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Magnan C, Morsli M, Salipante F, Thiry B, Attar JE, Maio MD, Safaria M, Tran TA, Dunyach-Remy C, Ory J, Richaud-Morel B, Sotto A, Pantel A, Lavigne JP. Emergence of multidrug-resistant Staphylococcus haemolyticus in neonatal intensive care unit in Southern France, a genomic study. Emerg Microbes Infect 2024; 13:2353291. [PMID: 38738561 PMCID: PMC11132433 DOI: 10.1080/22221751.2024.2353291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 05/03/2024] [Indexed: 05/14/2024]
Abstract
An emergence of multidrug-resistant (MDR) Staphylococcus haemolyticus has been observed in the neonatal intensive care unit (NICU) of Nîmes University Hospital in southern France. A case-control analysis was conducted on 96 neonates, to identify risk factors associated with S. haemolyticus infection, focusing on clinical outcomes. Forty-eight MDR S. haemolyticus strains, isolated from neonates between October 2019 and July 2022, were investigated using routine in vitro procedures and whole-genome sequencing. Additionally, five S. haemolyticus isolates from adult patients were sequenced to identify clusters circulating within the hospital environment. The incidence of neonatal S. haemolyticus was significantly associated with low birth weight, lower gestational age, and central catheter use (p < 0.001). Sepsis was the most frequent clinical manifestation in this series (20/46, 43.5%) and was associated with five deaths. Based on whole-genome analysis, three S. haemolyticus genotypes were predicted: ST1 (6/53, 11%), ST25 (3/53, 5.7%), and ST29 (44/53, 83%), which included the subcluster II-A, predominantly emerging in the neonatal department. All strains were profiled in silico to be resistant to methicillin, erythromycin, aminoglycosides, and fluoroquinolones, consistent with in vitro antibiotic susceptibility tests. Moreover, in silico prediction of biofilm formation and virulence-encoding genes supported the association of ST29 with severe clinical outcomes, while the persistence in the NICU could be explained by the presence of antiseptic and heavy metal resistance-encoding genes. The clonality of S. haemolyticus ST29 subcluster II-A isolates confirms healthcare transmission causing severe infections. Based on these results, reinforced hygiene measures are necessary to eradicate the nosocomial transmission of MDR strains.
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Affiliation(s)
- Chloé Magnan
- VBIC, Univ Montpellier, INSERM U1047, Department of Microbiology and Hospital Hygiene, CHU Nîmes, Univ. Montpellier, Nîmes, France
| | - Madjid Morsli
- VBIC, Univ Montpellier, INSERM U1047, Department of Microbiology and Hospital Hygiene, CHU Nîmes, Univ. Montpellier, Nîmes, France
| | - Florian Salipante
- Department of Biostatistics, Epidemiology, Public Health and Innovation in Methodology, CHU Nîmes, Univ. Montpellier, Nîmes, France
| | - Blandine Thiry
- VBIC, Univ Montpellier, INSERM U1047, Department of Microbiology and Hospital Hygiene, CHU Nîmes, Univ. Montpellier, Nîmes, France
| | - Julie El Attar
- VBIC, Univ Montpellier, INSERM U1047, Department of Microbiology and Hospital Hygiene, CHU Nîmes, Univ. Montpellier, Nîmes, France
| | - Massimo Di Maio
- Neonatal Pediatrics Department, CHU Nîmes, Univ. Montpellier, Nîmes, France
| | - Maryam Safaria
- Neonatal Pediatrics Department, CHU Nîmes, Univ. Montpellier, Nîmes, France
| | - Tu-Anh Tran
- Department of Paediatrics, CHU Nîmes, Nîmes, France
| | - Catherine Dunyach-Remy
- VBIC, Univ Montpellier, INSERM U1047, Department of Microbiology and Hospital Hygiene, CHU Nîmes, Univ. Montpellier, Nîmes, France
| | - Jérôme Ory
- VBIC, Univ Montpellier, INSERM U1047, Department of Microbiology and Hospital Hygiene, CHU Nîmes, Univ. Montpellier, Nîmes, France
| | - Brigitte Richaud-Morel
- VBIC, Univ Montpellier, INSERM U1047, Department of Microbiology and Hospital Hygiene, CHU Nîmes, Univ. Montpellier, Nîmes, France
| | - Albert Sotto
- VBIC, Univ Montpellier, INSERM U1047, Department of Infectious Diseases, CHU Nîmes, Univ. Montpellier, Nîmes, France
| | - Alix Pantel
- VBIC, Univ Montpellier, INSERM U1047, Department of Microbiology and Hospital Hygiene, CHU Nîmes, Univ. Montpellier, Nîmes, France
| | - Jean-Philippe Lavigne
- VBIC, Univ Montpellier, INSERM U1047, Department of Microbiology and Hospital Hygiene, CHU Nîmes, Univ. Montpellier, Nîmes, France
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Katahira K, Gotoh Y, Kasama K, Yoshimura D, Itoh T, Shimauchi C, Tajiri A, Hayashi T. Mobile genetic element-driven genomic changes in a community-associated methicillin-resistant Staphylococcus aureus clone during its transmission in a regional community outbreak in Japan. Microb Genom 2024; 10. [PMID: 39017043 DOI: 10.1099/mgen.0.001272] [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: 07/18/2024] Open
Abstract
Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) infections are now a public health concern in both community and healthcare settings worldwide. We previously identified a suspected case of a maternity clinic-centred outbreak of CA-MRSA skin infection in a regional community in Japan by PFGE-based analysis. In this study, we performed genome sequence-based analyses of 151 CA-MRSA isolates, which included not only outbreak-related isolates that we previously defined based on identical or similar PFGE patterns but also other isolates obtained during the same period in the same region. Our analysis accurately defined 133 isolates as outbreak-related isolates, collectively called the TDC clone. They belonged to a CA-MRSA lineage in clonal complex (CC) 30, known as the South West Pacific (SWP) clone. A high-resolution phylogenetic analysis of these isolates combined with their epidemiological data revealed that the TDC clone was already present and circulating in the region before the outbreak was recognized, and only the isolates belonging to two sublineages (named SL4 and SL5) were directly involved in the outbreak. Long persistence in patients/carriers and frequent intrahousehold transmission of the TDC clone were also revealed by this analysis. Moreover, by systematic analyses of the genome changes that occurred in this CA-MRSA clone during transmission in the community, we revealed that most variations were associated with mobile genetic elements (MGEs). Variant PFGE types were generated by alterations of prophages and genomic islands or insertion sequence (IS)-mediated insertion of a plasmid or a sequence of unknown origin. Dynamic changes in plasmid content, which were linked to changes in antimicrobial resistance profiles in specific isolates, were generated by frequent gain and loss of plasmids, most of which were self-transmissible or mobilizable. The introduction of IS256 by a plasmid (named pTDC02) into sublineage SL5 led to SL5-specific amplification of IS256, and amplified IS256 copies were involved in some of the structural changes of chromosomes and plasmids and generated variations in the repertoire of virulence-related genes in limited isolates. These data revealed how CA-MRSA genomes change during transmission in the community and how MGEs are involved in this process.
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Affiliation(s)
- Katsuyuki Katahira
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
- Department of Respiratory Medicine, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
- Department of Respiratory Medicine, NHO Omuta Hospital, Tachibana, Omuta City 837-0911, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kentaro Kasama
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Dai Yoshimura
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Takehiko Itoh
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Chieko Shimauchi
- Department of Nursing Humanics I, Miyazaki Prefectural Nursing University, Manabino, Miyazaki 880-0929, Japan
| | - Akihiko Tajiri
- Tajiri Dermatology Clinic, Kiyotake, Miyazaki 889-1067, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
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Diversity and Dissemination of Methicillin-Resistant Staphylococcus aureus (MRSA) Genotypes in Southeast Asia. Trop Med Infect Dis 2022; 7:tropicalmed7120438. [PMID: 36548693 PMCID: PMC9781663 DOI: 10.3390/tropicalmed7120438] [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: 11/14/2022] [Revised: 12/09/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a successful pathogen that has achieved global dissemination, with high prevalence rates in Southeast Asia. A huge diversity of clones has been reported in this region, with MRSA ST239 being the most successful lineage. Nonetheless, description of MRSA genotypes circulating in the Southeast Asia region has, until now, remained poorly compiled. In this review, we aim to provide a better understanding of the molecular epidemiology and distribution of MRSA clones in 11 Southeast Asian countries: Singapore, Malaysia, Thailand, Vietnam, Cambodia, Lao People's Democratic Republic (PDR), Myanmar, Philippines, Indonesia, Brunei Darussalam, and Timor-Leste. Notably, while archaic multidrug-resistant hospital-associated (HA) MRSAs, such as the ST239-III and ST241-III, were prominent in the region during earlier observations, these were then largely replaced by the more antibiotic-susceptible community-acquired (CA) MRSAs, such as ST22-IV and PVL-positive ST30-IV, in recent years after the turn of the century. Nonetheless, reports of livestock-associated (LA) MRSAs remain few in the region.
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Phylodynamic signatures in the emergence of community-associated MRSA. Proc Natl Acad Sci U S A 2022; 119:e2204993119. [PMID: 36322765 PMCID: PMC9659408 DOI: 10.1073/pnas.2204993119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Community-associated, methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) lineages have emerged in many geographically distinct regions around the world during the past 30 y. Here, we apply consistent phylodynamic methods across multiple community-associated MRSA lineages to describe and contrast their patterns of emergence and dissemination. We generated whole-genome sequencing data for the Australian sequence type (ST) ST93-MRSA-IV from remote communities in Far North Queensland and Papua New Guinea, and the Bengal Bay ST772-MRSA-V clone from metropolitan communities in Pakistan. Increases in the effective reproduction number (R<sub>e</sub>) and sustained transmission (R<sub>e</sub> > 1) coincided with spread of progenitor methicillin-susceptible <i>S. aureus</i> (MSSA) in remote northern Australian populations, dissemination of the ST93-MRSA-IV genotype into population centers on the Australian East Coast, and subsequent importation into the highlands of Papua New Guinea and Far North Queensland. Applying the same phylodynamic methods to existing lineage datasets, we identified common signatures of epidemic growth in the emergence and epidemiological trajectory of community-associated <i>S. aureus</i> lineages from America, Asia, Australasia, and Europe. Surges in R<sub>e</sub> were observed at the divergence of antibiotic-resistant strains, coinciding with their establishment in regional population centers. Epidemic growth was also observed among drug-resistant MSSA clades in Africa and northern Australia. Our data suggest that the emergence of community-associated MRSA in the late 20th century was driven by a combination of antibiotic-resistant genotypes and host epidemiology, leading to abrupt changes in lineage-wide transmission dynamics and sustained transmission in regional population centers.
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Didelot X, Parkhill J. A scalable analytical approach from bacterial genomes to epidemiology. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210246. [PMID: 35989600 PMCID: PMC9393561 DOI: 10.1098/rstb.2021.0246] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 02/17/2022] [Indexed: 12/21/2022] Open
Abstract
Recent years have seen a remarkable increase in the practicality of sequencing whole genomes from large numbers of bacterial isolates. The availability of this data has huge potential to deliver new insights into the evolution and epidemiology of bacterial pathogens, but the scalability of the analytical methodology has been lagging behind that of the sequencing technology. Here we present a step-by-step approach for such large-scale genomic epidemiology analyses, from bacterial genomes to epidemiological interpretations. A central component of this approach is the dated phylogeny, which is a phylogenetic tree with branch lengths measured in units of time. The construction of dated phylogenies from bacterial genomic data needs to account for the disruptive effect of recombination on phylogenetic relationships, and we describe how this can be achieved. Dated phylogenies can then be used to perform fine-scale or large-scale epidemiological analyses, depending on the proportion of cases for which genomes are available. A key feature of this approach is computational scalability and in particular the ability to process hundreds or thousands of genomes within a matter of hours. This is a clear advantage of the step-by-step approach described here. We discuss other advantages and disadvantages of the approach, as well as potential improvements and avenues for future research. This article is part of a discussion meeting issue 'Genomic population structures of microbial pathogens'.
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Affiliation(s)
- Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry CV4 7AL, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
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6
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Zhu H, Luo H, Zhong Q, Cao X, Gu S, Peng S, Xiao Y, Chen Y, Hang Y, Fang X, Zou S, Yu F, Hu L. Comparison of Molecular Characteristics Between Methicillin-Resistant and -Susceptible Staphylococcus aureus Clinical Isolates by Whole-Genome Sequencing. Infect Drug Resist 2022; 15:2949-2958. [PMID: 35706925 PMCID: PMC9190744 DOI: 10.2147/idr.s359654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 05/12/2022] [Indexed: 11/23/2022] Open
Abstract
Introduction The transmission of methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-susceptible Staphylococcus aureus (MSSA) are great public health concern worldwide. To better understand S. aureus evolution and dissemination, we compared the molecular features of MSSA and MRSA isolates. Methods In this study, 74 MSSA and 102 MRSA non-duplicate isolates were recovered from clinical samples between 2016 and 2020. Molecular epidemiology, antimicrobial resistance determinants, and virulence gene profiles were carried out by whole-genome sequencing (WGS). Results Twenty distinct sequence types were identified in MRSA isolates, with the most common being ST59, ST630, and ST338. The major genotypes of MSSA were ST188 and ST7. The toxin genes clfA, sek, and seq were significantly associated with MRSA, while splA/B, clfB, map, sdrC/D, and sem-sen-seo-seu were detected more frequently in MSSA isolates than MRSA (P < 0.05). The tst positive isolates were more commonly identified in CC1 and CC72, whereas lukE/D was mainly found in the CC7, CC15, CC88, and completely absent in CC59 clones. Conclusion Our results compared the genetic diversity between MRSA and MSSA strains, suggesting efforts to fight infections caused by MSSA need to be intensified due to MSSA isolates carrying wide range of virulence factors. Comparative epidemiological studies of large populations of MSSA and MRSA will be necessary in the future to understand how MSSA and MRSA populations may co-evolve and interact in the future.
