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Bellis KL, Dissanayake OM, Harrison EM, Aggarwal D. Community methicillin-resistant Staphylococcus aureus outbreaks in areas of low prevalence. Clin Microbiol Infect 2024:S1198-743X(24)00286-6. [PMID: 38897351 DOI: 10.1016/j.cmi.2024.06.006] [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: 01/31/2024] [Revised: 05/21/2024] [Accepted: 06/10/2024] [Indexed: 06/21/2024]
Abstract
BACKGROUND Community-acquired (CA), community-onset methicillin-resistant Staphylococcus aureus (CO-MRSA) infection presents a significant public health challenge, even where MRSA rates are historically lower. Despite successes in reducing hospital-onset MRSA, CO-MRSA rates are increasing globally, with a need to understand this trend, and the potential risk factors for re-emergence. OBJECTIVES This review aims to explore the characteristics of outbreaks of community-acquired community-onset methicillin-resistant Staphylococcus aureus in low-prevalence areas, to understand the factors involved in its rise, and to translate this knowledge into public health policy and further research needs. SOURCES PubMed, EMBASE, and Google Scholar were searched using combinations of the terms 'transmission', 'acquisition', 'community-acquired', 'MRSA', 'CA-MRSA', 'low prevalence', 'genomic', 'outbreak', 'colonisation', and 'carriage'. Wherever evidence was limited, additional articles were sought specifically, via PubMed searches. Papers where materials were not available in English were excluded. CONTENT Challenges in defining low-prevalence areas and the significance of exposure to various risk factors for community acquisition, such as healthcare settings, travel, livestock, and environmental factors, are discussed. The importance of genomic surveillance in identifying outbreak strains and understanding the transmission dynamics is highlighted, along with the need for robust public health policies and control measures. IMPLICATIONS The findings emphasise the complexity of CO-MRSA transmission and the necessity of a multifaceted approach in low-prevalence areas. This includes integrated and systematic surveillance of hospital-onset-, CO-, and livestock-associated MRSA, as has been effective in some Northern European countries. The evolution of CO-MRSA underscores the need for global collaboration, routine genomic surveillance, and comprehensive antimicrobial stewardship to mitigate the rise of CO-MRSA and address the broader challenge of antimicrobial resistance. These efforts are crucial for maintaining low MRSA prevalence and managing the increasing burden of CO-MRSA in both low and higher prevalence regions.
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Affiliation(s)
- Katherine L Bellis
- Department of Medicine, University of Cambridge, Hills Rd, Cambridge, UK; Wellcome Sanger Institute, Parasites and Microbes, Hinxton, Saffron Walden, UK
| | - Oshani M Dissanayake
- University College London, Global Business School for Health, Gower St, London, UK
| | - Ewan M Harrison
- Department of Medicine, University of Cambridge, Hills Rd, Cambridge, UK; Wellcome Sanger Institute, Parasites and Microbes, Hinxton, Saffron Walden, UK
| | - Dinesh Aggarwal
- Department of Medicine, University of Cambridge, Hills Rd, Cambridge, UK; Wellcome Sanger Institute, Parasites and Microbes, Hinxton, Saffron Walden, UK; Department of Medicine, Cambridge University Hospital NHS Foundation Trust, Hills Rd, Cambridge, UK.
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Silvola J, Gröndahl-Yli-Hannuksela K, Hirvioja T, Rantakokko-Jalava K, Rintala E, Auranen K, Junnila J, Marttila H, Lindholm L, Vuopio J. Whole genome sequencing reveals new links between spa t172/CC59 methicillin-resistant Staphylococcus aureus cases in low-endemicity region of Southwest Finland, 2007‒2016. Sci Rep 2022; 12:21326. [PMID: 36494398 PMCID: PMC9734107 DOI: 10.1038/s41598-022-25556-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) rates have remained relatively low in Finland. In Southwest Finland, however, annual MRSA incidence increased from 12 to 25/100,000 between 2007 and 2016 with spa t172 strain causing one fourth (237/983) of all cases. This provoked us to study the molecular epidemiology of t172-MRSA, aiming to better understand the transmission of this strain type. We combined epidemiological data and whole genome sequencing (WGS) of a set of 64 (27%, 64/237) t172-MRSA isolates covering 10 years. Isolates represented sporadic and index cases of all identified healthcare-associated outbreaks (HAOs) and family clusters (FCs). Among the included 62 isolates, core-genome MLST analysis revealed eight genomic clusters comprising 24 (38.7%) isolates and 38 (61.3%) non-clustered isolates. Cluster 1 comprised ten and the remaining seven clusters two isolates each, respectively. Two epidemiologically distinct HAOs were linked in cluster 1. FCs were involved in all clusters. All strains were associated with epidemic clonal complex CC59. We were able to confirm the spread of several successful t172-MRSA subclones in regional healthcare and the community. WGS complemented routine surveillance by revealing undetected links between t172-MRSA cases. Targeted, WGS-based typing could enhance MRSA surveillance without the need for routine WGS diagnostics.
