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Okoh EB, Payne M, Lan R, Riegler M, Chapman TA, Bogema DR. A Multilocus Sequence Typing Scheme for Rapid Identification of Xanthomonas citri Based on Whole-Genome Sequencing Data. PHYTOPATHOLOGY 2024; 114:1480-1489. [PMID: 38669587 DOI: 10.1094/phyto-12-23-0490-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
Xanthomonas citri is a plant-pathogenic bacterium associated with a diverse range of host plant species. It has undergone substantial reclassification and currently consists of 14 different subspecies or pathovars that are responsible for a wide range of plant diseases. Whole-genome sequencing (WGS) provides a cutting-edge advantage over other diagnostic techniques in epidemiological and evolutionary studies of X. citri because it has a higher discriminatory power and is replicable across laboratories. WGS also allows for the improvement of multilocus sequence typing (MLST) schemes. In this study, we used genome sequences of Xanthomonas isolates from the NCBI RefSeq database to develop a seven-gene MLST scheme that yielded 19 sequence types (STs) that correlated with phylogenetic clades of X. citri subspecies or pathovars. Using this MLST scheme, we examined 2,911 Xanthomonas species assemblies from NCBI GenBank and identified 15 novel STs from 37 isolates that were misclassified in NCBI. In total, we identified 545 X. citri assemblies from GenBank with 95% average nucleotide identity to the X. citri type strain, and all were classified as one of the 34 STs. All MLST classifications correlated with a phylogenetic position inferred from alignments using 92 conserved genes. We observed several instances where strains from different pathovars formed closely related monophyletic clades and shared the same ST, indicating that further investigation of the validity of these pathovars is required. Our MLST scheme described here is a robust tool for rapid classification of X. citri pathovars using WGS and a powerful method for further comprehensive taxonomic revision of X. citri pathovars.
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Affiliation(s)
- Efenaide B Okoh
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW 2568, Australia
| | - Michael Payne
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, NSW, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, NSW, Australia
| | - Markus Riegler
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Toni A Chapman
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW 2568, Australia
| | - Daniel R Bogema
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW 2568, Australia
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Klaper K, Tlapák H, Selb R, Jansen K, Heuer D. Integrated molecular, phenotypic and epidemiological surveillance of antimicrobial resistance in Neisseria gonorrhoeae in Germany. Int J Med Microbiol 2024; 314:151611. [PMID: 38309143 DOI: 10.1016/j.ijmm.2024.151611] [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] [Revised: 01/17/2024] [Accepted: 01/22/2024] [Indexed: 02/05/2024] Open
Abstract
Numbers of infections with Neisseria gonorrhoeae are among the top three sexually transmitted infections (STI) worldwide. In addition, the emergence and spread of antimicrobial resistance (AMR) in Neisseria gonorrhoeae pose an important public-health issue. The integration of genomic, phenotypic and epidemiological data to monitor Neisseria gonorrhoeae fosters our understanding of the emergence and spread of AMR in Neisseria gonorrhoeae and helps to inform therapy guidelines and intervention strategies. Thus, the Gonococcal resistance surveillance (Go-Surv-AMR) was implemented at the Robert Koch Institute in Germany in 2021 to obtain molecular, phenotypic and epidemiological data on Neisseria gonorrhoeae isolated in Germany. Here, we describe the structure and aims of Go-Surv-AMR. Furthermore, we point out future directions of Go-Surv-AMR to improve the integrated genomic surveillance of Neisseria gonorrhoeae. In this context we discuss current and prospective sequencing approaches and the information derived from their application. Moreover, we highlight the importance of combining phenotypic and WGS data to monitor the evolution of AMR in Neisseria gonorrhoeae in Germany. The implementation and constant development of techniques and tools to improve the genomic surveillance of Neisseria gonorrhoeae will be important in coming years.
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Affiliation(s)
- Kathleen Klaper
- Department Infectious Diseases, Unit 18 `Sexually transmitted bacterial pathogens and HIV´, Robert Koch Institute, Berlin, Germany
| | - Hana Tlapák
- Department Infectious Diseases, Unit 18 `Sexually transmitted bacterial pathogens and HIV´, Robert Koch Institute, Berlin, Germany
| | - Regina Selb
- Department of Infectious Disease Epidemiology, Unit 34 `'HIV/AIDS, STI and Blood-borne Infections´, Robert Koch Institute, Berlin, Germany
| | - Klaus Jansen
- Department of Infectious Disease Epidemiology, Unit 34 `'HIV/AIDS, STI and Blood-borne Infections´, Robert Koch Institute, Berlin, Germany
| | - Dagmar Heuer
- Department Infectious Diseases, Unit 18 `Sexually transmitted bacterial pathogens and HIV´, Robert Koch Institute, Berlin, Germany.
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Song M, Li Q, Liu C, Wang P, Qin F, Zhang L, Fan Y, Shao H, Chen G, Yang M. A comprehensive technology strategy for microbial identification and contamination investigation in the sterile drug manufacturing facility-a case study. Front Microbiol 2024; 15:1327175. [PMID: 38410390 PMCID: PMC10895062 DOI: 10.3389/fmicb.2024.1327175] [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: 10/24/2023] [Accepted: 01/30/2024] [Indexed: 02/28/2024] Open
Abstract
Objective A comprehensive strategy for microbial identification and contamination investigation during sterile drug manufacturing was innovatively established in this study, mainly based on MALDI-TOF MS for the identification and complemented by sequencing technology on strain typing. Methods It was implemented to monitor the bacterial contamination of a sterile drug manufacturing facility, including its bacterial distribution features and patterns. In three months, two hundred ninety-two samples were collected covering multiple critical components of raw materials, personnel, environment, and production water. Results Based on our strategy, the bacterial profile across the production process was determined: 241/292 bacterial identities were obtained, and Staphylococcus spp. (40.25%), Micrococcus spp.(11.20%), Bacillus spp. (8.30%), Actinobacteria (5.81%), and Paenibacillus spp. (4.56%) are shown to be the most dominant microbial contaminants. With 75.8% species-level and 95.4% genus-level identification capability, MALDI-TOF MS was promising to be a first-line tool for environmental monitoring routine. Furthermore, to determine the source of the most frequently occurring Staphylococcus cohnii, which evidenced a widespread presence in the entire process, a more discriminating S. cohnii whole-genome SNP typing method was developed to track the transmission routes. Phylogenetic analysis based on SNP results indicated critical environment contamination is highly relevant to personnel flow in this case. The strain typing results provide robust and accurate information for the following risk assessment step and support effective preventive and corrective measures. Conclusion In general, the strategy presented in this research will facilitate the development of improved production and environmental control processes for the pharmaceutical industry, and give insights about how to provide more sound and reliable evidence for the optimization of its control program.