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Affiliation(s)
- Hongying Zhu
- Department of Clinical Laboratory Medicine, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Hong Luo
- Department of Clinical Laboratory Medicine, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Qiaoshi Zhong
- Department of Clinical Laboratory Medicine, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Xingwei Cao
- Department of Clinical Laboratory Medicine, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Shumin Gu
- Department of Clinical Laboratory Medicine, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Suqin Peng
- Department of Clinical Laboratory Medicine, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Yanping Xiao
- Department of Clinical Laboratory Medicine, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Yanhui Chen
- Department of Clinical Laboratory Medicine, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Yaping Hang
- Department of Clinical Laboratory Medicine, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Xueyao Fang
- Department of Clinical Laboratory Medicine, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Shan Zou
- Department of Clinical Laboratory Medicine, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Fangyou Yu
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji UniversitySchool of Medicine, Shanghai, 200082, People's Republic of China
| | - Longhua Hu
- Department of Clinical Laboratory Medicine, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
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Kondo S, Phokhaphan P, Tongsima S, Ngamphiw C, Phornsiricharoenphant W, Ruangchai W, Disratthakit A, Tingpej P, Mahasirimongkol S, Lulitanond A, Apisarnthanarak A, Palittapongarnpim P. Molecular characterization of methicillin-resistant Staphylococcus aureus genotype ST764-SCCmec type II in Thailand. Sci Rep 2022; 12:2085. [PMID: 35136112 PMCID: PMC8826912 DOI: 10.1038/s41598-022-05898-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 01/05/2022] [Indexed: 12/16/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a significant causative agent of hospital-acquired infections. We characterized MRSA isolated from August 2012 to July 2015 from Thammasat University Hospital. Genotypic characterization of MRSA SCCmec type II and III isolates were scrutinized by whole genome sequencing (WGS). The WGS data revealed that the MRSA SCCmec type II isolates belonged to ST764 previously reported mainly in Japan. All of tested isolates contained ACME Type II′, SaPIn2, SaPIn3, seb, interrupted SA1320, and had a virulence gene profile similar to Japan MRSA ST764. Rigorous surveillance of MRSA strains is imperative in Thailand to arrest its potential spread.
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Affiliation(s)
- Sumalee Kondo
- Faculty of Medicine, Thammasat University, Pathum Thani, 12120, Thailand.
| | - Pimonwan Phokhaphan
- National Biobank of Thailand (NBT), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Sissades Tongsima
- National Biobank of Thailand (NBT), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Chumpol Ngamphiw
- National Biobank of Thailand (NBT), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | | | - Wuthiwat Ruangchai
- Pornchai Matangkasombut Center for Microbial Genomics, Mahidol University, Bangkok, 10400, Thailand
| | - Areeya Disratthakit
- Medical Life Science Institute, Ministry of Public Health, Nonthaburi, 11000, Thailand
| | - Pholawat Tingpej
- Faculty of Medicine, Thammasat University, Pathum Thani, 12120, Thailand
| | | | - Aroonlug Lulitanond
- Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, 40002, Thailand
| | | | - Prasit Palittapongarnpim
- Pornchai Matangkasombut Center for Microbial Genomics, Mahidol University, Bangkok, 10400, Thailand.
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Gatt YE, Margalit H. Common Adaptive Strategies Underlie Within-Host Evolution of Bacterial Pathogens. Mol Biol Evol 2021; 38:1101-1121. [PMID: 33118035 PMCID: PMC7947768 DOI: 10.1093/molbev/msaa278] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Within-host adaptation is a hallmark of chronic bacterial infections, involving substantial genomic changes. Recent large-scale genomic data from prolonged infections allow the examination of adaptive strategies employed by different pathogens and open the door to investigate whether they converge toward similar strategies. Here, we compiled extensive data of whole-genome sequences of bacterial isolates belonging to miscellaneous species sampled at sequential time points during clinical infections. Analysis of these data revealed that different species share some common adaptive strategies, achieved by mutating various genes. Although the same genes were often mutated in several strains within a species, different genes related to the same pathway, structure, or function were changed in other species utilizing the same adaptive strategy (e.g., mutating flagellar genes). Strategies exploited by various bacterial species were often predicted to be driven by the host immune system, a powerful selective pressure that is not species specific. Remarkably, we find adaptive strategies identified previously within single species to be ubiquitous. Two striking examples are shifts from siderophore-based to heme-based iron scavenging (previously shown for Pseudomonas aeruginosa) and changes in glycerol-phosphate metabolism (previously shown to decrease sensitivity to antibiotics in Mycobacterium tuberculosis). Virulence factors were often adaptively affected in different species, indicating shifts from acute to chronic virulence and virulence attenuation during infection. Our study presents a global view on common within-host adaptive strategies employed by different bacterial species and provides a rich resource for further studying these processes.
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Affiliation(s)
- Yair E Gatt
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hanah Margalit
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
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A narrative review of single-nucleotide polymorphism detection methods and their application in studies of Staphylococcus aureus. JOURNAL OF BIO-X RESEARCH 2021. [DOI: 10.1097/jbr.0000000000000071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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10
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Longitudinal whole-genome based comparison of carriage and infection associated Staphylococcus aureus in northern Australian dialysis clinics. PLoS One 2021; 16:e0245790. [PMID: 33544742 PMCID: PMC7864423 DOI: 10.1371/journal.pone.0245790] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 01/07/2021] [Indexed: 11/19/2022] Open
Abstract
Background The study objective was to reveal reservoirs potentially leading to Staphylococcus aureus infections in haemodialysis clinic clients in the tropical north of the Australian Northern Territory (NT). This client population are primarily Aboriginal Australians who have a greater burden of ill health than other Australians. Reservoir identification will enhance infection control in this client group, including informing potential S. aureus decolonisation strategies. Methods and findings The study participants were 83 clients of four haemodialysis clinics in the Darwin region of the NT, and 46 clinical staff and researchers who had contact with the clinic clients. The study design was longitudinal, encompassing swabbing of anatomical sites at two month intervals to yield carriage isolates, and also progressive collection of infection isolates. Swab sampling was performed for all participants, and infection isolates collected for dialysis clients only. Analysis was based on the comparison of 139 carriage isolates and 27 infection isolates using whole genome sequencing. Genome comparisons were based on of 20,651 genome-wide orthologous SNPs, presence/absence of the mecA and pvl genes, and inferred multilocus sequence type and clonal complex. Pairs of genomes meeting the definition of “not discriminated” were classed as defining potential transmission events. The primary outcome was instances of potential transmission between a carriage site other than a skin lesion and an infection site, in the same individual. Three such instances were identified. Two involved ST762 (CC1) PVL- MRSA, and one instance ST121 PVL+ MSSA. Three additional instances were identified where the carriage strains were derived from skin lesions. Also identified were six instances of potential transmission of a carriage strains between participants, including transmission of strains between dialysis clients and staff/researchers, and one potential transmission of a clinical strain between participants. There were frequent occurrences of longitudinal persistence of carriage strains in individual participants, and two examples of the same strain causing infection in the same participants at different times. Strains associated with infections and skin lesions were enriched for PVL and mecA in comparison to strains associated with long term carriage. Conclusions This study indicated that strains differ with respect to propensity to stably colonise sites such as the nose, and cause skin infections. PVL+ strains were associated with infection and skin lesions and were almost absent from the carriage sites. PVL- MRSA (mainly CC1) strains were associated with infection and also with potential transmission events involving carriage sites, while PVL- MSSA were frequently observed to stably colonise individuals without causing infection, and to be rarely transmitted. Current clinical guidelines for dialysis patients suggest MRSA decolonisation. Implementation in this client group may impact infections by PVL- MRSA, but may have little effect on infection by PVL+ strains. In this study, the PVL+ strains were predominant causes of infection but rarely colonised typical carriage sites such as the nose, and in the case of ST121, were MSSA. The important reservoirs for infection by PVL+ strains appeared to be prior infections.
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11
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Kombe IK, Agoti CN, Munywoki PK, Baguelin M, Nokes DJ, Medley GF. Integrating epidemiological and genetic data with different sampling intensities into a dynamic model of respiratory syncytial virus transmission. Sci Rep 2021; 11:1463. [PMID: 33446831 PMCID: PMC7809427 DOI: 10.1038/s41598-021-81078-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 01/04/2021] [Indexed: 01/06/2023] Open
Abstract
Respiratory syncytial virus (RSV) is responsible for a significant burden of severe acute lower respiratory tract illness in children under 5 years old; particularly infants. Prior to rolling out any vaccination program, identification of the source of infant infections could further guide vaccination strategies. We extended a dynamic model calibrated at the individual host level initially fit to social-temporal data on shedding patterns to include whole genome sequencing data available at a lower sampling intensity. The study population was 493 individuals (55 aged < 1 year) distributed across 47 households, observed through one RSV season in coastal Kenya. We found that 58/97 (60%) of RSV-A and 65/125 (52%) of RSV-B cases arose from infection probably occurring within the household. Nineteen (45%) infant infections appeared to be the result of infection by other household members, of which 13 (68%) were a result of transmission from a household co-occupant aged between 2 and 13 years. The applicability of genomic data in studies of transmission dynamics is highly context specific; influenced by the question, data collection protocols and pathogen under investigation. The results further highlight the importance of pre-school and school-aged children in RSV transmission, particularly the role they play in directly infecting the household infant. These age groups are a potential RSV vaccination target group.
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Affiliation(s)
- Ivy K Kombe
- KEMRI-Wellcome Trust Research Programme, KEMRI Centre for Geographical Medical Research-Coast, P.O. Box 230-80108, Kilifi, Kenya.
| | - Charles N Agoti
- KEMRI-Wellcome Trust Research Programme, KEMRI Centre for Geographical Medical Research-Coast, P.O. Box 230-80108, Kilifi, Kenya
| | - Patrick K Munywoki
- KEMRI-Wellcome Trust Research Programme, KEMRI Centre for Geographical Medical Research-Coast, P.O. Box 230-80108, Kilifi, Kenya
| | - Marc Baguelin
- Centre for Mathematical Modelling of Infectious Disease and Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, WC1H 9SH, UK
| | - D James Nokes
- KEMRI-Wellcome Trust Research Programme, KEMRI Centre for Geographical Medical Research-Coast, P.O. Box 230-80108, Kilifi, Kenya.,School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, CV4 7AL, UK
| | - Graham F Medley
- Centre for Mathematical Modelling of Infectious Disease and Department of Global Health and Development, London School of Hygiene and Tropical Medicine, London, WC1H 9SH, UK
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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: 66] [Impact Index Per Article: 16.5] [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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Pilot study of a combined genomic and epidemiologic surveillance program for hospital-acquired multidrug-resistant pathogens across multiple hospital networks in Australia. Infect Control Hosp Epidemiol 2020; 42:573-581. [PMID: 34008484 DOI: 10.1017/ice.2020.1253] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
OBJECTIVES To conduct a pilot study implementing combined genomic and epidemiologic surveillance for hospital-acquired multidrug-resistant organisms (MDROs) to predict transmission between patients and to estimate the local burden of MDRO transmission. DESIGN Pilot prospective multicenter surveillance study. SETTING The study was conducted in 8 university hospitals (2,800 beds total) in Melbourne, Australia (population 4.8 million), including 4 acute-care, 1 specialist cancer care, and 3 subacute-care hospitals. METHODS All clinical and screening isolates from hospital inpatients (April 24 to June 18, 2017) were collected for 6 MDROs: vanA VRE, MRSA, ESBL Escherichia coli (ESBL-Ec) and Klebsiella pneumoniae (ESBL-Kp), and carbapenem-resistant Pseudomonas aeruginosa (CRPa) and Acinetobacter baumannii (CRAb). Isolates were analyzed and reported as routine by hospital laboratories, underwent whole-genome sequencing at the central laboratory, and were analyzed using open-source bioinformatic tools. MDRO burden and transmission were assessed using combined genomic and epidemiologic data. RESULTS In total, 408 isolates were collected from 358 patients; 47.5% were screening isolates. ESBL-Ec was most common (52.5%), then MRSA (21.6%), vanA VRE (15.7%), and ESBL-Kp (7.6%). Most MDROs (88.3%) were isolated from patients with recent healthcare exposure.Combining genomics and epidemiology identified that at least 27.1% of MDROs were likely acquired in a hospital; most of these transmission events would not have been detected without genomics. The highest proportion of transmission occurred with vanA VRE (88.4% of patients). CONCLUSIONS Genomic and epidemiologic data from multiple institutions can feasibly be combined prospectively, providing substantial insights into the burden and distribution of MDROs, including in-hospital transmission. This analysis enables infection control teams to target interventions more effectively.