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Affiliation(s)
- Jaakko Silvola
- grid.1374.10000 0001 2097 1371Institute of Biomedicine, University of Turku, Turku, Finland
| | | | - Tiina Hirvioja
- grid.410552.70000 0004 0628 215XDepartment of Hospital Hygiene & Infection Control, Turku University Hospital, Turku, Finland
| | - Kaisu Rantakokko-Jalava
- grid.410552.70000 0004 0628 215XClinical Microbiology Laboratory, Turku University Hospital, Turku, Finland
| | - Esa Rintala
- grid.410552.70000 0004 0628 215XDepartment of Hospital Hygiene & Infection Control, Turku University Hospital, Turku, Finland
| | - Kari Auranen
- grid.1374.10000 0001 2097 1371Department of Mathematics and Statistics and Department of Clinical Medicine, University of Turku, Turku, Finland
| | - Jenna Junnila
- grid.1374.10000 0001 2097 1371Institute of Biomedicine, University of Turku, Turku, Finland
| | - Harri Marttila
- grid.410552.70000 0004 0628 215XDepartment of Hospital Hygiene & Infection Control, Turku University Hospital, Turku, Finland
| | - Laura Lindholm
- grid.14758.3f0000 0001 1013 0499Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Jaana Vuopio
- grid.1374.10000 0001 2097 1371Institute of Biomedicine, University of Turku, Turku, Finland ,grid.410552.70000 0004 0628 215XClinical Microbiology Laboratory, Turku University Hospital, Turku, Finland ,grid.14758.3f0000 0001 1013 0499Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
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3
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Zuo H, Uehara Y, Lu Y, Sasaki T, Hiramatsu K. Genetic and phenotypic diversity of methicillin-resistant Staphylococcus aureus among Japanese inpatients in the early 1980s. Sci Rep 2021; 11:5447. [PMID: 33686133 PMCID: PMC7940613 DOI: 10.1038/s41598-021-84481-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 02/16/2021] [Indexed: 01/02/2023] Open
Abstract
To trace the linkage between Japanese healthcare-associated methicillin-resistant Staphylococcus aureus (HA-MRSA) strains in the early 1980s and the 2000s onward, we performed molecular characterizations using mainly whole-genome sequencing. Among the 194 S. aureus strains isolated, 20 mecA-positive MRSA (10.3%), 8 mecA-negative MRSA (4.1%) and 3 mecA-positive methicillin-susceptible S. aureus (MSSA) (1.5%) strains were identified. The most frequent sequence type (ST) was ST30 (n = 11), followed by ST5 (n = 8), ST81 (n = 4), and ST247 (n = 3). Rates of staphylococcal cassette chromosome mec (SCCmec) types I, II, and IV composed 65.2%, 13.0%, and 17.4% of isolates, respectively. Notably, 73.3% of SCCmec type I strains were susceptible to imipenem unlike SCCmec type II strains (0%). ST30-SCCmec I (n = 7) and ST5-SCCmec I (n = 5) predominated, whereas only two strains exhibited imipenem-resistance and were tst-positive ST5-SCCmec II, which is the current Japanese HA-MRSA genotype. All ST30 strains shared the common ancestor strain 55/2053, which caused the global pandemic of Panton-Valentine leukocidin-positive MSSA in Europe and the United States in the 1950s. Conspicuously more heterogeneous, the population of HA-MRSA clones observed in the 1980s, including the ST30-SCCmec I clone, has shifted to the current homogeneous population of imipenem-resistant ST5-SCCmec II clones, probably due to the introduction of new antimicrobials.
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Affiliation(s)
- Hui Zuo
- Department of Microbiology, Juntendo University Faculty of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Yuki Uehara
- Department of Microbiology, Juntendo University Faculty of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan.
- Department of Clinical Laboratory, St Luke's International Hospital, Tokyo, Japan.
- Department of Infectious Diseases, St Luke's International Hospital, Tokyo, Japan.
- Center for Infection Control Science Research, Juntendo University Graduate School of Medicine, Tokyo, Japan.
| | - Yujie Lu
- Center for Infection Control Science Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Takashi Sasaki
- Center for Infection Control Science Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Animal Research Center, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Keiichi Hiramatsu
- Department of Microbiology, Juntendo University Faculty of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
- Center for Infection Control Science Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
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4
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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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Ikeuchi K, Adachi E, Sasaki T, Suzuki M, Lim LA, Saito M, Koga M, Tsutsumi T, Kido Y, Uehara Y, Yotsuyanagi H. An Outbreak of USA300 Methicillin-Resistant Staphylococcus aureus Among People With HIV in Japan. J Infect Dis 2020; 223:610-620. [PMID: 33057717 DOI: 10.1093/infdis/jiaa651] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 10/09/2020] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND USA300 produces Panton-Valentin leucocidin (PVL) and is known as a predominant community-associated methicillin-resistant Staphylococcus aureus (MRSA) strain in the United States, but it was extremely rare in Japan. We report here an outbreak of USA300 in people with HIV (PWH) in Tokyo, Japan. METHODS We analyzed the cases of PVL-MRSA infection between 2010 and 2020 and screened for nasal colonization of PVL-MRSA in PWH who visited an HIV/AIDS referral hospital from December 2019 to March 2020. Whole-genome sequencing-based single nucleotide polymorphism (SNP) analysis was performed on these isolates. RESULTS During the study period, a total of 21 PVL-MRSA infections in 14 patients were identified after 2014. The carriage prevalence was 4.3% (12/277) and PVL-MRSA carriers were more likely to have sexually transmitted infections (STIs) within a year compared with patients who had neither a history of PVL-MRSA infection nor colonization (33.3% [4/12] vs 10.1% [26/258]; P = .03). SNP analysis showed that all 26 isolates were ST8-SCCmecIVa-USA300. Twenty-four isolates were closely related (≤100 SNP differences) and had the nonsynonymous SNPs associated with carbohydrate metabolism and antimicrobial tolerance. CONCLUSIONS An outbreak of USA300 has been occurring among PWH in Tokyo and a history of STI was a risk of colonization.
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Affiliation(s)
- Kazuhiko Ikeuchi
- IMSUT Hospital, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Eisuke Adachi
- IMSUT Hospital, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Takashi Sasaki
- Animal Research Center, Sapporo Medical University School of Medicine, Sapporo City, Hokkaido, Japan
| | - Masato Suzuki
- IMSUT Hospital, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Lay Ahyoung Lim
- IMSUT Hospital, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Makoto Saito
- IMSUT Hospital, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Michiko Koga
- IMSUT Hospital, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Takeya Tsutsumi
- IMSUT Hospital, The University of Tokyo, Minato-ku, Tokyo, Japan
| | | | - Yuki Uehara
- St Luke's International Hospital, Chuo-ku, Tokyo, Japan
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6
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Tsujiwaki A, Hisata K, Tohyama Y, Matsunaga N, Uehara Y, Sasaki T, Hiramatsu K, Shimizu T. Epidemiology of methicillin-resistant Staphylococcus aureus in a Japanese neonatal intensive care unit. Pediatr Int 2020; 62:911-919. [PMID: 32215993 DOI: 10.1111/ped.14241] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 03/17/2020] [Accepted: 03/19/2020] [Indexed: 11/30/2022]
Abstract
BACKGROUND There have been few reports on the genetic structure of the current population of methicillin-resistant Staphylococcus aureus (MRSA) from neonatal intensive care units (NICUs) in Japan. In the present study we conducted a molecular epidemiological analysis based on whole genome sequencing against MRSA strains in a Japanese NICU. METHODS We performed genotyping by whole genome sequencing, polymerase chain reaction-based typing of Staphylococcal cassette chromosome mec (SCCmec) and polymerase chain reaction-based open-reading frame typing against 57 MRSA strains from fecal or nasal specimens from NICU patients in Juntendo University Shizuoka Hospital in 2013-2014. RESULTS Forty-nine MRSA strains (86.0%) exhibited a clonal complex (CC) 1, and were divided into three sequence types (STs): ST2725 (n = 25), ST2764 (n = 21), and ST1 (n = 3). All CC1 MRSA strains had SCCmec IVa, and were resistant to new quinolones, which are limited in pediatric use, suggesting that these strains were derived from adult MRSA clones. Single nucleotide polymorphism differences of both ≤10 and >100 nucleotides were observed by pairwise, single nucleotide polymorphism analysis among ST2725 and ST2764 MRSA strains, respectively. Seven ST8 MRSA strains (12.2%) were isolated, and no strain exhibiting the Japanese hospital-associated MRSA genotype (ST5/SCCmec II) was isolated in this study. CONCLUSIONS Our molecular epidemiological analysis suggested that ST2725 and ST2764 MRSA strains had genetic diversity that could not be explained only by a recent transmission event in the NICU. These MRSA clones might be disseminated in other Japanese hospital facilities as new endemic clones. Our results are expected to contribute to the improvement of infection control measures of MRSA in NICUs.