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Affiliation(s)
- Minghui Song
- NMPA Key Laboratory for Testing Technology of Pharmaceutical Microbiology, Shanghai Institute for Food and Drug Control, Shanghai, China
- Shanghai Quality Inspection and Testing Center for Innovative Biological Products, Shanghai, China
| | - Qiongqiong Li
- NMPA Key Laboratory for Testing Technology of Pharmaceutical Microbiology, Shanghai Institute for Food and Drug Control, Shanghai, China
- Shanghai Quality Inspection and Testing Center for Innovative Biological Products, Shanghai, China
| | - Chengzhi Liu
- Hangzhou Digital-Micro Biotech Co., Ltd., Hangzhou, China
| | - Peien Wang
- NMPA Key Laboratory for Testing Technology of Pharmaceutical Microbiology, Shanghai Institute for Food and Drug Control, Shanghai, China
- Shanghai Quality Inspection and Testing Center for Innovative Biological Products, Shanghai, China
| | - Feng Qin
- NMPA Key Laboratory for Testing Technology of Pharmaceutical Microbiology, Shanghai Institute for Food and Drug Control, Shanghai, China
| | - Lichun Zhang
- Shanghai SPH New Asia Pharmaceutical Co., Ltd., Shanghai, China
| | - Yiling Fan
- NMPA Key Laboratory for Testing Technology of Pharmaceutical Microbiology, Shanghai Institute for Food and Drug Control, Shanghai, China
- Shanghai Quality Inspection and Testing Center for Innovative Biological Products, Shanghai, China
- China State Institute of Pharmaceutical Industry Co., Ltd., Shanghai, China
| | - Hong Shao
- NMPA Key Laboratory for Testing Technology of Pharmaceutical Microbiology, Shanghai Institute for Food and Drug Control, Shanghai, China
- Shanghai Quality Inspection and Testing Center for Innovative Biological Products, Shanghai, China
| | - Guiliang Chen
- China State Institute of Pharmaceutical Industry Co., Ltd., Shanghai, China
- Shanghai Center for Drug Evaluation and Inspection, Shanghai, China
| | - Meicheng Yang
- NMPA Key Laboratory for Testing Technology of Pharmaceutical Microbiology, Shanghai Institute for Food and Drug Control, Shanghai, China
- China State Institute of Pharmaceutical Industry Co., Ltd., Shanghai, China
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Ham H, Park DS. New Insights and Approach Toward the Genetic Diversity and Strain Typing of Erwinia pyrifoliae Based on rsxC, an Electron Transport Gene. PLANT DISEASE 2024; 108:296-301. [PMID: 37669173 DOI: 10.1094/pdis-03-23-0475-sc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Erwinia pyrifoliae, a causal agent of black shoot blight in apple and pear trees, is a plant pathogenic bacterium first reported in South Korea. The symptoms of black shoot blight are very similar to those of the fire blight disease in apple and pear trees caused by E. amylovora, as E. pyrifoliae has a genetically very close relationship with E. amylovora. Recently, there have been reports that E. pyrifoliae causes disease in European strawberries, resulting in severe fruit loss that aroused great concern about its spread, distribution, and host range. Therefore, it is essential to establish a trustworthy approach to understanding the distribution patterns of E. pyrifoliae based on the genetic background to strengthen the barrier of potential spreading risks, although advanced methods have been provided to accurately detect E. pyrifoliae and E. amylovora. Consequently, this study discovered a noble and noteworthy gene, rsxC, capable of providing the pathogen genotype by comparing E. pyrifoliae genomic sequences in the international representative genome archive. Different numbers of 40-unit amino acid repeats in this gene among the strains induced intraspecific traits in RsxC. By comparing their repeat pattern, E. pyrifoliae isolates were divided into two main groups, branching into several clades via sequence alignment of 35 E. pyrifoliae isolates from various apple orchards from 2020 to 2021 in South Korea. The newly discovered quadraginta amino acid repeat within this gene would be a valuable genetic touchstone for determining the genotype and distribution pattern of E. pyrifoliae strains, ultimately leading to exploring their evolution. The function of amino acid repeats and the biological significance of strains need to be elucidated further.