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Whole-genome sequencing as part of national and international surveillance programmes for antimicrobial resistance: a roadmap. BMJ Glob Health 2020; 5:e002244. [PMID: 33239336 PMCID: PMC7689591 DOI: 10.1136/bmjgh-2019-002244] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/18/2020] [Accepted: 03/27/2020] [Indexed: 12/26/2022] Open
Abstract
The global spread of antimicrobial resistance (AMR) and lack of novel alternative treatments have been declared a global public health emergency by WHO. The greatest impact of AMR is experienced in resource-poor settings, because of lack of access to alternative antibiotics and because the prevalence of multidrug-resistant bacterial strains may be higher in low-income and middle-income countries (LMICs). Intelligent surveillance of AMR infections is key to informed policy decisions and public health interventions to counter AMR. Molecular surveillance using whole-genome sequencing (WGS) can be a valuable addition to phenotypic surveillance of AMR. WGS provides insights into the genetic basis of resistance mechanisms, as well as pathogen evolution and population dynamics at different spatial and temporal scales. Due to its high cost and complexity, WGS is currently mainly carried out in high-income countries. However, given its potential to inform national and international action plans against AMR, establishing WGS as a surveillance tool in LMICs will be important in order to produce a truly global picture. Here, we describe a roadmap for incorporating WGS into existing AMR surveillance frameworks, including WHO Global Antimicrobial Resistance Surveillance System, informed by our ongoing, practical experiences developing WGS surveillance systems in national reference laboratories in Colombia, India, Nigeria and the Philippines. Challenges and barriers to WGS in LMICs will be discussed together with a roadmap to possible solutions.
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15
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Acosta F, Fernández-Cruz A, Maus SR, Sola-Campoy PJ, Marín M, Cercenado E, Sierra O, Muñoz P, García de Viedma D, Pérez-Lago L. In-Depth Study of a Nosocomial Outbreak Caused by Extensively Drug-Resistant Pseudomonas aeruginosa Using Whole Genome Sequencing Coupled With a Polymerase Chain Reaction Targeting Strain-Specific Single Nucleotide Polymorphisms. Am J Epidemiol 2020; 189:841-849. [PMID: 32128575 DOI: 10.1093/aje/kwaa025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 02/21/2020] [Indexed: 12/23/2022] Open
Abstract
In 2013-2014, an outbreak involving 14 patients infected by an extensively drug-resistant strain of Pseudomonas aeruginosa was detected in a hospital in Madrid, Spain. Our objective was to evaluate an alternative strategy for investigating the outbreak in depth by means of molecular and genomic approaches. Pulsed-field gel electrophoresis (PFGE) was applied as a first-line approach, followed by a more refined whole genome sequencing analysis. Single nucleotide polymorphisms identified by whole genome sequencing were used to design a specific polymerase chain reaction (PCR) for screening unsuspected cases infected by the outbreak strain. Whole genome sequencing alerted us to the existence of greater genetic diversity than was initially assumed, splitting the PFGE-associated outbreak isolates into 4 groups, 2 of which represented coincidental transmission unrelated to the outbreak. A multiplex allele-specific PCR targeting outbreak-specific single nucleotide polymorphisms was applied to 290 isolates, which allowed us to identify 25 additional cases related to the outbreak during 2011-2017. Whole genome sequencing coupled with an outbreak-strain-specific PCR enabled us to markedly redefine the initial picture of the outbreak by 1) ruling out initially suspected cases, 2) defining likely independent coincidental transmission events, 3) predating the starting point of the outbreak, 4) capturing new unsuspected cases, and 5) revealing that the outbreak was still active.
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16
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Nakamura Y, Takahashi H, Takaya A, Inoue Y, Katayama Y, Kusuya Y, Shoji T, Takada S, Nakagawa S, Oguma R, Saito N, Ozawa N, Nakano T, Yamaide F, Dissanayake E, Suzuki S, Villaruz A, Varadarajan S, Matsumoto M, Kobayashi T, Kono M, Sato Y, Akiyama M, Otto M, Matsue H, Núñez G, Shimojo N. Staphylococcus Agr virulence is critical for epidermal colonization and associates with atopic dermatitis development. Sci Transl Med 2020; 12:eaay4068. [PMID: 32641488 PMCID: PMC7426015 DOI: 10.1126/scitranslmed.aay4068] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 06/12/2020] [Indexed: 01/07/2023]
Abstract
Atopic dermatitis (AD) is commonly associated with colonization by Staphylococcus aureus in the affected skin. To understand the role of S. aureus in the development of AD, we performed whole-genome sequencing of S. aureus strains isolated from the cheek skin of 268 Japanese infants 1 and 6 months after birth. About 45% of infants were colonized with S. aureus at 1 month regardless of AD outcome. In contrast, skin colonization by S. aureus at 6 months of age increased the risk of developing AD. Acquisition of dysfunctional mutations in the S. aureus Agr quorum-sensing (QS) system was primarily observed in strains from 6-month-old infants who did not develop AD. Expression of a functional Agr system in S. aureus was required for epidermal colonization and the induction of AD-like inflammation in mice. Thus, retention of functional S. aureus agr virulence during infancy is associated with pathogen skin colonization and the development of AD.
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Affiliation(s)
- Yuumi Nakamura
- Department of Dermatology, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan.
- Cutaneous Immunology, Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan
| | - Hiroki Takahashi
- Medical Mycology Research Center, Chiba University, Chiba 260-8673, Japan
- Molecular Chirality Research Center, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
| | - Akiko Takaya
- Laboratory of Microbiology and Immunology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan
| | - Yuzaburo Inoue
- Department of Pediatrics, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan
| | - Yuki Katayama
- Department of Dermatology, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan
| | - Yoko Kusuya
- Medical Mycology Research Center, Chiba University, Chiba 260-8673, Japan
| | - Tatsuma Shoji
- Laboratory of Microbiology and Immunology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan
| | - Sanami Takada
- Department of Dermatology, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan
| | - Seitaro Nakagawa
- Department of Dermatology, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan
| | - Rena Oguma
- Department of Dermatology, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan
| | - Nobuko Saito
- Department of Dermatology, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan
| | - Naoko Ozawa
- Department of Pediatrics, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan
| | - Taiji Nakano
- Department of Pediatrics, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan
| | - Fumiya Yamaide
- Department of Pediatrics, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan
| | - Eishika Dissanayake
- Department of Pediatrics, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan
| | - Shuichi Suzuki
- Department of Pediatrics, Shimoshizu National Hospital, Chiba 284-0003, Japan
| | - Amer Villaruz
- Pathogen Molecular Genetics Section, Laboratory of Human Bacterial Pathogenesis, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Saranyaraajan Varadarajan
- Department of Pathology and Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Masanori Matsumoto
- Department of Pathology and Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Tomoko Kobayashi
- Department of Dermatology, Nagoya University Graduate School of Medicine, Aichi 466-8550, Japan
| | - Michihiro Kono
- Department of Dermatology, Nagoya University Graduate School of Medicine, Aichi 466-8550, Japan
| | - Yasunori Sato
- Department of Global Clinical Research, Chiba University Graduate School of Medicine, Chiba 260-0870, Japan
| | - Masashi Akiyama
- Department of Dermatology, Nagoya University Graduate School of Medicine, Aichi 466-8550, Japan
| | - Michael Otto
- Pathogen Molecular Genetics Section, Laboratory of Human Bacterial Pathogenesis, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hiroyuki Matsue
- Department of Dermatology, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan
- Medical Mycology Research Center, Chiba University, Chiba 260-8673, Japan
| | - Gabriel Núñez
- Department of Pathology and Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Naoki Shimojo
- Department of Pediatrics, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan
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Cassidy R, Kypraios T, O'Neill PD. Modelling, Bayesian inference, and model assessment for nosocomial pathogens using whole-genome-sequence data. Stat Med 2020; 39:1746-1765. [PMID: 32142587 PMCID: PMC7217057 DOI: 10.1002/sim.8510] [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: 08/12/2019] [Revised: 01/15/2020] [Accepted: 01/31/2020] [Indexed: 12/28/2022]
Abstract
Whole‐genome sequencing of pathogens in outbreaks of infectious disease provides the potential to reconstruct transmission pathways and enhance the information contained in conventional epidemiological data. In recent years, there have been numerous new methods and models developed to exploit such high‐resolution genetic data. However, corresponding methods for model assessment have been largely overlooked. In this article, we develop both new modelling methods and new model assessment methods, specifically by building on the work of Worby et al. Although the methods are generic in nature, we focus specifically on nosocomial pathogens and analyze a dataset collected during an outbreak of MRSA in a hospital setting.
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Affiliation(s)
- Rosanna Cassidy
- School of Mathematical Sciences, University of Nottingham, Nottingham, UK
| | - Theodore Kypraios
- School of Mathematical Sciences, University of Nottingham, Nottingham, UK
| | - Philip D O'Neill
- School of Mathematical Sciences, University of Nottingham, Nottingham, UK
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18
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Dabetic NM, Todorovic VM, Djuricic ID, Antic Stankovic JA, Basic ZN, Vujovic DS, Sobajic SS. Grape Seed Oil Characterization: A Novel Approach for Oil Quality Assessment. EUR J LIPID SCI TECH 2020. [DOI: 10.1002/ejlt.201900447] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Nevena M. Dabetic
- Department of Bromatology, Faculty of PharmacyUniversity of Belgrade Vojvode Stepe 450 Belgrade 11221 Serbia
| | - Vanja M. Todorovic
- Department of Bromatology, Faculty of PharmacyUniversity of Belgrade Vojvode Stepe 450 Belgrade 11221 Serbia
| | - Ivana D. Djuricic
- Department of Bromatology, Faculty of PharmacyUniversity of Belgrade Vojvode Stepe 450 Belgrade 11221 Serbia
| | - Jelena A. Antic Stankovic
- Department of Microbiology and Immunology, Faculty of PharmacyUniversity of Belgrade Vojvode Stepe 450 Belgrade 11221 Serbia
| | - Zorica N. Basic
- Institute of HygieneMilitary Medical Academy Crnotravska 17 Belgrade 11040 Serbia
| | - Dragan S. Vujovic
- Department of Viticulture, Faculty of AgricultureUniversity of Belgrade Nemanjina 6 Belgrade 11080 Serbia
| | - Sladjana S. Sobajic
- Department of Bromatology, Faculty of PharmacyUniversity of Belgrade Vojvode Stepe 450 Belgrade 11221 Serbia
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Raven KE, Blane B, Kumar N, Leek D, Bragin E, Coll F, Parkhill J, Peacock SJ. Defining metrics for whole-genome sequence analysis of MRSA in clinical practice. Microb Genom 2020; 6:e000354. [PMID: 32228804 PMCID: PMC7276698 DOI: 10.1099/mgen.0.000354] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 02/24/2020] [Indexed: 12/26/2022] Open
Abstract
Bacterial sequencing will become increasingly adopted in routine microbiology laboratories. Here, we report the findings of a technical evaluation of almost 800 clinical methicillin-resistant Staphylococcus aureus (MRSA) isolates, in which we sought to define key quality metrics to support MRSA sequencing in clinical practice. We evaluated the accuracy of mapping to a generic reference versus clonal complex (CC)-specific mapping, which is more computationally challenging. Focusing on isolates that were genetically related (<50 single nucleotide polymorphisms (SNPs)) and belonged to prevalent sequence types, concordance between these methods was 99.5 %. We use MRSA MPROS0386 to control for base calling accuracy by the sequencer, and used multiple repeat sequences of the control to define a permitted range of SNPs different to the mapping reference for this control (equating to 3 standard deviations from the mean). Repeat sequences of the control were also used to demonstrate that SNP calling was most accurate across differing coverage depths (above 35×, the lowest depth in our study) when the depth required to call a SNP as present was at least 4-8×. Using 786 MRSA sequences, we defined a robust measure for mec gene detection to reduce false-positives arising from contamination, which was no greater than 2 standard deviations below the average depth of coverage across the genome. Sequencing from bacteria harvested from clinical plates runs an increased risk of contamination with the same or different species, and we defined a cut-off of 30 heterozygous sites >50 bp apart to identify same-species contamination for MRSA. These metrics were combined into a quality-control (QC) flowchart to determine whether sequence runs and individual clinical isolates passed QC, which could be adapted by future automated analysis systems to enable rapid hands-off sequence analysis by clinical laboratories.
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Affiliation(s)
- Kathy E. Raven
- Department of Medicine, University of Cambridge, Box 157 Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0QQ, UK
| | - Beth Blane
- Department of Medicine, University of Cambridge, Box 157 Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0QQ, UK
| | - Narender Kumar
- Department of Medicine, University of Cambridge, Box 157 Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0QQ, UK
| | - Danielle Leek
- Department of Medicine, University of Cambridge, Box 157 Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0QQ, UK
| | - Eugene Bragin
- Next Gen Diagnostics LLC (NGD), Mountain View, CA and Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Francesc Coll
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK
| | - Sharon J. Peacock
- Department of Medicine, University of Cambridge, Box 157 Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0QQ, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
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20
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Abdelbary MMH, Feil EJ, Senn L, Petignat C, Prod’hom G, Schrenzel J, François P, Werner G, Layer F, Strommenger B, Pantosti A, Monaco M, Denis O, Deplano A, Grundmann H, Blanc DS. Phylogeographical Analysis Reveals the Historic Origin, Emergence, and Evolutionary Dynamics of Methicillin-Resistant Staphylococcus aureus ST228. Front Microbiol 2020; 11:2063. [PMID: 32983046 PMCID: PMC7479193 DOI: 10.3389/fmicb.2020.02063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 08/05/2020] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Methicillin-resistant Staphylococcus aureus (MRSA) is a common healthcare-associated pathogen that remains a major public health concern. Sequence type 228 (ST228) was first described in Germany and spread to become a successful MRSA clone in several European countries. In 2000, ST228 emerged in Lausanne and has subsequently caused several large outbreaks. Here, we describe the evolutionary history of this clone and identify the genetic changes underlying its expansion in Switzerland. MATERIALS AND METHODS We aimed to understand the phylogeographic and demographic dynamics of MRSA ST228/ST111 by sequencing 530 representative isolates of this clone that were collected from 14 European countries between 1997 and 2012. RESULTS The phylogenetic analysis revealed distinct lineages of ST228 isolates associated with specific geographic origins. In contrast, isolates of ST111, which is a single locus variant of ST228 sharing the same spa type t041, formed a monophyletic cluster associated with multiple countries. The evidence points to a German origin of the sampled population, with the basal German lineage being characterized by spa type t001. The highly successful Swiss ST228 lineage diverged from this progenitor clone through the loss of the aminoglycoside-streptothricin resistance gene cluster and the gain of mupirocin resistance. This lineage was introduced first in Geneva and was subsequently introduced into Lausanne. CONCLUSION Our results reveal the radiation of distinct lineages of MRSA ST228 from a German progenitor, as the clone spread into different European countries. In Switzerland, ST228 was introduced first in Geneva and was subsequently introduced into Lausanne.