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Affiliation(s)
- Atsushi Tsujiwaki
- Department of Pediatrics and Adolescent Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Ken Hisata
- Department of Pediatrics and Adolescent Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yudai Tohyama
- Department of Pediatrics and Adolescent Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Nobuaki Matsunaga
- Department of Pediatrics and Adolescent Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yuki Uehara
- Department of Infection Control Science, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Takashi Sasaki
- Department of Infection Control Science, Juntendo University Graduate School of Medicine, Tokyo, Japan.,Animal Research Center, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Keiichi Hiramatsu
- Department of Infection Control Science, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Toshiaki Shimizu
- Department of Pediatrics and Adolescent Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
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Yuan DH, Xing JF, Luan MW, Ji KK, Guo J, Xie SQ, Zhang YM. DNA N6-Methyladenine Modification in Wild and Cultivated Soybeans Reveals Different Patterns in Nucleus and Cytoplasm. Front Genet 2020; 11:736. [PMID: 32849778 PMCID: PMC7398112 DOI: 10.3389/fgene.2020.00736] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 06/18/2020] [Indexed: 01/16/2023] Open
Abstract
DNA 6mA modification, an important newly discovered epigenetic mark, plays a crucial role in organisms and has been attracting more and more attention in recent years. The soybean is economically the most important bean in the world, providing vegetable protein for millions of people. However, the distribution pattern and function of 6mA in soybean are still unknown. In this study, we decoded 6mA modification to single-nucleotide resolution in wild and cultivated soybeans, and compared the 6mA differences between cytoplasmic and nuclear genomes and between wild and cultivated soybeans. The motif of 6mA in the nuclear genome was conserved across the two kinds of soybeans, and ANHGA was the most dominant motif in wild and cultivated soybeans. Genes with 6mA modification in the nucleus had higher expression than those without modification. Interestingly, 6mA distribution patterns in cytoplasm for each soybean were significantly different from those in nucleus, which was reported for the first time in soybean. Our research provides a new insight in the deep analysis of cytoplasmic genomic DNA modification in plants.
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Affiliation(s)
- De-Hui Yuan
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jian-Feng Xing
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Hainan University, Haikou, China
| | - Mei-Wei Luan
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Hainan University, Haikou, China
| | - Kai-Kai Ji
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Hainan University, Haikou, China
| | - Jun Guo
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Hainan University, Haikou, China
| | - Shang-Qian Xie
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Hainan University, Haikou, China
| | - Yuan-Ming Zhang
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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8
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Ma X, Li Y, Liang Y, Liu Y, Yu L, Li C, Liu Q, Chen L. Development of a DNA microarray assay for rapid detection of fifteen bacterial pathogens in pneumonia. BMC Microbiol 2020; 20:177. [PMID: 32576241 PMCID: PMC7310556 DOI: 10.1186/s12866-020-01842-3] [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: 02/11/2020] [Accepted: 06/03/2020] [Indexed: 01/25/2023] Open
Abstract
Background The rapid identification of pathogenic bacteria is important for determining an appropriate antimicrobial therapy for pneumonia, but traditional bacterial culture is time-consuming and labourious. The aim of this study was to develop and evaluate a DNA microarray assay for the simultaneous detection of fifteen bacterial species directly from respiratory tract specimens in patients with pneumonia. These species included Streptococcus pneumoniae, Staphylococcus aureus, Haemophilus influenzae, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii, Mycoplasma pneumoniae, Enterococcus faecalis, Enterococcus faecium, Enterobacter cloacae, Stenotrophomonas maltophilia, Burkholderia cepacia, Legionella pneumophila and Chlamydia pneumoniae. The 16S rDNA genes and other specific genes of each pathogen were chosen as the amplification targets, amplified via multiplex polymerase chain reaction (PCR), and hybridized to oligonucleotide probes in a microarray. Results The DNA microarray detection limit was 103 copies/μL. Nineteen standard strains and 119 clinical isolates were correctly detected with our microarray, and 3 nontarget species from 4 clinical isolates were not detected. Additionally, bacterial pathogens were accurately identified when two or three bacterial targets were mixed together. Furthermore, the results for 99.4% (156/157) of clinical specimens were the same as those from a conventional assay. Conclusions We developed a DNA microarray that could simultaneously detect various bacterial pathogens in pneumonia. The method described here has the potential to provide considerable labour and time savings due to its ability to screen for 15 bacterial pathogens simultaneously.
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Affiliation(s)
- Xiuqing Ma
- Department of Pulmonary & Critical Care Medicine, Chinese PLA General Hospital, Beijing, China
| | - Yanqin Li
- Department of Pulmonary & Critical Care Medicine, Chinese PLA General Hospital, Beijing, China
| | - Yuan Liang
- Department of Pulmonary & Critical Care Medicine, Chinese PLA General Hospital, Beijing, China
| | - Yang Liu
- Department of Pulmonary & Critical Care Medicine, Chinese PLA General Hospital, Beijing, China
| | - Ling Yu
- Department of Pulmonary & Critical Care Medicine, Chinese PLA General Hospital, Beijing, China
| | - Chunsun Li
- Department of Pulmonary & Critical Care Medicine, Chinese PLA General Hospital, Beijing, China
| | - Qiqi Liu
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Liangan Chen
- Department of Pulmonary & Critical Care Medicine, Chinese PLA General Hospital, Beijing, China.
