domestic epidemiological investigations of multidrug resistance (MDR) profiles.
Collapse
Affiliation(s)
- Carla L Schwan
- Department of Animal Sciences and Industry, Food Science Institute, Kansas State University, Manhattan, KS, United States
| | - Sara Lomonaco
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States
| | - Leonardo M Bastos
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
| | - Peter W Cook
- Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Joshua Maher
- Department of Animal Sciences and Industry, Food Science Institute, Kansas State University, Manhattan, KS, United States
| | - Valentina Trinetta
- Department of Animal Sciences and Industry, Food Science Institute, Kansas State University, Manhattan, KS, United States
| | - Manreet Bhullar
- Department of Horticulture and Natural Resources, Kansas State University, Olathe, KS, United States
| | - Randall K Phebus
- Department of Animal Sciences and Industry, Food Science Institute, Kansas State University, Manhattan, KS, United States
| | - Sara Gragg
- Department of Animal Sciences and Industry, Food Science Institute, Kansas State University, Manhattan, KS, United States
| | - Justin Kastner
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, United States
| | - Jessie L Vipham
- Department of Animal Sciences and Industry, Food Science Institute, Kansas State University, Manhattan, KS, United States
| |
Collapse
|
34
|
Beaudry MS, Thomas JC, Baptista RP, Sullivan AH, Norfolk W, Devault A, Enk J, Kieran TJ, Rhodes OE, Perry-Dow KA, Rose LJ, Bayona-Vásquez NJ, Oladeinde A, Lipp EK, Sanchez S, Glenn TC. Escaping the fate of Sisyphus: assessing resistome hybridization baits for antimicrobial resistance gene capture. Environ Microbiol 2021; 23:7523-7537. [PMID: 34519156 DOI: 10.1111/1462-2920.15767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/03/2021] [Accepted: 09/07/2021] [Indexed: 11/30/2022]
Abstract
Finding, characterizing and monitoring reservoirs for antimicrobial resistance (AMR) is vital to protecting public health. Hybridization capture baits are an accurate, sensitive and cost-effective technique used to enrich and characterize DNA sequences of interest, including antimicrobial resistance genes (ARGs), in complex environmental samples. We demonstrate the continued utility of a set of 19 933 hybridization capture baits designed from the Comprehensive Antibiotic Resistance Database (CARD)v1.1.2 and Pathogenicity Island Database (PAIDB)v2.0, targeting 3565 unique nucleotide sequences that confer resistance. We demonstrate the efficiency of our bait set on a custom-made resistance mock community and complex environmental samples to increase the proportion of on-target reads as much as >200-fold. However, keeping pace with newly discovered ARGs poses a challenge when studying AMR, because novel ARGs are continually being identified and would not be included in bait sets designed prior to discovery. We provide imperative information on how our bait set performs against CARDv3.3.1, as well as a generalizable approach for deciding when and how to update hybridization capture bait sets. This research encapsulates the full life cycle of baits for hybridization capture of the resistome from design and validation (both in silico and in vitro) to utilization and forecasting updates and retirement.
