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Fernandez JE, Egli A, Overesch G, Perreten V. Time-calibrated phylogenetic and chromosomal mobilome analyses of Staphylococcus aureus CC398 reveal geographical and host-related evolution. Nat Commun 2024; 15:5526. [PMID: 38951499 PMCID: PMC11217367 DOI: 10.1038/s41467-024-49644-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 06/13/2024] [Indexed: 07/03/2024] Open
Abstract
An international collection of Staphylococcus aureus of clonal complex (CC) 398 from diverse hosts spanning all continents and a 30 year-period is studied based on whole-genome sequencing (WGS) data. The collection consists of publicly available genomic data from 2994 strains and 134 recently sequenced Swiss methicillin-resistant S. aureus (MRSA) CC398 strains. A time-calibrated phylogeny reveals the presence of distinct phylogroups present in Asia, North and South America and Europe. European MRSA diverged from methicillin-susceptible S. aureus (MSSA) at the beginning of the 1950s. Two major European phylogroups (EP4 and EP5), which diverged approximately 1974, are the main drivers of MRSA CC398 spread in Europe. Within EP5, an emergent MRSA lineage spreading among the European horse population (EP5-Leq) diverged approximately 1996 from the pig lineage (EP5-Lpg), and also contains human-related strains. EP5-Leq is characterized by staphylococcal cassette chromosome mec (SCCmec) IVa and spa type t011 (CC398-IVa-t011), and EP5-Lpg by CC398-SCCmecVc-t011. The lineage-specific antibiotic resistance and virulence gene patterns are mostly mediated by the acquisition of mobile genetic elements like SCCmec, S. aureus Genomic Islands (SaGIs), prophages and transposons. Different combinations of virulence factors are present on S. aureus pathogenicity islands (SaPIs), and novel antimicrobial resistance gene containing elements are associated with certain lineages expanding in Europe. This WGS-based analysis reveals the actual evolutionary trajectory and epidemiological trend of the international MRSA CC398 population considering host, temporal, geographical and molecular factors. It provides a baseline for global WGS-based One-Health studies of adaptive evolution of MRSA CC398 as well as for local outbreak investigations.
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Affiliation(s)
- Javier Eduardo Fernandez
- Division of Molecular Bacterial Epidemiology and Infectious Diseases, Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Adrian Egli
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Gudrun Overesch
- Center for Zoonoses, Animal Bacterial Diseases and Antimicrobial Resistance, Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Vincent Perreten
- Division of Molecular Bacterial Epidemiology and Infectious Diseases, Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
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2
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Mauffrey F, Bertelli C, Greub G, Senn L, Blanc DS. Genomic evolution of ST228 SCCmec-I MRSA 10 years after a major nosocomial outbreak. J Clin Microbiol 2024:e0020324. [PMID: 38934681 DOI: 10.1128/jcm.00203-24] [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: 02/12/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
In this study, we investigated the genomic changes in a major methicillin-resistant Staphylococcus aureus (MRSA) clone following a significant outbreak at a hospital. Whole-genome sequencing of MRSA isolates was utilized to explore the genomic evolution of post-outbreak MRSA strains. The epidemicity of the clone declined over time, coinciding with the introduction of multimodal infection control measures. A genome-wide association study (GWAS) identified multiple genes significantly associated with either high or low epidemic success, indicating alterations in mobilome, virulence, and defense mechanisms. Random Forest models pinpointed a gene related to fibrinogen binding as the most influential predictor of epidemicity. The decline of the MRSA clone may be attributed to various factors, including the implementation of new infection control measures, single nucleotide polymorphisms accumulation, and the genetic drift of a given clone. This research underscores the complex dynamics of MRSA clones, emphasizing the multifactorial nature of their evolution. The decline in epidemicity seems linked to alterations in the clone's genetic profile, with a probable shift towards decreased virulence and adaptation to long-term carriage. Understanding the genomic basis for the decline of epidemic clones is crucial to develop effective strategies for their surveillance and management, as well as to gain insights into the evolutionary dynamics of pathogen genomes.
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Affiliation(s)
- Florian Mauffrey
- Infection Prevention and Control Unit, Infectious Diseases Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Claire Bertelli
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Laurence Senn
- Infection Prevention and Control Unit, Infectious Diseases Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Dominique S Blanc
- Infection Prevention and Control Unit, Infectious Diseases Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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3
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Campbell K, Kowalski CH, Kohler KM, Barber MF. Evolution of polyamine resistance in Staphylococcus aureus through modulation of potassium transport. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.15.599172. [PMID: 38915543 PMCID: PMC11195161 DOI: 10.1101/2024.06.15.599172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Microbes must adapt to diverse biotic and abiotic factors encountered in host environments. Polyamines are an abundant class of aliphatic molecules that play essential roles in fundamental cellular processes across the tree of life. Surprisingly, the bacterial pathogen Staphylococcus aureus is highly sensitive to polyamines encountered during infection, and acquisition of a polyamine resistance locus has been implicated in spread of the prominent USA300 methicillin-resistant S. aureus lineage. At present, alternative pathways of polyamine resistance in staphylococci are largely unknown. Here we applied experimental evolution to identify novel mechanisms and consequences of S. aureus adaption when exposed to increasing concentrations of the polyamine spermine. Evolved populations of S. aureus exhibited striking evidence of parallel adaptation, accumulating independent mutations in the potassium transporter genes ktrA and ktrD. Mutations in either ktrA or ktrD are sufficient to confer polyamine resistance and function in an additive manner. Moreover, we find that ktr mutations provide increased resistance to multiple classes of unrelated cationic antibiotics, suggesting a common mechanism of resistance. Consistent with this hypothesis, ktr mutants exhibit alterations in cell surface charge indicative of reduced affinity and uptake of cationic molecules. Finally, we observe that laboratory-evolved ktr mutations are also present in diverse natural S. aureus isolates, suggesting these mutations may contribute to antimicrobial resistance during human infections. Collectively this study identifies a new role for potassium transport in S. aureus polyamine resistance with consequences for susceptibility to both host-derived and clinically-used antimicrobials.
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Affiliation(s)
- Killian Campbell
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR USA
- Department of Biology, University of Oregon, Eugene, OR USA
| | | | - Kristin M. Kohler
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR USA
| | - Matthew F. Barber
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR USA
- Department of Biology, University of Oregon, Eugene, OR USA
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4
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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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5
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Houtak G, Bouras G, Nepal R, Shaghayegh G, Cooksley C, Psaltis AJ, Wormald PJ, Vreugde S. The intra-host evolutionary landscape and pathoadaptation of persistent Staphylococcus aureus in chronic rhinosinusitis. Microb Genom 2023; 9. [PMID: 38010322 DOI: 10.1099/mgen.0.001128] [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] [Indexed: 11/29/2023] Open
Abstract
Chronic rhinosinusitis (CRS) is a common chronic sinonasal mucosal inflammation associated with Staphylococcus aureus biofilm and relapsing infections. This study aimed to determine rates of S. aureus persistence and pathoadaptation in CRS patients by investigating the genomic relatedness and antibiotic resistance/tolerance in longitudinally collected S. aureus clinical isolates. A total of 68 S. aureus paired isolates (34 pairs) were sourced from 34 CRS patients at least 6 months apart. Isolates were grown into 48 h biofilms and tested for tolerance to antibiotics. A hybrid sequencing strategy was used to obtain high-quality reference-grade assemblies of all isolates. Single nucleotide variants (SNV) divergence in the core genome and sequence type clustering were used to analyse the relatedness of the isolate pairs. Single nucleotide and structural genome variations, plasmid similarity, and plasmid copy numbers between pairs were examined. Our analysis revealed that 41 % (14/34 pairs) of S. aureus isolates were persistent, while 59 % (20/34 pairs) were non-persistent. Persistent isolates showed episode-specific mutational changes over time with a bias towards events in genes involved in adhesion to the host and mobile genetic elements such as plasmids, prophages, and insertion sequences. Furthermore, a significant increase in the copy number of conserved plasmids of persistent strains was observed. This was accompanied by a significant increase in biofilm tolerance against all tested antibiotics, which was linked to a significant increase in biofilm biomass over time, indicating a potential biofilm pathoadaptive process in persistent isolates. In conclusion, our study provides important insights into the mutational changes during S. aureus persistence in CRS patients highlighting potential pathoadaptive mechanisms in S. aureus persistent isolates culminating in increased biofilm biomass.
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Affiliation(s)
- Ghais Houtak
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, Australia
| | - George Bouras
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, Australia
| | - Roshan Nepal
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, Australia
| | - Gohar Shaghayegh
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, Australia
| | - Clare Cooksley
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, Australia
| | - Alkis James Psaltis
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, Australia
| | - Peter-John Wormald
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, Australia
| | - Sarah Vreugde
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, Australia
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6
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Kumar G, Engle K. Natural products acting against S. aureus through membrane and cell wall disruption. Nat Prod Rep 2023; 40:1608-1646. [PMID: 37326041 DOI: 10.1039/d2np00084a] [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] [Indexed: 06/17/2023]
Abstract
Covering: 2015 to 2022Staphylococcus aureus (S. aureus) is responsible for several community and hospital-acquired infections with life-threatening complications such as bacteraemia, endocarditis, meningitis, liver abscess, and spinal cord epidural abscess. In recent decades, the abuse and misuse of antibiotics in humans, animals, plants, and fungi and the treatment of nonmicrobial diseases have led to the rapid emergence of multidrug-resistant pathogens. The bacterial wall is a complex structure consisting of the cell membrane, peptidoglycan cell wall, and various associated polymers. The enzymes involved in bacterial cell wall synthesis are established antibiotic targets and continue to be a central focus for antibiotic development. Natural products play a vital role in drug discovery and development. Importantly, natural products provide a starting point for active/lead compounds that sometimes need modification based on structural and biological properties to meet the drug criteria. Notably, microorganisms and plant metabolites have contributed as antibiotics for noninfectious diseases. In this study, we have summarized the recent advances in understanding the activity of the drugs or agents of natural origin that directly inhibit the bacterial membrane, membrane components, and membrane biosynthetic enzymes by targeting membrane-embedded proteins. We also discussed the unique aspects of the active mechanisms of established antibiotics or new agents.
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Affiliation(s)
- Gautam Kumar
- Department of Natural Products, Chemical Sciences, National Institute of Pharmaceutical Education and Research-Hyderabad, Hyderabad, Balanagar, 500037, India.
| | - Kritika Engle
- Department of Natural Products, Chemical Sciences, National Institute of Pharmaceutical Education and Research-Hyderabad, Hyderabad, Balanagar, 500037, India.
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7
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Ladner JT, Sahl JW. Towards a post-pandemic future for global pathogen genome sequencing. PLoS Biol 2023; 21:e3002225. [PMID: 37527248 PMCID: PMC10393143 DOI: 10.1371/journal.pbio.3002225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023] Open
Abstract
Pathogen genome sequencing has become a routine part of our response to active outbreaks of infectious disease and should be an important part of our preparations for future epidemics. In this Essay, we discuss the innovations that have enabled routine pathogen genome sequencing, as well as how genome sequences can be used to understand and control the spread of infectious disease. We also explore the impact of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic on the field of pathogen genomics and outline the challenges we must address to further improve the utility of pathogen genome sequencing in the future.
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Affiliation(s)
- Jason T Ladner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jason W Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
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8
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Papudeshi B, Rusch DB, VanInsberghe D, Lively CM, Edwards RA, Bashey F. Host Association and Spatial Proximity Shape but Do Not Constrain Population Structure in the Mutualistic Symbiont Xenorhabdus bovienii. mBio 2023:e0043423. [PMID: 37154562 DOI: 10.1128/mbio.00434-23] [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: 05/10/2023] Open
Abstract
To what extent are generalist species cohesive evolutionary units rather than a compilation of recently diverged lineages? We examine this question in the context of host specificity and geographic structure in the insect pathogen and nematode mutualist Xenorhabdus bovienii. This bacterial species partners with multiple nematode species across two clades in the genus Steinernema. We sequenced the genomes of 42 X. bovienii strains isolated from four different nematode species and three field sites within a 240-km2 region and compared them to globally available reference genomes. We hypothesized that X. bovienii would comprise several host-specific lineages, such that bacterial and nematode phylogenies would be largely congruent. Alternatively, we hypothesized that spatial proximity might be a dominant signal, as increasing geographic distance might lower shared selective pressures and opportunities for gene flow. We found partial support for both hypotheses. Isolates clustered largely by nematode host species but did not strictly match the nematode phylogeny, indicating that shifts in symbiont associations across nematode species and clades have occurred. Furthermore, both genetic similarity and gene flow decreased with geographic distance across nematode species, suggesting differentiation and constraints on gene flow across both factors, although no absolute barriers to gene flow were observed across the regional isolates. Several genes associated with biotic interactions were found to be undergoing selective sweeps within this regional population. The interactions included several insect toxins and genes implicated in microbial competition. Thus, gene flow maintains cohesiveness across host associations in this symbiont and may facilitate adaptive responses to a multipartite selective environment. IMPORTANCE Microbial populations and species are notoriously hard to delineate. We used a population genomics approach to examine the population structure and the spatial scale of gene flow in Xenorhabdus bovienii, an intriguing species that is both a specialized mutualistic symbiont of nematodes and a broadly virulent insect pathogen. We found a strong signature of nematode host association, as well as evidence for gene flow connecting isolates associated with different nematode host species and collected from distinct study sites. Furthermore, we saw signatures of selective sweeps for genes involved with nematode host associations, insect pathogenicity, and microbial competition. Thus, X. bovienii exemplifies the growing consensus that recombination not only maintains cohesion but can also allow the spread of niche-beneficial alleles.