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Affiliation(s)
- Hyeonheui Ham
- Crop Protection Division, National Institute of Agricultural Sciences, Wanju-gun 55365, Republic of Korea
| | - Dong Suk Park
- Crop Protection Division, National Institute of Agricultural Sciences, Wanju-gun 55365, Republic of Korea
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Jiang JH, Cameron DR, Nethercott C, Aires-de-Sousa M, Peleg AY. Virulence attributes of successful methicillin-resistant Staphylococcus aureus lineages. Clin Microbiol Rev 2023; 36:e0014822. [PMID: 37982596 PMCID: PMC10732075 DOI: 10.1128/cmr.00148-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a leading cause of severe and often fatal infections. MRSA epidemics have occurred in waves, whereby a previously successful lineage has been replaced by a more fit and better adapted lineage. Selection pressures in both hospital and community settings are not uniform across the globe, which has resulted in geographically distinct epidemiology. This review focuses on the mechanisms that trigger the establishment and maintenance of current, dominant MRSA lineages across the globe. While the important role of antibiotic resistance will be mentioned throughout, factors which influence the capacity of S. aureus to colonize and cause disease within a host will be the primary focus of this review. We show that while MRSA possesses a diverse arsenal of toxins including alpha-toxin, the success of a lineage involves more than just producing toxins that damage the host. Success is often attributed to the acquisition or loss of genetic elements involved in colonization and niche adaptation such as the arginine catabolic mobile element, as well as the activity of regulatory systems, and shift metabolism accordingly (e.g., the accessory genome regulator, agr). Understanding exactly how specific MRSA clones cause prolonged epidemics may reveal targets for therapies, whereby both core (e.g., the alpha toxin) and acquired virulence factors (e.g., the Panton-Valentine leukocidin) may be nullified using anti-virulence strategies.
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Affiliation(s)
- Jhih-Hang Jiang
- Department of Microbiology, Infection Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - David R. Cameron
- Department of Biomedical Research, University of Bern, Bern, Switzerland
| | - Cara Nethercott
- Department of Microbiology, Infection Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Marta Aires-de-Sousa
- Laboratory of Molecular Genetics, Institutode Tecnologia Químicae Biológica António Xavier (ITQB-NOVA), Universidade Nova de Lisboa, Oeiras, Portugal
- Escola Superior de Saúde da Cruz Vermelha Portuguesa-Lisboa (ESSCVP-Lisboa), Lisbon, Portugal
| | - Anton Y. Peleg
- Department of Microbiology, Infection Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Centre to Impact Antimicrobial Resistance, Monash University, Clayton, Melbourne, Victoria, Australia
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Peña-Mosca F, Dean C, Machado V, Fernandes L, Pinedo P, Doster E, Heins B, Sharpe K, Ray T, Feijoo V, Antunes A, Baumann C, Wehri T, Noyes N, Caixeta L. Investigation of intramammary infections in primiparous cows during early lactation on organic dairy farms. J Dairy Sci 2023; 106:9377-9392. [PMID: 37641314 DOI: 10.3168/jds.2022-23036] [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: 11/15/2022] [Accepted: 06/25/2023] [Indexed: 08/31/2023]
Abstract
Previous studies have shown that organically raised dairy cows have an increased prevalence of Staphylococcus aureus compared with conventionally raised dairy cows. However, little information exists about the dynamics of intramammary infection (IMI) in primiparous cows during early lactation on organic dairy farms. The objective of this study was to describe the IMI dynamics of primiparous cows on certified organic farms during early lactation. This longitudinal study enrolled 503 primiparous cows from 5 organic dairy farms from February 2019 to January 2020. Quarter-level milk samples were collected aseptically on a weekly basis during the first 5 wk of lactation. Samples were pooled by cow and time point into composite samples inside a sterilized laminar hood and submitted for microbiological culture. For each of the different microorganisms identified, we estimated the prevalence in each postpartum sample, period prevalence (PP), cumulative incidence, and persistence of IMI. Logistic regression models were used to investigate whether the prevalence of IMI differed by farm or sampling time points and whether IMI persistence differed between detected microorganisms. Our findings revealed a high prevalence of Staphylococcus aureus (PP = 18.9%), non-aureus staphylococci and closely related mammaliicoccal species (PP = 52.1%), and Streptococcus spp. and Streptococcus-like organisms (PP = 32.1%) within the study population. The prevalence of these microorganisms varied significantly between farms. Staphylococcus aureus and Staphylococcus chromogenes exhibited significantly higher IMI persistence compared with other detected bacterial taxa, confirming the divergent epidemiological behavior in terms of IMI chronicity across different microorganisms. This study improves our understanding of the epidemiology of mastitis-causing pathogens in organically raised primiparous cows, which can be used to tailor mastitis control plans for this unique yet growing subpopulation of dairy cows.
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Affiliation(s)
- Felipe Peña-Mosca
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN 55108
| | - Chris Dean
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN 55108
| | - Vinicius Machado
- Department of Animal Science, University of Minnesota, Saint Paul, MN 55108
| | - Leticia Fernandes
- Department of Animal Science, University of Minnesota, Saint Paul, MN 55108
| | - Pablo Pinedo
- Department of Veterinary Sciences, Texas Tech University, Lubbock, TX 79409
| | - Enrique Doster
- Department of Veterinary Sciences, Texas Tech University, Lubbock, TX 79409
| | - Bradley Heins
- Department of Animal Sciences, Colorado State University, Fort Collins, CO 80521
| | - Kirsten Sharpe
- Department of Animal Sciences, Colorado State University, Fort Collins, CO 80521
| | - Tui Ray
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN 55108
| | - Victoria Feijoo
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN 55108
| | - Acir Antunes
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN 55108
| | - Carol Baumann
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN 55108
| | - Thomas Wehri
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN 55108
| | - Noelle Noyes
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN 55108
| | - Luciano Caixeta
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN 55108.