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Affiliation(s)
- Mohamed M. H. Abdelbary
- Service of Hospital Preventive Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- Division of Oral Microbiology and Immunology, Department of Operative Dentistry, Periodontology and Preventive Dentistry, RWTH Aachen University Hospital, Aachen, Germany
| | - Edward J. Feil
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Laurence Senn
- Service of Hospital Preventive Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Christiane Petignat
- Service of Hospital Preventive Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Guy Prod’hom
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Jacques Schrenzel
- Bacteriology Laboratory, Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | - Patrice François
- Bacteriology Laboratory, Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | - Guido Werner
- National Reference Centre for Staphylococci and Enterococci, Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany
| | - Franziska Layer
- National Reference Centre for Staphylococci and Enterococci, Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany
| | - Birgit Strommenger
- National Reference Centre for Staphylococci and Enterococci, Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany
| | - Annalisa Pantosti
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Monica Monaco
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Olivier Denis
- National Reference Centre-Staphylococcus aureus, Department of Microbiology, Hôpital Erasme, Université libre de Bruxelles, Brussels, Belgium
- Laboratory of Microbiology, CHU UCL Namur, Université catholique de Louvain, Yvoir, Belgium
| | - Ariane Deplano
- National Reference Centre-Staphylococcus aureus, Department of Microbiology, Hôpital Erasme, Université libre de Bruxelles, Brussels, Belgium
| | - Hajo Grundmann
- Department of Infectious Diseases Epidemiology, The University of Groningen, Groningen, Netherlands
| | - Dominique S. Blanc
- Service of Hospital Preventive Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- *Correspondence: Dominique S. Blanc,
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Giulieri SG, Tong SYC, Williamson DA. Using genomics to understand meticillin- and vancomycin-resistant Staphylococcus aureus infections. Microb Genom 2020; 6:e000324. [PMID: 31913111 PMCID: PMC7067033 DOI: 10.1099/mgen.0.000324] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 12/12/2019] [Indexed: 12/15/2022] Open
Abstract
Resistance to meticillin and vancomycin in Staphylococcus aureus significantly complicates the management of severe infections like bacteraemia, endocarditis or osteomyelitis. Here, we review the molecular mechanisms and genomic epidemiology of resistance to these agents, with a focus on how genomics has provided insights into the emergence and evolution of major meticillin-resistant S. aureus clones. We also provide insights on the use of bacterial whole-genome sequencing to inform management of S. aureus infections and for control of transmission at the hospital and in the community.
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Affiliation(s)
- Stefano G. Giulieri
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Infectious Disease Department, Austin Health, Melbourne, Australia
| | - Steven Y. C. Tong
- Victorian Infectious Disease Service, Royal Melbourne Hospital, and Doherty Department University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
- Menzies School of Health Research, Darwin, Australia
| | - Deborah A. Williamson
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne at the Peter Doherty Institute of Infection and Immunity, Melbourne, Australia
- Microbiology, Royal Melbourne Hospital, Melbourne, Australia
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Abstract
Staphylococci, and in particular Staphylococcus aureus, cause an extensive variety of infections in a range of hosts. The comprehensive analysis of staphylococcal genomes reveals mechanisms controlling the organism's biology, pathobiology, and dissemination. Whole-genome sequencing technologies led to a quantum leap in our understanding of bacterial genomes. The recent cost reduction of sequencing has resulted in unprecedented volumes of genomic information about S. aureus, one of the most sequenced bacterial species. Collecting, comparing, and interpreting big data is challenging, but fascinating insights have emerged. For example, it is becoming clearer which selective pressures staphylococci face in their habitats and which mechanisms allow this pathogen to adapt, survive, and spread. A key theme is the constant evolution of staphylococci as they alter their genome, exchange DNA, and adapt to new environments, leading to the emergence of increasingly successful, antibiotic-resistant, immune-evading, and host-adapted colonizers and pathogens. This article introduces the structure of staphylococcal genomes, details how genomes vary between strains, outlines the mechanisms of genetic variation, and describes the features of successful clones.
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Affiliation(s)
- Jodi A Lindsay
- St. George's, University of London, Institute of Infection and Immunity, London, United Kingdom
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Barcudi D, Sosa EJ, Lamberghini R, Garnero A, Tosoroni D, Decca L, Gonzalez L, Kuyuk MA, Lopez T, Herrero I, Cortes P, Figueroa M, Egea AL, Gagetti P, Fernandez Do Porto DA, Corso A, Turjanski AG, Bocco JL, Sola C. MRSA dynamic circulation between the community and the hospital setting: New insights from a cohort study. J Infect 2019; 80:24-37. [PMID: 31606351 DOI: 10.1016/j.jinf.2019.10.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 09/09/2019] [Accepted: 10/03/2019] [Indexed: 12/21/2022]
Abstract
Dissemination of methicillin-resistant-Staphylococcus aureus/(MRSA) is a worldwide concern both in hospitals [healthcare-associated-(HA)-MRSA] and communities [community-associated-(CA)-MRSA]. Knowledge on when and where MRSA colonization is acquired and what clones are involved is necessary, to focus efforts for prevention of hospital-acquired MRSA-infections. METHODS A prospective/longitudinal cohort study was performed in eight Argentina hospitals (Cordoba/ October-December/2014). Surveillance cultures for MRSA (nose-throat-inguinal) were obtained on admission and at discharge. MRSA strains were genetically typed as CA-MRSAG and HA-MRSAG genotypes. RESULTS Overall, 1419 patients were screened and 534 stayed at hospital for ≥3 days. S. aureus admission prevalence was 30.9% and 4.2% for MRSA. Overall MRSA acquisition rate was 2.3/1000 patient-days-at-risk with a MRSA acquisition prevalence of 1.96% (95%CI: 1.0%-3.4%); 3.2% of patients were discharged back to community with MRSA. CA-MRSAG accounted for 84.6% of imported, 100.0% of hospital-acquired and 94% of discharged MRSA strains. Most imported and acquired MRSA strains belonged to two major epidemic CA-MRSA clones spread in Argentina: PFGEtypeI-ST5-IVa-t311-PVL+ and PFGEtypeN/ST30-IVc-t019-PVL+. CONCLUSIONS CA-MRSA clones, particularly ST5-IV-PVL+ and ST30-IV-PVL+, with main reservoir in the community, not only enter but also are truly acquired within hospital, causing healthcare-associated-hospital-onset infections, having a transmission capacity greater or similar than HA-MRSAG. This information is essential to develop appropriate MRSA infection prevention-control programs, considering hospital and community.
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Affiliation(s)
- Danilo Barcudi
- Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI) CONICET and Universidad Nacional de Córdoba; Departamento de Bioquímica Clínica; Facultad de Ciencias Químicas; Haya de La Torre y Medina Allende, Ciudad Universitaria, X5000-Córdoba, Argentina
| | - Ezequiel J Sosa
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, CONICET, Ciudad Universitaria, Pabellón 2, C1428EHA Ciudad de Buenos Aires, Argentina; Instituto de Química Biológica de La Facultad de Ciencias Exactas y Naturales (IQUIBICEN)-CONICET, Ciudad Universitaria, Pabellón 2, C1428EHA Ciudad de Buenos Aires, Argentina
| | - Ricardo Lamberghini
- Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Bajada Pucará 2025, X5000 Córdoba, Argentina; Hospital Guillermo Rawson, Bajada Pucará 2025, X5000 Córdoba, Argentina
| | - Analía Garnero
- Hospital de Niños de la Santísima Trinidad de Córdoba, Córdoba, Bajada Pucará 787, X5000 ANN, Argentina
| | - Dario Tosoroni
- Facultad de Medicina, Universidad Católica de Córdoba, Jacinto Ríos 555, X5004ASK Córdoba, Argentina
| | - Laura Decca
- Clínica Regional del SUD-Río IV, Av. Italia 1262, X5800 Río Cuarto, Córdoba, Argentina
| | - Liliana Gonzalez
- Hospital Infantil Municipal de Córdoba, Juan Antonio Lavalleja 3050, X5000 Córdoba, Argentina
| | - María A Kuyuk
- Hospital Militar Córdoba, Cruz Roja Argentina 1114, X5000 Córdoba, Argentina
| | - Teresa Lopez
- Hospital Guillermo Rawson, Bajada Pucará 2025, X5000 Córdoba, Argentina
| | - Ivana Herrero
- Hospital de Urgencias, Catamarca 441, X5000 Córdoba, Argentina
| | - Paulo Cortes
- Hospital Pediátrico del Niño Jesús, Av. Castro Barros 650, X5000HTT Córdoba, Argentina
| | - Myrian Figueroa
- Hospital Misericordia, Nuevo Siglo, Belgrano 1502, X5000 Córdoba, Argentina
| | - Ana L Egea
- Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI) CONICET and Universidad Nacional de Córdoba; Departamento de Bioquímica Clínica; Facultad de Ciencias Químicas; Haya de La Torre y Medina Allende, Ciudad Universitaria, X5000-Córdoba, Argentina
| | - Paula Gagetti
- Servicio Antimicrobianos, Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS "Dr. Carlos G. Malbrán", Av. Vélez Sarsfield 563, C1282AFF Ciudad Autónoma de Buenos Aires, Argentina
| | - Darío A Fernandez Do Porto
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, CONICET, Ciudad Universitaria, Pabellón 2, C1428EHA Ciudad de Buenos Aires, Argentina; Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Ciudad de Buenos Aires, Argentina
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- The members of the Study Group are listed in the Acknowledgments section, where the participants of each hospital and their affiliations are described
| | - Alejandra Corso
- Servicio Antimicrobianos, Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS "Dr. Carlos G. Malbrán", Av. Vélez Sarsfield 563, C1282AFF Ciudad Autónoma de Buenos Aires, Argentina
| | - Adrián G Turjanski
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Ciudad de Buenos Aires, Argentina
| | - José L Bocco
- Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI) CONICET and Universidad Nacional de Córdoba; Departamento de Bioquímica Clínica; Facultad de Ciencias Químicas; Haya de La Torre y Medina Allende, Ciudad Universitaria, X5000-Córdoba, Argentina
| | - Claudia Sola
- Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI) CONICET and Universidad Nacional de Córdoba; Departamento de Bioquímica Clínica; Facultad de Ciencias Químicas; Haya de La Torre y Medina Allende, Ciudad Universitaria, X5000-Córdoba, Argentina.
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24
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Hall MD, Holden MT, Srisomang P, Mahavanakul W, Wuthiekanun V, Limmathurotsakul D, Fountain K, Parkhill J, Nickerson EK, Peacock SJ, Fraser C. Improved characterisation of MRSA transmission using within-host bacterial sequence diversity. eLife 2019; 8:46402. [PMID: 31591959 PMCID: PMC6954020 DOI: 10.7554/elife.46402] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 10/01/2019] [Indexed: 12/31/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) transmission in the hospital setting has been a frequent subject of investigation using bacterial genomes, but previous approaches have not yet fully utilised the extra deductive power provided when multiple pathogen samples are acquired from each host. Here, we used a large dataset of MRSA sequences from multiply-sampled patients to reconstruct colonisation of individuals in a high-transmission setting in a hospital in Thailand. We reconstructed transmission trees for MRSA. We also investigated transmission between anatomical sites on the same individual, finding that this either occurs repeatedly or involves a wide transmission bottleneck. We examined the between-subject bottleneck, finding considerable variation in the amount of diversity transmitted. Finally, we compared our approach to the simpler method of identifying transmission pairs using single nucleotide polymorphism (SNP) counts. This suggested that the optimum threshold for identifying a pair is 39 SNPs, if sensitivities and specificities are equally weighted.
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Affiliation(s)
- Matthew D Hall
- Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Matthew Tg Holden
- School of Medicine, University of St Andrews, St Andrews, United Kingdom
| | - Pramot Srisomang
- Department of Pediatrics, Sunpasitthiprasong Hospital, Ubon Ratchathani, Thailand
| | - Weera Mahavanakul
- Department of Medicine, Sunpasitthiprasong Hospital, Ubon Ratchathani, Thailand
| | - Vanaporn Wuthiekanun
- Mahidol Oxford Tropical Medicine Research Unit, Mahidol University, Salaya, Thailand
| | | | - Kay Fountain
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Emma K Nickerson
- Department of Infectious Diseases, Cambridge University Hospitals NHS Foundation, Cambridge, United Kingdom
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
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25
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Gotoh Y, Taniguchi T, Yoshimura D, Katsura K, Saeki Y, Hirabara Y, Fukuda M, Takajo I, Tomida J, Kawamura Y, Ogura Y, Itoh T, Misawa N, Okayama A, Hayashi T. Multi-step genomic dissection of a suspected intra-hospital Helicobacter cinaedi outbreak. Microb Genom 2019; 4. [PMID: 30629483 PMCID: PMC6412056 DOI: 10.1099/mgen.0.000236] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Helicobacter cinaedi is an emerging pathogen causing bacteraemia and cellulitis. Nosocomial transmission of this microbe has been described, but detailed molecular-epidemiological analyses have not been performed. Here, we describe the results of a multi-step genome-wide phylogenetic analysis of a suspected intra-hospital outbreak of H. cinaedi that occurred in a hospital in Japan. The outbreak was recognized by the infectious control team (ICT) of the hospital as a sudden increase in H. cinaedi bacteraemia. ICT defined this outbreak case based on 16S rRNA sequence data and epidemiological information, but were unable to determine the source and route of the infections. We therefore re-investigated this case using whole-genome sequencing (WGS). We first performed a species-wide analysis using publicly available genome sequences to understand the level of genomic diversity of this under-studied species. The clusters identified were then separately analysed using the genome sequence of a representative strain in each cluster as a reference. These analyses provided a high-level phylogenetic resolution of each cluster, identified a confident set of outbreak isolates, and discriminated them from other closely related but distinct clones, which were locally circulating and invaded the hospital during the same period. By considering the epidemiological data, possible strain transmission chains were inferred, which highlighted the role of asymptomatic carriers or environmental contamination. The emergence of a subclone with increased resistance to fluoroquinolones in the outbreak was also recognized. Our results demonstrate the impact of the use of a closely related genome as a reference to maximize the power of WGS.