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Affiliation(s)
- Bhavya Papudeshi
- Flinders Accelerator for Microbiome Exploration, Flinders University, Adelaide, Australia
- National Centre for Genome Analysis Support, Pervasive Institute of Technology, Indiana University, Bloomington, Indiana, USA
| | - Douglas B Rusch
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana, USA
| | | | - Curtis M Lively
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Robert A Edwards
- Flinders Accelerator for Microbiome Exploration, Flinders University, Adelaide, Australia
| | - Farrah Bashey
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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9
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Zhou K, Xue CX, Xu T, Shen P, Wei S, Wyres KL, Lam MMC, Liu J, Lin H, Chen Y, Holt KE, Xiao Y. A point mutation in recC associated with subclonal replacement of carbapenem-resistant Klebsiella pneumoniae ST11 in China. Nat Commun 2023; 14:2464. [PMID: 37117217 PMCID: PMC10147710 DOI: 10.1038/s41467-023-38061-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 04/13/2023] [Indexed: 04/30/2023] Open
Abstract
Adaptation to selective pressures is crucial for clinically important pathogens to establish epidemics, but the underlying evolutionary drivers remain poorly understood. The current epidemic of carbapenem-resistant Klebsiella pneumoniae (CRKP) poses a significant threat to public health. In this study we analyzed the genome sequences of 794 CRKP bloodstream isolates collected in 40 hospitals in China between 2014 and 2019. We uncovered a subclonal replacement in the predominant clone ST11, where the previously prevalent subclone OL101:KL47 was replaced by O2v1:KL64 over time in a stepwise manner. O2v1:KL64 carried a higher load of mobile genetic elements, and a point mutation exclusively detected in the recC of O2v1:KL64 significantly promotes recombination proficiency. The epidemic success of O2v1:KL64 was further associated with a hypervirulent sublineage with enhanced resistance to phagocytosis, sulfamethoxazole-trimethoprim, and tetracycline. The phenotypic alterations were linked to the overrepresentation of hypervirulence determinants and antibiotic genes conferred by the acquisition of an rmpA-positive pLVPK-like virulence plasmid and an IncFII-type multidrug-resistant plasmid, respectively. The dissemination of the sublineage was further promoted by more frequent inter-hospital transmission. The results collectively demonstrate that the expansion of O2v1:KL64 is correlated to a repertoire of genomic alterations convergent in a subpopulation with evolutionary advantages.
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Affiliation(s)
- Kai Zhou
- Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital (Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, China.
| | - Chun-Xu Xue
- Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital (Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, China
| | - Tingting Xu
- Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital (Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, China
| | - Ping Shen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Sha Wei
- Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital (Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, China
| | - Kelly L Wyres
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | - Margaret M C Lam
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | - Jinquan Liu
- Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital (Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, China
| | - Haoyun Lin
- Department of Clinical Laboratory, Shenzhen People's Hospital, Shenzhen, China
| | - Yunbo Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Kathryn E Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Yonghong Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China.
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10
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Key FM, Khadka VD, Romo-González C, Blake KJ, Deng L, Lynn TC, Lee JC, Chiu IM, García-Romero MT, Lieberman TD. On-person adaptive evolution of Staphylococcus aureus during treatment for atopic dermatitis. Cell Host Microbe 2023; 31:593-603.e7. [PMID: 37054679 PMCID: PMC10263175 DOI: 10.1016/j.chom.2023.03.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 02/14/2023] [Accepted: 03/10/2023] [Indexed: 04/15/2023]
Abstract
The opportunistic pathogen Staphylococcus aureus frequently colonizes the inflamed skin of people with atopic dermatitis (AD) and worsens disease severity by promoting skin damage. Here, we show, by longitudinally tracking 23 children treated for AD, that S. aureus adapts via de novo mutations during colonization. Each patient's S. aureus population is dominated by a single lineage, with infrequent invasion by distant lineages. Mutations emerge within each lineage at rates similar to those of S. aureus in other contexts. Some variants spread across the body within months, with signatures of adaptive evolution. Most strikingly, mutations in capsule synthesis gene capD underwent parallel evolution in one patient and across-body sweeps in two patients. We confirm that capD negativity is more common in AD than in other contexts, via reanalysis of S. aureus genomes from 276 people. Together, these findings highlight the importance of the mutation level when dissecting the role of microbes in complex disease.
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Affiliation(s)
- Felix M Key
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Veda D Khadka
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Carolina Romo-González
- Experimental Bacteriology Laboratory, National Institute for Pediatrics, Mexico City, Mexico
| | - Kimbria J Blake
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Liwen Deng
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Tucker C Lynn
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jean C Lee
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Isaac M Chiu
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | | | - Tami D Lieberman
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute, Massachusetts Institute of Technology, Cambridge, MA, USA; Ragon Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
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11
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Kumar G, Kiran Tudu A. Tackling multidrug-resistant Staphylococcus aureus by natural products and their analogues acting as NorA efflux pump inhibitors. Bioorg Med Chem 2023; 80:117187. [PMID: 36731248 DOI: 10.1016/j.bmc.2023.117187] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 01/29/2023]
Abstract
Staphylococcus aureus (S. aureus) is a pathogen responsible for various community and hospital-acquired infections with life-threatening complications like bacteraemia, endocarditis, meningitis, liver abscess, and spinal cord epidural abscess. Antibiotics have been used to treat microbial infections since the introduction of penicillin in 1940. In recent decades, the abuse and misuse of antibiotics in humans, animals, plants, and fungi, including the treatment of non-microbial diseases, have led to the rapid emergence of multidrug-resistant pathogens with increased virulence. Bacteria have developed several complementary mechanisms to avoid the effects of antibiotics. These mechanisms include chemical transformations and enzymatic inactivation of antibiotics, modification of antibiotics' target site, and reduction of intracellular antibiotics concentration by changes in membrane permeability or by the overexpression of efflux pumps (EPs). The strategy to check antibiotic resistance includes synthesis of the antibiotic analogues, or antibiotics are given in combination with the adjuvant. The inhibitors of multidrug EPs are considered promising alternative therapeutic options with the potential to revive the effects of antibiotics and reduce bacterial virulence. Natural products played a vital role in drug discovery and significantly contributed to the area of infectious diseases. Also, natural products provide lead compounds that sometimes need modification based on structural and biological properties to meet the drug criteria. This review discusses natural products and their derived compounds as NorA efflux pump inhibitors (EPIs).
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Affiliation(s)
- Gautam Kumar
- Department of Natural Products, Chemical Sciences, National Institute of Pharmaceutical Education and Research-Hyderabad, Hyderabad, Balanagar, Telangana 500037, India.
| | - Asha Kiran Tudu
- Department of Natural Products, Chemical Sciences, National Institute of Pharmaceutical Education and Research-Hyderabad, Hyderabad, Balanagar, Telangana 500037, India
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12
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Li X, He F, Wang Z, Xing B. Roadmap of environmental health research on emerging contaminants: Inspiration from the studies on engineered nanomaterials. ECO-ENVIRONMENT & HEALTH (ONLINE) 2022; 1:181-197. [PMID: 38075596 PMCID: PMC10702922 DOI: 10.1016/j.eehl.2022.10.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 10/04/2022] [Accepted: 10/11/2022] [Indexed: 01/25/2024]
Abstract
Research on the environmental health of emerging contaminants is critical to understand their risks before causing severe harm. However, the low environmental concentrations, complex behaviors, and toxicology of emerging contaminants present enormous challenges for researchers. Here, we reviewed the research on the environmental health of engineered nanomaterials (ENMs), one of the typical emerging contaminants, to enlighten pathways for future research on emerging contaminants at their initial exploratory stage. To date, some developed pretreatment methods and detection technologies have been established for the determination of ENMs in natural environments. The mechanisms underlying the transfer and transformation of ENMs have been systematically explored in laboratory studies. The mechanisms of ENMs-induced toxicity have also been preliminarily clarified at genetic, cellular, individual, and short food chain levels, providing not only a theoretical basis for revealing the risk change and environmental health effects of ENMs in natural environments but also a methodological guidance for studying environmental health of other emerging contaminants. Nonetheless, due to the interaction of multiple environmental factors and the high diversity of organisms in natural environments, health effects observed in laboratory studies likely differ from those in natural environments. We propose a holistic approach and mesocosmic model ecosystems to systematically carry out environmental health research on emerging contaminants, obtaining data that determine the objectivity and accuracy of risk assessment.
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Affiliation(s)
- Xiaona Li
- Institute of Environmental Processes and Pollution Control, and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Jiangnan University, Wuxi 214122, China
| | - Feng He
- Institute of Environmental Processes and Pollution Control, and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Jiangnan University, Wuxi 214122, China
| | - Zhenyu Wang
- Institute of Environmental Processes and Pollution Control, and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Jiangnan University, Wuxi 214122, China
| | - Baoshan Xing
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA 01003, United States
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13
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A Review of Next Generation Sequencing Methods and its Applications in Laboratory Diagnosis. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2022. [DOI: 10.22207/jpam.16.2.45] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Next-generation sequencing (NGS) is a new technology used to detect the sequence of DNA and RNA and to detect mutations or variations of significance. NGS generates large quantities of sequence data within a short time duration. The various types of sequencing includes Sanger Sequencing, Pyrosequencing, Sequencing by Synthesis (Illumina), Ligation (SoLID), Single molecule Fluorescent Sequencing (Helicos), Single molecule Real time Sequencing (Pacbio), Semiconductor sequencing (Ion torrent technology), Nanopore sequencing and fourth generation sequencing. These methods of sequencing have been modified and improved over the years such that it has become cost effective and accessible to diagnostic laboratories. Management of Outbreaks, rapid identification of bacteria, molecular case finding, taxonomy, detection of the zoonotic agents and guiding prevention strategies in HIV outbreaks are just a few of the many applications of Next Generation sequencing in clinical microbiology.
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14
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Lister AP, Highmore CJ, Hanrahan N, Read J, Munro APS, Tan S, Allan RN, Faust SN, Webb JS, Mahajan S. Multi-Excitation Raman Spectroscopy for Label-Free, Strain-Level Characterization of Bacterial Pathogens in Artificial Sputum Media. Anal Chem 2022; 94:669-677. [DOI: 10.1021/acs.analchem.1c02501] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Adam P. Lister
- School of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, SO17 1BJ Southampton, United Kingdom
- National Biofilms Innovation Centre (NBIC) and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Callum J. Highmore
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, SO17 1BJ Southampton, United Kingdom
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Niall Hanrahan
- School of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, SO17 1BJ Southampton, United Kingdom
- National Biofilms Innovation Centre (NBIC) and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - James Read
- School of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, SO17 1BJ Southampton, United Kingdom
- National Biofilms Innovation Centre (NBIC) and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Alasdair P. S. Munro
- NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Samuel Tan
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Raymond N. Allan
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, SO17 1BJ Southampton, United Kingdom
- NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
- School of Pharmacy, Faculty of Health and Life Sciences, De Montfort University, Leicester LE1 9BH, UK
| | - Saul N. Faust
- NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
- National Biofilms Innovation Centre (NBIC) and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Jeremy S. Webb
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, SO17 1BJ Southampton, United Kingdom
- National Biofilms Innovation Centre (NBIC) and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Sumeet Mahajan
- School of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, SO17 1BJ Southampton, United Kingdom
- National Biofilms Innovation Centre (NBIC) and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
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Evolutionary Processes Driving the Rise and Fall of Staphylococcus aureus ST239, a Dominant Hybrid Pathogen. mBio 2021; 12:e0216821. [PMID: 34903061 PMCID: PMC8669471 DOI: 10.1128/mbio.02168-21] [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] [Indexed: 02/07/2023] Open
Abstract
Selection plays a key role in the spread of antibiotic resistance, but the evolutionary drivers of clinically important resistant strains remain poorly understood. Here, we use genomic analyses and competition experiments to study Staphylococcus aureus ST239, a prominent MRSA strain that is thought to have been formed by large-scale recombination between ST8 and ST30. Genomic analyses allowed us to refine the hybrid model for the origin of ST239 and to date the origin of ST239 to 1920 to 1945, which predates the clinical introduction of methicillin in 1959. Although purifying selection has dominated the evolution of ST239, parallel evolution has occurred in genes involved in antibiotic resistance and virulence, suggesting that ST239 has evolved toward an increasingly pathogenic lifestyle. Crucially, ST239 isolates have low competitive fitness relative to both ST8 and ST30 isolates, supporting the idea that fitness costs have driven the demise of this once-dominant pathogen strain.
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16
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Dietrich A, Steffens U, Sass P, Bierbaum G. The hypersusceptible antibiotic screening strain Staphylococcus aureus SG511-Berlin harbors multiple mutations in regulatory genes. Int J Med Microbiol 2021; 311:151545. [PMID: 34896903 DOI: 10.1016/j.ijmm.2021.151545] [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: 08/17/2021] [Revised: 12/01/2021] [Accepted: 12/05/2021] [Indexed: 10/19/2022] Open
Abstract
The genetic plasticity of Staphylococcus aureus has facilitated the evolution of many virulent and drug-resistant strains. Here we present the sequence of the 2.74 Mbp genome of S. aureus SG511-Berlin, which is frequently used for antibiotic screening. Although S. aureus SG511 and the related methicillin-resistant S. aureus MRSA252 share a high similarity in their core genomes, indicated by an average nucleotide identity (ANI) of 99.83%, the accessory genomes of these strains differed, as nearly no mobile elements and resistance determinants were identified in the genome of S. aureus SG511. Susceptibility testing showed that S. aureus SG511 was susceptible to most of the tested antibiotics of different classes. Intriguingly, and in contrast to the standard laboratory strain S. aureus HG001, S. aureus SG511 was even hyper-susceptible towards cell wall and membrane targeting agents, with the exception of the MurA-inhibitor fosfomycin. In depth comparative genome analysis revealed that, in addition to the loss of function mutation in the antibiotic sensor histidine kinase gene graS, further mutations had occurred in the lysyltransferase gene mprF, the structural giant protein gene ebh, and the regulator genes codY and saeR, which might contribute to antibiotic susceptibility. In addition, an insertion element in agrC abolishes Agr-activity in S. aureus SG511, and the spa and sarS genes, which encode the surface protein SpA and its transcriptional regulator, were deleted. Thus, the lack of mobile resistance genes together with multiple mutations affecting cell envelope morphology may render S. aureus SG511 hyper-susceptible towards most cell wall targeting agents.
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Affiliation(s)
- Alina Dietrich
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Medical Faculty, 53127 Bonn, Germany.
| | - Ursula Steffens
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Medical Faculty, 53127 Bonn, Germany.
| | - Peter Sass
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Medical Faculty, 53127 Bonn, Germany.
| | - Gabriele Bierbaum
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Medical Faculty, 53127 Bonn, Germany.
