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Huang YC, Chen CJ, Kuo AJ, Hwang KR, Chien CC, Lee CY, Wu TH, Ko WC, Hsueh PR. Dissemination of meticillin-resistant Staphylococcus aureus sequence type 8 (USA300) in Taiwan. J Hosp Infect 2024; 149:108-118. [PMID: 38782057 DOI: 10.1016/j.jhin.2024.04.024] [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: 01/13/2024] [Revised: 04/23/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND In Taiwan, sequence type (ST) 239 and ST59 were two major clones among meticillin-resistant Staphylococcus aureus (MRSA) clinical isolates in the past two decades. USA300 (ST8) prevailed in the Americas but not in outside areas. Recently USA300 (ST8) emerged and was increasingly identified in Taiwan; we thus conducted an island-wide study to explore the role of USA300 among MRSA isolates. METHODS One hundred MRSA bloodstream isolates identified in 2020 from each of the six participating hospitals in Taiwan were collected and characterized. The first 10 ST8 isolates from each hospital were further analysed by whole-genome sequencing. RESULTS Of the 590 confirmed MRSA isolates, a total of 22 pulsotypes and 21 STs were identified. The strain of pulsotype AI/ST8 was the most common lineage identified, accounting for 187 isolates (31.7%) and dominating in five of six hospitals, followed by pulsotype A/ST239 (14.7%), pulsotype C/ST59 (13.9%) and pulsotype D/ST59 (9.2%). Of the 187 pulsotype AI/ST8 isolates, 184 isolates were characterized as USA300 and clustered in three major sub-pulsotypes, accounting for 78%. Ninety per cent of the 60 ST8 isolates for whole-genome sequencing were clustered in three major clades. CONCLUSIONS In 2020, USA300 became the most common clone of MRSA in Taiwan, accounting for >30% of MRSA bloodstream isolates island wide. Most of USA300 isolates circulating in Taiwan might have been imported on multiple occasions and evolved into at least three successful local clades. MRSA USA300 has successfully established its role in Taiwan, an area outside of the Americas.
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Affiliation(s)
- Y-C Huang
- Department of Pediatrics, Chang Gung Memorial Hospital at Linkou, Taoyuan City, Taiwan; College of Medicine, Chang Gung University, Taoyuan City, Taiwan.
| | - C-J Chen
- Department of Pediatrics, Chang Gung Memorial Hospital at Linkou, Taoyuan City, Taiwan; College of Medicine, Chang Gung University, Taoyuan City, Taiwan
| | - A-J Kuo
- College of Medicine, Chang Gung University, Taoyuan City, Taiwan; Department of Laboratory Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan City, Taiwan
| | - K-R Hwang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan City, Taiwan; Department of Laboratory Medicine, Chang Gung Memorial Hospital at Keelung, Keelung City, Taiwan
| | - C-C Chien
- Department of Laboratory Medicine, Chang Gung Memorial Hospital at Kaohsiung, Kaohsiung City, Taiwan
| | - C-Y Lee
- Department of Pediatrics, Chang Bing Show Chwan Memorial Hospital, Changhua County, Taiwan
| | - T-H Wu
- Department of Pediatrics, Chang Hua Show Chwan Memorial Hospital, Changhua, Taiwan
| | - W-C Ko
- Department of Medicine, National Cheng Kung University Hospital, Tainan City, Taiwan
| | - P-R Hsueh
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan; Departments of Laboratory Medicine and Internal Medicine, China Medical University Hospital, Taichung, Taiwan; School of Medicine, China Medical University, Taichung, Taiwan
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2
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Thiede SN, Snitkin ES, Trick W, Payne D, Aroutcheva A, Weinstein RA, Popovich KJ. Genomic Epidemiology Suggests Community Origins of Healthcare-Associated USA300 Methicillin-Resistant Staphylococcus aureus. J Infect Dis 2022; 226:157-166. [PMID: 35172338 PMCID: PMC9612791 DOI: 10.1093/infdis/jiac056] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/14/2022] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Hospital-onset (HO) methicillin-resistant Staphylococcus aureus (MRSA) infections have declined over the past decade due to infection control strategies; community-onset (CO) and healthcare-associated community-onset (HACO) MRSA, particularly USA300, has declined less. We examined the role of community strains to explain the difference. METHODS We performed whole-genome sequencing (WGS) on MRSA clinical isolates from Cook County Health patients during 2011-2014. We defined infections as CO, HO, or HACO epidemiologically. We integrated genomic, community exposure, and statewide hospital discharge data to infer MRSA origin. RESULTS Among 1020 individuals with available WGS, most were USA300 wound infections (580 CO, 143 HO, 297 HACO). USA300 HO, CO, and HACO infections were intermixed on the USA300 phylogeny, consistent with common strains circulating across community and healthcare settings. Community exposures (eg, substance abuse, incarceration, homelessness) were associated with HACO and HO infections, and genetically linked individuals from both groups had little overlap in healthcare facilities, supporting community origins. Most repeat infections-over months to years-occurred in individuals persistently carrying their own strains. These individuals were more likely to have genetic linkages, suggesting a role of persistent colonization in transmission. CONCLUSIONS Efforts to reduce presumed nosocomial USA300 spread may require understanding and controlling community sources and transmission networks, particularly for repeat infections.