Collapse
Affiliation(s)
- Megan S Beaudry
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA
| | - Jesse C Thomas
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA.,Savannah River Ecology Laboratory, University of Georgia, Aiken, SC, 29808, USA
| | - Rodrigo P Baptista
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA.,Center for Tropical and Emerging Diseases, University of Georgia, Athens, GA, 30602, USA
| | - Amanda H Sullivan
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA.,Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| | - William Norfolk
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA
| | - Alison Devault
- Daicel Arbor Biosciences, 5840 Interface Dr., Suite 101, Ann Arbor, MI, 48103, USA
| | - Jacob Enk
- Daicel Arbor Biosciences, 5840 Interface Dr., Suite 101, Ann Arbor, MI, 48103, USA
| | - Troy J Kieran
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA
| | - Olin E Rhodes
- Savannah River Ecology Laboratory, University of Georgia, Aiken, SC, 29808, USA.,Odum School of Ecology, University of Georgia, Athens, GA, 30602, USA
| | - K Allison Perry-Dow
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Laura J Rose
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Natalia J Bayona-Vásquez
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA.,Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA.,Division of Natural Science and Mathematics, Oxford College, Emory University, Oxford, GA, 30054, USA
| | - Adelumola Oladeinde
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, USDA Agricultural Research Service, Athens, GA, 30605, USA
| | - Erin K Lipp
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA
| | - Susan Sanchez
- Department of Infectious Diseases, University of Georgia, Athens, GA, 30602, USA
| | - Travis C Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA.,Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| |
Collapse
|
35
|
Garner CD, Brazelton de Cardenas J, Suganda S, Hayden RT. Accuracy of Broad-Panel PCR-Based Bacterial Identification for Blood Cultures in a Pediatric Oncology Population. Microbiol Spectr 2021; 9:e0022121. [PMID: 34232100 PMCID: PMC8552719 DOI: 10.1128/spectrum.00221-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/05/2021] [Indexed: 11/20/2022] Open
Abstract
Bloodstream infections are a major cause of morbidity and mortality and result in significant costs to health care systems. Rapid identification of the causative agent of bloodstream infections is critical for patient treatment and improved outcomes. Multiplex PCR systems that provide bacterial identification directly from the blood culture bottle allow for earlier detection of pathogens. The GenMark Dx ePlex blood culture identification (BCID) panels have an expanded number of targets for both identification and genotypic markers of antimicrobial resistance. The performance of the ePlex BCID Gram-negative (GN) and Gram-positive (GP) panels were evaluated in a predominantly pediatric oncology population. A total of 112 blood cultures were tested by the ePlex BCID GN and GP panels and results were compared to those from standard-of-care testing. Accuracy for on-panel organisms was 89% (CI, 76% to 95%) for the Gram-positive panel, with four misidentifications and one not detected, and 93% (CI, 82% to 98%) for the Gram-negative panel, with two misidentifications and one not detected. The results showed good overall performance of these panels for rapid, accurate detection of bloodstream pathogens in this high-risk population. IMPORTANCE Bloodstream infections are a major cause of morbidity and mortality and result in significant costs to health care systems. Rapid identification of the causative agent of bloodstream infections is critical for patient treatment and improved outcomes. Multiplex PCR systems that provide bacterial identification directly from the blood culture bottle allow for earlier characterization of pathogens. The GenMark Dx ePlex blood culture identification (BCID) panels, recently cleared by the FDA, have an expanded number of targets for both identification and resistance, much larger than other, automated, broad-panel PCR assays. The performance of the ePlex BCID Gram-negative and Gram-positive panels was evaluated in a predominantly pediatric oncology population, providing a unique look at its performance in a high-risk group, where rapid diagnostic information for bloodstream infections could be of particular value for clinical care providers.
Collapse
Affiliation(s)
- C. D. Garner
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | | | - S. Suganda
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - R. T. Hayden
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| |
Collapse
|
36
|
Culture-Free Detection of Antibiotic Resistance Markers from Native Patient Samples by Hybridization Capture Sequencing. Microorganisms 2021; 9:microorganisms9081672. [PMID: 34442751 PMCID: PMC8398375 DOI: 10.3390/microorganisms9081672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/29/2021] [Accepted: 08/03/2021] [Indexed: 01/04/2023] Open
Abstract
The increasing incidence of antimicrobial resistance (AMR) is a major global challenge. Routine techniques for molecular AMR marker detection are largely based on low-plex PCR and detect dozens to hundreds of AMR markers. To allow for comprehensive and sensitive profiling of AMR markers, we developed a capture-based next generation sequencing (NGS) workflow featuring a novel AMR marker panel based on the curated AMR database ARESdb. Our primary objective was to compare the sensitivity of target enrichment-based AMR marker detection to metagenomics sequencing. Therefore, we determined the limit of detection (LOD) in synovial fluid and urine samples across four key pathogens. We further demonstrated proof-of-concept for AMR marker profiling from septic samples using a selection of urine samples with confirmed monoinfection. The results showed that the capture-based workflow is more sensitive and requires lower sequencing depth compared with metagenomics sequencing, allowing for comprehensive AMR marker detection with an LOD of 1000 CFU/mL. Combining the ARESdb AMR panel with 16S rRNA gene sequencing allowed for the culture-free detection of bacterial taxa and AMR markers directly from septic patient samples at an average sensitivity of 99%. Summarizing, the newly developed ARESdb AMR panel may serve as a valuable tool for comprehensive and sensitive AMR marker detection.