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17
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Chen H, Yin Y, van Dorp L, Shaw LP, Gao H, Acman M, Yuan J, Chen F, Sun S, Wang X, Li S, Zhang Y, Farrer RA, Wang H, Balloux F. Drivers of methicillin-resistant Staphylococcus aureus (MRSA) lineage replacement in China. Genome Med 2021; 13:171. [PMID: 34711267 PMCID: PMC8555231 DOI: 10.1186/s13073-021-00992-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 10/17/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Methicillin-resistant Staphylococcus aureus (MRSA) is a major nosocomial pathogen subdivided into lineages termed sequence types (STs). Since the 1950s, successive waves of STs have appeared and replaced previously dominant lineages. One such event has been occurring in China since 2013, with community-associated (CA-MRSA) strains including ST59 largely replacing the previously dominant healthcare-associated (HA-MRSA) ST239. We previously showed that ST59 isolates tend to have a competitive advantage in growth experiments against ST239. However, the underlying genomic and phenotypic drivers of this replacement event are unclear. METHODS Here, we investigated the replacement of ST239 using whole-genome sequencing data from 204 ST239 and ST59 isolates collected in Chinese hospitals between 1994 and 2016. We reconstructed the evolutionary history of each ST and considered two non-mutually exclusive hypotheses for ST59 replacing ST239: antimicrobial resistance (AMR) profile and/or ability to colonise and persist in the environment through biofilm formation. We also investigated the differences in cytolytic activity, linked to higher virulence, between STs. We performed an association study using the presence and absence of accessory virulence genes. RESULTS ST59 isolates carried fewer AMR genes than ST239 and showed no evidence of evolving towards higher AMR. Biofilm production was marginally higher in ST59 overall, though this effect was not consistent across sub-lineages so is unlikely to be a sole driver of replacement. Consistent with previous observations of higher virulence in CA-MRSA STs, we observed that ST59 isolates exhibit significantly higher cytolytic activity than ST239 isolates, despite carrying on average fewer putative virulence genes. Our association study identified the chemotaxis inhibitory protein (chp) as a strong candidate for involvement in the increased virulence potential of ST59. We experimentally validated the role of chp in increasing the virulence potential of ST59 by creating Δchp knockout mutants, confirming that ST59 can carry chp without a measurable impact on fitness. CONCLUSIONS Our results suggest that the ongoing replacement of ST239 by ST59 in China is not associated to higher AMR carriage or biofilm production. However, the increase in ST59 prevalence is concerning since it is linked to a higher potential for virulence, aided by the carriage of the chp gene.
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Affiliation(s)
- Hongbin Chen
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, 100044, China
- UCL Genetics Institute, University College London, Gower Street, London, WC1E 6BT, UK
| | - Yuyao Yin
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, 100044, China
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, Gower Street, London, WC1E 6BT, UK.
| | - Liam P Shaw
- UCL Genetics Institute, University College London, Gower Street, London, WC1E 6BT, UK
- Department of Zoology, University of Oxford, Oxford, OX1 3SZ, UK
| | - Hua Gao
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, 100044, China
| | - Mislav Acman
- UCL Genetics Institute, University College London, Gower Street, London, WC1E 6BT, UK
| | - Jizhen Yuan
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, 100044, China
- The No. 971 Hospital of People's Liberation Army Navy, Qingdao, 266000, Shandong, China
| | - Fengning Chen
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, 100044, China
| | - Shijun Sun
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, 100044, China
| | - Xiaojuan Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, 100044, China
| | - Shuguang Li
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, 100044, China
| | - Yawei Zhang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, 100044, China
| | - Rhys A Farrer
- UCL Genetics Institute, University College London, Gower Street, London, WC1E 6BT, UK
- Medical Research Council Centre for Medical Mycology at the University of Exeter, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK
| | - Hui Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, 100044, China.
| | - Francois Balloux
- UCL Genetics Institute, University College London, Gower Street, London, WC1E 6BT, UK.
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18
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Comparative Genomic Analysis Provides Insights into the Evolution and Genetic Diversity of Community-Genotype Sequence Type 72 Staphylococcus aureus Isolates. mSystems 2021; 6:e0098621. [PMID: 34491085 PMCID: PMC8547429 DOI: 10.1128/msystems.00986-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Staphylococcus aureus sequence type (ST) 72, the predominant community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) lineage in South Korea, has emerged as a major cause of bloodstream infection in hospital settings. However, relatively little information is available regarding the genomic characteristics and dissemination of ST72. Here, we characterized the whole-genome sequence of 24 ST72 isolates from China, along with 83 ST72 genomes from global sources. Of these 107 ST72 isolates, 63 were MRSA and 44 were methicillin-susceptible S. aureus (MSSA). Phylogenetic analysis revealed four distinct clades (A, B, C, and D), of which clade D contained only MSSA isolates. By characterizing the evolutionary dynamics of the ST72 lineage, we found that the MRSA from China might not have developed from the MSSA in China. Furthermore, we observed both international transmission of ST72 isolates and interregional transmission within China. The distributions of the SCCmec and spa types of isolates differed among clades. Additionally, in silico analyses revealed that the distributions of resistance genes, virulence genes, and mobile genetic elements (MGEs) also differed among isolates of the four clades. This was especially true for clade D isolates, which had the lowest level of antimicrobial resistance and had obtained specific virulence genes such as tsst-1 by acquisition of specific MGEs. Notably, ST72 MRSA isolates were more antibiotic resistant than ST72 MSSA isolates, but comparably virulent. Our findings provide insight into the potential transmission and genotypic features of ST72 clones across the globe. IMPORTANCE Understanding the evolution and dissemination of community-genotype ST72 Staphylococcus aureus isolates is important, as isolates of this lineage have rapidly spread into hospital settings and caused serious health issues. In this study, we first carried out genome-wide analysis of 107 global ST72 isolates to characterize the evolution and genetic diversity of the ST72 lineage. We found that the MSSA lineage in China might have evolved independently from the MRSA isolates from China, and that ST72 isolates have the potential to undergo both international transmission and interregional transmission within China. The diversity of isolates correlated with distinct acquisitions of SCCmec elements, antibiotic resistance genes, virulence genes, and mobile genetic elements. The comprehensive information on the ST72 lineage emerging from this study will enable improved therapeutic approaches and rapid molecular diagnosis.
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Calland JK, Pascoe B, Bayliss SC, Mourkas E, Berthenet E, Thorpe HA, Hitchings MD, Feil EJ, Corander J, Blaser MJ, Falush D, Sheppard SK. Quantifying bacterial evolution in the wild: A birthday problem for Campylobacter lineages. PLoS Genet 2021; 17:e1009829. [PMID: 34582435 PMCID: PMC8500405 DOI: 10.1371/journal.pgen.1009829] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 10/08/2021] [Accepted: 09/20/2021] [Indexed: 11/20/2022] Open
Abstract
Measuring molecular evolution in bacteria typically requires estimation of the rate at which nucleotide changes accumulate in strains sampled at different times that share a common ancestor. This approach has been useful for dating ecological and evolutionary events that coincide with the emergence of important lineages, such as outbreak strains and obligate human pathogens. However, in multi-host (niche) transmission scenarios, where the pathogen is essentially an opportunistic environmental organism, sampling is often sporadic and rarely reflects the overall population, particularly when concentrated on clinical isolates. This means that approaches that assume recent common ancestry are not applicable. Here we present a new approach to estimate the molecular clock rate in Campylobacter that draws on the popular probability conundrum known as the 'birthday problem'. Using large genomic datasets and comparative genomic approaches, we use isolate pairs that share recent common ancestry to estimate the rate of nucleotide change for the population. Identifying synonymous and non-synonymous nucleotide changes, both within and outside of recombined regions of the genome, we quantify clock-like diversification to estimate synonymous rates of nucleotide change for the common pathogenic bacteria Campylobacter coli (2.4 x 10-6 s/s/y) and Campylobacter jejuni (3.4 x 10-6 s/s/y). Finally, using estimated total rates of nucleotide change, we infer the number of effective lineages within the sample time frame-analogous to a shared birthday-and assess the rate of turnover of lineages in our sample set over short evolutionary timescales. This provides a generalizable approach to calibrating rates in populations of environmental bacteria and shows that multiple lineages are maintained, implying that large-scale clonal sweeps may take hundreds of years or more in these species.
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Affiliation(s)
- Jessica K. Calland
- The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
| | - Ben Pascoe
- The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
| | - Sion C. Bayliss
- The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
| | - Evangelos Mourkas
- The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
| | - Elvire Berthenet
- French National Reference Center for Campylobacters and Helicobacters, University of Bordeaux, Bordeaux, France
- Institute of Life Sciences, Swansea University Medical School, Swansea University, Singleton Park, Swansea, United Kingdom
| | - Harry A. Thorpe
- The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
- Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Matthew D. Hitchings
- Institute of Life Sciences, Swansea University Medical School, Swansea University, Singleton Park, Swansea, United Kingdom
| | - Edward J. Feil
- The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Department of Mathematics and Statistics, Helsinki Institute for Information Technology, University of Helsinki, Helsinki, Finland
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Martin J. Blaser
- Center for Advanced Biotechnology and Medicine, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Daniel Falush
- Centre for Microbes, Development and Health, Institute Pasteur of Shanghai, Shanghai, China
- * E-mail: (DF); (SKS)
| | - Samuel K. Sheppard
- The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- * E-mail: (DF); (SKS)
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20
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Jiang N, Wyres KL, Li J, Feßler AT, Krüger H, Wang Y, Holt KE, Schwarz S, Wu C. Evolution and genomic insight into methicillin-resistant Staphylococcus aureus ST9 in China. J Antimicrob Chemother 2021; 76:1703-1711. [PMID: 33822977 DOI: 10.1093/jac/dkab106] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 03/13/2021] [Indexed: 12/11/2022] Open
Abstract
OBJECTIVES To reconstruct the evolutionary history and genomic epidemiology of Staphylococcus aureus ST9 in China. METHODS Using WGS analysis, we described the phylogeny of 131 S. aureus ST9 isolates collected between 2002 and 2016 from 11 provinces in China, including six clinical samples from Taiwan. We also investigated the complex structure and distribution of the lsa(E)-carrying multiresistance gene cluster, and genotyped prophages in the genomes of the ST9 isolates. RESULTS ST9 was subdivided into one major (n = 122) and one minor (n = 9) clade. Bayesian phylogeny predicted the divergence of ST9 isolates in pig farming in China as early as 1987, which then evolved rapidly in the following three decades. ST9 isolates shared similar multiresistance properties, which were likely acquired before the ST9 emergence in China. The accessory genome is highly conserved, and ST9 harboured similar sets of phages, but lacked certain virulence genes. CONCLUSIONS Host exchange and regional transmission of ST9 have occurred between pigs and humans. Pig rearing and trading might have favoured gene exchanges between ST9 isolates. Resistance genes, obtained from the environment and other isolates, were stably integrated into the chromosomal DNA. The abundance of resistance genes among ST9 is likely attributed to the extensive use of antimicrobial agents in livestock. Phages are present in the genomes of ST9 and may play a role in the rapid evolution of this ST. Although human ST9 infections are rare, ST9 isolates may constitute a potential risk to public health as a repository of antimicrobial resistance genes.
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Affiliation(s)
- Nansong Jiang
- Beijing Key Laboratory of Detection Technology for Animal Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Kelly L Wyres
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia
| | - Jun Li
- Beijing Key Laboratory of Detection Technology for Animal Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China.,Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Beijing, China
| | - Andrea T Feßler
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Henrike Krüger
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Yang Wang
- Beijing Key Laboratory of Detection Technology for Animal Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Kathryn E Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia.,Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
| | - Stefan Schwarz
- Beijing Key Laboratory of Detection Technology for Animal Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China.,Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Congming Wu
- Beijing Key Laboratory of Detection Technology for Animal Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
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21
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Wang W, Baker M, Hu Y, Xu J, Yang D, Maciel-Guerra A, Xue N, Li H, Yan S, Li M, Bai Y, Dong Y, Peng Z, Ma J, Li F, Dottorini T. Whole-Genome Sequencing and Machine Learning Analysis of Staphylococcus aureus from Multiple Heterogeneous Sources in China Reveals Common Genetic Traits of Antimicrobial Resistance. mSystems 2021; 6:e0118520. [PMID: 34100643 PMCID: PMC8579812 DOI: 10.1128/msystems.01185-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 05/10/2021] [Indexed: 12/27/2022] Open
Abstract
Staphylococcus aureus is a worldwide leading cause of numerous diseases ranging from food-poisoning to lethal infections. Methicillin-resistant S. aureus (MRSA) has been found capable of acquiring resistance to most antimicrobials. MRSA is ubiquitous and diverse even in terms of antimicrobial resistance (AMR) profiles, posing a challenge for treatment. Here, we present a comprehensive study of S. aureus in China, addressing epidemiology, phylogenetic reconstruction, genomic characterization, and identification of AMR profiles. The study analyzes 673 S. aureus isolates from food as well as from hospitalized and healthy individuals. The isolates have been collected over a 9-year period, between 2010 and 2018, from 27 provinces across China. By whole-genome sequencing, Bayesian divergence analysis, and supervised machine learning, we reconstructed the phylogeny of the isolates and compared them to references from other countries. We identified 72 sequence types (STs), of which, 29 were novel. We found 81 MRSA lineages by multilocus sequence type (MLST), spa, staphylococcal cassette chromosome mec element (SCCmec), and Panton-Valentine leukocidin (PVL) typing. In addition, novel variants of SCCmec type IV hosting extra metal and antimicrobial resistance genes, as well as a new SCCmec type, were found. New Bayesian dating of the split times of major clades showed that ST9, ST59, and ST239 in China and European countries fell in different branches, whereas this pattern was not observed for the ST398 clone. On the contrary, the clonal transmission of ST398 was more intermixed in regard to geographic origin. Finally, we identified genetic determinants of resistance to 10 antimicrobials, discriminating drug-resistant bacteria from susceptible strains in the cohort. Our results reveal the emergence of Chinese MRSA lineages enriched of AMR determinants that share similar genetic traits of antimicrobial resistance across human and food, hinting at a complex scenario of evolving transmission routes. IMPORTANCE Little information is available on the epidemiology and characterization of Staphylococcus aureus in China. The role of food is a cause of major concern: staphylococcal foodborne diseases affect thousands every year, and the presence of resistant Staphylococcus strains on raw retail meat products is well documented. We studied a large heterogeneous data set of S. aureus isolates from many provinces of China, isolated from food as well as from individuals. Our large whole-genome collection represents a unique catalogue that can be easily meta-analyzed and integrated with further studies and adds to the library of S. aureus sequences in the public domain in a currently underrepresented geographical region. The new Bayesian dating of the split times of major drug-resistant enriched clones is relevant in showing that Chinese and European methicillin-resistant S. aureus (MRSA) have evolved differently. Our machine learning approach, across a large number of antibiotics, shows novel determinants underlying resistance and reveals frequent resistant traits in specific clonal complexes, highlighting the importance of particular clonal complexes in China. Our findings substantially expand what is known of the evolution and genetic determinants of resistance in food-associated S. aureus in China and add crucial information for whole-genome sequencing (WGS)-based surveillance of S. aureus.