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Bezdicek M, Hanslikova J, Nykrynova M, Dufkova K, Kocmanova I, Kubackova P, Mayer J, Lengerova M. New Multilocus Sequence Typing Scheme for Enterococcus faecium Based on Whole Genome Sequencing Data. Microbiol Spectr 2023; 11:e0510722. [PMID: 37306567 PMCID: PMC10434285 DOI: 10.1128/spectrum.05107-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 05/24/2023] [Indexed: 06/13/2023] Open
Abstract
The MLST scheme currently used for Enterococcus faecium typing was designed in 2002 and is based on putative gene functions and Enterococcus faecalis gene sequences available at that time. As a result, the original MLST scheme does not correspond to the real genetic relatedness of E. faecium strains and often clusters genetically distant strains to the same sequence types (ST). Nevertheless, typing has a significant impact on the subsequent epidemiological conclusions and introduction of appropriate epidemiological measures, thus it is crucial to use a more accurate MLST scheme. Based on the genome analysis of 1,843 E. faecium isolates, a new scheme, consisting of 8 highly discriminative loci, was created in this study. These strains were divided into 421 STs using the new MLST scheme, as opposed to 223 STs assigned by the original MLST scheme. The proposed MLST has a discriminatory power of D = 0.983 (CI95% 0.981 to 0.984), compared to the original scheme's D = 0.919 (CI95% 0.911 to 0.927). Moreover, we identified new clonal complexes with our newly designed MLST scheme. The scheme proposed here is available within the PubMLST database. Although whole genome sequencing availability has increased rapidly, MLST remains an integral part of clinical epidemiology, mainly due to its high standardization and excellent robustness. In this study, we proposed and validated a new MLST scheme for E. faecium, which is based on genome-wide data and thus reflects the tested isolates' more accurate genetic similarity. IMPORTANCE Enterococcus faecium is one of the most important pathogens causing health care associated infections. One of the main reasons for its clinical importance is a rapidly spreading resistance to vancomycin and linezolid, which significantly complicates antibiotic treatment of infections caused by such resistant strains. Monitoring the spread and relationships between resistant strains causing severe conditions represents an important tool for implementing appropriate preventive measures. Therefore, there is an urgent need to establish a robust method enabling strain monitoring and comparison at the local, national, and global level. Unfortunately, the current, extensively used MLST scheme does not reflect the real genetic relatedness between individual strains and thus does not provide sufficient discriminatory power. This can lead directly to incorrect epidemiological measures due to insufficient accuracy and biased results.
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Affiliation(s)
- Matej Bezdicek
- Department of Internal Medicine - Haematology and Oncology, University Hospital Brno, Brno, Czech Republic
- Department of Internal Medicine - Haematology and Oncology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jana Hanslikova
- Department of Internal Medicine - Haematology and Oncology, University Hospital Brno, Brno, Czech Republic
| | - Marketa Nykrynova
- Department of Internal Medicine - Haematology and Oncology, University Hospital Brno, Brno, Czech Republic
- Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic
| | - Kristyna Dufkova
- Department of Internal Medicine - Haematology and Oncology, University Hospital Brno, Brno, Czech Republic
- Department of Internal Medicine - Haematology and Oncology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Iva Kocmanova
- Department of Clinical Microbiology and Immunology, University Hospital Brno, Brno, Czech Republic
| | - Petra Kubackova
- Department of Clinical Microbiology and Immunology, University Hospital Brno, Brno, Czech Republic
| | - Jiri Mayer
- Department of Internal Medicine - Haematology and Oncology, University Hospital Brno, Brno, Czech Republic
- Department of Internal Medicine - Haematology and Oncology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Martina Lengerova
- Department of Internal Medicine - Haematology and Oncology, University Hospital Brno, Brno, Czech Republic
- Department of Internal Medicine - Haematology and Oncology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
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Pongchaikul P, Romero R, Mongkolsuk P, Vivithanaporn P, Wongsurawat T, Jenjaroenpun P, Nitayanon P, Thaipisuttikul I, Kamlungkuea T, Singsaneh A, Santanirand P, Chaemsaithong P. Genomic analysis of Enterococcus faecium strain RAOG174 associated with acute chorioamnionitis carried antibiotic resistance gene: is it time for precise microbiological identification for appropriate antibiotic use? BMC Genomics 2023; 24:405. [PMID: 37468842 DOI: 10.1186/s12864-023-09511-1] [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: 04/26/2023] [Accepted: 07/09/2023] [Indexed: 07/21/2023] Open
Abstract
BACKGROUND Preterm labor syndrome is associated with high perinatal morbidity and mortality, and intra-amniotic infection is a cause of preterm labor. The standard identification of causative microorganisms is based on the use of biochemical phenotypes, together with broth dilution-based antibiotic susceptibility from organisms grown in culture. However, such methods could not provide an accurate epidemiological aspect and a genetic basis of antimicrobial resistance leading to an inappropriate antibiotic administration. Hybrid genome assembly is a combination of short- and long-read sequencing, which provides better genomic resolution and completeness for genotypic identification and characterization. Herein, we performed a hybrid whole genome assembly sequencing of a pathogen associated with acute histologic chorioamnionitis in women presenting with PPROM. RESULTS We identified Enterococcus faecium, namely E. faecium strain RAOG174, with several antibiotic resistance genes, including vancomycin and aminoglycoside. Virulence-associated genes and potential bacteriophage were also identified in this genome. CONCLUSION We report herein the first study demonstrating the use of hybrid genome assembly and genomic analysis to identify E. faecium ST17 as a pathogen associated with acute histologic chorioamnionitis. The analysis provided several antibiotic resistance-associated genes/mutations and mobile genetic elements. The occurrence of E. faecium ST17 raised the awareness of the colonization of clinically relevant E. faecium and the carrying of antibiotic resistance. This finding has brought the advantages of genomic approach in the identification of the bacterial species and antibiotic resistance gene for E. faecium for appropriate antibiotic use to improve maternal and neonatal care.
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Affiliation(s)
- Pisut Pongchaikul
- Chakri Naruebodindra Medical Institute, Faculty of Medicine Ramathibodi Hospital Mahidol University, Samut Prakan, Thailand
- Integrative Computational BioScience Center, Mahidol University, Nakhon Pathom, Thailand
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Roberto Romero
- Pregnancy Research Branch (formerly The Perinatology Research Branch, NICHD/NIH/DHHS, in Detroit, Michigan, USA, has been renamed as the Pregnancy Research Branch, NICHD/NIH/DHHS), Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, United States Department of Health and Human Services, Bethesda, MD, USA
- Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, United States Department of Health and Human Services, Detroit, MI, USA
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, USA
| | - Paninee Mongkolsuk
- Chakri Naruebodindra Medical Institute, Faculty of Medicine Ramathibodi Hospital Mahidol University, Samut Prakan, Thailand
| | - Pornpun Vivithanaporn
- Chakri Naruebodindra Medical Institute, Faculty of Medicine Ramathibodi Hospital Mahidol University, Samut Prakan, Thailand
| | - Thidathip Wongsurawat
- Division of Medical Bioinformatics, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Piroon Jenjaroenpun
- Division of Medical Bioinformatics, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Perapon Nitayanon
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Iyarit Thaipisuttikul
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Threebhorn Kamlungkuea
- Department of Obstetrics and Gynecology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Arunee Singsaneh
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Pitak Santanirand
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Piya Chaemsaithong
- Department of Obstetrics and Gynecology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.