Collapse
|
37
|
Sharma D, Sharma A, Singh B, Verma SK. Pan-proteome profiling of emerging and re-emerging zoonotic pathogen Orientia tsutsugamushi for getting insight into microbial pathogenesis. Microb Pathog 2021; 158:105103. [PMID: 34298125 DOI: 10.1016/j.micpath.2021.105103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 07/13/2021] [Accepted: 07/16/2021] [Indexed: 01/21/2023]
Abstract
With the occurrence and evolution of antibiotic and multidrug resistance in bacteria most of the existing remedies are becoming ineffective. The pan-proteome exploration of the bacterial pathogens helps to identify the wide spectrum therapeutic targets which will be effective against all strains in a species. The current study is focused on the pan-proteome profiling of zoonotic pathogen Orientia tsutsugamushi (Ott) for the identification of potential therapeutic targets. The pan-proteome of Ott is estimated to be extensive in nature that has 1429 protein clusters, out of which 694 were core, 391 were accessory, and 344 were unique. It was revealed that 622 proteins were essential, 222 proteins were virulent factors, and 42 proteins were involved in antibiotic resistance. The potential therapeutic targets were further classified into eleven broad classes among which gene expression and regulation, transport, and metabolism were dominant. The biological interactome analysis of therapeutic targets revealed that an ample amount of interactions were present among the proteins involved in DNA replication, ribosome assembly, cellwall metabolism, cell division, and antimicrobial resistance. The predicted therapeutic targets from the pan-proteome of Ott are involved in various biological processes, virulence, and antibiotic resistance; hence envisioned as potential candidates for drug discovery to combat scrub typhus.
Collapse
Affiliation(s)
- Dixit Sharma
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Kangra, Himachal Pradesh, 176206, India.
| | - Ankita Sharma
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Kangra, Himachal Pradesh, 176206, India
| | - Birbal Singh
- ICAR-Indian Veterinary Research Institute, Regional Station, Palampur, Himachal Pradesh, 176061, India
| | - Shailender Kumar Verma
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Kangra, Himachal Pradesh, 176206, India
| |
Collapse
|
38
|
Preparation and Antimicrobial Activity of Chitosan and Its Derivatives: A Concise Review. Molecules 2021; 26:molecules26123694. [PMID: 34204251 PMCID: PMC8233993 DOI: 10.3390/molecules26123694] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 06/10/2021] [Accepted: 06/12/2021] [Indexed: 12/12/2022] Open
Abstract
Despite the advantages presented by synthetic polymers such as strength and durability, the lack of biodegradability associated with the persistence in the environment for a long time turned the attention of researchers to natural polymers. Being biodegradable, biopolymers proved to be extremely beneficial to the environment. At present, they represent an important class of materials with applications in all economic sectors, but also in medicine. They find applications as absorbers, cosmetics, controlled drug delivery, tissue engineering, etc. Chitosan is one of the natural polymers which raised a strong interest for researchers due to some exceptional properties such as biodegradability, biocompatibility, nontoxicity, non-antigenicity, low-cost and numerous pharmacological properties as antimicrobial, antitumor, antioxidant, antidiabetic, immunoenhancing. In addition to this, the free amino and hydroxyl groups make it susceptible to a series of structural modulations, obtaining some derivatives with different biomedical applications. This review approaches the physico-chemical and pharmacological properties of chitosan and its derivatives, focusing on the antimicrobial potential including mechanism of action, factors that influence the antimicrobial activity and the activity against resistant strains, topics of great interest in the context of the concern raised by the available therapeutic options for infections, especially with resistant strains.