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Affiliation(s)
- Yasuhiro Gotoh
- 1Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan.,2Previous address: Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Takako Taniguchi
- 3Laboratory of Veterinary Public Health, Department of Veterinary Medical Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Dai Yoshimura
- 4Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Tokyo, Japan
| | - Keisuke Katsura
- 5Frontier Science Research Center, University of Miyazaki, Miyazaki, Japan
| | - Yuji Saeki
- 6Center for Infection Control, University of Miyazaki Hospital, Miyazaki, Japan
| | - Yasutoshi Hirabara
- 6Center for Infection Control, University of Miyazaki Hospital, Miyazaki, Japan
| | - Mayumi Fukuda
- 6Center for Infection Control, University of Miyazaki Hospital, Miyazaki, Japan
| | - Ichiro Takajo
- 6Center for Infection Control, University of Miyazaki Hospital, Miyazaki, Japan
| | - Junko Tomida
- 7Department of Microbiology, School of Pharmacy, Aichi Gakuin University, Nagoya, Japan
| | - Yoshiaki Kawamura
- 7Department of Microbiology, School of Pharmacy, Aichi Gakuin University, Nagoya, Japan
| | - Yoshitoshi Ogura
- 1Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan.,2Previous address: Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Takehiko Itoh
- 4Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Tokyo, Japan
| | - Naoaki Misawa
- 3Laboratory of Veterinary Public Health, Department of Veterinary Medical Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan.,8Faculty of Agriculture, University of Miyazaki Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - Akihiko Okayama
- 6Center for Infection Control, University of Miyazaki Hospital, Miyazaki, Japan.,9Department of Rheumatology, Infectious Diseases and Laboratory Medicine, University of Miyazaki, Miyazaki, Japan
| | - Tetsuya Hayashi
- 1Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan.,2Previous address: Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
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26
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Amoako DG, Somboro AM, Abia ALK, Allam M, Ismail A, Bester L, Essack SY. Genomic analysis of methicillin-resistant Staphylococcus aureus isolated from poultry and occupational farm workers in Umgungundlovu District, South Africa. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 670:704-716. [PMID: 30909047 DOI: 10.1016/j.scitotenv.2019.03.110] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 03/06/2019] [Accepted: 03/07/2019] [Indexed: 06/09/2023]
Abstract
This study detected methicillin-resistant Staphylococcus aureus (MRSA) isolates circulating in poultry and farm workers at an intensive poultry production system in uMgungundlovu, South Africa and established the genetic relatedness and characteristics of the isolates using whole genome sequencing (WGS). A total of 145 S. aureus were isolated from poultry (120) and occupational workers (25) in the "farm to fork" continuum (farm, transport, slaughterhouse, and retail points). Twelve MRSA (12/145; 8.3%) isolates were found in the poultry food-chain. MRSA isolates were subjected to antibiotic susceptibility testing against a panel of 20 antibiotics using the broth dilution method and their whole genome was sequenced via the Illumina MiSeq. All the MRSA isolates were multi-drug resistant (MDR) and carried the mecA gene on the SCCmec mobile genetic element (MGE). The majority (11/12) of the MRSA isolates circulating between humans and animals in the continuum belonged to a human-associated clone, ST612-CC8-t1257-SCCmec_IVd (2B), previously reported in South Africa. Other MGEs present in the isolates included: plasmid replicons based on Rep 7 and 20, insertion sequences (IS1182), and prophages (phi2958PVL). Genomic analysis identified a distinct acquired antibiotic resistome in the clone, which accurately predicted the phenotypic antibiograms. Phylogenetic analysis clustered the isolates within the major cluster (I), suggesting the spread of the local dominant multidrug resistance MRSA clone ST612-CC8-t1257-SCCmec_IVd (2B) between humans and animals along the 'farm to fork' continuum. The findings of this study suggest the need to establish appropriate control measures to curb the spread of MDR-MRSA in the food chain.
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Affiliation(s)
- Daniel Gyamfi Amoako
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
| | - Anou Moise Somboro
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
| | - Akebe Luther King Abia
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Pretoria, South Africa.
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Pretoria, South Africa.
| | - Linda Bester
- Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
| | - Sabiha Yusuf Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
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27
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Humphreys H, Coleman D. Contribution of whole-genome sequencing to understanding of the epidemiology and control of meticillin-resistant Staphylococcus aureus. J Hosp Infect 2019; 102:189-199. [DOI: 10.1016/j.jhin.2019.01.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 01/29/2019] [Indexed: 02/06/2023]
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28
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De Backer S, Xavier B, Vanjari L, Coppens J, Lammens C, Vemu L, Carevic B, Hryniewicz W, Jorens P, Kumar-Singh S, Lee A, Harbarth S, Schrenzel J, Tacconelli E, Goossens H, Malhotra-Kumar S. Remarkable geographical variations between India and Europe in carriage of the staphylococcal surface protein-encoding sasX/sesI and in the population structure of methicillin-resistant Staphylococcus aureus belonging to clonal complex 8. Clin Microbiol Infect 2019; 25:628.e1-628.e7. [DOI: 10.1016/j.cmi.2018.07.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 07/10/2018] [Accepted: 07/23/2018] [Indexed: 10/28/2022]
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29
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Baines SL, Jensen SO, Firth N, Gonçalves da Silva A, Seemann T, Carter GP, Williamson DA, Howden BP, Stinear TP. Remodeling of pSK1 Family Plasmids and Enhanced Chlorhexidine Tolerance in a Dominant Hospital Lineage of Methicillin-Resistant Staphylococcus aureus. Antimicrob Agents Chemother 2019; 63:e02356-18. [PMID: 30783008 PMCID: PMC6496109 DOI: 10.1128/aac.02356-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 02/08/2019] [Indexed: 12/29/2022] Open
Abstract
Staphylococcus aureus is a significant human pathogen whose evolution and adaptation have been shaped in part by mobile genetic elements (MGEs), facilitating the global spread of extensive antimicrobial resistance. However, our understanding of the evolutionary dynamics surrounding MGEs, in particular, how changes in the structure of multidrug resistance (MDR) plasmids may influence important staphylococcal phenotypes, is incomplete. Here, we undertook a population and functional genomics study of 212 methicillin-resistant S. aureus (MRSA) sequence type 239 (ST239) isolates collected over 32 years to explore the evolution of the pSK1 family of MDR plasmids, illustrating how these plasmids have coevolved with and contributed to the successful adaptation of this persistent MRSA lineage. Using complete genomes and temporal phylogenomics, we reconstructed the evolution of the pSK1 family lineage from its emergence in the late 1970s and found that multiple structural variants have arisen. Plasmid maintenance and stability were linked to IS256- and IS257-mediated chromosomal integration and disruption of the plasmid replication machinery. Overlaying genomic comparisons with phenotypic susceptibility data for gentamicin, trimethoprim, and chlorhexidine, it appeared that pSK1 has contributed to enhanced resistance in ST239 MRSA isolates through two mechanisms: (i) acquisition of plasmid-borne resistance mechanisms increasing the rates of gentamicin resistance and reduced chlorhexidine susceptibility and (ii) changes in the plasmid configuration linked with further enhancement of chlorhexidine tolerance. While the exact mechanism of enhanced tolerance remains elusive, this research has uncovered a potential evolutionary response of ST239 MRSA to biocides, one of which may contribute to the ongoing persistence and adaptation of this lineage within health care institutions.
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Affiliation(s)
- Sarah L Baines
- Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Slade O Jensen
- Microbiology and Infectious Diseases, School of Medicine, Ingham Institute for Applied Medical Research, University of Western Sydney, Sydney, New South Wales, Australia
| | - Neville Firth
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Anders Gonçalves da Silva
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Torsten Seemann
- Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Glen P Carter
- Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Deborah A Williamson
- Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
- Infectious Diseases Department, Austin Health, Melbourne, Victoria, Australia
| | - Timothy P Stinear
- Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
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30
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Antimicrobial-resistant Gram-negative colonization in infants from a neonatal intensive care unit in Thailand. J Hosp Infect 2019; 103:151-155. [PMID: 30995491 PMCID: PMC6863035 DOI: 10.1016/j.jhin.2019.04.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 04/04/2019] [Indexed: 11/23/2022]
Abstract
Antimicrobial-resistant Gram-negative bacteria are a major cause of morbidity and mortality in hospitalized neonates in South and South-East Asia. This study aimed to determine the dynamics of colonization with antimicrobial-resistant Gram-negative bacteria amongst patients in a neonatal intensive care unit (NICU) in Thailand. From 97 enrolled patients, 52% were colonized by an extended-spectrum β-lactamase (ESBL) organism at some point during their stay and 64% were colonized by a carbapenem-resistant organism. Rapid acquisition of ESBL-positive and carbapenem-resistant organisms was found. Once colonized with an antibiotic-resistant organism, patients remained colonized for the remainder of their NICU stay.
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31
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Desvillechabrol D, Bouchier C, Kennedy S, Cokelaer T. Sequana coverage: detection and characterization of genomic variations using running median and mixture models. Gigascience 2018; 7:5091804. [PMID: 30192951 PMCID: PMC6275460 DOI: 10.1093/gigascience/giy110] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 08/23/2018] [Indexed: 11/30/2022] Open
Abstract
Background In addition to mapping quality information, the Genome coverage contains valuable biological information such as the presence of repetitive regions, deleted genes, or copy number variations (CNVs). It is essential to take into consideration atypical regions, trends (e.g., origin of replication), or known and unknown biases that influence coverage. It is also important that reported events have robust statistics (e.g. z-score) associated with their detections as well as precise location. Results We provide a stand-alone application, sequana_coverage, that reports genomic regions of interest (ROIs) that are significantly over- or underrepresented in high-throughput sequencing data. Significance is associated with the events as well as characteristics such as length of the regions. The algorithm first detrends the data using an efficient running median algorithm. It then estimates the distribution of the normalized genome coverage with a Gaussian mixture model. Finally, a z-score statistic is assigned to each base position and used to separate the central distribution from the ROIs (i.e., under- and overcovered regions). A double thresholds mechanism is used to cluster the genomic ROIs. HTML reports provide a summary with interactive visual representations of the genomic ROIs with standard plots and metrics. Genomic variations such as single-nucleotide variants or CNVs can be effectively identified at the same time.
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Affiliation(s)
| | - Christiane Bouchier
- Institut Pasteur - Pole Biomics - 25-28 Rue du Docteur Roux, 75015 Paris, France
| | - Sean Kennedy
- Institut Pasteur - Pole Biomics - 25-28 Rue du Docteur Roux, 75015 Paris, France
| | - Thomas Cokelaer
- Institut Pasteur - Pole Biomics - 25-28 Rue du Docteur Roux, 75015 Paris, France.,Institut Pasteur - Bioinformatics and Biostatistics Hub - C3BI, USR 3756 IP CNRS - Paris, France
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32
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Manara S, Pasolli E, Dolce D, Ravenni N, Campana S, Armanini F, Asnicar F, Mengoni A, Galli L, Montagnani C, Venturini E, Rota-Stabelli O, Grandi G, Taccetti G, Segata N. Whole-genome epidemiology, characterisation, and phylogenetic reconstruction of Staphylococcus aureus strains in a paediatric hospital. Genome Med 2018; 10:82. [PMID: 30424799 PMCID: PMC6234625 DOI: 10.1186/s13073-018-0593-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 10/29/2018] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Staphylococcus aureus is an opportunistic pathogen and a leading cause of nosocomial infections. It can acquire resistance to all the antibiotics that entered the clinics to date, and the World Health Organization defined it as a high-priority pathogen for research and development of new antibiotics. A deeper understanding of the genetic variability of S. aureus in clinical settings would lead to a better comprehension of its pathogenic potential and improved strategies to contrast its virulence and resistance. However, the number of comprehensive studies addressing clinical cohorts of S. aureus infections by simultaneously looking at the epidemiology, phylogenetic reconstruction, genomic characterisation, and transmission pathways of infective clones is currently low, thus limiting global surveillance and epidemiological monitoring. METHODS We applied whole-genome shotgun sequencing (WGS) to 184 S. aureus isolates from 135 patients treated in different operative units of an Italian paediatric hospital over a timespan of 3 years, including both methicillin-resistant S. aureus (MRSA) and methicillin-sensitive S. aureus (MSSA) from different infection types. We typed known and unknown clones from their genomes by multilocus sequence typing (MLST), Staphylococcal Cassette Chromosome mec (SCCmec), Staphylococcal protein A gene (spa), and Panton-Valentine Leukocidin (PVL), and we inferred their whole-genome phylogeny. We explored the prevalence of virulence and antibiotic resistance genes in our cohort, and the conservation of genes encoding vaccine candidates. We also performed a timed phylogenetic investigation for a potential outbreak of a newly emerging nosocomial clone. RESULTS The phylogeny of the 135 single-patient S. aureus isolates showed a high level of diversity, including 80 different lineages, and co-presence of local, global, livestock-associated, and hypervirulent clones. Five of these clones do not have representative genomes in public databases. Variability in the epidemiology is mirrored by variability in the SCCmec cassettes, with some novel variants of the type IV cassette carrying extra antibiotic resistances. Virulence and resistance genes were unevenly distributed across different clones and infection types, with highly resistant and lowly virulent clones showing strong association with chronic diseases, and highly virulent strains only reported in acute infections. Antigens included in vaccine formulations undergoing clinical trials were conserved at different levels in our cohort, with only a few highly prevalent genes fully conserved, potentially explaining the difficulty of developing a vaccine against S. aureus. We also found a recently diverged ST1-SCCmecIV-t127 PVL- clone suspected to be hospital-specific, but time-resolved integrative phylogenetic analysis refuted this hypothesis and suggested that this quickly emerging lineage was acquired independently by patients. CONCLUSIONS Whole genome sequencing allowed us to study the epidemiology and genomic repertoire of S. aureus in a clinical setting and provided evidence of its often underestimated complexity. Some virulence factors and clones are specific of disease types, but the variability and dispensability of many antigens considered for vaccine development together with the quickly changing epidemiology of S. aureus makes it very challenging to develop full-coverage therapies and vaccines. Expanding WGS-based surveillance of S. aureus to many more hospitals would allow the identification of specific strains representing the main burden of infection and therefore reassessing the efforts for the discovery of new treatments and clinical practices.