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Affiliation(s)
- Wei Wang
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Michelle Baker
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Leicestershire, United Kingdom
| | - Yue Hu
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Leicestershire, United Kingdom
| | - Jin Xu
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Dajin Yang
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | | | - Ning Xue
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Leicestershire, United Kingdom
| | - Hui Li
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Shaofei Yan
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Menghan Li
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Yao Bai
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Yinping Dong
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Zixin Peng
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Jinjing Ma
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
- School of Chemistry and Chemical Engineering, Anqing Normal University, Anqing, Anhui, China
| | - Fengqin Li
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Tania Dottorini
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Leicestershire, United Kingdom
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Coagulase-negative staphylococci release a purine analog that inhibits Staphylococcus aureus virulence. Nat Commun 2021; 12:1887. [PMID: 33767207 PMCID: PMC7994395 DOI: 10.1038/s41467-021-22175-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 03/01/2021] [Indexed: 01/08/2023] Open
Abstract
Coagulase-negative staphylococci and Staphylococcus aureus colonize similar niches in mammals and conceivably compete for space and nutrients. Here, we report that a coagulase-negative staphylococcus, Staphylococcus chromogenes ATCC43764, synthesizes and secretes 6-thioguanine (6-TG), a purine analog that suppresses S. aureus growth by inhibiting de novo purine biosynthesis. We identify a 6-TG biosynthetic gene cluster in S. chromogenes and other coagulase-negative staphylococci including S. epidermidis, S. pseudintermedius and S. capitis. Recombinant S. aureus strains harbouring this operon produce 6-TG and, when used in subcutaneous co-infections in mice with virulent S. aureus USA300, protect the host from necrotic lesion formation. Used prophylactically, 6-TG reduces necrotic skin lesions in mice infected with USA300, and this effect is mediated by abrogation of toxin production. RNAseq analyses reveal that 6-TG downregulates expression of genes coding for purine biosynthesis, the accessory gene regulator (agr) and ribosomal proteins in S. aureus, providing an explanation for its effect on toxin production. Coagulase-negative staphylococci and Staphylococcus aureus colonize similar niches in mammals. Here, Chin et al. show that a coagulase-negative staphylococcus secretes 6-thioguanine, a purine analog that suppresses S. aureus growth and virulence by inhibiting de novo purine biosynthesis and toxin production.
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Di Gregorio S, Haim MS, Vielma Vallenilla J, Cohen V, Rago L, Gulone L, Aanensen DM, Argimón S, Mollerach M. Genomic Epidemiology of CC30 Methicillin-Resistant Staphylococcus aureus Strains from Argentina Reveals Four Major Clades with Distinctive Genetic Features. mSphere 2021; 6:e01297-20. [PMID: 33692199 PMCID: PMC8546718 DOI: 10.1128/msphere.01297-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/10/2021] [Indexed: 11/20/2022] Open
Abstract
Staphylococcus aureus clonal complex 30 (CC30) has given rise to epidemics worldwide and is one of the most prevalent lineages in Argentina, represented by sequence type 30 methicillin-resistant S. aureus SCCmec type IV (ST30-MRSA-IV). ST30-MRSA-IV has displaced previous prevalent clones in the country and demonstrated increased virulence. Despite the burden of infections caused by ST30-MRSA-IV both in hospitals and in communities in Argentina, no detailed genome-based characterization of this clone is available to date. In this study, we used whole-genome sequencing (WGS) to evaluate the genetic diversity, population structure, and genomic characteristics of 190 CC30-MRSA strains circulating in Argentina between 2004 and 2015. Phylogenetic analysis revealed the existence of 4 major clades: ARG-1 (CC30-MRSA-IVc-spa t012), ARG-2 (ST30-MRSA-IVc-spa t021 related), ARG-3 (ST30-MRSA-IVh/j-spa t021 and related), and ARG-4 (CC30-MRSA-IVc-spa t019 and related). The clades were characterized by different distributions of antimicrobial resistance determinants, virulence genes, and mobile genetic elements (MGEs). While ARG-1 and ARG-4 were related to global epidemic MRSA-16 (EMRSA-16) and South West Pacific (SWP) clones, respectively, ARG-3 was phylogenetically distinct from previously defined CC30 epidemic clones. ARG-4, the most prevalent and geographically disseminated in the collection (N = 164), was characterized by specific MGEs and chromosomal mutations that might have contributed to its virulence and success. To our knowledge, this is the first genomic epidemiology study of CC30-MRSA in Argentina, which will serve as baseline genomic data going forward to inform public health measures for infection prevention and control.IMPORTANCE The rise in prevalence of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is of public health concern. In Argentina, several studies documented a shift in the epidemiology of CA-MRSA since 2009, with clonal complex 30 (CC30) and, in particular, sequence type 30 MRSA SCCmec type IV (ST30-MRSA-IV) replacing other clones both in communities and in hospitals and possibly displaying increased virulence. By sequencing the whole genomes of 190 CC30 MRSA isolates recovered from Argentina between 2005 and 2015, we showed that they represented a diverse population composed of 4 major clades. The predominant clade evolved from the South West Pacific clone but has acquired a distinct repertoire of mobile genetic elements, virulence genes, and chromosomal mutations that might play a role in its success. Our work is the first extensive genomic study of CC30 S. aureus in Argentina and will contribute not only to the development of genomic surveillance in the region but also to our understanding of the global epidemiology of this pathogen.
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Affiliation(s)
- Sabrina Di Gregorio
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina
| | - María Sol Haim
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Jesús Vielma Vallenilla
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina
| | - Victoria Cohen
- The Centre for Genomic Pathogen Surveillance (CGPS), Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Lucía Rago
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina
| | - Lucía Gulone
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - David M Aanensen
- The Centre for Genomic Pathogen Surveillance (CGPS), Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Silvia Argimón
- The Centre for Genomic Pathogen Surveillance (CGPS), Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Marta Mollerach
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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Manyahi J, Moyo SJ, Aboud S, Langeland N, Blomberg B. Predominance of PVL-negative community-associated methicillin-resistant Staphylococcus aureus sequence type 8 in newly diagnosed HIV-infected adults, Tanzania. Eur J Clin Microbiol Infect Dis 2021; 40:1477-1485. [PMID: 33586013 PMCID: PMC8206053 DOI: 10.1007/s10096-021-04160-2] [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: 08/26/2020] [Accepted: 01/11/2021] [Indexed: 11/24/2022]
Abstract
Difficult-to-treat infections caused by methicillin-resistant Staphylococcus aureus (MRSA) are of concern in people living with HIV infection as they are more vulnerable to infection. We aimed to identify molecular characteristics of MRSA colonizing newly diagnosed HIV-infected adults in Tanzania. Individuals newly diagnosed with HIV infection were recruited in Dar es Salaam, Tanzania, from April 2017 to May 2018, as part of the randomized clinical trial CoTrimResist (ClinicalTrials.gov identifier: NCT03087890). Nasal/nasopharyngeal isolates of Staphylococcus aureus were susceptibility tested by disk diffusion method, and cefoxitin-resistant isolates were characterized by short-reads whole genome sequencing. Four percent (22/537) of patients carried MRSA in the nose/nasopharynx. MRSA isolates were frequently resistant towards gentamicin (95%), ciprofloxacin (91%), and erythromycin (82%) but less often towards trimethoprim-sulfamethoxazole (9%). Seventy-three percent had inducible clindamycin resistance. Erythromycin-resistant isolates harbored ermC (15/18) and LmrS (3/18) resistance genes. Ciprofloxacin resistance was mediated by mutations of the quinolone resistance-determining region (QRDR) sequence in the gyrA (S84L) and parC (S80Y) genes. All isolates belonged to the CC8 and ST8-SCCmecIV MRSA clone. Ninety-five percent of the MRSA isolates were spa-type t1476, and one exhibited spa-type t064. All isolates were negative for Panton-Valentine leucocidin (PVL) and arginine catabolic mobile element (ACME) type 1. All ST8-SCCmecIV-spa-t1476 MRSA clones from Tanzania were unrelated to the globally successful USA300 clone. Carriage of ST8 MRSA (non-USA300) was common among newly diagnosed HIV-infected adults in Tanzania. Frequent co-resistance to non-beta lactam antibiotics limits therapeutic options when infection occurs.
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Affiliation(s)
- Joel Manyahi
- Department of Clinical Science, University of Bergen, Bergen, Norway. .,National Advisory Unit for Tropical Infectious Diseases, Department of Medicine, Haukeland University Hospital, Bergen, Norway. .,Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, MUHAS, P.O. Box 65001, Dar es Salaam, Tanzania.
| | - Sabrina J Moyo
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, MUHAS, P.O. Box 65001, Dar es Salaam, Tanzania
| | - Said Aboud
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, MUHAS, P.O. Box 65001, Dar es Salaam, Tanzania
| | - Nina Langeland
- Department of Clinical Science, University of Bergen, Bergen, Norway.,National Advisory Unit for Tropical Infectious Diseases, Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Bjørn Blomberg
- Department of Clinical Science, University of Bergen, Bergen, Norway.,National Advisory Unit for Tropical Infectious Diseases, Department of Medicine, Haukeland University Hospital, Bergen, Norway
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25
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Valiente-Mullor C, Beamud B, Ansari I, Francés-Cuesta C, García-González N, Mejía L, Ruiz-Hueso P, González-Candelas F. One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads. PLoS Comput Biol 2021; 17:e1008678. [PMID: 33503026 PMCID: PMC7870062 DOI: 10.1371/journal.pcbi.1008678] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 02/08/2021] [Accepted: 01/05/2021] [Indexed: 12/17/2022] Open
Abstract
Mapping of high-throughput sequencing (HTS) reads to a single arbitrary reference genome is a frequently used approach in microbial genomics. However, the choice of a reference may represent a source of errors that may affect subsequent analyses such as the detection of single nucleotide polymorphisms (SNPs) and phylogenetic inference. In this work, we evaluated the effect of reference choice on short-read sequence data from five clinically and epidemiologically relevant bacteria (Klebsiella pneumoniae, Legionella pneumophila, Neisseria gonorrhoeae, Pseudomonas aeruginosa and Serratia marcescens). Publicly available whole-genome assemblies encompassing the genomic diversity of these species were selected as reference sequences, and read alignment statistics, SNP calling, recombination rates, dN/dS ratios, and phylogenetic trees were evaluated depending on the mapping reference. The choice of different reference genomes proved to have an impact on almost all the parameters considered in the five species. In addition, these biases had potential epidemiological implications such as including/excluding isolates of particular clades and the estimation of genetic distances. These findings suggest that the single reference approach might introduce systematic errors during mapping that affect subsequent analyses, particularly for data sets with isolates from genetically diverse backgrounds. In any case, exploring the effects of different references on the final conclusions is highly recommended. Mapping consists in the alignment of reads (i.e., DNA fragments) obtained through high-throughput genome sequencing to a previously assembled reference sequence. It is a common practice in genomic studies to use a single reference for mapping, usually the ‘reference genome’ of a species—a high-quality assembly. However, the selection of an optimal reference is hindered by intrinsic intra-species genetic variability, particularly in bacteria. It is known that genetic differences between the reference genome and the read sequences may produce incorrect alignments during mapping. Eventually, these errors could lead to misidentification of variants and biased reconstruction of phylogenetic trees (which reflect ancestry between different bacterial lineages). To our knowledge, this is the first work to systematically examine the effect of different references for mapping on the inference of tree topology as well as the impact on recombination and natural selection inferences. Furthermore, the novelty of this work relies on a procedure that guarantees that we are evaluating only the effect of the reference. This effect has proved to be pervasive in the five bacterial species that we have studied and, in some cases, alterations in phylogenetic trees could lead to incorrect epidemiological inferences. Hence, the use of different reference genomes may be prescriptive to assess the potential biases of mapping.
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Affiliation(s)
- Carlos Valiente-Mullor
- Joint Research Unit “Infection and Public Health” FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
| | - Beatriz Beamud
- Joint Research Unit “Infection and Public Health” FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
- * E-mail: (BB); (FG-C)
| | - Iván Ansari
- Joint Research Unit “Infection and Public Health” FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
| | - Carlos Francés-Cuesta
- Joint Research Unit “Infection and Public Health” FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
| | - Neris García-González
- Joint Research Unit “Infection and Public Health” FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
| | - Lorena Mejía
- Joint Research Unit “Infection and Public Health” FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - Paula Ruiz-Hueso
- Joint Research Unit “Infection and Public Health” FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
| | - Fernando González-Candelas
- Joint Research Unit “Infection and Public Health” FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
- CIBER in Epidemiology and Public Health, Valencia, Spain
- * E-mail: (BB); (FG-C)
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26
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Masim ML, Argimón S, Espiritu HO, Magbanua MA, Lagrada ML, Olorosa AM, Cohen V, Gayeta JM, Jeffrey B, Abudahab K, Hufano CM, Sia SB, Holden MT, Stelling J, Aanensen DM, Carlos CC. Genomic surveillance of methicillin-resistant Staphylococcus aureus in the Philippines,
2013-2014. Western Pac Surveill Response J 2021; 12:6-16. [PMID: 34094618 PMCID: PMC8143927 DOI: 10.5365/wpsar.2020.11.1.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) remains one of the leading causes of both nosocomial and community infections worldwide. In the Philippines, MRSA rates have remained above 50% since 2010, but resistance to other antibiotics, including vancomycin, is low. The MRSA burden can be partially attributed to pathogen-specific characteristics of the circulating clones, but little was known about the S. aureus clones circulating in the Philippines. We sequenced the whole genomes of 116 S. aureus isolates collected in 2013-2014 within the Antimicrobial Resistance Surveillance Program. The multilocus sequence type, spa type, SCCmec type, presence of antimicrobial resistance (AMR) determinants and virulence genes and relatedness between the isolates were all derived from the sequence data. The concordance between phenotypic and genotypic resistance was also determined. The MRSA population in the Philippines comprised a limited number of genetic clones, including several international epidemic clones, such as CC30-spa-t019-SCCmec-IV-PVL+, CC5-SCCmec-typeIV and ST239-spa-t030-SCCmec-typeIII. The CC30 genomes were related to the South-West Pacific clone but formed a distinct, diverse lineage, with evidence of global dissemination. We showed independent acquisition of resistance to sulfamethoxazole/trimethoprim in various locations and genetic clones but mostly in paediatric patients with invasive infections. The concordance between phenotypic and genotypic resistance was 99.68% overall for eight antibiotics in seven classes. We have made the first comprehensive genomic survey of S. aureus in the Philippines, which bridges the gap in genomic data from the Western Pacific Region and will constitute the genetic background for contextualizing prospective surveillance.