Collapse
|
39
|
Structural, functional, resistome and pathogenicity profiling of the Cooum river. Microb Pathog 2021; 158:105048. [PMID: 34139279 DOI: 10.1016/j.micpath.2021.105048] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/12/2021] [Accepted: 06/06/2021] [Indexed: 01/26/2023]
Abstract
The microbial community's structure and functions determine the health, quality, and anthropogenic conditions of the river ecosystems. The presence of Bacteria such as Arcobacter spp, Escherichia spp, and Campylobacters spp, have been shown to reflect the poor water quality of rivers. Apprehension of the microbial community in polluted water bodies is significant because it affects human health and the environment. Culture-independent metagenomic and metatranscriptomic approaches employed in the current study of the Cooum river unraveled the taxonomic classification of diverse microbes, including archaea, bacteria, viruses, and phages. The presence of abundant Macellibacteroides fermentans, Arcobacter bivolvorium, Arcobacter butzleri, Methanothrix soenhngeii, and Bacteroides graminisolvens were noted. Viruses and phages like Caudovirales, Human mastadenovirus C, Siphoviridae, Escherichia phage, Erwinia phage, Synechoccus phage, and Vibrio phage were relatively predominant. Various metabolic pathways like methane, sulfur, and nitrogen metabolism adopted by the microbiome confer dangerous gases. Mechanisms such as secretory systems, signal transduction, Chemotaxis, quorum sensing, transportation of chemicals and ions were significantly enriched. The microbes expressed antimicrobial resistance mechanisms as identified from the genes encoding beta-lactamase enzymes and aminoglycoside phosphotransferase enzymes. Metal resistance mechanisms against copper, tellurium, chromium, and cadmium were plentiful. Presence of human pathogens interactions with Yersinia pestis, Campylobacter jejuni, Escherichia coli, Helicobacter pylori, and Francisella tularensis subsp. tularensis suggested the possibilities of transmission of pathogenesis to humans. The current study is the first to apprehend the detailed microbiome composition of one of the highly polluted rivers in South India. The study elaborated the microbiome's structure, functions, and metabolic potential at a specific site of the polluted river.
Collapse
|
40
|
Beaudry MS, Wang J, Kieran TJ, Thomas J, Bayona-Vásquez NJ, Gao B, Devault A, Brunelle B, Lu K, Wang JS, Rhodes OE, Glenn TC. Improved Microbial Community Characterization of 16S rRNA via Metagenome Hybridization Capture Enrichment. Front Microbiol 2021; 12:644662. [PMID: 33986735 PMCID: PMC8110821 DOI: 10.3389/fmicb.2021.644662] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/22/2021] [Indexed: 01/04/2023] Open
Abstract
Environmental microbial diversity is often investigated from a molecular perspective using 16S ribosomal RNA (rRNA) gene amplicons and shotgun metagenomics. While amplicon methods are fast, low-cost, and have curated reference databases, they can suffer from amplification bias and are limited in genomic scope. In contrast, shotgun metagenomic methods sample more genomic regions with fewer sequence acquisition biases, but are much more expensive (even with moderate sequencing depth) and computationally challenging. Here, we develop a set of 16S rRNA sequence capture baits that offer a potential middle ground with the advantages from both approaches for investigating microbial communities. These baits cover the diversity of all 16S rRNA sequences available in the Greengenes (v. 13.5) database, with no sequence having <78% sequence identity to at least one bait for all segments of 16S. The use of our baits provide comparable results to 16S amplicon libraries and shotgun metagenomic libraries when assigning taxonomic units from 16S sequences within the metagenomic reads. We demonstrate that 16S rRNA capture baits can be used on a range of microbial samples (i.e., mock communities and rodent fecal samples) to increase the proportion of 16S rRNA sequences (average > 400-fold) and decrease analysis time to obtain consistent community assessments. Furthermore, our study reveals that bioinformatic methods used to analyze sequencing data may have a greater influence on estimates of community composition than library preparation method used, likely due in part to the extent and curation of the reference databases considered. Thus, enriching existing aliquots of shotgun metagenomic libraries and obtaining modest numbers of reads from them offers an efficient orthogonal method for assessment of bacterial community composition.