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9
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Uehara Y, Sasaki T, Baba T, Lu Y, Imajo E, Sato Y, Tanno S, Furuichi M, Kawada M, Hiramatsu K. Regional outbreak of community-associated methicillin-resistant Staphylococcus aureus ST834 in Japanese children. BMC Infect Dis 2019; 19:35. [PMID: 30626342 PMCID: PMC6327381 DOI: 10.1186/s12879-018-3646-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 12/20/2018] [Indexed: 12/01/2022] Open
Abstract
Background Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) infection has recently become a challenging problem worldwide and in Japan. We experienced 10 pediatric patients infected with CA-MRSA and hospitalized from 2011 to 2014 in a tertiary care hospital in Saitama, Japan, and assessed the characteristic of the strains using a whole genome sequencing (WGS)-based approach. Methods CA-MRSA strains isolated from infected patients who required hospitalization for treatment were evaluated in this study. Antimicrobial susceptibility tests, molecular typing by PCR and pulse-field gel electrophoresis (PFGE) were performed to characterize MRSA strains. WGS was performed for detailed genetic analysis. Results A total of 582 MRSA strains (35.2%) were identified among 1625 S. aureus strains collected during the study period. Ten MRSA strains (1.7%) were defined as CA-MRSA clinically, and all were isolated from pediatric patients. All strains mainly caused purulent lymphadenitis, were susceptible to fluoroquinolone and tetracycline, exhibited sequence type (ST) 834 or its single-locus variants and contained staphylococcal cassette chromosome mec (SCCmec) type IVc. Phylogenic analysis by PFGE and WGS revealed close relatedness of all strains, with the number of single nucleotide polymorphisms ranging from 35 to 119 by WGS. Out of the ten strains, nine possessed the genomic island SaPISaitama2 containing tst, sec and sel genes. SaPISaitama2 comprises a mosaic of genomic islands SaPIm4 and SaPIm1 harbored by a hospital-associated MRSA strain Mu50. Conclusions This study describes a regional outbreak of ST834-related CA-MRSA in children with a unique pathogenicity island in Japan. Pediatric patient tropism of this clone could be enhanced by susceptibility to fluoroquinolones and tetracyclines, which cannot be prescribed to children. Electronic supplementary material The online version of this article (10.1186/s12879-018-3646-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuki Uehara
- Department of Infection Control Science, Juntendo University Graduate School of Medicine, 2-1-1, Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan. .,Department of Microbiology, Juntendo University Faculty of Medicine, 2-1-1, Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan. .,Department of General Medicine, Juntendo University Faculty of Medicine, 2-1-1, Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan.
| | - Takashi Sasaki
- Department of Microbiology, Juntendo University Faculty of Medicine, 2-1-1, Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan.,Infection Control Science Research Center, Juntendo University Graduate School of Medicine, 2-1-1, Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Tadashi Baba
- Department of Microbiology, Juntendo University Faculty of Medicine, 2-1-1, Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan.,Infection Control Science Research Center, Juntendo University Graduate School of Medicine, 2-1-1, Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Yujie Lu
- Infection Control Science Research Center, Juntendo University Graduate School of Medicine, 2-1-1, Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Eri Imajo
- Department of Laboratory Medicine, Saitama City Hospital, 2460, Mimuro, Midori-ku, Saitama, 336-8522, Japan
| | - Yuka Sato
- Department of Laboratory Medicine, Saitama City Hospital, 2460, Mimuro, Midori-ku, Saitama, 336-8522, Japan
| | - Shigeru Tanno
- Department of Laboratory Medicine, Saitama City Hospital, 2460, Mimuro, Midori-ku, Saitama, 336-8522, Japan
| | - Munehiro Furuichi
- Division of Infectious Diseases, Department of Medical Subspecialties, National Center for Child Health and Development, 2-10-1, Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Miki Kawada
- Department of Infectious Diseases, Saitama City Hospital, 2460, Mimuro, Midori-ku, Saitama, 336-8522, Japan
| | - Keiichi Hiramatsu
- Department of Infection Control Science, Juntendo University Graduate School of Medicine, 2-1-1, Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan.,Department of Microbiology, Juntendo University Faculty of Medicine, 2-1-1, Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan.,Infection Control Science Research Center, Juntendo University Graduate School of Medicine, 2-1-1, Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
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10
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Collins A, Wakeland EK, Raj P, Kim MS, Kim J, Tareen NG, Copley LAB. The impact of Staphylococcus aureus genomic variation on clinical phenotype of children with acute hematogenous osteomyelitis. Heliyon 2018; 4:e00674. [PMID: 30003165 PMCID: PMC6039886 DOI: 10.1016/j.heliyon.2018.e00674] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 05/18/2018] [Accepted: 06/26/2018] [Indexed: 11/27/2022] Open
Abstract
Background Children with acute hematogenous osteomyelitis (AHO) have a broad spectrum of illness ranging from mild to severe. The purpose of this study is to evaluate the impact of genomic variation of Staphylococcus aureus on clinical phenotype of affected children and determine which virulence genes correlate with severity of illness. Methods De novo whole genome sequencing was conducted for a strain of Community Acquired Methicillin Resistant Staphylococcus aureus (CA-MRSA), using PacBio Hierarchical Genome Assembly Process (HGAP) from 6 Single Molecule Real Time (SMRT) Cells, as a reference for DNA library assembly of 71 Staphylococcus aureus isolates from children with AHO. Virulence gene annotation was based on exhaustive literature review and genomic data in NCBI for Staphylococcus aureus. Clinical phenotype was assessed using a validated severity score. Kruskal-Wallis rank sum test determined association between clinical severity and virulence gene presence using False Discovery Rate (FDR), significance <0.01. Results PacBio produced an assembled genome of 2,898,306 bp and 2054 Open Reading Frames (ORFs). Annotation confirmed 201 virulence genes. Statistical analysis of gene presence by clinical severity found 40 genes significantly associated with severity of illness (FDR ≤0.009). MRSA isolates encoded a significantly greater number of virulence genes than did MSSA (p < 0.0001). Phylogenetic analysis by maximum likelihood (PAML) demonstrated the relatedness of genomic distance to clinical phenotype. Conclusions The Staphylococcus aureus genome contains virulence genes which are significantly associated with severity of illness in children with osteomyelitis. This study introduces a novel reference strain and detailed annotation of Staphylococcus aureus virulence genes. While this study does not address bacterial gene expression, a platform is created for future transcriptome investigations to elucidate the complex mechanisms involved in childhood osteomyelitis.