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Affiliation(s)
- Melissa L. Masim
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, Philippines
- These authors contributed equally to this work
| | - Silvia Argimón
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, England, United Kingdom of Great Britain and Northern Ireland
- These authors contributed equally to this work
| | - Holly O. Espiritu
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, Philippines
| | - Mariane A. Magbanua
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, Philippines
| | - Marietta L. Lagrada
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, Philippines
| | - Agnettah M. Olorosa
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, Philippines
| | - Victoria Cohen
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, England, United Kingdom of Great Britain and Northern Ireland
| | - June M. Gayeta
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, Philippines
| | - Benjamin Jeffrey
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, England, United Kingdom of Great Britain and Northern Ireland
| | - Khalil Abudahab
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, England, United Kingdom of Great Britain and Northern Ireland
| | - Charmian M. Hufano
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, Philippines
| | - Sonia B. Sia
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, Philippines
| | - Matthew T.G. Holden
- University of St Andrews School of Medicine, St Andrews, Scotland, United Kingdom of Great Britain and Northern Ireland
| | - John Stelling
- Brigham and Women’s Hospital, Boston (MA), United States of America
| | - David M. Aanensen
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, England, United Kingdom of Great Britain and Northern Ireland
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, England, United Kingdom of Great Britain and Northern Ireland
- These authors contributed equally to this work
| | - Celia C. Carlos
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, Philippines
- These authors contributed equally to this work
| | - on behalf of the Philippines Antimicrobial Resistance Surveillance Program
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, Philippines
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, England, United Kingdom of Great Britain and Northern Ireland
- University of St Andrews School of Medicine, St Andrews, Scotland, United Kingdom of Great Britain and Northern Ireland
- Brigham and Women’s Hospital, Boston (MA), United States of America
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, England, United Kingdom of Great Britain and Northern Ireland
- These authors contributed equally to this work
- These authors contributed equally to this work
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27
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Coll F, Raven KE, Knight GM, Blane B, Harrison EM, Leek D, Enoch DA, Brown NM, Parkhill J, Peacock SJ. Definition of a genetic relatedness cutoff to exclude recent transmission of meticillin-resistant Staphylococcus aureus: a genomic epidemiology analysis. LANCET MICROBE 2020; 1:e328-e335. [PMID: 33313577 PMCID: PMC7721685 DOI: 10.1016/s2666-5247(20)30149-x] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Background Whole-genome sequencing (WGS) can be used in genomic epidemiology investigations to confirm or refute outbreaks of bacterial pathogens, and to support targeted and efficient infection control interventions. We aimed to define a genetic relatedness cutoff, quantified as a number of single-nucleotide polymorphisms (SNP), for meticillin-resistant Staphylococcus aureus (MRSA), above which recent (ie, within 6 months) patient-to-patient transmission could be ruled out. Methods We did a retrospective genomic and epidemiological analysis of MRSA data from two prospective observational cohort studies in the UK to establish SNP cutoffs for genetic relatedness, above which recent transmission was unlikely. We used three separate approaches to calculate these thresholds. First, we applied a linear mixed model to estimate the S aureus substitution rate and 95th percentile within-host diversity in a cohort in which multiple isolates were sequenced per individual. Second, we applied a simulated transmission model to this same genomic dataset. Finally, in a second cohort, we determined the genetic distance (ie, the number of SNPs) that would capture 95% of epidemiologically linked cases. We applied the three approaches to both whole-genome and core-genome sequences. Findings In the linear mixed model, the estimated substitution rate was roughly 5 whole-genome SNPs (wgSNPs) or 3 core-genome SNPs (cgSNPs) per genome per year, and the 95th percentile within-host diversity was 19 wgSNPs or 10 cgSNPs. The combined SNP cutoffs for detection of MRSA transmission within 6 months per this model were thus 24 wgSNPs or 13 cgSNPs. The simulated transmission model suggested that cutoffs of 17 wgSNPs or 12 cgSNPs would detect 95% of MRSA transmission events within the same timeframe. Finally, in the second cohort, cutoffs of 22 wgSNPs or 11 cgSNPs captured 95% of epidemiologically linked cases within 6 months. Interpretation On the basis of our results, we propose conservative cutoffs of 25 wgSNPs or 15 cgSNPS above which transmission of MRSA within the previous 6 months can be ruled out. These cutoffs could potentially be used as part of a genomic sequencing approach to the management of outbreaks of MRSA in conjunction with traditional epidemiological techniques. Funding UK Department of Health, Wellcome Trust, UK National Institute for Health Research.
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Affiliation(s)
- Francesc Coll
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Correspondence to: Dr Francesc Coll, Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
| | - Kathy E Raven
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Gwenan M Knight
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Beth Blane
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Ewan M Harrison
- Department of Medicine, University of Cambridge, Cambridge, UK
- Human Genetics Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Danielle Leek
- Department of Medicine, University of Cambridge, Cambridge, UK
| | | | | | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Cambridge, UK
- Public Health England, London, UK
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Crandall H, Kapusta A, Killpack J, Heyrend C, Nilsson K, Dickey M, Daly JA, Ampofo K, Pavia AT, Mulvey MA, Yandell M, Hulten KG, Blaschke AJ. Clinical and molecular epidemiology of invasive Staphylococcus aureus infection in Utah children; continued dominance of MSSA over MRSA. PLoS One 2020; 15:e0238991. [PMID: 32946486 PMCID: PMC7500648 DOI: 10.1371/journal.pone.0238991] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 08/27/2020] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Invasive Staphylococcus aureus infections are a common cause of morbidity and mortality in children. In the early 2000's the proportion of infections due the methicillin-resistant S. aureus (MRSA) increased rapidly. We described the clinical and molecular epidemiology of invasive S. aureus disease in a pediatric population. METHODS We prospectively identified children in Utah with invasive S. aureus infections. Medical records were reviewed to determine diagnosis and clinical characteristics. Isolates were genotyped using multi-locus sequence typing. The presence of genes encoding the Panton-Valentine leukocidin (PVL) was determined using polymerase chain reaction. RESULTS Over a 4-year period between January 2009 and December 2012, we identified 357 children, hospitalized at Primary Children's Hospital, with invasive S. aureus infections and isolates available for the study. Methicillin-susceptible S. aureus (MSSA) caused 79% of disease, while MRSA caused only 21% of disease. Mortality associated with invasive S. aureus infection was 3.6%. The most common diagnoses were osteoarticular infections (38%) followed by central line associated blood stream infections (19%) and pneumonia (12%). We identified 41 multi-locus sequence types. The majority of isolates belonged to 6 predominant clonal complexes (CC5, CC8, CC15, CC30, CC45, CC59). PVL was present in a minority (16%) of isolates, of which most were ST8 MRSA. CONCLUSIONS MSSA was the primary cause of invasive S. aureus infections at our institution throughout the study period. A limited number of predominant strains accounted for the majority of invasive disease. The classic virulence factor PVL was uncommon in MSSA isolates. Further study is needed to improve our understanding of S. aureus virulence and disease pathogenesis.
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Affiliation(s)
- Hillary Crandall
- Division of Pediatric Critical Care, Department of Pediatrics, University of Utah, Salt Lake City, Utah, United States of America
- * E-mail:
| | - Aurélie Kapusta
- Division of Pediatric Infectious Diseases, Department of Pediatrics, University of Utah, Salt Lake City, Utah, United States of America
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Jarrett Killpack
- Division of Pediatric Infectious Diseases, Department of Pediatrics, University of Utah, Salt Lake City, Utah, United States of America
| | - Carly Heyrend
- Primary Children’s Hospital, Salt Lake City, Utah, United States of America
| | - Kody Nilsson
- Division of Pediatric Infectious Diseases, Department of Pediatrics, University of Utah, Salt Lake City, Utah, United States of America
| | - Mandy Dickey
- Primary Children’s Hospital, Salt Lake City, Utah, United States of America
| | - Judy A. Daly
- Primary Children’s Hospital, Salt Lake City, Utah, United States of America
- Department of Pathology, University of Utah, Salt Lake City, Utah, United States of America
| | - Krow Ampofo
- Division of Pediatric Infectious Diseases, Department of Pediatrics, University of Utah, Salt Lake City, Utah, United States of America
| | - Andrew T. Pavia
- Division of Pediatric Infectious Diseases, Department of Pediatrics, University of Utah, Salt Lake City, Utah, United States of America
| | - Matthew A. Mulvey
- Department of Pathology, University of Utah, Salt Lake City, Utah, United States of America
| | - Mark Yandell
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
- Department of Human Genetics, USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, Utah, United States of America
| | - Kristina G. Hulten
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Anne J. Blaschke
- Division of Pediatric Infectious Diseases, Department of Pediatrics, University of Utah, Salt Lake City, Utah, United States of America
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Arning N, Wilson DJ. The past, present and future of ancient bacterial DNA. Microb Genom 2020; 6:mgen000384. [PMID: 32598277 PMCID: PMC7478633 DOI: 10.1099/mgen.0.000384] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/18/2020] [Indexed: 12/12/2022] Open
Abstract
Groundbreaking studies conducted in the mid-1980s demonstrated the possibility of sequencing ancient DNA (aDNA), which has allowed us to answer fundamental questions about the human past. Microbiologists were thus given a powerful tool to glimpse directly into inscrutable bacterial history, hitherto inaccessible due to a poor fossil record. Initially plagued by concerns regarding contamination, the field has grown alongside technical progress, with the advent of high-throughput sequencing being a breakthrough in sequence output and authentication. Albeit burdened with challenges unique to the analysis of bacteria, a growing number of viable sources for aDNA has opened multiple avenues of microbial research. Ancient pathogens have been extracted from bones, dental pulp, mummies and historical medical specimens and have answered focal historical questions such as identifying the aetiological agent of the black death as Yersinia pestis. Furthermore, ancient human microbiomes from fossilized faeces, mummies and dental plaque have shown shifts in human commensals through the Neolithic demographic transition and industrial revolution, whereas environmental isolates stemming from permafrost samples have revealed signs of ancient antimicrobial resistance. Culminating in an ever-growing repertoire of ancient genomes, the quickly expanding body of bacterial aDNA studies has also enabled comparisons of ancient genomes to their extant counterparts, illuminating the evolutionary history of bacteria. In this review we summarize the present avenues of research and contextualize them in the past of the field whilst also pointing towards questions still to be answered.
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Affiliation(s)
- Nicolas Arning
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford, OX3 7LF, UK
| | - Daniel J. Wilson
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford, OX3 7LF, UK
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30
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Dreisbach A, Wang M, van der Kooi-Pol MM, Reilman E, Koedijk DGAM, Mars RAT, Duipmans J, Jonkman M, Benschop JJ, Bonarius HPJ, Groen H, Hecker M, Otto A, Bäsell K, Bernhardt J, Back JW, Becher D, Buist G, van Dijl JM. Tryptic Shaving of Staphylococcus aureus Unveils Immunodominant Epitopes on the Bacterial Cell Surface. J Proteome Res 2020; 19:2997-3010. [DOI: 10.1021/acs.jproteome.0c00043] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Annette Dreisbach
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P. O. Box 30001, 9700 RB Groningen, the Netherlands
| | - Min Wang
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P. O. Box 30001, 9700 RB Groningen, the Netherlands
| | - Magdalena M. van der Kooi-Pol
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P. O. Box 30001, 9700 RB Groningen, the Netherlands
| | - Ewoud Reilman
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P. O. Box 30001, 9700 RB Groningen, the Netherlands
| | - Dennis G. A. M. Koedijk
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P. O. Box 30001, 9700 RB Groningen, the Netherlands
| | - Ruben A. T. Mars
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P. O. Box 30001, 9700 RB Groningen, the Netherlands
| | - José Duipmans
- Department of Dermatology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9700 RB Groningen, the Netherlands
| | - Marcel Jonkman
- Department of Dermatology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9700 RB Groningen, the Netherlands
| | - Joris J. Benschop
- Pepscan Therapeutics BV, P. O. Box 2098, 8203 AB Lelystad, the Netherlands
| | | | - Herman Groen
- IQ Therapeutics, Rozenburglaan 13a, 9727 DL Groningen, the Netherlands
| | - Michael Hecker
- Institut für Mikrobiologie, Ernst-Moritz-Arndt Universität Greifswald, Friedrich-Ludwig-Jahn-Str. 15, D-17489 Greifswald, Germany
| | - Andreas Otto
- Institut für Mikrobiologie, Ernst-Moritz-Arndt Universität Greifswald, Friedrich-Ludwig-Jahn-Str. 15, D-17489 Greifswald, Germany
| | - Katrin Bäsell
- Institut für Mikrobiologie, Ernst-Moritz-Arndt Universität Greifswald, Friedrich-Ludwig-Jahn-Str. 15, D-17489 Greifswald, Germany
| | - Jörg Bernhardt
- Institut für Mikrobiologie, Ernst-Moritz-Arndt Universität Greifswald, Friedrich-Ludwig-Jahn-Str. 15, D-17489 Greifswald, Germany
| | - Jaap Willem Back
- Pepscan Therapeutics BV, P. O. Box 2098, 8203 AB Lelystad, the Netherlands
| | - Dörte Becher
- Institut für Mikrobiologie, Ernst-Moritz-Arndt Universität Greifswald, Friedrich-Ludwig-Jahn-Str. 15, D-17489 Greifswald, Germany
| | - Girbe Buist
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P. O. Box 30001, 9700 RB Groningen, the Netherlands
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P. O. Box 30001, 9700 RB Groningen, the Netherlands
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Wirth T, Wong V, Vandenesch F, Rasigade JP. Applied phyloepidemiology: Detecting drivers of pathogen transmission from genomic signatures using density measures. Evol Appl 2020; 13:1513-1525. [PMID: 32684973 PMCID: PMC7359849 DOI: 10.1111/eva.12991] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 04/04/2020] [Accepted: 04/13/2020] [Indexed: 02/06/2023] Open
Abstract
Understanding the driving forces of an epidemic is key to inform intervention strategies against it. Correlating measures of the epidemic success of a pathogen with ancillary parameters such as its drug resistance profile provides a flexible tool to identify such driving forces. The recently described time‐scaled haplotypic density (THD) method facilitates the inference of a pathogen's epidemic success from genetic data. Contrary to demogenetic approaches that define success in an aggregated fashion, the THD computes an independent index of success for each isolate in a collection. Modeling this index using multivariate regression, thus, allows us to control for various sources of bias and to identify independent predictors of success. We illustrate the use of THD to address key questions regarding three exemplary epidemics of multidrug‐resistant (MDR) bacterial lineages, namely Mycobacterium tuberculosis Beijing, Salmonella Typhi H58, and Staphylococcus aureus ST8 (including ST8‐USA300 MRSA), based on previously published, international genetic datasets. In each case, THD analysis allowed to identify the impact, or lack thereof, of various factors on the epidemic success, independent of confounding by population structure and geographic distribution. Our results suggest that rifampicin resistance drives the MDR Beijing epidemic and that fluoroquinolone resistance drives the S. aureus ST8/USA300 epidemic, in line with previous evidence of a lack of resistance‐associated fitness cost in these pathogens. Conversely, fluoroquinolone resistance measurably hampered the success of S. Typhi H58 and non‐H58. These findings illustrate how THD can help leverage the massive genomic datasets generated by molecular epidemiology studies to address new questions. THD implementation for the R platform is available at https://github.com/rasigadelab/thd.