Collapse
Affiliation(s)
- Megan S. Beaudry
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States
| | - Jincheng Wang
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States
| | - Troy J. Kieran
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States
| | - Jesse Thomas
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States
- Savannah River Ecology Laboratory, University of Georgia, Aiken, SC, United States
| | - Natalia J. Bayona-Vásquez
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States
| | - Bei Gao
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States
| | | | | | - Kun Lu
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States
| | - Jia-Sheng Wang
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States
| | - Olin E. Rhodes
- Savannah River Ecology Laboratory, University of Georgia, Aiken, SC, United States
| | - Travis C. Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States
| |
Collapse
|
41
|
Genome-Based Targeted Sequencing as a Reproducible Microbial Community Profiling Assay. mSphere 2021; 6:6/2/e01325-20. [PMID: 33827913 PMCID: PMC8546724 DOI: 10.1128/msphere.01325-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Current sequencing-based methods for profiling microbial communities rely on marker gene (e.g., 16S rRNA) or metagenome shotgun sequencing (mWGS) analysis. We present an approach based on a single-primer extension reaction using a highly multiplexed oligonucleotide probe pool. This approach, termed MA-GenTA (microbial abundances from genome tagged analysis), enables quantitative, straightforward, cost-effective microbiome profiling that combines desirable features of both 16S rRNA and mWGS strategies. The use of multiple probes per target genome and rigorous probe design criteria enabled robust determination of relative abundance. To test the utility of the MA-GenTA assay, probes were designed for 830 genome sequences representing bacteria present in mouse stool specimens. Comparison of the MA-GenTA data with mWGS data demonstrated excellent correlation down to 0.01% relative abundance and a similar number of organisms detected per sample. Despite the incompleteness of the reference database, nonmetric multidimensional scaling (NMDS) clustering based on the Bray-Curtis dissimilarity metric of sample groups was consistent between MA-GenTA, mWGS, and 16S rRNA data sets. MA-GenTA represents a potentially useful new method for microbiome community profiling based on reference genomes. IMPORTANCE New methods for profiling the microbial communities can create new approaches to understanding the composition and function of those communities. In this study, we combined bacterial genome-specific probe design with a highly multiplexed single primer extension reaction as a new method to profile microbial communities, using stool from various mouse strains as a test case. This method, termed MA-GenTA, was benchmarked against 16S rRNA gene sequencing and metagenome sequencing methods and delivered similar relative abundance and clustering data. Since the probes were generated from reference genomes, MA-GenTA was also able to provide functional pathway data for the stool microbiome in the assayed samples. The method is more informative than 16S rRNA analysis while being less costly than metagenome shotgun sequencing.
Collapse
|
42
|
The Effect of the Effluent from a Small-Scale Conventional Wastewater Treatment Plant Treating Municipal Wastewater on the Composition and Abundance of the Microbial Community, Antibiotic Resistome, and Pathogens in the Sediment and Water of a Receiving Stream. WATER 2021. [DOI: 10.3390/w13060865] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The effluents of wastewater treatment plants (WWTPs) are major contributors of nutrients, microbes—including those carrying antibiotic resistance genes (ARGs)—and pathogens to receiving waterbodies. The effect of the effluent of a small-scale activated sludge WWTP treating municipal wastewater on the composition and abundance of the microbial community as well as the antibiotic resistome and pathogens in the sediment and water of the receiving stream and river was studied using metagenome sequencing and a quantitative approach. Elevated Bacteroidetes proportions in the prokaryotic community, heightened sulfonamide and aminoglycoside resistance determinants proportions, and an increase of up to three orders of magnitude of sul1–sul2–aadA–blaOXA2 gene cluster abundances were recorded in stream water and sediments 0.3 km downstream of a WWTP discharge point. Further downstream, a gradual recovery of affected microbial communities along a distance gradient from WWTP was recorded, culminating in the mostly comparable state of river water and sediment parameters 3.7 km downstream of WWTP and stream water and sediments upstream of the WWTP discharge point. Archaea, especially Methanosarcina, Methanothrix, and Methanoregula, formed a substantial proportion of the microbial community of WWTP effluent as well as receiving stream water and sediment, and were linked to the spread of ARGs. Opportunistic environmental-origin pathogens were predominant in WWTP effluent and receiving stream bacterial communities, with Citrobacter freundii proportion being especially elevated in the close vicinity downstream of the WWTP discharge point.
Collapse
|
43
|
Amino Acid k-mer Feature Extraction for Quantitative Antimicrobial Resistance (AMR) Prediction by Machine Learning and Model Interpretation for Biological Insights. BIOLOGY 2020; 9:biology9110365. [PMID: 33126516 PMCID: PMC7694136 DOI: 10.3390/biology9110365] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/17/2020] [Accepted: 10/19/2020] [Indexed: 12/31/2022]
Abstract
Machine learning algorithms can learn mechanisms of antimicrobial resistance from the data of DNA sequence without any a priori information. Interpreting a trained machine learning algorithm can be exploited for validating the model and obtaining new information about resistance mechanisms. Different feature extraction methods, such as SNP calling and counting nucleotide k-mers have been proposed for presenting DNA sequences to the model. However, there are trade-offs between interpretability, computational complexity and accuracy for different feature extraction methods. In this study, we have proposed a new feature extraction method, counting amino acid k-mers or oligopeptides, which provides easier model interpretation compared to counting nucleotide k-mers and reaches the same or even better accuracy in comparison with different methods. Additionally, we have trained machine learning algorithms using different feature extraction methods and compared the results in terms of accuracy, model interpretability and computational complexity. We have built a new feature selection pipeline for extraction of important features so that new AMR determinants can be discovered by analyzing these features. This pipeline allows the construction of models that only use a small number of features and can predict resistance accurately.