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Affiliation(s)
- Serena Manara
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Edoardo Pasolli
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Daniela Dolce
- Cystic Fibrosis Center, Interdisciplinary Specialist Department, Anna Meyer Children's University Hospital, Florence, Italy
| | - Novella Ravenni
- Cystic Fibrosis Center, Interdisciplinary Specialist Department, Anna Meyer Children's University Hospital, Florence, Italy
| | - Silvia Campana
- Cystic Fibrosis Center, Interdisciplinary Specialist Department, Anna Meyer Children's University Hospital, Florence, Italy
| | | | | | - Alessio Mengoni
- Department of Biology, University of Florence, Florence, Italy
| | - Luisa Galli
- Department of Health Sciences, University of Florence, Florence, Italy
- Infectious Diseases Unit, Anna Meyer Children's University Hospital, Florence, Italy
| | - Carlotta Montagnani
- Infectious Diseases Unit, Anna Meyer Children's University Hospital, Florence, Italy
| | - Elisabetta Venturini
- Infectious Diseases Unit, Anna Meyer Children's University Hospital, Florence, Italy
| | - Omar Rota-Stabelli
- Department of Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Guido Grandi
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Giovanni Taccetti
- Cystic Fibrosis Center, Interdisciplinary Specialist Department, Anna Meyer Children's University Hospital, Florence, Italy
| | - Nicola Segata
- Centre for Integrative Biology, University of Trento, Trento, Italy.
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Price JR, Crook DW, Walker AS, Peto TEA, Llewelyn MJ, Paul J. Staphylococcus aureus in critical care - Authors' reply. THE LANCET. INFECTIOUS DISEASES 2018; 17:580-581. [PMID: 28555579 DOI: 10.1016/s1473-3099(17)30269-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 04/27/2017] [Indexed: 10/19/2022]
Affiliation(s)
- James R Price
- Department of Microbiology and Infection, Royal Sussex County Hospital, Brighton, UK.
| | - Derrick W Crook
- Nuffield Department of Clinical Medicine, Experimental Medicine Division, John Radcliffe Hospital, Oxford, UK; National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK; Public Health England, London, UK
| | - A Sarah Walker
- Nuffield Department of Clinical Medicine, Experimental Medicine Division, John Radcliffe Hospital, Oxford, UK; National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Timothy E A Peto
- Nuffield Department of Clinical Medicine, Experimental Medicine Division, John Radcliffe Hospital, Oxford, UK; National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Martin J Llewelyn
- Department of Microbiology and Infection, Royal Sussex County Hospital, Brighton, UK; Division of Medicine, Brighton and Sussex Medical School, Falmer, UK
| | - John Paul
- Department of Microbiology and Infection, Royal Sussex County Hospital, Brighton, UK; Public Health England, Royal Sussex County Hospital, Brighton, UK
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Quantifying the relative effect of environmental contamination on surgical ward MRSA incidence: An exploratory analysis. Infect Dis Health 2018. [DOI: 10.1016/j.idh.2018.02.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Smit PW, Stoesser N, Pol S, van Kleef E, Oonsivilai M, Tan P, Neou L, Turner C, Turner P, Cooper BS. Transmission Dynamics of Hyper-Endemic Multi-Drug Resistant Klebsiella pneumoniae in a Southeast Asian Neonatal Unit: A Longitudinal Study With Whole Genome Sequencing. Front Microbiol 2018; 9:1197. [PMID: 29951041 PMCID: PMC5996243 DOI: 10.3389/fmicb.2018.01197] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Accepted: 05/16/2018] [Indexed: 11/13/2022] Open
Abstract
Background:Klebsiella pneumoniae is an important and increasing cause of life-threatening disease in hospitalized neonates. Third generation cephalosporin resistance (3GC-R) is frequently a marker of multi-drug resistance, and can complicate management of infections. 3GC-R K. pneumoniae is hyper-endemic in many developing country settings, but its epidemiology is poorly understood and prospective studies of endemic transmission are lacking. We aimed to determine the transmission dynamics of 3GC-R K. pneumoniae in a newly opened neonatal unit (NU) in Cambodia and to address the following questions: what is the diversity of 3GC-R K. pneumoniae both within- and between-host; to what extent is high carriage prevalence driven by ward-based transmission; and to what extent can environmental contamination explain patterns of patient acquisition. Methods: We performed a prospective longitudinal study between September and November 2013. Rectal swabs from consented patients were collected upon NU admission and every 3 days thereafter. Morphologically different colonies from swabs growing cefpodoxime-resistant K. pneumoniae were selected for whole-genome sequencing (WGS). Results: One hundred and fifty-eight samples from 37 patients and 7 environmental sites were collected. 32/37 (86%) patients screened positive for 3GC-R K. pneumoniae and 93 colonies from 119 swabs were successfully sequenced. Isolates were resistant to a median of six (range 3-9) antimicrobials. WGS revealed high diversity; pairwise distances between isolates from the same patient were either 0-1 SNV or >1,000 SNVs; 19/32 colonized patients harbored K. pneumoniae colonies differing by >1000 SNVs. Diverse lineages accounted for 18 probable importations to the NU and nine probable transmission clusters involving 19/37 (51%) of screened patients. Median cluster size was five patients (range 3-9). Seven out of 46 environmental swabs (15%) were positive for 3GC-R K. pneumoniae. Environmental sources were plausible sources for acquisitions in 2/9 transmission clusters, though in both cases other patients were also plausible sources. Conclusion: The epidemiology of 3GC-R K. pneumoniae was characterized by multiple introductions, high within- and between host diversity and a dense network of cross-infection, with half of screened neonates part of a transmission cluster. We found no evidence to suggest that environmental contamination was playing a dominant role in transmission.
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Affiliation(s)
- Pieter W Smit
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Headington, United Kingdom.,Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Nicole Stoesser
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital (Level 5), Headington, United Kingdom.,John Radcliffe Hospital Microbiology Laboratory, John Radcliffe Hospital (Level 7), Headington, United Kingdom
| | - Sreymom Pol
- Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Esther van Kleef
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Headington, United Kingdom.,Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Mathupanee Oonsivilai
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Pisey Tan
- Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Leakhena Neou
- Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Claudia Turner
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Headington, United Kingdom.,Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Paul Turner
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Headington, United Kingdom.,Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Ben S Cooper
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Headington, United Kingdom.,Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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Kinross P, Petersen A, Skov R, Van Hauwermeiren E, Pantosti A, Laurent F, Voss A, Kluytmans J, Struelens MJ, Heuer O, Monnet DL. Livestock-associated meticillin-resistant Staphylococcus aureus (MRSA) among human MRSA isolates, European Union/European Economic Area countries, 2013. ACTA ACUST UNITED AC 2018; 22. [PMID: 29113628 PMCID: PMC5710135 DOI: 10.2807/1560-7917.es.2017.22.44.16-00696] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Currently, surveillance of livestock-associated meticillin-resistant Staphylococcus aureus (LA-MRSA) in humans in Europe is not systematic but mainly event-based. In September 2014, the European Centre for Disease Prevention and Control (ECDC) initiated a questionnaire to collect data on the number of LA-MRSA from human samples (one isolate per patient) from national/regional reference laboratories in European Union/European Economic Area (EU/EEA) countries in 2013. Identification of LA-MRSA as clonal complex (CC) 398 by multilocus sequence typing (MLST) was preferred, although surrogate methods such as spa-typing were also accepted. The questionnaire was returned by 28 laboratories in 27 EU/EEA countries. Overall, LA-MRSA represented 3.9% of 13,756 typed MRSA human isolates, but it represented ≥ 10% in five countries (Belgium, Denmark, Spain, the Netherlands and Slovenia). Seven of the reference laboratories did not type MRSA isolates in 2013. To monitor the dispersion of LA-MRSA and facilitate targeted control measures, we advocate periodic systematic surveys or integrated multi-sectorial surveillance.
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Affiliation(s)
- Pete Kinross
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Andreas Petersen
- European Programme for Public Health Microbiology (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden.,Statens Serum Institut, Copenhagen, Denmark
| | | | | | | | - Frédéric Laurent
- International Center for Infectiology Research (CIRI), INSERM, Lyon, France
| | - Andreas Voss
- Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Jan Kluytmans
- University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Marc J Struelens
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Ole Heuer
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Dominique L Monnet
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
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- The members of the group are listed at the end of the article
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A Systematic Review of the Burden of Multidrug-Resistant Healthcare-Associated Infections Among Intensive Care Unit Patients in Southeast Asia: The Rise of Multidrug-Resistant Acinetobacter baumannii. Infect Control Hosp Epidemiol 2018; 39:525-533. [PMID: 29580299 DOI: 10.1017/ice.2018.58] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVETo summarize the clinical burden (cumulative incidence, prevalence, case fatality rate and length of stay) and economic burden (healthcare cost) of healthcare-associated infections (HAIs) due to multidrug-resistant organisms (MDROs) among patients in intensive care units (ICUs) in Southeast Asia.DESIGNSystematic review.METHODSWe conducted a comprehensive literature search in PubMed, EMBASE, CINAHL, EconLit, and the Cochrane Library databases from their inception through September 30, 2016. Clinical and economic burdens and study quality were assessed for each included study.RESULTSIn total, 41 studies met our inclusion criteria; together, 22,876 ICU patients from 7 Southeast Asian countries were included. The cumulative incidence of HAI caused by A. baumannii (AB) in Southeast Asia is substantially higher than has been reported in other regions, especially carbapenem-resistant AB (CRAB; 64.91%) and multidrug-resistant AB (MDR-AB) (58.51%). Evidence of a dose-response relationship between different degrees of drug resistance and excess mortality due to AB infections was observed. Adjusted odds ratios were 1.23 (95% confidence interval [CI], 0.51-3.00) for MDR-AB, 1.72 (95% CI, 0.77-3.80) for extensively drug-resistant AB (XDR-AB), and 1.82 (95% CI, 0.55-6.00) for pandrug-resistant AB (PDR-AB). There is, however, a paucity of published data on additional length of stay and costs attributable to MDROs.CONCLUSIONSThis review highlights the challenges in addressing MDROs in Southeast Asia, where HAIs caused by MDR gram-negative bacteria are abundant and have a strong impact on society. With our findings, we hope to draw the attention of clinicians and policy makers to the problem of antibiotic resistance and to issue a call for action in the management of MDROs.Infect Control Hosp Epidemiol 2018;39:525-533.
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Durand G, Javerliat F, Bes M, Veyrieras JB, Guigon G, Mugnier N, Schicklin S, Kaneko G, Santiago-Allexant E, Bouchiat C, Martins-Simões P, Laurent F, Van Belkum A, Vandenesch F, Tristan A. Routine Whole-Genome Sequencing for Outbreak Investigations of Staphylococcus aureus in a National Reference Center. Front Microbiol 2018; 9:511. [PMID: 29616014 PMCID: PMC5869177 DOI: 10.3389/fmicb.2018.00511] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 03/06/2018] [Indexed: 11/25/2022] Open
Abstract
The French National Reference Center for Staphylococci currently uses DNA arrays and spa typing for the initial epidemiological characterization of Staphylococcus aureus strains. We here describe the use of whole-genome sequencing (WGS) to investigate retrospectively four distinct and virulent S. aureus lineages [clonal complexes (CCs): CC1, CC5, CC8, CC30] involved in hospital and community outbreaks or sporadic infections in France. We used a WGS bioinformatics pipeline based on de novo assembly (reference-free approach), single nucleotide polymorphism analysis, and on the inclusion of epidemiological markers. We examined the phylogeographic diversity of the French dominant hospital-acquired CC8-MRSA (methicillin-resistant S. aureus) Lyon clone through WGS analysis which did not demonstrate evidence of large-scale geographic clustering. We analyzed sporadic cases along with two outbreaks of a CC1-MSSA (methicillin-susceptible S. aureus) clone containing the Panton–Valentine leukocidin (PVL) and results showed that two sporadic cases were closely related. We investigated an outbreak of PVL-positive CC30-MSSA in a school environment and were able to reconstruct the transmission history between eight families. We explored different outbreaks among newborns due to the CC5-MRSA Geraldine clone and we found evidence of an unsuspected link between two otherwise distinct outbreaks. Here, WGS provides the resolving power to disprove transmission events indicated by conventional methods (same sequence type, spa type, toxin profile, and antibiotic resistance profile) and, most importantly, WGS can reveal unsuspected transmission events. Therefore, WGS allows to better describe and understand outbreaks and (inter-)national dissemination of S. aureus lineages. Our findings underscore the importance of adding WGS for (inter-)national surveillance of infections caused by virulent clones of S. aureus but also substantiate the fact that technological optimization at the bioinformatics level is still urgently needed for routine use. However, the greatest limitation of WGS analysis is the completeness and the correctness of the reference database being used and the conversion of floods of data into actionable results. The WGS bioinformatics pipeline (EpiSeqTM) we used here can easily generate a uniform database and associated metadata for epidemiological applications.