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Affiliation(s)
- Thierry Wirth
- Institut de Systématique, Evolution, Biodiversité UMR-CNRS 7205 Muséum National d'Histoire Naturelle Université Pierre et Marie Curie Université des Antilles Ecole Pratique des Hautes Etudes Sorbonne Universités Paris France.,EPHE PSL University Paris France
| | - Vanessa Wong
- Cambridge Institute for Medical Research Welcome Trust Center Cambridge UK
| | - François Vandenesch
- CIRI INSERM U1111 CNRS UMR5308 ENS Lyon University of Lyon Lyon France.,Institut des Agents Infectieux Hospices Civils de Lyon Lyon France
| | - Jean-Philippe Rasigade
- CIRI INSERM U1111 CNRS UMR5308 ENS Lyon University of Lyon Lyon France.,Institut des Agents Infectieux Hospices Civils de Lyon Lyon France
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32
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Pang R, Wu S, Zhang F, Huang J, Wu H, Zhang J, Li Y, Ding Y, Zhang J, Chen M, Wei X, Zhang Y, Gu Q, Zhou Z, Liang B, Li W, Wu Q. The Genomic Context for the Evolution and Transmission of Community-Associated Staphylococcus aureus ST59 Through the Food Chain. Front Microbiol 2020; 11:422. [PMID: 32256477 PMCID: PMC7090029 DOI: 10.3389/fmicb.2020.00422] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 02/27/2020] [Indexed: 12/16/2022] Open
Abstract
Sequence type 59 (ST59) is a predominant clonal lineage of community-acquired, methicillin-resistant Staphylococcus aureus (CA-MRSA) in Asia. Despite its increasing clinical relevance in China, the evolution and geographic expansion of ST59 has been relatively uncared for. Previous study has shown that ST59 was the predominant clone in food-related MRSA in China. This study compared the genomes of 87 clonal complex (CC) 59 S. aureus isolates sourced from food chain and infection cases to reconstruct the molecular evolution and geographical spread of ST59. Accordingly, three major sub-clades of ST59 were identified and these did not correlate with isolation source or location. Phylogenetic analysis estimated that ST59 in mainland China diverged from a most common recent ancestor around 1974, and most of the cases of cross-country transmission occurred between 1987 and 2000. Notably, two recent events of cross-country transmission through the food chain were observed, the isolates from these events diverged within relatively short time intervals. These isolates also showed high similarity in terms of their core genome, accessory genes, and antibiotic resistance patterns. These findings provide a valuable insight into the potential route of ST59 expansion in China and indicate a need for robust food chain surveillance to prevent the spread of this pathogen.
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Affiliation(s)
- Rui Pang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Shi Wu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Feng Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Jiahui Huang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Haoming Wu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Junhui Zhang
- Department of Food Science and Technology, Jinan University, Guangzhou, China
| | - Yanping Li
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yu Ding
- Department of Food Science and Technology, Jinan University, Guangzhou, China
| | - Jumei Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Moutong Chen
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xianhu Wei
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Youxiong Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qihui Gu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Zhenwen Zhou
- Clinical Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Bingshao Liang
- Clinical Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Wenzhi Li
- Infinitus (China) Company Ltd., Jiangmen, China
| | - Qingping Wu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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33
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Zhang AZ, Negoescu D, Munoz-Zanzi C. When and what to test for: A cost-effectiveness analysis of febrile illness test-and-treat strategies in the era of responsible antibiotic use. PLoS One 2020; 15:e0227409. [PMID: 31914143 PMCID: PMC6948826 DOI: 10.1371/journal.pone.0227409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 12/18/2019] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Febrile illness caused by viral and bacterial diseases (e.g., dengue and leptospirosis) often have similar symptoms and are difficult to differentiate without diagnostic tests. If not treated appropriately, patients may experience serious complications. The question of what diagnostic tests to make available to providers in order to inform antibiotic therapy remains an open problem for health services facing limited resources. METHODS AND FINDINGS We formulated the problem of minimizing the weighted average of antibiotic underuse and overuse to inform the optimal diagnostic test and antibiotic treatment options for given occurrence probabilities of several bacterial and viral infections. We modeled the weight of antibiotic overuse as a monetary penalty per unnecessarily administered course, which we varied in both the base case and sensitivity analysis. Detailed Markov cohort models of febrile illness progression were used to estimate the weight of antibiotic underuse. The model accounted for multiple infections simultaneously and incorporated test, treatment, and other direct and indirect costs, as well as the effect of delays in seeking care and test turnaround times. We used the Markov models to numerically estimate disability-adjusted life years (DALYs), pre-penalty costs, and likelihood of antibiotics overuse per patient for fifteen different strategies in two example settings in Thailand, one with a higher probability of bacterial infections (Northern Thailand, Scenario A) and one with a higher probability of viral infections (Bangkok, Scenario B). We found that empirical antibiotic treatment to all patients always incurs the lowest pre-penalty cost (Scenario A: $47.5/patient, $100.6/patient, $149.5/patient for patients seeking care on day one, day four, and day ten respectively; Scenario B: $94.1/patient, $108.7/patient, $122.1/patient on day one, day four, and day ten respectively), and the lowest DALYs, (Scenario A: 0.2 DALYs/patient, 0.9 DALYs/patient, 1.7 DALYs/patient on day one, day four, and day ten, respectively; Scenario B: 0.5 DALYs/patient, 0.7 DALYs/patient, 0.9 DALYs/patient on day one, day four, and day ten, respectively). However, such strategy resulted in the highest proportion of antibiotic overuse per patient (Scenario A: 38.1%, 19.3%, 7.5% on day one, day four, and day ten, respectively; Scenario B: 82.9%, 42.1%, 16.3% on day one, day four, and day ten, respectively). Consequently, empirical antibiotic treatment became suboptimal with antibiotic overuse penalties above $12,800/course, $18,400/course, $23,900/course for patients presenting on day one, day four, and day ten in Scenario A and above $1,100/course, $1,500/course, $1,600/course for patients presenting on day one, day four, and day ten in Scenario B. CONCLUSIONS Empirical antibiotic treatment to all patients provided the best outcomes if antibiotic overuse was not the primary concern or if presenting with viral disease (such as dengue) was unlikely. Empirical antibiotic treatment to severe patients only was in most cases not beneficial. Otherwise, strategies involving diagnostic tests became optimal. In particular, our results indicated that single test strategies (bacterial RDT or viral PCR) were optimal in regions with a greater probability of presenting with viral infection. PCR-led strategies (e.g., parallel bacterial PCR, or multiplex PCR) are robust under parameter uncertainty (e.g., with uncertain disease occurrence probabilities).
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Affiliation(s)
- Anthony Zhenhuan Zhang
- College of Science and Engineering, Industrial and System Engineering, University of Minnesota, Minneapolis, Minnesota, United States of America
- * E-mail: (AZZ); (CMZ)
| | - Diana Negoescu
- College of Science and Engineering, Industrial and System Engineering, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Claudia Munoz-Zanzi
- School of Public Health, Division of Environmental Health Sciences, University of Minnesota, Minneapolis, Minnesota, United States of America
- * E-mail: (AZZ); (CMZ)
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Methicillin-resistant Staphylococcus aureus: an overview of basic and clinical research. Nat Rev Microbiol 2020; 17:203-218. [PMID: 30737488 DOI: 10.1038/s41579-018-0147-4] [Citation(s) in RCA: 878] [Impact Index Per Article: 219.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most successful modern pathogens. The same organism that lives as a commensal and is transmitted in both health-care and community settings is also a leading cause of bacteraemia, endocarditis, skin and soft tissue infections, bone and joint infections and hospital-acquired infections. Genetically diverse, the epidemiology of MRSA is primarily characterized by the serial emergence of epidemic strains. Although its incidence has recently declined in some regions, MRSA still poses a formidable clinical threat, with persistently high morbidity and mortality. Successful treatment remains challenging and requires the evaluation of both novel antimicrobials and adjunctive aspects of care, such as infectious disease consultation, echocardiography and source control. In this Review, we provide an overview of basic and clinical MRSA research and summarize the expansive body of literature on the epidemiology, transmission, genetic diversity, evolution, surveillance and treatment of MRSA.
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35
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Sewell DK. Analysis of network interventions with an application to hospital-acquired infections. Stat Med 2019; 38:5376-5390. [PMID: 31631371 DOI: 10.1002/sim.8373] [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: 11/19/2018] [Revised: 08/20/2019] [Accepted: 08/24/2019] [Indexed: 11/06/2022]
Abstract
Regional interventions to prevent the spread of hospital-acquired infections, vaccination campaigns, and information dissemination strategies are examples of treatment interventions applied to members of a network with the intent of effecting a network-wide change. In designing clinical trials or determining policy changes, it may not be cost effective or otherwise possible to treat all actors of a network. There is a notable lack of study designs and statistical frameworks with which to plan a network-wide intervention in this context and analyze the resulting data. This paper builds off of the network autocorrelation model in order to provide such a framework for a pre-post study design. We derive key quantitative measures of the network-wide treatment effect, exact formulas for power analyses of these measures, and extensions for the context in which the network is unknown. As the treatment assignation is part of the network-wide treatment, we provide methods for determining the assignation which optimizes the overall treatment effect over all members of the network subject to any arbitrary set of implementation costs and cost constraint. We implement these methods on Clostridioides difficile data for the state of California, where the hospitals are linked through patient sharing.
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Affiliation(s)
- Daniel K Sewell
- Department of Biostatistics, University of Iowa, Iowa City, Iowa
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36
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Kristinsdottir I, Haraldsson A, Thorkelsson T, Haraldsson G, Kristinsson KG, Larsen J, Larsen AR, Thors V. MRSA outbreak in a tertiary neonatal intensive care unit in Iceland. Infect Dis (Lond) 2019; 51:815-823. [PMID: 31507231 DOI: 10.1080/23744235.2019.1662083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Introduction: Preventing the spread of methicillin-resistant Staphylococcus aureus (MRSA) and understanding the pathophysiology and transmission is essential. This study describes an MRSA outbreak in a neonatal intensive care unit in Reykjavik, Iceland at a time where no screening procedures were active. Materials and methods: After isolating MRSA in the neonatal intensive care unit in 2015, neonates, staff members and parents of positive patients were screened and environmental samples collected. The study period was from 14 April 2015 until 31 August 2015. Antimicrobial susceptibility testing, spa-typing and whole genome sequencing were done on MRSA isolates. Results: During the study period, 96/143 admitted patients were screened for colonization. Non-screened infants had short admissions not including screening days. MRSA was isolated from nine infants and seven parents. All tested staff members were negative. Eight infants and six parents carried MRSA ST30-IVc with spa-type t253 and one infant and its parent carried MRSA CC9-IVa (spa-type t4845) while most environmental samples were MRSA CC9-IVa (spa-type t4845). Whole genome sequencing revealed close relatedness between all ST30-IVc and CC9-IVa isolates, respectively. All colonized infants received decolonization treatment, but 3/9 were still positive when last sampled. Discussion: The main outbreak source was a single MRSA ST30-IVc (spa-type t253), isolated for the first time in Iceland. A new CC9-IVa (spa-type t4845) was also identified, most abundant on environmental surfaces but only in one patient. The reason for the differences in the epidemiology of the two strains is not clear. The study highlights a need for screening procedures in high-risk settings and guidelines for neonatal decolonization.
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Affiliation(s)
| | - Asgeir Haraldsson
- Faculty of Medicine, University of Iceland , Reykjavík , Iceland.,Children's Hospital Iceland, Landspitali University Hospital , Reykjavík , Iceland
| | - Thordur Thorkelsson
- Faculty of Medicine, University of Iceland , Reykjavík , Iceland.,Children's Hospital Iceland, Landspitali University Hospital , Reykjavík , Iceland
| | - Gunnsteinn Haraldsson
- Faculty of Medicine, University of Iceland , Reykjavík , Iceland.,Department of Clinical Microbiology, Landspitali University Hospital , Reykjavík , Iceland
| | - Karl G Kristinsson
- Faculty of Medicine, University of Iceland , Reykjavík , Iceland.,Department of Clinical Microbiology, Landspitali University Hospital , Reykjavík , Iceland
| | - Jesper Larsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institute , Copenhagen , Denmark
| | - Anders Rhod Larsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institute , Copenhagen , Denmark
| | - Valtyr Thors
- Faculty of Medicine, University of Iceland , Reykjavík , Iceland.,Children's Hospital Iceland, Landspitali University Hospital , Reykjavík , Iceland
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37
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Tracking Staphylococcus aureus in the intensive care unit using whole-genome sequencing. J Hosp Infect 2019; 103:13-20. [PMID: 31039382 DOI: 10.1016/j.jhin.2019.04.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 04/22/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Staphylococcus aureus remains an important bacterial pathogen worldwide. This study utilized known staphylococcal epidemiology to track S. aureus between different ecological reservoirs in one 10-bed intensive care unit (ICU). METHODS Selected hand-touch surfaces, staff hands and air were screened systematically 10 times during 10 months, with patients screened throughout the study. S. aureus isolates were subjected to spa typing and epidemiological analyses, followed by whole-genome sequencing to provide single nucleotide polymorphism (SNP) data. RESULTS Multiple transmission pathways between patients and reservoirs were investigated. There were 34 transmission events, of which 29 were highly related (<25 SNPs) and five were possibly related (<50 SNPs). Twenty (59%) transmission events occurred between colonized patients and their own body sites (i.e. autogenous spread); four (12%) were associated with cross-transmission between patients; four (12%) occurred between patients and hand-touch sites (bedrails and intravenous pump); four (12%) linked airborne S. aureus with staff hands and bedrail; and two (6%) linked bed tables, bedrail and cardiac monitor. CONCLUSION Colonized patients are responsible for repeated introduction of new S. aureus into the ICU, whereupon a proportion spread to hand-touch sites in (or near) the patient zone. This short-term reservoir for S. aureus imposes a colonization/infection risk for subsequent patients. More than half of ICU-acquired S. aureus infection originated from the patients' own flora, while staff hands and air were rarely implicated in onward transmission. Control of staphylococcal infection in the ICU is best served by patient screening, systematic cleaning of hand-touch surfaces and continued emphasis on hand hygiene.