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Mizusawa M, Carroll KC. Recent updates in the development of molecular assays for the rapid identification and susceptibility testing of MRSA. Expert Rev Mol Diagn 2023; 23:679-699. [PMID: 37419696 DOI: 10.1080/14737159.2023.2234823] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 06/22/2023] [Accepted: 07/06/2023] [Indexed: 07/09/2023]
Abstract
INTRODUCTION Methicillin-resistant Staphylococcus aureus (MRSA) is a frequent cause of healthcare- and community-associated infections. Nasal carriage of MRSA is a risk factor for subsequent MRSA infections. Increased morbidity and mortality are associated with MRSA infections and screening and diagnostic tests for MRSA play an important role in clinical management. AREAS COVERED A literature search was conducted in PubMed and supplemented by citation searching. In this article, we provide a comprehensive review of molecular-based methods for MRSA screening and diagnostic tests including individual nucleic acid detection assays, syndromic panels, and sequencing technologies with a focus on their analytical performance. EXPERT OPINION Molecular based-assays for the detection of MRSA have improved in terms of accuracy and availability. Rapid turnaround enables earlier contact isolation and decolonization for MRSA. The availability of syndromic panel tests that include MRSA as a target has expanded from positive blood cultures to pneumonia and osteoarticular infections. Sequencing technologies allow detailed characterizations of novel methicillin-resistance mechanisms that can be incorporated into future assays. Next generation sequencing is capable of diagnosing MRSA infections that cannot be identified by conventional methods and metagenomic next-generation sequencing (mNGS) assays will likely move closer to implementation as front-line diagnostics in the near future.
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Affiliation(s)
- Masako Mizusawa
- Monmouth Medical Center, Rutgers University Robert Wood Johnson Medical School, Long Branch, NJ, USA
| | - Karen C Carroll
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Neves A, Walther D, Martin-Campos T, Barbie V, Bertelli C, Blanc D, Bouchet G, Erard F, Greub G, Hirsch HH, Huber M, Kaiser L, Leib SL, Leuzinger K, Lazarevic V, Mäusezahl M, Molina J, Neher RA, Perreten V, Ramette A, Roloff T, Schrenzel J, Seth-Smith HMB, Stephan R, Terumalai D, Wegner F, Egli A. The Swiss Pathogen Surveillance Platform - towards a nation-wide One Health data exchange platform for bacterial, viral and fungal genomics and associated metadata. Microb Genom 2023; 9. [PMID: 37171846 DOI: 10.1099/mgen.0.001001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Abstract
The Swiss Pathogen Surveillance Platform (SPSP) is a shared secure surveillance platform between human and veterinary medicine, to also include environmental and foodborne isolates. It enables rapid and detailed transmission monitoring and outbreak surveillance of pathogens using whole genome sequencing data and associated metadata. It features controlled data access, complex dynamic queries, dedicated dashboards and automated data sharing with international repositories, providing actionable results for public health and the vision to improve societal well-being and health.
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Affiliation(s)
- Aitana Neves
- SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Daniel Walther
- SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | | | - Valerie Barbie
- SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Claire Bertelli
- Clinical Microbiology, University Hospital Lausanne, Lausanne, Switzerland
| | - Dominique Blanc
- Hospital Epidemiology, University Hospital Lausanne, Lausanne, Switzerland
| | - Gérard Bouchet
- SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Frédéric Erard
- SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Gilbert Greub
- Clinical Microbiology, University Hospital Lausanne, Lausanne, Switzerland
| | - Hans H Hirsch
- Clinical Virology, University Hospital Basel, Basel, Switzerland
- Department of Biomedicine, Transplantation & Clinical Virology, University of Basel, Basel, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Laurent Kaiser
- Virology, University Hospital Geneva, Geneva, Switzerland
| | - Stephen L Leib
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Karoline Leuzinger
- Clinical Virology, University Hospital Basel, Basel, Switzerland
- Department of Biomedicine, Transplantation & Clinical Virology, University of Basel, Basel, Switzerland
| | | | | | - Jorge Molina
- SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Richard A Neher
- Biozentrum, University of Basel, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Alban Ramette
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Tim Roloff
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Jacques Schrenzel
- Genomic Research Laboratory, University of Geneva, Geneva, Switzerland
| | | | - Roger Stephan
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | | | - Fanny Wegner
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Adrian Egli
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
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11
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Morin-Le Bihan A, Le Neindre K, Dejoies L, Piau C, Donnio PY, Ménard G. Use of the quantitative antibiogram method for assessing nosocomial transmission of ESBL-producing Enterobacteriaceae in a French hospital. J Hosp Infect 2023; 135:132-138. [PMID: 36918068 DOI: 10.1016/j.jhin.2023.01.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/19/2023] [Accepted: 01/24/2023] [Indexed: 03/13/2023]
Abstract
BACKGROUND ESBL-producing Enterobacteriaceae (eESBL) have a high prevalence in hospitals but real-time monitoring of nosocomial acquisition through conventional typing methods is challenging. Moreover, patient-to-patient transmission varies between the main species, namely Escherichia coli, and Klebsiella pneumoniae, then questioning the relevance of applying identical preventive measures. AIM To detect eESBL cross-transmission events (CTE) using combination of quantitative antibiogram with epidemiological data (combined-QA), and to rule on the effectiveness of standard or contact precautions for eESBL species. METHODS First, a validation set was used to confirm the relevance of the combined-QA by comparison to a combination of pulsed-field gel electrophoresis and epidemiological data (combined-PFGE). Secondly, a four-year retrospective analysis was conducted to detect eESBL-CTE in hospitalized patients. Two species were screened i.e. ESBL-E. coli (ESBL-Ec), and ESBL-K. pneumoniae (ESBL-Kp). During the study, only standard precautions were applied to ESBL-Ec patients whereas contact precautions were retained for ESBL-Kp. FINDINGS As a proof of concept, results between the two combined methods for the detection of CTE were identical for E. coli, and similar to at least 75% for K. pneumoniae. During the retrospective analysis, 722 patients with ESBL-Ec isolates and 280 with ESBL-Kp isolates were included. Nine CTE were identified for E. coli and 23 for K. pneumoniae, implying 20 (2.7%) and 36 (12.8%) patients, respectively. CONCLUSION The QA-combined method constitutes a rapid tool for epidemiological surveillance to detect CTE. In our hospital, standard precautions are sufficient to prevent acquisition of ESBL-Ec whereas contact precautions must be implemented to prevent acquisition of ESBL-Kp.