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Affiliation(s)
| | | | - Michèle Bes
- National Reference Center for Staphylococci, Hospices Civils de Lyon, Lyon, France
| | | | | | | | | | - Gaël Kaneko
- Data Analytics Unit, bioMérieux, Marcy-I'Étoile, France
| | | | - Coralie Bouchiat
- National Reference Center for Staphylococci, Hospices Civils de Lyon, Lyon, France
| | | | - Frederic Laurent
- National Reference Center for Staphylococci, Hospices Civils de Lyon, Lyon, France
| | | | - François Vandenesch
- National Reference Center for Staphylococci, Hospices Civils de Lyon, Lyon, France
| | - Anne Tristan
- National Reference Center for Staphylococci, Hospices Civils de Lyon, Lyon, France
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Henderson A, Nimmo GR. Control of healthcare- and community-associated MRSA: recent progress and persisting challenges. Br Med Bull 2018; 125:25-41. [PMID: 29190327 DOI: 10.1093/bmb/ldx046] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 10/31/2017] [Indexed: 12/31/2022]
Abstract
BACKGROUND Healthcare adapted meticillin-resistant Staphylococcus aureus (MRSA) has spread to hospitals around the world over 50 years. More recently, other strains of MRSA have emerged with the ability to spread in the community and infect otherwise healthy individuals. Morbidity and mortality associated with MRSA remains high and its control in both the healthcare and community setting has proven challenging. SOURCES OF DATA Pubmed (Medline). AREAS OF AGREEMENT The use of targeted screening and decolonization, hand hygiene and antimicrobial stewardship is supported by the most robust studies, though many studies have implemented bundles for effective healthcare-associated (HA)-MRSA control. AREAS OF CONTENTION Universal screening, universal decolonization and contact precautions for HA-MRSA control are supported by less evidence. Some interventions may not be cost-effective. Contact precautions may be associated with potential for patient harm. Evidence for effective control community acquired (CA)-MRSA is largely lacking. GROWING POINTS Programmes that focus on implementing bundles of interventions aimed at targeting HA-MRSA are more likely to be effective, with an emphasis on hand hygiene as a key component. Control of CA-MRSA is likely to be more difficult to achieve and relies on prevalence, risk factors and community healthcare interactions on a broader scale. AREAS TIMELY FOR DEVELOPING RESEARCH Further research in the area of CA-MRSA in particular is required. Antimicrobial stewardship for both CA and HA-MRSA is promising, as is the role of whole genome sequencing in characterizing transmission. However, further work is required to assess their long-term roles in controlling MRSA. With many institutions applying widespread use of chlorhexidine washes, monitoring for chlorhexidine resistance is paramount to sustaining efforts at controlling MRSA.
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Affiliation(s)
- Andrew Henderson
- Infection Management Services, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia.,School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland 4067, Australia.,University of Queensland Centre for Clinical Research, Herston, Queensland 4029, Australia
| | - Graeme R Nimmo
- Pathology Queensland Central Laboratory, Herston, Queensland 4029, Australia.,School of Medicine, Griffith University, Southport 4222, Queensland, Australia
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Daliri EBM, Wei S, Oh DH, Lee BH. The human microbiome and metabolomics: Current concepts and applications. Crit Rev Food Sci Nutr 2018; 57:3565-3576. [PMID: 27767329 DOI: 10.1080/10408398.2016.1220913] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The mammalian gastrointestinal tract has co-developed with a large number of microbes in a symbiotic relationship over millions of years. Recent studies indicate that indigenous bacteria are intimate with the intestine and play essential roles in health and disease. In the quest to maintain a stable niche, these prokaryotes influence multiple host metabolic pathways, resulting from an interactive host-microbiota metabolic signaling and impacting strongly on the metabolic phenotypes of the host. Since dysbiosis of the gut bacteria result in alteration in the levels of certain microbial and host co-metabolites, identifying these markers could enhance early detection of diseases. Also, identification of these metabolic fingerprints could give us clues as to how to manipulate the microbiome to promote health or treat diseases. This review provides an overview of our current knowledge of the microbiome and metablomics, applications and the future perspectives.
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Affiliation(s)
- Eric Banan-Mwine Daliri
- a Department of Food Science and Biotechnology , Kangwon National University , Chuncheon , South Korea
| | - Shuai Wei
- a Department of Food Science and Biotechnology , Kangwon National University , Chuncheon , South Korea
| | - Deog H Oh
- a Department of Food Science and Biotechnology , Kangwon National University , Chuncheon , South Korea
| | - Byong H Lee
- a Department of Food Science and Biotechnology , Kangwon National University , Chuncheon , South Korea.,b Department of Food Science/Agricultural Chemistry , McGill University , Ste.-Anne-de-Bellevue , Quebec , Canada
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Li T, Huang M, Song Z, Zhang H, Chen C. Biological characteristics and conjugated antigens of ClfA A-FnBPA and CP5 in Staphylococcus aureus. CANADIAN JOURNAL OF VETERINARY RESEARCH = REVUE CANADIENNE DE RECHERCHE VETERINAIRE 2018; 82:48-54. [PMID: 29382968 PMCID: PMC5764038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 02/27/2017] [Indexed: 06/07/2023]
Abstract
To obtain immunogenic conjugate antigens, adipic acid dihydrazide (ADH), as a bridge, and 1-ethyl-3-(3-dimethylaminopropyl) carbodiimidehydrochloride (EDAC), as a coupling agent, were used to conjugate the purified fusion protein, clumping factor A-fibronectin binding protein ClfA A-FnBPA, and type 5 capsular polysaccharide (CP5). The conjugates were mixed with an adjuvant, and mice were immunized 3 times and challenged with Staphylococcus aureus 1 week later. Antibody titers were determined by indirect enzyme-linked immunosorbent assay (ELISA). At 14 days after the first immunization, antibodies against the purified protein and conjugate were detected; after 28 days, antibody levels increased; and a week after the third immunization, antibody levels continued to increase. However, the conjugate antibody titers were higher than those of the purified protein during the study, and no IgG antibodies against purified CP5 were detected during the entire experiment. The protection rate increased to 90% in the conjugate group, indicating that the conjugate imparts a relatively higher protective efficacy than the purified protein and purified CP5.
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Affiliation(s)
| | | | | | | | - Chuangfu Chen
- Address all correspondence to Dr. Chuangfu Chen; telephone: +86-0993-2058002; fax: +86-0993-2058002; e-mail:
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After the deluge: mining Staphylococcus aureus genomic data for clinical associations and host-pathogen interactions. Curr Opin Microbiol 2017; 41:43-50. [PMID: 29197673 DOI: 10.1016/j.mib.2017.11.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 11/04/2017] [Accepted: 11/16/2017] [Indexed: 01/31/2023]
Abstract
The genome of Staphylococcus aureus has rapidly become one the most frequently sequenced among bacteria, with more than 40000 genome sequences uploaded to public databases. Computational resources required for analysis and quality assessment have lagged behind accumulation of sequence data. Improved analytic pipelines, in combination with the development of customized S. aureus reference databases, can be used to inform S. aureus biology and potentially predict clinical outcome. Here, we review the currently available data about S. aureus genome in public databases, and discuss their potential utility for understanding S. aureus evolution. Also discussed are ways to overcome challenges to the application of whole-genome sequencing data for prevention and management of S. aureus disease.
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Toleman MS, Watkins ER, Williams T, Blane B, Sadler B, Harrison EM, Coll F, Parkhill J, Nazareth B, Brown NM, Peacock SJ. Investigation of a Cluster of Sequence Type 22 Methicillin-Resistant Staphylococcus aureus Transmission in a Community Setting. Clin Infect Dis 2017; 65:2069-2077. [PMID: 29077854 PMCID: PMC5850418 DOI: 10.1093/cid/cix539] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Whole-genome sequencing (WGS) has typically been used to confirm or refute hospital/ward outbreaks of methicillin-resistant Staphylococcus aureus (MRSA) identified through routine practice. However, appropriately targeted WGS strategies that identify routinely "undetectable" transmission remain the ultimate aim. METHODS WGS of MRSA isolates sent to a regional microbiological laboratory was performed as part of a 12-month prospective observational study. Phylogenetic analyses identified a genetically related cluster of E-MRSA15 isolated from patients registered to the same general practice (GP) surgery. This led to an investigation to identify epidemiological links, find additional cases, and determine potential for ongoing transmission. RESULTS We identified 15 MRSA-positive individuals with 27 highly related MRSA isolates who were linked to the GP surgery, 2 of whom died with MRSA bacteremia. Of the 13 cases that were further investigated, 11 had attended a leg ulcer/podiatry clinic. Cases lacked epidemiological links to hospitals, suggesting that transmission occurred elsewhere. Environmental and staff screening at the GP surgery did not identify an ongoing source of infection. CONCLUSIONS Surveillance in the United Kingdom shows that the proportion of MRSA bacteremias apportioned to hospitals is decreasing, suggesting the need for greater focus on the detection of MRSA outbreaks and transmission in the community. This case study confirms that the typically nosocomial lineage (E-MRSA15) can transmit within community settings. Our study exemplifies the continued importance of WGS in detecting outbreaks, including those which may be missed by routine practice, and suggests that universal WGS of bacteremia isolates may help detect outbreaks in low-surveillance settings.
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Affiliation(s)
- Michelle S Toleman
- University of Cambridge
- Wellcome Trust Sanger Institute, Hinxton
- Cambridge University Hospitals NHS Foundation Trust
| | | | | | | | - Belinda Sadler
- Infection Prevention and Control, Cambridgeshire and Peterborough Clinical Commissioning Group
| | | | | | | | | | - Nicholas M Brown
- Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, United Kingdom
| | - Sharon J Peacock
- University of Cambridge
- Wellcome Trust Sanger Institute, Hinxton
- Cambridge University Hospitals NHS Foundation Trust
- London School of Hygiene and Tropical Medicine
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Stanczak-Mrozek KI, Laing KG, Lindsay JA. Resistance gene transfer: induction of transducing phage by sub-inhibitory concentrations of antimicrobials is not correlated to induction of lytic phage. J Antimicrob Chemother 2017; 72:1624-1631. [PMID: 28369562 PMCID: PMC5437526 DOI: 10.1093/jac/dkx056] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 02/01/2017] [Indexed: 12/22/2022] Open
Abstract
Objectives: Horizontal gene transfer of antimicrobial resistance (AMR) genes between clinical isolates via transduction is poorly understood. MRSA are opportunistic pathogens resistant to all classes of antimicrobial agents but currently no strains are fully drug resistant. AMR gene transfer between Staphylococcus aureus isolates is predominantly due to generalized transduction via endogenous bacteriophage, and recent studies have suggested transfer is elevated during host colonization. The aim was to investigate whether exposure to sub-MIC concentrations of antimicrobials triggers bacteriophage induction and/or increased efficiency of AMR gene transfer. Methods: Isolates from MRSA carriers were exposed to nine antimicrobials and supernatants were compared for lytic phage particles and ability to transfer an AMR gene. A new technology, droplet digital PCR, was used to measure the concentration of genes in phage particles. Results: All antibiotics tested induced lytic phage and AMR gene transduction, although the ratio of transducing particles to lytic particles differed substantially for each antibiotic. Mupirocin induced the highest ratio of transducing versus lytic particles. Gentamicin and novobiocin reduced UV-induced AMR transduction. The genes carried in phage particles correlated with AMR transfer or lytic particle activity, suggesting antimicrobials influence which DNA sequences are packaged into phage particles. Conclusions: Sub-inhibitory antibiotics induce AMR gene transfer between clinical MRSA, while combination therapy with an inhibiting antibiotic could potentially alter AMR gene packaging into phage particles, reducing AMR transfer. In a continually evolving environment, pathogens have an advantage if they can transfer DNA while lowering the risk of lytic death.