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Szafrańska AK, Junker V, Steglich M, Nübel U. Rapid cell division of Staphylococcus aureus during colonization of the human nose. BMC Genomics 2019; 20:229. [PMID: 30894139 PMCID: PMC6425579 DOI: 10.1186/s12864-019-5604-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 03/13/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Staphylococcus aureus is an important opportunistic pathogen and a commensal bacterium, thriving in the nasal cavities of 20% of the human population. Little is known about the dynamics of asymptomatic colonization and the occasional transition to infectious disease. RESULTS In this study, we inferred that S. aureus cells replicate every one to three hours on average while colonizing the human nose, based on two independent lines of genomic evidence. First, we collected nasal swab samples from human subjects, extracted and sequenced metagenomic DNA, and analyzed the distribution of sequencing coverage along the staphylococcal chromosome. Calibration of this data by comparison to a laboratory culture enabled measuring S. aureus cell division rates in nasal samples. Second, we applied mutation accumulation experiments paired with genome sequencing to measure spontaneous mutation rates at a genome scale. Relating these mutation rates to annual evolutionary rates confirmed that nasal S. aureus continuously pass several thousand cell divisions per year when averaged over large, globally distributed populations and over many years, corresponding to generation times of less than two hours. CONCLUSIONS The cell division rates we determined were higher than the fastest documented rates during fulminant disease progression (in a mouse model of systemic infection) and much higher than those previously measured in expectorated sputum from cystic fibrosis patients. This paper supplies absolute in-vivo generation times for an important bacterial commensal, indicating that colonization of the human upper respiratory tract is characterized by a highly dynamic equilibrium between bacterial growth and removal.
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Affiliation(s)
- Anna K Szafrańska
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, 38124, Braunschweig, Germany.,German Center for Infection Research (DZIF), Braunschweig site, Germany
| | - Vera Junker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, 38124, Braunschweig, Germany
| | - Matthias Steglich
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, 38124, Braunschweig, Germany.,German Center for Infection Research (DZIF), Braunschweig site, Germany
| | - Ulrich Nübel
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, 38124, Braunschweig, Germany. .,German Center for Infection Research (DZIF), Braunschweig site, Germany. .,Braunschweig Integrated Centre of Systems Biology (BRICS), Technical University Braunschweig, Braunschweig, Germany.
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Sharma H, Smith D, Turner CE, Game L, Pichon B, Hope R, Hill R, Kearns A, Sriskandan S. Clinical and Molecular Epidemiology of Staphylococcal Toxic Shock Syndrome in the United Kingdom. Emerg Infect Dis 2019; 24. [PMID: 29350159 PMCID: PMC5782905 DOI: 10.3201/eid2402.170606] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Staphylococcal toxic shock syndrome (TSS) was originally described in menstruating women and linked to TSS toxin 1 (TSST-1)-producing Staphylococcus aureus. Using UK national surveillance data, we ascertained clinical, molecular and superantigenic characteristics of TSS cases. Average annual TSS incidence was 0.07/100,000 population. Patients with nonmenstrual TSS were younger than those with menstrual TSS but had the same mortality rate. Children <16 years of age accounted for 39% of TSS cases, most caused by burns and skin and soft tissue infections. Nonmenstrual TSS is now more common than menstrual TSS in the UK, although both types are strongly associated with the tst+ clonal complex (CC) 30 methicillin-sensitive S. aureus lineage, which accounted for 49.4% of all TSS and produced more TSST-1 and superantigen bioactivity than did tst+ CC30 methicillin-resistant S. aureus strains. Better understanding of this MSSA lineage and infections in children could focus interventions to prevent TSS in the future.
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Read TD, Petit RA, Yin Z, Montgomery T, McNulty MC, David MZ. USA300 Staphylococcus aureus persists on multiple body sites following an infection. BMC Microbiol 2018; 18:206. [PMID: 30518317 PMCID: PMC6282268 DOI: 10.1186/s12866-018-1336-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 11/12/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND USA300 methicillin-resistant Staphylococcus aureus (MRSA) is a community- and hospital-acquired pathogen that frequently causes infections but also can survive on the human body asymptomatically as a part of the normal microbiota. We devised a comparative genomic strategy to track colonizing USA300 at different body sites after an initial infection. We sampled ST8 S. aureus from subjects at the site of a first known MRSA infection. Within 60 days of this infection and again 12 months later, each subject was tested for asymptomatic colonization in the nose, throat and perirectal region. 93 S. aureus strains underwent whole genome shotgun sequencing. RESULTS Among 28 subjects at the initial sampling time, we isolated S. aureus from the nose, throat and perirectal sites from 15, 11 and 15 of them, respectively. Twelve months later we isolated S. aureus from 9 subjects, with 6, 3 and 3 strains from the nose, throat and perirectal area, respectively. Genome sequencing revealed that 23 patients (ages 0-66 years) carried USA300 intra-subject lineages (ISLs), defined as having an index infection isolate and closely related colonizing strains. Pairwise distance between strains in different ISLs was 48 to 162 single nucleotide polymorphisms (SNPs) across the core regions of the chromosome, whereas within the same ISL it was 0 to 26 SNPs. Strains in ISLs from the same subject differed in plasmid and prophage content, and contained deletions that removed the mecA-containing SCCmec and ACME regions. Five strains contained frameshift mutations in agr toxin-regulating genes. Persistence of an ISL was not associated with clinical or demographic subject characteristics. We inferred that colonization with the ISL occurred about 18 weeks before the first assessment of asymptomatic colonization. CONCLUSIONS Clonal lineages of USA300 may continue to colonize people at one or more anatomic sites up to a year after an initial infection and experience loss of the SCCmec, loss and gain of other mobile genetic elements, and mutations in the agr operon.
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Affiliation(s)
- Timothy D. Read
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA USA
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA USA
| | - Robert A. Petit
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA USA
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA USA
| | - Zachary Yin
- Department of Pediatrics, Section of Infectious Diseases, University of Chicago, Chicago, IL USA
| | - Tuyaa Montgomery
- Department of Pediatrics, Section of Infectious Diseases, University of Chicago, Chicago, IL USA
| | - Moira C. McNulty
- Department of Medicine, Section of Infectious Diseases and Global Health, University of Chicago, Chicago, IL USA
| | - Michael Z. David
- Department of Medicine, Division of Infectious Diseases, University of Pennsylvania, Philadelphia, PA USA
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41
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Lakhundi S, Zhang K. Methicillin-Resistant Staphylococcus aureus: Molecular Characterization, Evolution, and Epidemiology. Clin Microbiol Rev 2018; 31:e00020-18. [PMID: 30209034 PMCID: PMC6148192 DOI: 10.1128/cmr.00020-18] [Citation(s) in RCA: 736] [Impact Index Per Article: 122.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Staphylococcus aureus, a major human pathogen, has a collection of virulence factors and the ability to acquire resistance to most antibiotics. This ability is further augmented by constant emergence of new clones, making S. aureus a "superbug." Clinical use of methicillin has led to the appearance of methicillin-resistant S. aureus (MRSA). The past few decades have witnessed the existence of new MRSA clones. Unlike traditional MRSA residing in hospitals, the new clones can invade community settings and infect people without predisposing risk factors. This evolution continues with the buildup of the MRSA reservoir in companion and food animals. This review focuses on imparting a better understanding of MRSA evolution and its molecular characterization and epidemiology. We first describe the origin of MRSA, with emphasis on the diverse nature of staphylococcal cassette chromosome mec (SCCmec). mecA and its new homologues (mecB, mecC, and mecD), SCCmec types (13 SCCmec types have been discovered to date), and their classification criteria are discussed. The review then describes various typing methods applied to study the molecular epidemiology and evolutionary nature of MRSA. Starting with the historical methods and continuing to the advanced whole-genome approaches, typing of collections of MRSA has shed light on the origin, spread, and evolutionary pathways of MRSA clones.
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Affiliation(s)
- Sahreena Lakhundi
- Centre for Antimicrobial Resistance, Alberta Health Services/Calgary Laboratory Services/University of Calgary, Calgary, Alberta, Canada
| | - Kunyan Zhang
- Centre for Antimicrobial Resistance, Alberta Health Services/Calgary Laboratory Services/University of Calgary, Calgary, Alberta, Canada
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
- Department of Medicine, University of Calgary, Calgary, Alberta, Canada
- The Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
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42
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Yi Y, Su L, Li B, Li S, Zhang B, Su Y. Analysis of the Genetic Diversity in Methicillin-ResistantStaphylococcus aureusIsolates from Bovine Subclinical Mastitis Case in Xinjiang, China. Foodborne Pathog Dis 2018; 15:568-575. [DOI: 10.1089/fpd.2018.2424] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Yuanyang Yi
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Lingling Su
- Feed Research Institute Xinjiang Academy of Animal Science, Urumqi, China
| | - Bin Li
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Shanchun Li
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Baojiang Zhang
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Yan Su
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
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Richardson EJ, Bacigalupe R, Harrison EM, Weinert LA, Lycett S, Vrieling M, Robb K, Hoskisson PA, Holden MTG, Feil EJ, Paterson GK, Tong SYC, Shittu A, van Wamel W, Aanensen DM, Parkhill J, Peacock SJ, Corander J, Holmes M, Fitzgerald JR. Gene exchange drives the ecological success of a multi-host bacterial pathogen. Nat Ecol Evol 2018; 2:1468-1478. [PMID: 30038246 PMCID: PMC7610605 DOI: 10.1038/s41559-018-0617-0] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 06/25/2018] [Indexed: 01/15/2023]
Abstract
The capacity for some pathogens to jump into different host-species populations is a major threat to public health and food security. Staphylococcus aureus is a multi-host bacterial pathogen responsible for important human and livestock diseases. Here, using a population-genomic approach, we identify humans as a major hub for ancient and recent S. aureus host-switching events linked to the emergence of endemic livestock strains, and cows as the main animal reservoir for the emergence of human epidemic clones. Such host-species transitions are associated with horizontal acquisition of genetic elements from host-specific gene pools conferring traits required for survival in the new host-niche. Importantly, genes associated with antimicrobial resistance are unevenly distributed among human and animal hosts, reflecting distinct antibiotic usage practices in medicine and agriculture. In addition to gene acquisition, genetic diversification has occurred in pathways associated with nutrient acquisition, implying metabolic remodelling after a host switch in response to distinct nutrient availability. For example, S. aureus from dairy cattle exhibit enhanced utilization of lactose-a major source of carbohydrate in bovine milk. Overall, our findings highlight the influence of human activities on the multi-host ecology of a major bacterial pathogen, underpinned by horizontal gene transfer and core genome diversification.
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Affiliation(s)
- Emily J Richardson
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.,Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Rodrigo Bacigalupe
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Ewan M Harrison
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Lucy A Weinert
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Samantha Lycett
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Manouk Vrieling
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | | | | | | | - Edward J Feil
- Milner Centre for Evolution, University of Bath, Bath, UK
| | - Gavin K Paterson
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Steven Y C Tong
- Victorian Infectious Disease Service, The Royal Melbourne Hospital and The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.,Menzies School of Health Research, Darwin, Australia
| | - Adebayo Shittu
- Department of Microbiology, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Willem van Wamel
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, Rotterdam, The Netherlands
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Hinxton, UK.,Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | | | | | - Jukka Corander
- Wellcome Trust Sanger Institute, Hinxton, UK.,Helsinki Institute for Information Technology, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.,Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Mark Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - J Ross Fitzgerald
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.
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Improved Subtyping of Staphylococcus aureus Clonal Complex 8 Strains Based on Whole-Genome Phylogenetic Analysis. mSphere 2018; 3:3/3/e00464-17. [PMID: 29720527 PMCID: PMC5932376 DOI: 10.1128/msphere.00464-17] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 11/12/2017] [Indexed: 12/12/2022] Open
Abstract
Staphylococcus aureus is a major human pathogen worldwide in both community and health care settings. Surveillance for S. aureus strains is important to our understanding of their spread and to informing infection prevention and control. Confusion surrounding the strain nomenclature of one of the most prevalent lineages of S. aureus, clonal complex 8 (CC8), and the imprecision of current tools for typing S. aureus make surveillance and source tracing difficult and sometimes misleading. In this study, we clarify the CC8 strain designations and propose a new typing scheme for CC8 isolates that is rapid and easy to use. This typing scheme is based on relatively stable genomic markers, and we demonstrate its superiority over traditional typing techniques. This scheme has the potential to greatly improve epidemiological investigations of S. aureus. Strains of Staphylococcus aureus in clonal complex 8 (CC8), including USA300, USA500, and the Iberian clone, are prevalent pathogens in the United States, both inside and outside health care settings. Methods for typing CC8 strains are becoming obsolete as the strains evolve and diversify, and whole-genome sequencing has shown that some strain types fall into multiple sublineages within CC8. In this study, we attempt to clarify the strain nomenclature of CC8, classifying the major strain types based on whole-genome sequence phylogenetics using both methicillin-resistant S. aureus (MRSA) and methicillin-susceptible S. aureus (MSSA) genomes. We show that isolates of the Archaic and Iberian clones from decades ago make up the most basal clade of the main CC8 lineages and that at least one successful lineage of CC8, made up mostly of MSSA, diverged before the other well-known strain types USA500 and USA300. We also show that the USA500 type includes two clades separated by the previously described “Canadian epidemic MRSA” strain CMRSA9, that one clade containing USA500 also contains the USA300 clade, and that the USA300-0114 strain type is not a monophyletic group. Additionally, we present a rapid, simple CC8 strain-typing scheme using real-time PCR assays that target single nucleotide polymorphisms (SNPs) derived from our CC8 phylogeny and show the significant benefit of using more stable genomic markers based on evolutionary lineages over traditional S. aureus typing techniques. This more accurate and accessible S. aureus typing system may improve surveillance and better inform the epidemiology of this very important pathogen. IMPORTANCEStaphylococcus aureus is a major human pathogen worldwide in both community and health care settings. Surveillance for S. aureus strains is important to our understanding of their spread and to informing infection prevention and control. Confusion surrounding the strain nomenclature of one of the most prevalent lineages of S. aureus, clonal complex 8 (CC8), and the imprecision of current tools for typing S. aureus make surveillance and source tracing difficult and sometimes misleading. In this study, we clarify the CC8 strain designations and propose a new typing scheme for CC8 isolates that is rapid and easy to use. This typing scheme is based on relatively stable genomic markers, and we demonstrate its superiority over traditional typing techniques. This scheme has the potential to greatly improve epidemiological investigations of S. aureus.