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Affiliation(s)
- Amélie Morin-Le Bihan
- CHU Rennes, SB2H (Service de Bactériologie-Hygiène Hospitalière), F-35000 Rennes, France
| | - Killian Le Neindre
- CHU Rennes, SB2H (Service de Bactériologie-Hygiène Hospitalière), F-35000 Rennes, France; INSERM, BRM (Bacterial RNAs and Medicine), University Rennes, UMR_S 1230, F-35000 Rennes, France
| | - Loren Dejoies
- CHU Rennes, SB2H (Service de Bactériologie-Hygiène Hospitalière), F-35000 Rennes, France; INSERM, BRM (Bacterial RNAs and Medicine), University Rennes, UMR_S 1230, F-35000 Rennes, France
| | - Caroline Piau
- CHU Rennes, SB2H (Service de Bactériologie-Hygiène Hospitalière), F-35000 Rennes, France
| | - Pierre-Yves Donnio
- CHU Rennes, SB2H (Service de Bactériologie-Hygiène Hospitalière), F-35000 Rennes, France; INSERM, BRM (Bacterial RNAs and Medicine), University Rennes, UMR_S 1230, F-35000 Rennes, France
| | - Guillaume Ménard
- CHU Rennes, SB2H (Service de Bactériologie-Hygiène Hospitalière), F-35000 Rennes, France; INSERM, BRM (Bacterial RNAs and Medicine), University Rennes, UMR_S 1230, F-35000 Rennes, France.
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12
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Montero-Vargas M, Saenz-Rojas A, Suárez-Esquivel M, Ramirez-Carvajal L. ASGARD+: A New Modular Platform for Bacterial Antibiotic-Resistant Analysis. Curr Protoc 2023; 3:e680. [PMID: 36892262 DOI: 10.1002/cpz1.680] [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: 03/10/2023]
Abstract
ASGARD+ (Accelerated Sequential Genome-analysis and Antibiotic Resistance Detection) is a command-line platform for automatic identification of antibiotic-resistance genes in bacterial genomes, providing an easy-to-use interface to process big batches of sequence files from whole genome sequencing, with minimal configuration. It also provides a CPU-optimization algorithm that reduces the processing time. This tool consists of two main protocols. The first one, ASGARD, is based on the identification and annotation of antimicrobial resistance elements directly from the short reads using different public databases. SAGA, enables the alignment, indexing, and mapping of whole-genome samples against a reference genome for the detection and call of variants, as well as the visualization of the results through the construction of a tree of SNPs. The application of both protocols is performed using just one short command and one configuration file based on JSON syntax, which modulates each pipeline step, allowing the user to do as many interventions as needed on the different software tools that are adapted to the pipeline. The modular ASGARD+ allows researchers with little experience in bioinformatic analysis and command-line use to quickly explore bacterial genomes in depth, optimizing analysis times and obtaining accurate results. © 2023 Wiley Periodicals LLC. Basic Protocol 1: ASGARD+ installation Basic Protocol 2: Configuration files general setup Basic Protocol 3: ASGARD execution Support Protocol: Results visualization with Phandango Basic Protocol 4: SAGA execution Alternative Protocol 1: Container installation Alternative Protocol 2: Run ASGARD and SAGA in container.