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Affiliation(s)
| | | | - William Trick
- Cook County Health, Rush University Medical Center, Chicago, Illinois, USA
| | - Darjai Payne
- Rush University Medical Center, Chicago, Illinois, USA
| | - Alla Aroutcheva
- Rush University Medical Center/Cook County Health, Chicago, Illinois, USA
| | - Robert A Weinstein
- Rush University Medical Center/Cook County Health, Chicago, Illinois, USA
| | - Kyle J Popovich
- Rush University Medical Center/Cook County Health, Chicago, Illinois, USA
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3
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Forrester JD, Cao S, Schaps D, Liou R, Patil A, Stave C, Sokolow SH, Leo GD. Influence of Socioeconomic and Environmental Determinants of Health on Human Infection and Colonization with Antibiotic-Resistant and Antibiotic-Associated Pathogens: A Scoping Review. Surg Infect (Larchmt) 2022; 23:209-225. [DOI: 10.1089/sur.2021.348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Joseph D. Forrester
- Division of General Surgery, Department of Surgery, Stanford University, Stanford, California, USA
| | - Siqi Cao
- School of Medicine, Stanford University, Stanford, California, USA
| | - Diego Schaps
- School of Medicine, Duke University, Durham, North Carolina, USA
| | - Raymond Liou
- School of Medicine, Stanford University, Stanford, California, USA
| | | | - Christopher Stave
- School of Medicine, Stanford University, Stanford, California, USA
- Lane Medical Library, Stanford University, Stanford, California, USA
| | - Susanne H. Sokolow
- Woods Institute for the Environment, Stanford University, Stanford, California, USA
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, California, USA
| | - Giulio De Leo
- Woods Institute for the Environment, Stanford University, Stanford, California, USA
- Hopkins Marine Station, Stanford University, Stanford, California, USA
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4
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Popovich KJ, Thiede SN, Zawitz C, Payne D, Aroutcheva A, Schoeny M, Green SJ, Snitkin ES, Weinstein RA. Genomic Analysis of Community Transmission Networks for MRSA among Females Entering a Large Inner-City Jail. Open Forum Infect Dis 2022; 9:ofac049. [PMID: 35211635 PMCID: PMC8863081 DOI: 10.1093/ofid/ofac049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 01/25/2022] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
It is unclear if there are differences in MRSA risk between sexes in high-risk populations.
Methods
Females incarcerated at the Cook County Jail were enrolled within 72 hours of intake. Surveillance cultures (nares, throat, groin) were collected to determine prevalence of MRSA colonization. A survey was administered to identify colonization predictors. Univariate and multivariate analyses were performed to identify predictors of colonization at intake. Genomic sequencing was performed on MRSA colonization and archived clinical isolates.
Results
250 women were enrolled (70% AA, 15% Hispanic) with 70% previously in jail. The prevalence of MRSA colonization at intake was 20%, with 42% of those colonized solely in the throat or groin. Univariate predictors of MRSA colonization at entrance were illicit drug use, unstable housing, engaging in anal sex, recent exchange of sex for drugs/money, and a higher number of recent sexual partners. With multivariate adjustment for race/ethnicity, use of needles for illicit drugs was a significant predictor of MRSA. Use of illicit drugs was also associated with inclusion in a genomic cluster.
Nares colonization was significantly associated with not being in a genomic cluster (18.8% vs 78.6%, p<0.001), whereas exclusive extra-nasal colonization was associated (OR 15.89, p<0.001).
Conclusion
We found that a high proportion (20%) of females entered jail colonized with MRSA, suggesting that previously reported sex disparities of a lower risk in women may not apply to high-risk populations. Our findings suggest high-risk activities or venues in the community for MRSA, with potential for directing sex-specific interventions.