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Affiliation(s)
- Angela Collins
- McLaren Medical Center, Department of Orthopaedic Surgery, Flint, Michigan, USA
| | - Edward K Wakeland
- University of Texas Southwestern, Department of Immunology, Dallas, Texas, USA
| | - Prithvi Raj
- University of Texas Southwestern, Department of Immunology, Dallas, Texas, USA
| | - Min S Kim
- University of Texas Southwestern, Department of Clinical Science, Dallas, Texas, USA
| | - Jiwoong Kim
- University of Texas Southwestern, Department of Clinical Science, Dallas, Texas, USA
| | - Naureen G Tareen
- Children's Health System of Texas, Department of Orthopaedic Surgery, Dallas, Texas, USA
| | - Lawson A B Copley
- University of Texas Southwestern, Department of Orthopaedic Surgery, Dallas, Texas, USA
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11
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van Belkum A, Rochas O. Laboratory-Based and Point-of-Care Testing for MSSA/MRSA Detection in the Age of Whole Genome Sequencing. Front Microbiol 2018; 9:1437. [PMID: 30008711 PMCID: PMC6034072 DOI: 10.3389/fmicb.2018.01437] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 06/11/2018] [Indexed: 12/28/2022] Open
Abstract
Staphylococcus aureus is an opportunistic pathogen of animals and humans that is capable of both colonizing and infecting its eukaryotic host. It is frequently detected in the clinical microbiology routine laboratory. S. aureus is capable of acquiring antibiotic resistance traits with ease and, given its rapid global dissemination, resistance to meticillin in S. aureus has received extensive coverage in the popular and medical press. The detection of meticillin-resistant versus meticillin-susceptible S. aureus (MRSA and MSSA) is of significant clinical importance. Detection of meticillin resistance is relatively straightforward since it is defined by a single determinant, penicillin-binding protein 2a', which exists in a limited number of genetic variants carried on various Staphylococcal Cassette Chromosomes mec. Diagnosis of MRSA and MSSA has evolved significantly over the past decades and there has been a strong shift from culture-based, phenotypic methods toward molecular detection, especially given the close correlation between the presence of the mec genes and phenotypic resistance. This brief review summarizes the current state of affairs concerning the mostly polymerase chain reaction-mediated detection of MRSA and MSSA in either the classical laboratory setting or at the point of care. The potential diagnostic impact of the currently emerging whole genome sequencing (WGS) technology will be discussed against a background of diagnostic, surveillance, and infection control parameters. Adequate detection of MSSA and MRSA is at the basis of any subsequent, more generic antibiotic susceptibility testing, epidemiological characterization, and detection of virulence factors, whether performed with classical technology or WGS analyses.
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Affiliation(s)
- Alex van Belkum
- Data Analytics Unit, bioMérieux, La Balme-les-Grottes, France
| | - Olivier Rochas
- Strategic Intelligence, Business Development Direction, bioMérieux, Marcy-l'Étoile, France
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12
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Millar EV, Rice GK, Elassal EM, Schlett CD, Bennett JW, Redden CL, Mor D, Law NN, Tribble DR, Hamilton T, Ellis MW, Bishop-Lilly KA. Genomic Characterization of USA300 Methicillin-Resistant Staphylococcus aureus (MRSA) to Evaluate Intraclass Transmission and Recurrence of Skin and Soft Tissue Infection (SSTI) Among High-Risk Military Trainees. Clin Infect Dis 2017; 65:461-468. [PMID: 28419202 PMCID: PMC5849051 DOI: 10.1093/cid/cix327] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 04/10/2017] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Military trainees are at increased risk for methicillin-resistant Staphylococcus aureus (MRSA) skin and soft tissue infection (SSTI). Whole genome sequencing (WGS) can refine our understanding of MRSA transmission and microevolution in congregate settings. METHODS We conducted a prospective case-control study of SSTI among US Army infantry trainees at Fort Benning, Georgia, from July 2012 to December 2014. We identified clusters of USA300 MRSA SSTI within select training classes and performed WGS on clinical isolates. We then linked genomic, phylogenetic, epidemiologic, and clinical data in order to evaluate intra- and interclass disease transmission. Furthermore, among cases of recurrent MRSA SSTI, we evaluated the intrahost relatedness of infecting strains. RESULTS Nine training classes with ≥5 cases of USA300 MRSA SSTI were selected. Eighty USA300 MRSA clinical isolates from 74 trainees, 6 (8.1%) of whom had recurrent infection, were subjected to WGS. We identified 2719 single nucleotide variants (SNVs). The overall median (range) SNV difference between isolates was 173 (1-339). Intraclass median SNV differences ranged from 23 to 245. Two phylogenetic clusters were suggestive of interclass MRSA transmission. One of these clusters stemmed from 2 classes that were separated by a 13-month period but housed in the same barracks. Among trainees with recurrent MRSA SSTI, the intrahost median SNV difference was 7.5 (1-48). CONCLUSIONS Application of WGS revealed intra- and interclass transmission of MRSA among military trainees. An interclass cluster between 2 noncontemporaneous classes suggests a long-term reservoir for MRSA in this setting.