Collapse
|
44
|
|
45
|
Wee BA, Muloi DM, van Bunnik BAD. Quantifying the transmission of antimicrobial resistance at the human and livestock interface with genomics. Clin Microbiol Infect 2020; 26:1612-1616. [PMID: 32979568 PMCID: PMC7721588 DOI: 10.1016/j.cmi.2020.09.019] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 09/05/2020] [Accepted: 09/11/2020] [Indexed: 12/27/2022]
Abstract
BACKGROUND Livestock have been implicated as a reservoir for antimicrobial resistance (AMR) that can spread to humans. Close proximity and ecological interfaces involving livestock have been posited as risk factors for the transmission of AMR. In spite of this, there are sparse data and limited agreement on the transmission dynamics that occur. OBJECTIVES To identify how genome sequencing approaches can be used to quantify the dynamics of AMR transmission at the human-livestock interface, and where current knowledge can be improved to better understand the impact of transmission on the spread of AMR. SOURCES Key articles investigating various aspects of AMR transmission at the human-livestock interface are discussed, with a focus on Escherichia coli. CONTENT We recapitulate the current understanding of the transmission of AMR between humans and livestock based on current genomic and epidemiological approaches. We discuss how the use of well-designed, high-resolution genome sequencing studies can improve our understanding of the human-livestock interface. IMPLICATIONS A better understanding of the human-livestock interface will aid in the development of evidence-based and effective One Health interventions that can ultimately reduce the burden of AMR in humans.
Collapse
Affiliation(s)
- Bryan A Wee
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom.
| | - Dishon M Muloi
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom; Centre for Immunity, Infection & Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom; International Livestock Research Institute, Nairobi, Kenya
| | - Bram A D van Bunnik
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom; Centre for Immunity, Infection & Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| |
Collapse
|
46
|
Ricker N, Spoja BS, May N, Chalmers G. Incorporating the plasmidome into antibiotic resistance surveillance in animal agriculture. Plasmid 2020; 113:102529. [PMID: 32771502 DOI: 10.1016/j.plasmid.2020.102529] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/06/2020] [Accepted: 07/11/2020] [Indexed: 12/25/2022]
Abstract
Mobile genetic elements (MGE) carrying resistance genes represent a unique challenge to risk assessment and surveillance of antimicrobial resistance (AMR). Yet determining the mobility of resistance genes within animal microbiomes is essential to evaluating the potential dissemination from livestock to potential human pathogens, as well as evaluating co-selection mechanisms that may impact persistence of resistance genes with changing antibiotic use patterns. Current surveillance efforts utilize phenotypic testing and sequencing of individual isolates for tracking of AMR in livestock. In this work, we investigated the utility of using long-read sequencing of the plasmids from mixed Enterobacterales enrichments of swine fecal samples as a surveillance strategy for AMR plasmids. Enrichments were performed in either MacConkey broth without selection or with selection by addition of tetracycline or ceftriaxone, and plasmids were extracted and sequenced in order to evaluate the diversity of plasmids enriched by each method. Intact resistance plasmids were successfully assembled, as well as complex resistance transposons carrying multiple repeated elements that would interfere with assembly by short read sequencing technologies. Comparison of the assembled plasmids with representatives from public databases confirmed the quality of the assemblies and also revealed the occurrence of IncI2 plasmids carrying blaCMY-2 in Ontario swine samples, which have not been found in previous studies.