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Affiliation(s)
- Kinga I Stanczak-Mrozek
- Institute for Infection and Immunity, St George's, University of London, Cranmer Terrace, London SW17 0RE, UK
| | - Ken G Laing
- Institute for Infection and Immunity, St George's, University of London, Cranmer Terrace, London SW17 0RE, UK
| | - Jodi A Lindsay
- Institute for Infection and Immunity, St George's, University of London, Cranmer Terrace, London SW17 0RE, UK
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45
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Coll F, Harrison EM, Toleman MS, Reuter S, Raven KE, Blane B, Palmer B, Kappeler ARM, Brown NM, Török ME, Parkhill J, Peacock SJ. Longitudinal genomic surveillance of MRSA in the UK reveals transmission patterns in hospitals and the community. Sci Transl Med 2017; 9:eaak9745. [PMID: 29070701 PMCID: PMC5683347 DOI: 10.1126/scitranslmed.aak9745] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 03/24/2017] [Accepted: 07/10/2017] [Indexed: 12/15/2022]
Abstract
Genome sequencing has provided snapshots of the transmission of methicillin-resistant Staphylococcus aureus (MRSA) during suspected outbreaks in isolated hospital wards. Scale-up to populations is now required to establish the full potential of this technology for surveillance. We prospectively identified all individuals over a 12-month period who had at least one MRSA-positive sample processed by a routine diagnostic microbiology laboratory in the East of England, which received samples from three hospitals and 75 general practitioner (GP) practices. We sequenced at least 1 MRSA isolate from 1465 individuals (2282 MRSA isolates) and recorded epidemiological data. An integrated epidemiological and phylogenetic analysis revealed 173 transmission clusters containing between 2 and 44 cases and involving 598 people (40.8%). Of these, 118 clusters (371 people) involved hospital contacts alone, 27 clusters (72 people) involved community contacts alone, and 28 clusters (157 people) had both types of contact. Community- and hospital-associated MRSA lineages were equally capable of transmission in the community, with instances of spread in households, long-term care facilities, and GP practices. Our study provides a comprehensive picture of MRSA transmission in a sampled population of 1465 people and suggests the need to review existing infection control policy and practice.
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Affiliation(s)
- Francesc Coll
- London School of Hygiene and Tropical Medicine, London, UK.
| | | | - Michelle S Toleman
- University of Cambridge, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Wellcome Trust Sanger Institute, Cambridge, UK
| | | | | | | | | | - A Ruth M Kappeler
- Public Health England, London, UK
- Papworth Hospital NHS Foundation Trust, Cambridge, UK
| | - Nicholas M Brown
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Public Health England, London, UK
| | - M Estée Török
- University of Cambridge, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Sharon J Peacock
- London School of Hygiene and Tropical Medicine, London, UK.
- University of Cambridge, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Wellcome Trust Sanger Institute, Cambridge, UK
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46
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Shankar N, Chow ALP, Oon J, Hsu LY, Ang B, Pang J, De Sessions PF, Periaswamy B, Tambyah PA, Teo DB, Tam CC. The epidemiology and transmission of methicillin-resistant Staphylococcus aureus in the community in Singapore: study protocol for a longitudinal household study. BMC Infect Dis 2017; 17:678. [PMID: 29020940 PMCID: PMC5637086 DOI: 10.1186/s12879-017-2793-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 10/04/2017] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND/AIM Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most common multidrug-resistant organisms in healthcare settings worldwide, but little is known about MRSA transmission outside of acute healthcare settings especially in Asia. We describe the methods for a prospective longitudinal study of MRSA prevalence and transmission. METHODS MRSA-colonized individuals were identified from MRSA admission screening at two tertiary hospitals and recruited together with their household contacts. Participants submitted self-collected nasal, axilla and groin (NAG) swabs by mail for MRSA culture at baseline and monthly thereafter for 6 months. A comparison group of households of MRSA-negative patients provided swab samples at one time point. In a validation sub-study, separate swabs from each site were collected from randomly selected individuals, to compare MRSA detection rates between swab sites, and between samples collected by participants versus those collected by trained research staff. Information on each participant's demographic information, medical status and medical history, past healthcare facilities usage and contacts, and personal interactions with others were collected using a self-administered questionnaire. DISCUSSION/CONCLUSION Understanding the dynamics of MRSA persistence and transmission in the community is crucial to devising and evaluating successful MRSA control strategies. Close contact with MRSA colonized patients may to be important for MRSA persistence in the community; evidence from this study on the extent of community MRSA could inform the development of household- or community-based interventions to reduce MRSA colonization of close contacts and subsequent re-introduction of MRSA into healthcare settings. Analysis of longitudinal data using whole-genome sequencing will yield further information regarding MRSA transmission within households, with significant implications for MRSA infection control outside acute hospital settings.
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Affiliation(s)
- Nivedita Shankar
- Saw Swee Hock School of Public Health, Tahir Foundation Building, 12 Science Drive 2, 11-01, Singapore, 117549, Singapore.
| | | | - Jolene Oon
- National University Hospital, Singapore, Singapore
| | - Li Yang Hsu
- Saw Swee Hock School of Public Health, Tahir Foundation Building, 12 Science Drive 2, 11-01, Singapore, 117549, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
| | - Brenda Ang
- Tan Tock Seng Hospital, Singapore, Singapore
| | - Junxiong Pang
- Saw Swee Hock School of Public Health, Tahir Foundation Building, 12 Science Drive 2, 11-01, Singapore, 117549, Singapore
| | | | | | | | | | - Clarence C Tam
- Saw Swee Hock School of Public Health, Tahir Foundation Building, 12 Science Drive 2, 11-01, Singapore, 117549, Singapore
- London School of Hygiene and Tropical Medicine, London, UK
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47
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Harkins CP, Pettigrew KA, Oravcová K, Gardner J, Hearn RMR, Rice D, Mather AE, Parkhill J, Brown SJ, Proby CM, Holden MTG. The Microevolution and Epidemiology of Staphylococcus aureus Colonization during Atopic Eczema Disease Flare. J Invest Dermatol 2017; 138:336-343. [PMID: 28951239 PMCID: PMC5780352 DOI: 10.1016/j.jid.2017.09.023] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 08/11/2017] [Accepted: 09/12/2017] [Indexed: 01/24/2023]
Abstract
Staphylococcus aureus is an opportunistic pathogen and variable component of the human microbiota. A characteristic of atopic eczema (AE) is colonization by S. aureus, with exacerbations associated with an increased bacterial burden of the organism. Despite this, the origins and genetic diversity of S. aureus colonizing individual patients during AE disease flares is poorly understood. To examine the microevolution of S. aureus colonization, we deep sequenced S. aureus populations from nine children with moderate to severe AE and 18 non-atopic children asymptomatically carrying S. aureus nasally. Colonization by clonal S. aureus populations was observed in both AE patients and control participants, with all but one of the individuals carrying colonies belonging to a single sequence type. Phylogenetic analysis showed that disease flares were associated with the clonal expansion of the S. aureus population, occurring over a period of weeks to months. There was a significant difference in the genetic backgrounds of S. aureus colonizing AE cases versus controls (Fisher exact test, P = 0.03). Examination of intra-host genetic heterogeneity of the colonizing S. aureus populations identified evidence of within-host selection in the AE patients, with AE variants being potentially selectively advantageous for intracellular persistence and treatment resistance.
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Affiliation(s)
- Catriona P Harkins
- School of Medicine, University of St Andrews, St Andrews, UK; Department of Dermatology, Ninewells Hospital, Dundee, UK; School of Medicine, University of Dundee, Dundee, UK.
| | | | - Katarina Oravcová
- School of Medicine, University of St Andrews, St Andrews, UK; Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - June Gardner
- Department of Dermatology, Ninewells Hospital, Dundee, UK
| | - R M Ross Hearn
- Department of Dermatology, Ninewells Hospital, Dundee, UK
| | - Debbie Rice
- Scottish Children's Research Network, MACH 2 Building, Level 5, Ninewells Hospital, Dundee, UK
| | - Alison E Mather
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Julian Parkhill
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Sara J Brown
- Department of Dermatology, Ninewells Hospital, Dundee, UK; Skin Research Group, Division of Cancer Research, School of Medicine, University of Dundee, UK
| | - Charlotte M Proby
- Department of Dermatology, Ninewells Hospital, Dundee, UK; School of Medicine, University of Dundee, Dundee, UK
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Vali L, Dashti AA, Mathew F, Udo EE. Characterization of Heterogeneous MRSA and MSSA with Reduced Susceptibility to Chlorhexidine in Kuwaiti Hospitals. Front Microbiol 2017; 8:1359. [PMID: 28775716 PMCID: PMC5517409 DOI: 10.3389/fmicb.2017.01359] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 07/04/2017] [Indexed: 11/20/2022] Open
Abstract
The objective of this investigation was to identify the lineages of MRSA and MSSA with reduced susceptibility to chlorhexidine in Kuwaiti hospitals. 121 clinical MRSA and 56 MSSA isolates were included in this study. Antimicrobial susceptibility testing was performed for a selection of agents including chlorhexidine and resistance genes were amplified and sequenced. PFGE, spa typing, and MLST were completed for a selection of isolates. The results showed SCCmec II, III, IV, and V were present in 0.8, 21.5, 69.4, and 8.3% of the MRSA isolates. agr-1Sa was the most prevalent type in both MSSA (48%) and MRSA (54%). Forty-five percentage of MRSA contained pvl and 39% contained lukE-lukD, however, as many as 86% of MSSA contained pvl and 96.4% contained lukE-lukD. qac A-C genes were identified in 12.3% of MRSA, norA was present in 82.6% and blaZ in 94.2%. Among MSSA only 5.4% harbored qacA, 83% contained norA, and 91% blaZ. Multi-drug resistant ST239/t945 lineage containing a qac gene was the most identified S. aureus. However, other lineages, including ST772-MRSA-V/t4867/pvl(+)qacC/smr and non-qac harboring lineages of ST217-MRSAIV/t3244/pvl(-), ST34-MSSA/t161/pvl(+), ST5-MSSA/t688/pvl(+), ST5-MSSA/t4867/norA(+), and ST672-MSSA/t003/pvl(-), also showed reduced susceptibility to chlorhexidine. The observed reduced susceptibility of non-qac dependent MSSA isolates to chlorhexidine suggests the involvement of other elements in promoting higher MBC (≥30 mg/L). Our results confirm that monitoring MSSA is essential as they may have the potential to survive low level biocide exposure.
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Affiliation(s)
- Leila Vali
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, Kuwait UniversitySulaibekhat, Kuwait
| | - Ali A. Dashti
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, Kuwait UniversitySulaibekhat, Kuwait
| | - Febine Mathew
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, Kuwait UniversitySulaibekhat, Kuwait
| | - Edet E. Udo
- Department of Medical Microbiology, Faculty of Medicine, Kuwait UniversitySulaibekhat, Kuwait
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49
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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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50
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Chow A, Lim VW, Khan A, Pettigrew K, Lye DCB, Kanagasabai K, Phua K, Krishnan P, Ang B, Marimuthu K, Hon PY, Koh J, Leong I, Parkhill J, Hsu LY, Holden MTG. MRSA Transmission Dynamics Among Interconnected Acute, Intermediate-Term, and Long-Term Healthcare Facilities in Singapore. Clin Infect Dis 2017; 64:S76-S81. [PMID: 28475785 PMCID: PMC5849126 DOI: 10.1093/cid/cix072] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Methicillin-resistant Staphylococcus aureus (MRSA) is the most common healthcare-associated multidrug-resistant organism. Despite the interconnectedness between acute care hospitals (ACHs) and intermediate- and long-term care facilities (ILTCFs), the transmission dynamics of MRSA between healthcare settings is not well understood. METHODS We conducted a cross-sectional study in a network comprising an ACH and 5 closely affiliated ILTCFs in Singapore. A total of 1700 inpatients were screened for MRSA over a 6-week period in 2014. MRSA isolates underwent whole-genome sequencing, with a pairwise single-nucleotide polymorphism (Hamming distance) cutoff of 60 core genome single-nucleotide polymorphisms used to define recent transmission clusters (clades) for the 3 major clones. RESULTS MRSA prevalence was significantly higher in intermediate-term (29.9%) and long-term (20.4%) care facilities than in the ACH (11.8%) (P < .001). The predominant clones were sequence type [ST] 22 (n = 183; 47.8%), ST45 (n = 129; 33.7%), and ST239 (n = 26; 6.8%), with greater diversity of STs in ILTCFs relative to the ACH. A large proportion of the clades in ST22 (14 of 21 clades; 67%) and ST45 (7 of 13; 54%) included inpatients from the ACH and ILTCFs. The most frequent source of the interfacility transmissions was the ACH (n = 28 transmission events; 36.4%). CONCLUSIONS MRSA transmission dynamics between the ACH and ILTCFs were complex. The greater diversity of STs in ILTCFs suggests that the ecosystem in such settings might be more conducive for intrafacility transmission events. ST22 and ST45 have successfully established themselves in ILTCFs. The importance of interconnected infection prevention and control measures and strategies cannot be overemphasized.
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Affiliation(s)
- Angela Chow
- Departments of Clinical Epidemiology and
- Saw Swee Hock School of Public Health and
| | | | - Ateeb Khan
- School of Medicine, University of St Andrews, Fife, and
| | | | - David C B Lye
- Infectious Diseases, Institute of Infectious Diseases and Epidemiology, and Departments of
- Yong Loo Lin School of Medicine, National University of Singapore
| | | | - Kelvin Phua
- Ang Mo Kio-Thye Hua Kwan Hospital, Singapore
| | | | - Brenda Ang
- Infectious Diseases, Institute of Infectious Diseases and Epidemiology, and Departments of
- Yong Loo Lin School of Medicine, National University of Singapore
| | - Kalisvar Marimuthu
- Infectious Diseases, Institute of Infectious Diseases and Epidemiology, and Departments of
- Yong Loo Lin School of Medicine, National University of Singapore
| | | | - Jocelyn Koh
- Ang Mo Kio-Thye Hua Kwan Hospital, Singapore
| | - Ian Leong
- Continuing and Community Care, Tan Tock Seng Hospital
| | - Julian Parkhill
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Li-Yang Hsu
- Infectious Diseases, Institute of Infectious Diseases and Epidemiology, and Departments of
- Saw Swee Hock School of Public Health and
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