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Affiliation(s)
- Eugene V Millar
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville
| | - Gregory K Rice
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville
- Naval Medical Research Center, Biological Defense Research Directorate, Fort Detrick
| | - Emad M Elassal
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville
| | - Carey D Schlett
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville
| | - Jason W Bennett
- Walter Reed Army Institute of Research, Silver Spring
- Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - Cassie L Redden
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville
- Naval Medical Research Center, Biological Defense Research Directorate, Fort Detrick
| | - Deepika Mor
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville
| | - Natasha N Law
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville
- Martin Army Community Hospital, Fort Benning, Georgia
| | - David R Tribble
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda
| | - Theron Hamilton
- Naval Medical Research Center, Biological Defense Research Directorate, Fort Detrick
| | - Michael W Ellis
- University of Toledo College of Medicine and Life Sciences, Ohio
| | - Kimberly A Bishop-Lilly
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville
- Naval Medical Research Center, Biological Defense Research Directorate, Fort Detrick
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13
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Demography and Intercontinental Spread of the USA300 Community-Acquired Methicillin-Resistant Staphylococcus aureus Lineage. mBio 2016; 7:e02183-15. [PMID: 26884428 PMCID: PMC4752609 DOI: 10.1128/mbio.02183-15] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) was recognized worldwide during the 1990s; in less than a decade, several genetically distinct CA-MRSA lineages carrying Panton-Valentine leukocidin genes have emerged on every continent. Most notably, in the United States, the sequence type 18-IV (ST8-IV) clone known as USA300 has become highly prevalent, outcompeting methicillin-susceptible S. aureus (MSSA) and other MRSA strains in both community and hospital settings. CA-MRSA bacteria are much less prevalent in Europe, where the European ST80-IV European CA-MRSA clone, USA300 CA-MRSA strains, and other lineages, such as ST22-IV, coexist. The question that arises is whether the USA300 CA-MRSA present in Europe (i) was imported once or on very few occasions, followed by a broad geographic spread, anticipating an increased prevalence in the future, or (ii) derived from multiple importations with limited spreading success. In the present study, we applied whole-genome sequencing to a collection of French USA300 CA-MRSA strains responsible for sporadic cases and micro-outbreaks over the past decade and United States ST8 MSSA and MRSA isolates. Genome-wide phylogenetic analysis demonstrated that the population structure of the French isolates is the product of multiple introductions dating back to the onset of the USA300 CA-MRSA clone in North America. Coalescent-based demography of the USA300 lineage shows that a strong expansion occurred during the 1990s concomitant with the acquisition of the arginine catabolic mobile element and antibiotic resistance, followed by a sharp decline initiated around 2008, reminiscent of the rise-and-fall pattern previously observed in the ST80 lineage. A future expansion of the USA300 lineage in Europe is therefore very unlikely. To trace the origin, evolution, and dissemination pattern of the USA300 CA-MRSA clone in France, we sequenced a collection of strains of this lineage from cases reported in France in the last decade and compared them with 431 ST8 strains from the United States. We determined that the French CA-MRSA USA300 sporadic and micro-outbreak isolates resulted from multiple independent introductions of the USA300 North American lineage. At a global level, in the transition from an MSSA lineage to a successful CA-MRSA clone, it first became resistant to multiple antibiotics and acquired the arginine catabolic mobile element and subsequently acquired resistance to fluoroquinolones, and these two steps were associated with a dramatic demographic expansion. This expansion was followed by the current stabilization and expected decline of this lineage. These findings highlight the significance of horizontal gene acquisitions and point mutations in the success of such disseminated clones and illustrate their cyclic and sporadic life cycle.
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14
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Sabirova JS, Hernalsteens JP, De Backer S, Xavier BB, Moons P, Turlej-Rogacka A, De Greve H, Goossens H, Malhotra-Kumar S. Fatty acid kinase A is an important determinant of biofilm formation in Staphylococcus aureus USA300. BMC Genomics 2015; 16:861. [PMID: 26502874 PMCID: PMC4623894 DOI: 10.1186/s12864-015-1956-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 09/25/2015] [Indexed: 01/09/2023] Open
Abstract
Background Methicillin-resistant Staphylococcus aureus (MRSA)-USA300 is notorious for its ability to cause community- and healthcare-acquired infections, which are even more difficult to treat when associated with a biofilm phenotype. We aimed to characterize the genetic determinants of biofilm formation in a USA300 skin abscess isolate (UAS391) that formed prolific biofilms. Methods USA300 S. aureus strains, TCH1516 and FPR3757, were found to be closely related based on whole genome mapping (Argus™ Optical Mapping System, Opgen Inc, Gaithersburg, USA) to UAS391 (96.3-99.1 % similarity, P=0.0151), however differed markedly in biofilm formation (P=0.0001) on a dynamic assay (BioFlux 200, Fluxion Biosciences, USA). Comparison of whole genome sequences of these strains identified differences in a total of 18 genes. Corresponding Tn (bursa aurealis-bearing) knockout mutants in these target genes were obtained from a publicly available mutant library of the same clonal lineage (USA300-JE2) and were characterized phenotypically for biofilm formation. Tn mutants showing significant differences in biofilm formation were utilized for transduction into a plasmid-cured erythromycin-sensitive derivative of UAS391 and for complementation experiments. All strains were tested on the dynamic assay, and 17h-biofilms were stained (SYTO9, Life Technologies) and fluorescence intensity quantified by microscopy (Zeiss, ImageJ). Gene expression levels in Tn and transduced mutants were studied by quantitative reverse transcriptase PCR (StepOnePlusTM, Applied Biosystems®). Results Comparison of the sequenced genomes of TCH1516, FPR3757 and UAS391 yielded a limited number of variant genes (n=18) that were hypothesized to account for the observed difference in biofilm-forming capacity. Screening of Tn mutants disrupted in these target genes identified one mutant (NE229) bearing a transposon insertion in SAUSA300_1119 (fakA), which exhibited increased biofilm formation similar to UAS391 (P=0.9320). Transduction experiments confirmed that fakA::Tn corresponded to 1.9- to 4.6-fold increase in biofilm formation depending on the USA300 strain background (P≤0.0007), while complementation of the TCH1516 wild-type fakA allele in UAS391 resulted in a 4.3-fold reduction in biofilm formation (P<0.0001). Conclusions This sequential approach, consisting of strain typing, genome comparison and functional genomics, identified fakA, a recently described fatty acid kinase in S. aureus that is essential for phospholipid synthesis and also impacts the transcription of numerous virulence factors, as a negative regulator of biofilm formation in S. aureus USA300. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1956-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- J S Sabirova
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium.,Viral Genetics Research Group, Vrije Universiteit Brussel, Brussels, Belgium
| | - J-P Hernalsteens
- Viral Genetics Research Group, Vrije Universiteit Brussel, Brussels, Belgium
| | - S De Backer
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - B B Xavier
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - P Moons
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - A Turlej-Rogacka
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - H De Greve
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Brussels, Belgium
| | - H Goossens
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - S Malhotra-Kumar
- Department of Medical Microbiology, Campus Drie Eiken, University of Antwerp, S6, Universiteitsplein 1, B-2610, Wilrijk, Belgium.