Collapse
Affiliation(s)
- N Ricker
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada.
| | - B S Spoja
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - N May
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - G Chalmers
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| |
Collapse
|
47
|
Slizovskiy IB, Mukherjee K, Dean CJ, Boucher C, Noyes NR. Mobilization of Antibiotic Resistance: Are Current Approaches for Colocalizing Resistomes and Mobilomes Useful? Front Microbiol 2020; 11:1376. [PMID: 32695079 PMCID: PMC7338343 DOI: 10.3389/fmicb.2020.01376] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 05/28/2020] [Indexed: 11/16/2022] Open
Abstract
Antimicrobial resistance (AMR) poses a global human and animal health threat, and predicting AMR persistence and transmission remains an intractable challenge. Shotgun metagenomic sequencing can help overcome this by enabling characterization of AMR genes within all bacterial taxa, most of which are uncultivatable in laboratory settings. Shotgun sequencing, therefore, provides a more comprehensive glance at AMR "potential" within samples, i.e., the "resistome." However, the risk inherent within a given resistome is predicated on the genomic context of various AMR genes, including their presence within mobile genetic elements (MGEs). Therefore, resistome risk stratification can be advanced if AMR profiles are considered in light of the flanking mobilizable genomic milieu (e.g., plasmids, integrative conjugative elements (ICEs), phages, and other MGEs). Because such mediators of horizontal gene transfer (HGT) are involved in uptake by pathogens, investigators are increasingly interested in characterizing that resistome fraction in genomic proximity to HGT mediators, i.e., the "mobilome"; we term this "colocalization." We explored the utility of common colocalization approaches using alignment- and assembly-based techniques, on clinical (human) and agricultural (cattle) fecal metagenomes, obtained from antimicrobial use trials. Ordination revealed that tulathromycin-treated cattle experienced a shift in ICE and plasmid composition versus untreated animals, though the resistome was unaffected during the monitoring period. Contrarily, the human resistome and mobilome composition both shifted shortly after antimicrobial administration, though this rebounded to pre-treatment status. Bayesian networks revealed statistical AMR-MGE co-occurrence in 19 and 2% of edges from the cattle and human networks, respectively, suggesting a putatively greater mobility potential of AMR in cattle feces. Conversely, using Mobility Index (MI) and overlap analysis, abundance of de novo-assembled contigs supporting resistomes flanked by MGE increased shortly post-exposure within human metagenomes, though > 40 days after peak dose such contigs were rare (∼2%). MI was not substantially altered by antimicrobial exposure across all cattle metagenomes, ranging 0.5-4.0%. We highlight that current alignment- and assembly-based methods estimating resistome mobility yield contradictory and incomplete results, likely constrained by approach-specific data inputs, and bioinformatic limitations. We discuss recent laboratory and computational advancements that may enhance resistome risk analysis in clinical, regulatory, and commercial applications.
Collapse
Affiliation(s)
- Ilya B Slizovskiy
- Food-Centric Corridor, Infectious Disease Laboratory, Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, United States
| | - Kingshuk Mukherjee
- Department of Computer and Information Science and Engineering, The Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, United States
| | - Christopher J Dean
- Food-Centric Corridor, Infectious Disease Laboratory, Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, United States
| | - Christina Boucher
- Department of Computer and Information Science and Engineering, The Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, United States
| | - Noelle R Noyes
- Food-Centric Corridor, Infectious Disease Laboratory, Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, United States
| |
Collapse
|
48
|
Molecular Characterization and Antimicrobial Susceptibilities of Nocardia Species Isolated from the Soil; A Comparison with Species Isolated from Humans. Microorganisms 2020; 8:microorganisms8060900. [PMID: 32549367 PMCID: PMC7355893 DOI: 10.3390/microorganisms8060900] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/05/2020] [Accepted: 06/11/2020] [Indexed: 01/08/2023] Open
Abstract
Nocardia species, one of the most predominant Actinobacteria of the soil microbiota, cause infection in humans following traumatic inoculation or inhalation. The identification, typing, phylogenetic relationship and antimicrobial susceptibilities of 38 soil Nocardia strains from Lara State, Venezuela, were studied by 16S rRNA and gyrB (subunit B of topoisomerase II) genes, multilocus sequence analysis (MLSA), whole-genome sequencing (WGS), and microdilution. The results were compared with those for human strains. Just seven Nocardia species with one or two strains each, except for Nocardia cyriacigeorgica with 29, were identified. MLSA confirmed the species assignments made by 16S rRNA and gyrB analyses (89.5% and 71.0% respectively), and grouped each soil strain with its corresponding reference and clinical strains, except for 19 N. cyriacigeorgica strains found at five locations which grouped into a soil-only cluster. The soil strains of N. cyriacigeorgica showed fewer gyrB haplotypes than the examined human strains (13 vs. 17) but did show a larger number of gyrB SNPs (212 vs. 77). Their susceptibilities to antimicrobials were similar except for beta-lactams, fluoroquinolones, minocycline, and clarithromycin, with the soil strains more susceptible to the first three (p ≤ 0.05). WGS was performed on four strains belonging to the soil-only cluster and on two outside it, and the results compared with public N. cyriacigeorgica genomes. The average nucleotide/amino acid identity, in silico genome-to-genome hybridization similarity, and the difference in the genomic GC content, suggest that some strains of the soil-only cluster may belong to a novel subspecies or even a new species (proposed name Nocardia venezuelensis).