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Affiliation(s)
- Kyle J Popovich
- Rush University Medical Center/Cook County Health, Chicago, IL, USA
| | | | - Chad Zawitz
- Cermak Health Services, Cook County Health, Chicago, IL, USA
| | - Darjai Payne
- Rush University Medical Center, Chicago, IL, USA
| | - Alla Aroutcheva
- Rush University Medical Center/Cook County Health, Chicago, IL, USA
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5
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Huang YC, Chen CJ. USA 300 (sequence type 8) became a major clone of methicillin-resistant Staphylococcus aureus in northern Taiwan. Int J Antimicrob Agents 2022; 59:106534. [DOI: 10.1016/j.ijantimicag.2022.106534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 01/11/2022] [Accepted: 01/19/2022] [Indexed: 11/05/2022]
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6
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Genomic Update of Phenotypic Prediction Rule for Methicillin-Resistant Staphylococcus aureus (MRSA) USA300 Discloses Jail Transmission Networks with Increased Resistance. Microbiol Spectr 2021; 9:e0037621. [PMID: 34287060 PMCID: PMC8552710 DOI: 10.1128/spectrum.00376-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a leading cause of health care-associated (HA) and community-associated (CA) infections. USA300 strains are historically CA-MRSA, while USA100 strains are HA-MRSA. Here, we update an antibiotic prediction rule to distinguish these two genotypes based on antibiotic resistance phenotype using whole-genome sequencing (WGS), a more discriminatory methodology than pulsed-field gel electrophoresis (PFGE). MRSA clinical isolates collected from 2007 to 2017 underwent WGS; associated epidemiologic data were ascertained. In developing the rule, we examined MRSA isolates that included a population with a history of incarceration. Performance characteristics of antibiotic susceptibility for predicting USA300 compared to USA100, as defined by WGS, were examined. Phylogenetic analysis was performed to examine resistant USA300 clades. We identified 275 isolates (221 USA300, 54 USA100). Combination susceptibility to clindamycin or levofloxacin performed the best overall (sensitivity 80.7%, specificity 75.9%) to identify USA300. The average number of antibiotic classes with resistance was higher for USA100 (3 versus 2, P < 0.001). Resistance to ≤2 classes was predictive for USA300 (area under the curve (AUC) 0.84, 95% confidence interval 0.78 to 0.90). Phylogenetic analysis identified a cluster of USA300 strains characterized by increased resistance among incarcerated individuals. Using a combination of clindamycin or levofloxacin susceptibility, or resistance to ≤2 antibiotic classes, was predictive of USA300 as defined by WGS. Increased resistance was observed among individuals with incarceration exposure, suggesting circulation of a more resistant USA300 clade among at-risk community networks. Our phenotypic prediction rule could be used as an epidemiologic tool to describe community and nosocomial shifts in USA300 MRSA and quickly identify emergence of lineages with increased resistance. IMPORTANCE Methicillin-resistant Staphylococcus aureus (MRSA) is an important cause of health care-associated (HA) and community-associated (CA) infections, but the epidemiology of these strains (USA100 and USA300, respectively) now overlaps in health care settings. Although sequencing technology has become more available, many health care facilities still lack the capabilities to perform these analyses. In this study, we update a simple prediction rule based on antibiotic resistance phenotype with integration of whole-genome sequencing (WGS) to predict strain type based on antibiotic resistance profiles that can be used in settings without access to molecular strain typing methods. This prediction rule has many potential epidemiologic applications, such as analysis of retrospective data sets, regional monitoring, and ongoing surveillance of CA-MRSA infection trends. We demonstrate application of this rule to identify an emerging USA300 strain with increased antibiotic resistance among incarcerated individuals that deviates from the rule.
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7
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Epidemiology of the Staphylococcus aureus CA-MRSA USA300 in Belgium. Eur J Clin Microbiol Infect Dis 2021; 40:2335-2347. [PMID: 34160741 DOI: 10.1007/s10096-021-04286-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 06/02/2021] [Indexed: 12/17/2022]
Abstract
The methicillin-resistant Staphylococcus aureus (MRSA) sequence type (ST) 8 Panton-Valentine toxin (PVL)-positive USA300 clone has a worldwide distribution. The USA300 North American (NA) variant, harbouring the arginine catabolic mobile element (ACME), is predominant in the USA while the Latin American (LV) variant is predominant in Northern South America. Both variants have failed to become endemic in Europe. We examined here the epidemiology of the USA300 clone in Belgium from 2006 to 2019. A total of 399 clonal complex 8 PVL-positive MRSA isolates received between 2006 and 2019 by the Belgian National Reference Laboratory for S. aureus were investigated for the presence of ACME. Selected ACME-positive (n=102) and ACME-negative (n=16) isolates were sequenced, characterized for the presence of several resistance and virulence molecular markers and subjected to phylogenetic analysis. A total of 300 isolates were USA300-NA (ACME-positive), while only 99 were ACME-negative. Most USA300-NA interspersed in the phylogeny analysis with isolates from other countries, suggesting multiple introductions. However, two big clades were maintained and spread over a decade, peaking between 2010 and 2017 to finally decrease. Few ACME-negative isolates, mainly related to trips to South America, were identified as USA300-LV. The remaining ACME-negative isolates were ST8 SCCmec IVb or ST923 SCCmec IVa (COL923). Two clades of the USA300-NA clone have successfully spread in Belgium, but seem to currently decrease. Related South American variants have been detected for the first time in Belgium, including the emerging COL923 clone.