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Affiliation(s)
- Maripaz Montero-Vargas
- Advanced Computing Laboratory (CNCA) of the National High Technology Center (CeNAT-CONARE), San Jose, Costa Rica
| | - Alex Saenz-Rojas
- Advanced Computing Laboratory (CNCA) of the National High Technology Center (CeNAT-CONARE), San Jose, Costa Rica
| | - Marcela Suárez-Esquivel
- Programa de Investigación en Enfermedades Tropicales (PIET), Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - Lizbeth Ramirez-Carvajal
- Former affiliation: National Laboratory of Veterinary Services (LANASEVE), Ministry of Agriculture of Costa Rica, Heredia, Costa Rica
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13
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Liu L, Peng H, Zhang N, Li M, Chen Z, Shang W, Hu Z, Wang Y, Yang Y, Wang D, Hu Q, Rao X. Genomic Epidemiology and Phenotypic Characterization of Staphylococcus aureus from a Tertiary Hospital in Tianjin Municipality, Northern China. Microbiol Spectr 2023; 11:e0420922. [PMID: 36786628 PMCID: PMC10100870 DOI: 10.1128/spectrum.04209-22] [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: 10/16/2022] [Accepted: 01/14/2023] [Indexed: 02/15/2023] Open
Abstract
Staphylococcus aureus remains a dangerous pathogen and poses a great threat to public health worldwide. The prevalence of the S. aureus clonotype is temporally and geographically variable. The genomic and phenotypic characteristics of S. aureus isolates in Tianjin, which is among the four big municipalities in China, are unclear. In the present study, 201 nonduplicate S. aureus isolates, including 70 methicillin-resistant S. aureus (MRSA) and 131 methicillin-susceptible S. aureus (MSSA), were collected from 2015 to 2021 in a tertiary hospital in Tianjin. Whole-genome sequencing of S. aureus isolates was carried out to investigate bacterial molecular characteristics, genomic phylogeny, antimicrobial resistance (AMR) gene carriage, and virulence factor gene distribution. The antibiotic resistance profiles, hemolytic activities, and biofilm formation abilities of the S. aureus isolates were also determined. In total, 31 distinct sequence types (STs) and 68 spa types were identified. ST59 (15.9%, 32/201) was the predominant clonotype, followed by ST398 (14.9%, 30/201) and several other major STs (ST1, ST5, ST6, ST22, ST25, ST188, and the newly emerging ST5527). ST59 and ST5527 mainly included MRSA isolates, while ST398 and the other major STs mainly included MSSA isolates. The unique characteristics of the S. aureus isolates belonging to the major STs were determined. ST59 isolates exhibited strong hemolytic activity, and ST398 strains had high biofilm formation capacity, while ST5527 isolates presented the greatest AMR. The genomic epidemiology and phenotypic characteristics of S. aureus isolates determined in this study will help in disease control in nosocomial environments. IMPORTANCE Staphylococcus aureus is an important bacterium pathogen in tertiary hospitals, which provide rich medical resources. Tianjin is one of the four municipalities in China with a population of more than 13 million. However, the epidemiology and molecular characteristics of S. aureus isolates in Tianjin are unknown. In this study, the genomic and phenotypic analyses were performed to investigate 201 S. aureus isolates collected from a tertiary hospital in Tianjin over a time span of 6 years. The refined analysis of predominant clones ST59, ST398, the newly emerging clone ST5527, as well as other major clones, will undoubtedly aid in the control and prevention of infections caused by S. aureus in tertiary hospitals.
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Affiliation(s)
- Lu Liu
- Department of Microbiology, School of Medicine, Chongqing University, Chongqing, China
| | - Huagang Peng
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University, Chongqing, China
| | - Naan Zhang
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University, Chongqing, China
| | - Mengyang Li
- Department of Microbiology, School of Medicine, Chongqing University, Chongqing, China
| | - Zhaozhe Chen
- Department of Clinical Laboratory, 983th hospital of PLA, Tianjin, China
| | - Weilong Shang
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University, Chongqing, China
| | - Zhen Hu
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University, Chongqing, China
| | - Yuting Wang
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University, Chongqing, China
| | - Yi Yang
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University, Chongqing, China
| | - Dongmei Wang
- Department of Clinical Laboratory, 983th hospital of PLA, Tianjin, China
| | - Qiwen Hu
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University, Chongqing, China
| | - Xiancai Rao
- Department of Microbiology, School of Medicine, Chongqing University, Chongqing, China
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University, Chongqing, China
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14
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Blasco L, de Aledo MG, Ortiz-Cartagena C, Blériot I, Pacios O, López M, Fernández-García L, Barrio-Pujante A, Hernández-Garcia M, Cantón R, Tomás M. Study of 32 new phage tail-like bacteriocins (pyocins) from a clinical collection of Pseudomonas aeruginosa and of their potential use as typing markers and antimicrobial agents. Sci Rep 2023; 13:117. [PMID: 36596850 PMCID: PMC9810705 DOI: 10.1038/s41598-022-27341-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 12/30/2022] [Indexed: 01/05/2023] Open
Abstract
Phage tail-like bacteriocins (PTLBs) are large proteomic structures similar to the tail phages. These structures function in bacterial competition by making pores in the membrane of their competitors. The PTLBs identified in Pseudomonas aeruginosa are known as R-type and F-type pyocins, which have a narrow spectrum of action. Their specificity is determined by the tail fiber and is closely related to the lipopolysaccharide type of the target competitor strain. In this study, the genome sequences of 32 clinical of P. aeruginosa clinical isolates were analysed to investigate the presence of R-type and F-type pyocins, and one was detected in all strains tested. The pyocins were classified into 4 groups on the basis of the tail fiber and also the homology, phylogeny and structure of the cluster components. A relationship was established between these groups and the sequence type and serotype of the strain of origin and finally the killing spectrum of the representative pyocins was determined showing a variable range of activity between 0 and 37.5%. The findings showed that these pyocins could potentially be used for typing of P. aeruginosa clinical isolates, on the basis of their genomic sequence and cluster structure, and also as antimicrobial agents.