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Campbell F, Strang C, Ferguson N, Cori A, Jombart T. When are pathogen genome sequences informative of transmission events? PLoS Pathog 2018; 14:e1006885. [PMID: 29420641 PMCID: PMC5821398 DOI: 10.1371/journal.ppat.1006885] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 02/21/2018] [Accepted: 01/18/2018] [Indexed: 01/19/2023] Open
Abstract
Recent years have seen the development of numerous methodologies for reconstructing transmission trees in infectious disease outbreaks from densely sampled whole genome sequence data. However, a fundamental and as of yet poorly addressed limitation of such approaches is the requirement for genetic diversity to arise on epidemiological timescales. Specifically, the position of infected individuals in a transmission tree can only be resolved by genetic data if mutations have accumulated between the sampled pathogen genomes. To quantify and compare the useful genetic diversity expected from genetic data in different pathogen outbreaks, we introduce here the concept of ‘transmission divergence’, defined as the number of mutations separating whole genome sequences sampled from transmission pairs. Using parameter values obtained by literature review, we simulate outbreak scenarios alongside sequence evolution using two models described in the literature to describe transmission divergence of ten major outbreak-causing pathogens. We find that while mean values vary significantly between the pathogens considered, their transmission divergence is generally very low, with many outbreaks characterised by large numbers of genetically identical transmission pairs. We describe the impact of transmission divergence on our ability to reconstruct outbreaks using two outbreak reconstruction tools, the R packages outbreaker and phybreak, and demonstrate that, in agreement with previous observations, genetic sequence data of rapidly evolving pathogens such as RNA viruses can provide valuable information on individual transmission events. Conversely, sequence data of pathogens with lower mean transmission divergence, including Streptococcus pneumoniae, Shigella sonnei and Clostridium difficile, provide little to no information about individual transmission events. Our results highlight the informational limitations of genetic sequence data in certain outbreak scenarios, and demonstrate the need to expand the toolkit of outbreak reconstruction tools to integrate other types of epidemiological data. The increasing availability of genetic sequence data has sparked an interest in using pathogen whole genome sequences to reconstruct the history of individual transmission events in an infectious disease outbreak. However, such methodologies rely on pathogen genomes mutating rapidly enough to discriminate between infected individuals, an assumption that remains to be investigated. To determine pathogen outbreaks for which genetic data is expected to be informative of transmission events, we introduce here the concept of ‘transmission divergence’, defined as the number of mutations separating pathogen genome sequences sampled from transmission pairs. We characterise transmission divergence of ten major outbreak causing pathogens using simulations and find significant variation between diseases, with viral outbreaks generally exhibiting higher transmission divergence than bacterial ones. We reconstruct these outbreaks using the R-packages outbreaker and phybreak and find that genetic sequence data, though useful for rapidly evolving pathogens, provides little to no information about outbreaks with low transmission divergence, such as Streptococcus pneumoniae and Shigella sonnei. Our results demonstrate the need to incorporate other sources of outbreak data, such as contact tracing data and spatial location data, into outbreak reconstruction tools.
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Affiliation(s)
- Finlay Campbell
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
- * E-mail: (FC); (TJ); (AC)
| | - Camilla Strang
- Centre for Preventive Medicine, Department of Epidemiology and Disease Surveillance, Animal Health Trust, Suffolk, United Kingdom
| | - Neil Ferguson
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | - Anne Cori
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
- * E-mail: (FC); (TJ); (AC)
| | - Thibaut Jombart
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
- * E-mail: (FC); (TJ); (AC)
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Ledda A, Price JR, Cole K, Llewelyn MJ, Kearns AM, Crook DW, Paul J, Didelot X. Re-emergence of methicillin susceptibility in a resistant lineage of Staphylococcus aureus. J Antimicrob Chemother 2018; 72:1285-1288. [PMID: 28108681 DOI: 10.1093/jac/dkw570] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 12/09/2016] [Indexed: 11/14/2022] Open
Abstract
Objectives MRSA is a leading cause of hospital-associated infection. Acquired resistance is encoded by the mecA gene or its homologue mecC , but little is known about the evolutionary dynamics involved in gain and loss of resistance. The objective of this study was to obtain an expanded understanding of Staphylococcus aureus methicillin resistance microevolution in vivo , by focusing on a single lineage. Methods We compared the whole-genome sequences of 231 isolates from a single epidemic lineage [clonal complex 30 (CC30) and spa -type t018] of S. aureus that caused an epidemic in the UK. Results We show that resistance to methicillin in this single lineage was gained on at least two separate occasions, one of which led to a clonal expansion around 1995 presumably caused by a selective advantage. Resistance was, however, subsequently lost in vivo by nine strains isolated between 2008 and 2012. We describe the genetic mechanisms involved in this loss of resistance and the imperfect relationship between genotypic and phenotypic resistance. Conclusions The recent re-emergence of methicillin susceptibility in this epidemic lineage suggests a significant fitness cost of resistance and reduced selective advantage following the introduction in the mid-2000s of MRSA hospital control measures throughout the UK.
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Affiliation(s)
- Alice Ledda
- Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place, London W2 1PG, UK
| | - James R Price
- Department of Infectious Diseases and Microbiology, Royal Sussex County Hospital, Brighton, UK
| | - Kevin Cole
- Department of Infectious Diseases and Microbiology, Royal Sussex County Hospital, Brighton, UK.,Public Health England, Microbiology, Royal Sussex County Hospital, Brighton, UK
| | - Martin J Llewelyn
- Department of Infectious Diseases and Microbiology, Royal Sussex County Hospital, Brighton, UK
| | - Angela M Kearns
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, National Infection Service, Public Health England, Colindale, UK
| | - Derrick W Crook
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - John Paul
- Public Health England, Microbiology, Royal Sussex County Hospital, Brighton, UK
| | - Xavier Didelot
- Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place, London W2 1PG, UK
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Anti-microbial and Anti-biofilm activity of a novel Dibenzyl (benzo[d] thiazol-2-yl (hydroxy) methyl) phosphonate by inducing protease expression in Staphylococcus aureus. Med Chem Res 2017. [DOI: 10.1007/s00044-017-2102-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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48
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Nübel U. Emergence and Spread of Antimicrobial Resistance: Recent Insights from Bacterial Population Genomics. Curr Top Microbiol Immunol 2017; 398:35-53. [PMID: 27738914 DOI: 10.1007/82_2016_505] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Driven by progress of DNA sequencing technologies, recent population genomics studies have revealed that several bacterial pathogens constitute 'measurably evolving populations'. As a consequence, it was possible to reconstruct the emergence and spatial spread of drug-resistant bacteria on the basis of temporally structured samples of bacterial genome sequences. Based on currently available data, some general inferences can be drawn across different bacterial species as follows: (1) Resistance to various antibiotics evolved years to decades earlier than had been anticipated on the basis of epidemiological surveillance data alone. (2) Resistance traits are more rapidly acquired than lost and commonly persist in bacterial populations for decades. (3) Global populations of drug-resistant pathogens are dominated by very few clones, yet the features enabling such spreading success have not been revealed, aside from antibiotic resistance. (4) Whole-genome sequencing proved very effective at identifying bacterial isolates as parts of the same transmission networks.
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Affiliation(s)
- Ulrich Nübel
- DZIF Group on Microbial Genome Research, Leibniz Institute DSMZ, Braunschweig, Germany. .,Technical University Braunschweig, Braunschweig, Germany. .,German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany.
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49
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Lax S, Sangwan N, Smith D, Larsen P, Handley KM, Richardson M, Guyton K, Krezalek M, Shogan BD, Defazio J, Flemming I, Shakhsheer B, Weber S, Landon E, Garcia-Houchins S, Siegel J, Alverdy J, Knight R, Stephens B, Gilbert JA. Bacterial colonization and succession in a newly opened hospital. Sci Transl Med 2017; 9:eaah6500. [PMID: 28539477 PMCID: PMC5706123 DOI: 10.1126/scitranslmed.aah6500] [Citation(s) in RCA: 180] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 02/27/2017] [Indexed: 11/02/2022]
Abstract
The microorganisms that inhabit hospitals may influence patient recovery and outcome, although the complexity and diversity of these bacterial communities can confound our ability to focus on potential pathogens in isolation. To develop a community-level understanding of how microorganisms colonize and move through the hospital environment, we characterized the bacterial dynamics among hospital surfaces, patients, and staff over the course of 1 year as a new hospital became operational. The bacteria in patient rooms, particularly on bedrails, consistently resembled the skin microbiota of the patient occupying the room. Bacterial communities on patients and room surfaces became increasingly similar over the course of a patient's stay. Temporal correlations in community structure demonstrated that patients initially acquired room-associated taxa that predated their stay but that their own microbial signatures began to influence the room community structure over time. The α- and β-diversity of patient skin samples were only weakly or nonsignificantly associated with clinical factors such as chemotherapy, antibiotic usage, and surgical recovery, and no factor except for ambulatory status affected microbial similarity between the microbiotas of a patient and their room. Metagenomic analyses revealed that genes conferring antimicrobial resistance were consistently more abundant on room surfaces than on the skin of the patients inhabiting those rooms. In addition, persistent unique genotypes of Staphylococcus and Propionibacterium were identified. Dynamic Bayesian network analysis suggested that hospital staff were more likely to be a source of bacteria on the skin of patients than the reverse but that there were no universal patterns of transmission across patient rooms.
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Affiliation(s)
- Simon Lax
- Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA
- Division of Biosciences, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Naseer Sangwan
- Division of Biosciences, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
- Microbiome Center, Department of Surgery, University of Chicago, A27 South Maryland Avenue, Chicago, IL 60637, USA
| | - Daniel Smith
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Peter Larsen
- Division of Biosciences, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Kim M Handley
- Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA
| | - Miles Richardson
- Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA
| | - Kristina Guyton
- Microbiome Center, Department of Surgery, University of Chicago, A27 South Maryland Avenue, Chicago, IL 60637, USA
| | - Monika Krezalek
- Microbiome Center, Department of Surgery, University of Chicago, A27 South Maryland Avenue, Chicago, IL 60637, USA
| | - Benjamin D Shogan
- Microbiome Center, Department of Surgery, University of Chicago, A27 South Maryland Avenue, Chicago, IL 60637, USA
| | - Jennifer Defazio
- Microbiome Center, Department of Surgery, University of Chicago, A27 South Maryland Avenue, Chicago, IL 60637, USA
| | - Irma Flemming
- Microbiome Center, Department of Surgery, University of Chicago, A27 South Maryland Avenue, Chicago, IL 60637, USA
| | - Baddr Shakhsheer
- Microbiome Center, Department of Surgery, University of Chicago, A27 South Maryland Avenue, Chicago, IL 60637, USA
| | - Stephen Weber
- Department of Medicine, University of Chicago, 5841 South Maryland Avenue, Chicago, IL 60637, USA
| | - Emily Landon
- Department of Medicine, University of Chicago, 5841 South Maryland Avenue, Chicago, IL 60637, USA
| | - Sylvia Garcia-Houchins
- Department of Medicine, University of Chicago, 5841 South Maryland Avenue, Chicago, IL 60637, USA
| | - Jeffrey Siegel
- Department of Civil Engineering, University of Toronto, 35 St. George Street, Toronto, Ontario M5S 1A4, Canada
- Dalla Lana School of Public Health, University of Toronto, 223 College Street, Toronto, Ontario M5T 1R4, Canada
| | - John Alverdy
- Microbiome Center, Department of Surgery, University of Chicago, A27 South Maryland Avenue, Chicago, IL 60637, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92037, USA
- Department of Computer Science and Engineering, University of California, San Diego, San Diego, CA 92037, USA
| | - Brent Stephens
- Department of Civil, Architectural and Environmental Engineering, Illinois Institute of Technology, 3201 South Dearborn Street, Chicago, IL 60616, USA
| | - Jack A Gilbert
- Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA.
- Division of Biosciences, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
- Microbiome Center, Department of Surgery, University of Chicago, A27 South Maryland Avenue, Chicago, IL 60637, USA
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Abstract
The community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) epidemic in the United States is largely attributable to the meteoric rise of a single clone, referred to as USA300. This strain not only spread across the United States in just a few years to become the predominant cause of staphylococcal disease, but it also appears to have increased the overall number of skin and soft-tissue infections (SSTIs), increasing the overall disease burden. While USA300 still constitutes a major public health burden, its prevalence may be decreasing in some parts of the United States. Other than an epidemic in South America due to a closely related strain, USA300 also seems to have been largely unable to establish itself as an endemic infection in other geographic locations. While there have been several hypotheses put forward to explain the enormous success of USA300, the reasons for its failures and its potential fall remain obscure. Far from being unique to USA300, the rise and fall of specific clones of S. aureus in human populations seems to be a common process that has occurred multiple times and in multiple locations. This review charts the rise of USA300 and the evidence that suggests that it may be in decline, and it considers how best to understand the future spread, containment, and possible extinction of CA-MRSA.
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Affiliation(s)
- Paul J Planet
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York.,Pediatric Infectious Disease Division, Children's Hospital of Philadelphia.,Perelman School of Medicine, University of Pennsylvania, Philadelphia
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