Collapse
|
49
|
Klowak JA, El Helou S, Pernica JM, Parker MJ, Surette M, Poinar H, Fox-Robichaud AE. Fast I(n)dentification of Pathogens in Neonates (FINDPATH-N): protocol for a prospective pilot cohort study of next-generation sequencing for pathogen identification in neonates with suspected sepsis. BMJ Paediatr Open 2020; 4:e000651. [PMID: 32518844 PMCID: PMC7254136 DOI: 10.1136/bmjpo-2020-000651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/19/2020] [Accepted: 03/20/2020] [Indexed: 11/13/2022] Open
Abstract
INTRODUCTION Sepsis is a major source of morbidity and mortality in neonates; however, identification of the causative pathogens is challenging. Many neonates have negative blood cultures despite clinical evidence of sepsis. Next-generation sequencing (NGS) is a high-throughput, parallel sequencing technique for DNA. Pathogen-targeted enrichment followed by NGS has the potential to be more sensitive and faster than current gold-standard blood culture. In this pilot study, we will test the feasibility and pathogen detection patterns of pathogen-targeted NGS in neonates with suspected sepsis. Additionally, the distribution and diagnostic accuracy of biomarkers cell-free DNA and protein C levels at two time points will be explored. METHODS AND ANALYSIS We will conduct a prospective, pilot observational study. Neonates over 1 kg with suspected sepsis from a single tertiary care children's hospital will be recruited for the study. Recruitment will be censored at 200 events or 6 months' duration. Two blood study samples will be taken: the first simultaneous to the blood culture (time=0 hour, for NGS and biomarkers) via an exception to consent (deferred consent) and another 24 hours later after prospective consent (biomarkers only). Neonates will be adjudicated into those with clinical sepsis, culture-proven sepsis and without sepsis based on clinical criteria. Feasibility parameters (eg, recruitment) and NGS process time will be reported.For analysis, NGS results will be described in aggregate, compared with the simultaneous blood culture (sensitivity and specificity) and reviewed via expert panel for plausibility. Pilot data for biomarker distribution and diagnostic accuracy (sensitivity and specificity) for distinguishing between septic and non-septic neonates will be reported. ETHICS AND DISSEMINATION Ethics approval has been granted by the Hamilton Integrated Research Ethics Board. We will seek publication of study results in peer-reviewed journals.
Collapse
Affiliation(s)
- Jennifer Ann Klowak
- Pediatrics, McMaster University, Hamilton, Ontario, Canada.,Pediatrics, McMaster Children's Hospital, Hamilton, Ontario, Canada
| | - Salhab El Helou
- Pediatrics, McMaster University, Hamilton, Ontario, Canada.,Pediatrics, McMaster Children's Hospital, Hamilton, Ontario, Canada
| | - Jeffrey M Pernica
- Pediatrics, McMaster University, Hamilton, Ontario, Canada.,Pediatrics, McMaster Children's Hospital, Hamilton, Ontario, Canada
| | - Melissa J Parker
- Pediatrics, McMaster University, Hamilton, Ontario, Canada.,Pediatrics, McMaster Children's Hospital, Hamilton, Ontario, Canada
| | | | - Hendrik Poinar
- Anthropology, McMaster University, Hamilton, Ontario, Canada
| | - Alison E Fox-Robichaud
- Medicine, McMaster University, Hamilton, Ontario, Canada.,Thrombosis and Atherosclerosis Research Institute, Hamilton, Ontario, Canada
| | | |
Collapse
|