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Affiliation(s)
- Lucía Blasco
- grid.8073.c0000 0001 2176 8535Microbiología Traslacional y Multidisciplinar (MicroTM)-Instituto de Investigación Biomédica (INIBIC), Servicio de Microbiología, Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain ,Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - Manuel González de Aledo
- grid.8073.c0000 0001 2176 8535Microbiología Traslacional y Multidisciplinar (MicroTM)-Instituto de Investigación Biomédica (INIBIC), Servicio de Microbiología, Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain ,Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - Concha Ortiz-Cartagena
- grid.8073.c0000 0001 2176 8535Microbiología Traslacional y Multidisciplinar (MicroTM)-Instituto de Investigación Biomédica (INIBIC), Servicio de Microbiología, Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain ,Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - Inés Blériot
- grid.8073.c0000 0001 2176 8535Microbiología Traslacional y Multidisciplinar (MicroTM)-Instituto de Investigación Biomédica (INIBIC), Servicio de Microbiología, Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain ,Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - Olga Pacios
- grid.8073.c0000 0001 2176 8535Microbiología Traslacional y Multidisciplinar (MicroTM)-Instituto de Investigación Biomédica (INIBIC), Servicio de Microbiología, Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain ,Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - María López
- grid.8073.c0000 0001 2176 8535Microbiología Traslacional y Multidisciplinar (MicroTM)-Instituto de Investigación Biomédica (INIBIC), Servicio de Microbiología, Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain ,Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - Laura Fernández-García
- grid.8073.c0000 0001 2176 8535Microbiología Traslacional y Multidisciplinar (MicroTM)-Instituto de Investigación Biomédica (INIBIC), Servicio de Microbiología, Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain ,Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - Antonio Barrio-Pujante
- grid.8073.c0000 0001 2176 8535Microbiología Traslacional y Multidisciplinar (MicroTM)-Instituto de Investigación Biomédica (INIBIC), Servicio de Microbiología, Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain ,Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - Marta Hernández-Garcia
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain ,Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Rafael Cantón
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain ,Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - María Tomás
- grid.8073.c0000 0001 2176 8535Microbiología Traslacional y Multidisciplinar (MicroTM)-Instituto de Investigación Biomédica (INIBIC), Servicio de Microbiología, Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain ,Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
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15
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Li L, Wang R, Qiao D, Zhou M, Jin P. Tracking the Outbreak of Carbapenem-Resistant Klebsiella pneumoniae in an Emergency Intensive Care Unit by Whole Genome Sequencing. Infect Drug Resist 2022; 15:6215-6224. [PMID: 36324669 PMCID: PMC9621004 DOI: 10.2147/idr.s386385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 10/19/2022] [Indexed: 11/05/2022] Open
Abstract
Purpose The spread of carbapenem-resistant Klebsiella pneumoniae (CRKP) has become a great threat to human health, especially in the intensive care unit. The aim of this study was to identify the origin and transmission route of a CRKP outbreak in an emergency intensive care unit (EICU), so as to provide prevention and control strategies for CRKP outbreak. Methods Between Mar and Jun 2018, 10 CRKP isolates from 5 patients in the EICU ward of Shanghai Ruijin hospital north were collected. Modified carbapenem inactivation method (mCIM) and whole-genome sequencing (WGS) were performed on all 10 CRKP isolates. By integrating the genomic and epidemiological data of our isolates and 9 CRKP isolates from an outbreak in another hospital, a putative transmission map was constructed. Results All 10 outbreak strains were carbapenemase positive in mCIM and belonged to the sequence type 11 (ST11) clone, harbored a set of resistance genes and virulence genes. The phylogenetic tree of CRKP isolates based on two outbreaks revealed that the initial isolate A1 in our EICU ward belonged to one branch of isolates in another hospital, this introductive isolate evolved and caused a subsequent outbreak in our EICU. Conclusion Integration of genomic and epidemiological data can yield a clear transmission map of CRKP outbreak. Monitoring the rapid evolution of CRKP at the early stage of outbreak, CRKP monitoring after patients are discharged, active surveillance of newly admitted patients, environmental hygiene and efficient antibiotic treatment may be the key to prevent and control of CRKP outbreak.
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Affiliation(s)
- Li Li
- Department of Clinical Laboratory, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, People’s Republic of China
| | - Renying Wang
- Department of Emergency, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, People’s Republic of China
| | - Dan Qiao
- Department of Clinical Laboratory, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, People’s Republic of China
| | - Min Zhou
- Department of Clinical Laboratory, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, People’s Republic of China
| | - Peipei Jin
- Department of Clinical Laboratory, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, People’s Republic of China,Correspondence: Peipei Jin, Department of Clinical Laboratory, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, 999 Xiwang Road, Shanghai, 201801, People’s Republic of China, Tel +86-21-67888999, Fax +86-21-64333548, Email
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16
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Raphenya AR, Robertson J, Jamin C, de Oliveira Martins L, Maguire F, McArthur AG, Hays JP. Datasets for benchmarking antimicrobial resistance genes in bacterial metagenomic and whole genome sequencing. Sci Data 2022; 9:341. [PMID: 35705638 PMCID: PMC9200708 DOI: 10.1038/s41597-022-01463-7] [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] [Received: 02/14/2022] [Accepted: 06/10/2022] [Indexed: 11/09/2022] Open
Abstract
Whole genome sequencing (WGS) is a key tool in identifying and characterising disease-associated bacteria across clinical, agricultural, and environmental contexts. One increasingly common use of genomic and metagenomic sequencing is in identifying the type and range of antimicrobial resistance (AMR) genes present in bacterial isolates in order to make predictions regarding their AMR phenotype. However, there are a large number of alternative bioinformatics software and pipelines available, which can lead to dissimilar results. It is, therefore, vital that researchers carefully evaluate their genomic and metagenomic AMR analysis methods using a common dataset. To this end, as part of the Microbial Bioinformatics Hackathon and Workshop 2021, a 'gold standard' reference genomic and simulated metagenomic dataset was generated containing raw sequence reads mapped against their corresponding reference genome from a range of 174 potentially pathogenic bacteria. These datasets and their accompanying metadata are freely available for use in benchmarking studies of bacteria and their antimicrobial resistance genes and will help improve tool development for the identification of AMR genes in complex samples.
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Affiliation(s)
- Amogelang R Raphenya
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, L8S 4K1, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4K1, Canada.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - James Robertson
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, N1G 3W4, Canada
| | - Casper Jamin
- Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Center, P. Debyelaan 25, 6229HX, Maastricht, the Netherlands
| | | | - Finlay Maguire
- Department of Community Health & Epidemiology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada.,Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada.,Shared Hospital Laboratory, Sunnybrook Health Sciences Centre, Toronto, Ontario, M4N 3M5, Canada
| | - Andrew G McArthur
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, L8S 4K1, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4K1, Canada.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - John P Hays
- Department of Medical Microbiology & Infectious Diseases, Erasmus University Medical Centre Rotterdam (Erasmus MC), Doctor Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands.
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