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15
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Gaviria-Agudelo C, Aroh C, Tareen N, Wakeland EK, Kim M, Copley LA. Genomic Heterogeneity of Methicillin Resistant Staphylococcus aureus Associated with Variation in Severity of Illness among Children with Acute Hematogenous Osteomyelitis. PLoS One 2015; 10:e0130415. [PMID: 26086671 PMCID: PMC4473274 DOI: 10.1371/journal.pone.0130415] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 05/20/2015] [Indexed: 11/23/2022] Open
Abstract
Introduction The association between severity of illness of children with osteomyelitis caused by Methicillin-resistant Staphylococcus aureus (MRSA) and genomic variation of the causative organism has not been previously investigated. The purpose of this study is to assess genomic heterogeneity among MRSA isolates from children with osteomyelitis who have diverse severity of illness. Materials and Methods Children with osteomyelitis were prospectively studied between 2010 and 2011. Severity of illness of the affected children was determined from clinical and laboratory parameters. MRSA isolates were analyzed with next generation sequencing (NGS) and optical mapping. Sequence data was used for multi-locus sequence typing (MLST), phylogenetic analysis by maximum likelihood (PAML), and identification of virulence genes and single nucleotide polymorphisms (SNP) relative to reference strains. Results The twelve children studied demonstrated severity of illness scores ranging from 0 (mild) to 9 (severe). All isolates were USA300, ST 8, SCC mec IVa MRSA by MLST. The isolates differed from reference strains by 2 insertions (40 Kb each) and 2 deletions (10 and 25 Kb) but had no rearrangements or copy number variations. There was a higher occurrence of virulence genes among study isolates when compared to the reference strains (p = 0.0124). There were an average of 11 nonsynonymous SNPs per strain. PAML demonstrated heterogeneity of study isolates from each other and from the reference strains. Discussion Genomic heterogeneity exists among MRSA isolates causing osteomyelitis among children in a single community. These variations may play a role in the pathogenesis of variation in clinical severity among these children.
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Affiliation(s)
- Claudia Gaviria-Agudelo
- Department of Pediatric Infectious Disease, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Chukwuemika Aroh
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Naureen Tareen
- Children’s Medical Center, Dallas, Texas, United States of America
| | - Edward K. Wakeland
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - MinSoo Kim
- Department of Biomedical Informatics, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
| | - Lawson A. Copley
- Children’s Medical Center, Dallas, Texas, United States of America
- Texas Scottish Rite Hospital for Children, Dallas, Texas, United States of America
- Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- * E-mail:
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16
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USA300 and USA500 clonal lineages of Staphylococcus aureus do not produce a capsular polysaccharide due to conserved mutations in the cap5 locus. mBio 2015; 6:mBio.02585-14. [PMID: 25852165 PMCID: PMC4453534 DOI: 10.1128/mbio.02585-14] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The surface capsular polysaccharide (CP) is a virulence factor that has been used as an antigen in several successful vaccines against bacterial pathogens. A vaccine has not yet been licensed against Staphylococcus aureus, although two multicomponent vaccines that contain CP antigens are in clinical trials. In this study, we evaluated CP production in USA300 methicillin-resistant S. aureus (MRSA) isolates that have become the predominant community-associated MRSA clones in the United States. We found that all 167 USA300 MRSA and 50 USA300 methicillin-susceptible S. aureus (MSSA) isolates were CP negative (CP−). Moreover, all 16 USA500 isolates, which have been postulated to be the progenitor lineage of USA300, were also CP−. Whole-genome sequence analysis of 146 CP− USA300 MRSA isolates revealed they all carry a cap5 locus with 4 conserved mutations compared with strain Newman. Genetic complementation experiments revealed that three of these mutations (in the cap5 promoter, cap5D nucleotide 994, and cap5E nucleotide 223) ablated CP production in USA300 and that Cap5E75 Asp, located in the coenzyme-binding domain, is essential for capsule production. All but three USA300 MSSA isolates had the same four cap5 mutations found in USA300 MRSA isolates. Most isolates with a USA500 pulsotype carried three of these four USA300-specific mutations, suggesting the fourth mutation occurred in the USA300 lineage. Phylogenetic analysis of the cap loci of our USA300 isolates as well as publicly available genomes from 41 other sequence types revealed that the USA300-specific cap5 mutations arose sequentially in S. aureus in a common ancestor of USA300 and USA500 isolates. The USA300 MRSA clone emerged as a community-associated pathogen in the United States nearly 20 years ago. Since then, it has rapidly disseminated and now causes health care-associated infections. This study shows that the CP-negative (CP−) phenotype has persisted among USA300 isolates and is a universal and characteristic trait of this highly successful MRSA lineage. It is important to note that a vaccine consisting solely of CP antigens would not likely demonstrate high efficacy in the U.S. population, where about half of MRSA isolates comprise USA300. Moreover, conversion of a USA300 strain to a CP-positive (CP+) phenotype is unlikely in vivo or in vitro since it would require the reversion of 3 mutations. We have also established that USA300 MSSA isolates and USA500 isolates are CP− and provide new insight into the evolution of the USA300 and USA500 lineages.
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17
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Transmission and microevolution of USA300 MRSA in U.S. households: evidence from whole-genome sequencing. mBio 2015; 6:e00054. [PMID: 25759497 PMCID: PMC4453535 DOI: 10.1128/mbio.00054-15] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
UNLABELLED Methicillin-resistant Staphylococcus aureus (MRSA) USA300 is a successful S. aureus clone in the United States and a common cause of skin and soft tissue infections (SSTIs). We performed whole-genome sequencing (WGS) of 146 USA300 MRSA isolates from SSTIs and colonization cultures obtained from an investigation conducted from 2008 to 2010 in Chicago and Los Angeles households that included an index case with an S. aureus SSTI. Identifying unique single nucleotide polymorphisms (SNPs) and analyzing whole-genome phylogeny, we characterized isolates to understand transmission dynamics, genetic relatedness, and microevolution of USA300 MRSA within the households. We also compared the 146 USA300 MRSA isolates from our study with the previously published genome sequences of the USA300 MRSA isolates from San Diego (n = 35) and New York City (n = 277). We found little genetic variation within the USA300 MRSA household isolates from Los Angeles (mean number of SNPs ± standard deviation, 17.6 ± 35; π nucleotide diversity, 3.1 × 10(-5)) or from Chicago (mean number of SNPs ± standard deviation, 12 ± 19; π nucleotide diversity, 3.1 × 10(-5)). The isolates within a household clustered into closely related monophyletic groups, suggesting the introduction into and transmission within each household of a single common USA300 ancestral strain. From a Bayesian evolutionary reconstruction, we inferred that USA300 persisted within households for 2.33 to 8.35 years prior to sampling. We also noted that fluoroquinolone-resistant USA300 clones emerged around 1995 and were more widespread in Los Angeles and New York City than in Chicago. Our findings strongly suggest that unique USA300 MRSA isolates are transmitted within households that contain an individual with an SSTI. Decolonization of household members may be a critical component of prevention programs to control USA300 MRSA spread in the United States. IMPORTANCE USA300, a virulent and easily transmissible strain of methicillin-resistant Staphylococcus aureus (MRSA), is the predominant community-associated MRSA clone in the United States. It most commonly causes skin infections but also causes necrotizing pneumonia and endocarditis. Strategies to limit the spread of MRSA in the community can only be effective if we understand the most common sources of transmission and the microevolutionary processes that provide a fitness advantage to MRSA. We performed a whole-genome sequence comparison of 146 USA300 MRSA isolates from Chicago and Los Angeles. We show that households represent a frequent site of transmission and a long-term reservoir of USA300 strains; individuals within households transmit the same USA300 strain among themselves. Our study also reveals that a large proportion of the USA300 isolates sequenced are resistant to fluoroquinolone antibiotics. The significance of this study is that if households serve as long-term reservoirs of USA300, household MRSA eradication programs may result in a uniquely effective control method.
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18
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Absence of patient-to-patient intrahospital transmission of Staphylococcus aureus as determined by whole-genome sequencing. mBio 2014; 5:e01692-14. [PMID: 25293757 PMCID: PMC4196229 DOI: 10.1128/mbio.01692-14] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Nosocomial transmission of pathogens is a major health care challenge. The increasing spread of antibiotic-resistant strains represents an ongoing threat to public health. Previous Staphylococcus aureus transmission studies have focused on transmission of S. aureus between asymptomatic carriers or used low-resolution typing methods such as multilocus sequence typing (MLST) or spa typing. To identify patient-to-patient intrahospital transmission using high-resolution genetic analysis, we sequenced the genomes of a consecutive set of 398 S. aureus isolates from sterile-site infections. The S. aureus strains were collected from four hospitals in the Houston Methodist Hospital System over a 6-month period. Importantly, we discovered no evidence of transmission of S. aureus between patients with sterile-site infections. The lack of intrahospital transmission may reflect a fundamental difference between day-to-day transmission events in the hospital setting and the more frequently studied outbreak scenarios. Previous studies have suggested that nosocomial transmission of S. aureus is common. Our data revealed an unexpected lack of evidence for intrahospital transmission of S. aureus between patients with invasive infections. This finding has important implications for hospital infection control and public health efforts. In addition, our data demonstrate that highly related pools of S. aureus strains exist in the community which may complicate outbreak investigations.
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19
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Molecular tracing of the emergence, diversification, and transmission of S. aureus sequence type 8 in a New York community. Proc Natl Acad Sci U S A 2014; 111:6738-43. [PMID: 24753569 DOI: 10.1073/pnas.1401006111] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
During the last 2 decades, community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) strains have dramatically increased the global burden of S. aureus infections. The pandemic sequence type (ST)8/pulsed-field gel type USA300 is the dominant CA-MRSA clone in the United States, but its evolutionary history and basis for biological success are incompletely understood. Here, we use whole-genome sequencing of 387 ST8 isolates drawn from an epidemiological network of CA-MRSA infections and colonizations in northern Manhattan to explore short-term evolution and transmission patterns. Phylogenetic analysis predicted that USA300 diverged from a most common recent ancestor around 1993. We found evidence for multiple introductions of USA300 and reconstructed the phylogeographic spread of isolates across neighborhoods. Using pair-wise single-nucleotide polymorphism distances as a measure of genetic relatedness between isolates, we observed that most USA300 isolates had become endemic in households, indicating their critical role as reservoirs for transmission and diversification. Using the maximum single-nucleotide polymorphism variability of isolates from within households as a threshold, we identified several possible transmission networks beyond households. Our study also revealed the evolution of a fluoroquinolone-resistant subpopulation in the mid-1990s and its subsequent expansion at a time of high-frequency outpatient antibiotic use. This high-resolution phylogenetic analysis of ST8 has documented the genomic changes associated with USA300 evolution and how some of its recent evolution has been shaped by antibiotic use. By integrating whole-genome sequencing with detailed epidemiological analyses, our study provides an important framework for delineating the full diversity and spread of USA300 and other emerging pathogens in large urban community populations.
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Evolution of community- and healthcare-associated methicillin-resistant Staphylococcus aureus. INFECTION GENETICS AND EVOLUTION 2013; 21:563-74. [PMID: 23648426 DOI: 10.1016/j.meegid.2013.04.030] [Citation(s) in RCA: 126] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Revised: 04/22/2013] [Accepted: 04/25/2013] [Indexed: 11/23/2022]
Abstract
Staphylococcus aureus is a prominent cause of human infections globally. The high prevalence of infections is compounded by antibiotic resistance--a significant problem for treatment. Methicillin-resistant S. aureus (MRSA) is endemic in hospitals and healthcare facilities worldwide, and is an increasingly common cause of community-associated bacterial infections in industrialized countries. Although much focus is placed on the role of S. aureus as a human pathogen, it is in fact a human commensal organism that has had a relatively long coexistence with the human host. Many S. aureus infections can be explained by host susceptibility or other predisposing risk factors. On the other hand, the emergence/re-emergence of successful S. aureus clones (referred to as epidemic waves) suggests a rapid bacterial adaption and evolution, which includes the emergence of antibiotic resistance and increased virulence and/or transmissibility. It is within this context that we review our understanding of selected S. aureus epidemic waves, and highlight the use of genome sequencing as a means to better understand the evolution of each lineage.
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