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8
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Staphylococcal Infections: Host and Pathogenic Factors. Microorganisms 2021; 9:microorganisms9051080. [PMID: 34069873 PMCID: PMC8157358 DOI: 10.3390/microorganisms9051080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 12/12/2022] Open
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9
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Popovich KJ, Thiede SN, Zawitz C, Aroutcheva A, Payne D, Janda W, Schoeny M, Green SJ, Snitkin ES, Weinstein RA. Genomic Epidemiology of MRSA During Incarceration at a Large Inner-City Jail. Clin Infect Dis 2021; 73:e3708-e3717. [PMID: 33395473 DOI: 10.1093/cid/ciaa1937] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 01/01/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Congregate settings, such as jails, may be a location where colonized detainees transmit MRSA. We examined MRSA acquisition during incarceration and characterized the genomic epidemiology of MRSA entering the jail and isolated during incarceration. METHODS Males incarcerated at the Cook County Jail were enrolled within 72 hours of intake and MRSA surveillance cultures collected. Detainees in jail at Day30 were re-cultured to determine MRSA acquisition. A survey was administered to identify acquisition predictors. Genomic sequencing of surveillance and clinical isolates was integrated with epidemiologic and jail location data to track MRSA transmission pathways. RESULTS 800 males were enrolled; 19% MRSA colonized at intake. Of 184 who reached Day30 visit, 12 acquired MRSA. Heroin use before entering (OR 3.67,p=0.05) and sharing personal items during incarceration (OR=4.92,p=.01) were predictors of acquisition. Sequenced clinical USA300 isolates (n=112) were more genetically similar than diverse intake USA300 strains (p<0.001), suggesting jail transmission. Four acquired colonization isolates were within 20 SNVs of other isolates; 4 were within 20SNVs of an intake isolate, 2 for an acquisition isolate, and 1 for a clinical isolate. Individuals with genetically similar isolates were more likely to have had overlapping stays in the same buildings. CONCLUSION There was a high MRSA burden entering jail. Genomic analysis of acquisition and clinical isolates suggests potential spread of incoming strains and networks of spread during incarceration, with spread often occurring among detainees housed in similar locations. Sharing personal items during incarceration is associated with MRSA acquisition and could be a focus for intervention.
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Affiliation(s)
- Kyle J Popovich
- Section of Infectious Diseases, Rush University Medical Center/ Cook County Health, Chicago, IL, USA
| | - Stephanie N Thiede
- Department of Microbiology and Immunology, University of Michigan, Chicago, IL, USA
| | - Chad Zawitz
- Section of Infectious Diseases, Stroger Hospital of Cook County/Cermak Health Services, Chicago, IL, USA
| | - Alla Aroutcheva
- Section of Infectious Diseases, Rush University Medical Center/Cook County Health, Chicago, IL, USA
| | - Darjai Payne
- Section of Infectious Diseases, Rush University Medical Center, Chicago, IL, USA
| | - William Janda
- Department of Pathology, Stroger Hospital of Cook County, Chicago, IL, USA
| | - Michael Schoeny
- College of Nursing, Community Systems and Mental Health Nursing, Rush University Medical Center, Chicago, IL, USA
| | - Stefan J Green
- Director, DNA Services Facility, University of SIllinois at Chicago, Chicago, IL, USA
| | - Evan S Snitkin
- Department of Microbiology and Immunology, Department of Medicine, Division of Infectious Diseases, University of Michigan, Chicago, IL, USA
| | - Robert A Weinstein
- Section of Infectious Diseases, Rush University Medical Center/Cook County Health, Chicago, IL, USA
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10
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Rose R, Nolan DJ, Moot S, Rodriguez C, Cross S, McCarter YS, Neilsen C, Lamers SL. Molecular surveillance of methicillin-resistant Staphylococcus aureus genomes in hospital unexpectedly reveals discordance between temporal and genetic clustering. Am J Infect Control 2021; 49:59-64. [PMID: 32565273 DOI: 10.1016/j.ajic.2020.06.180] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/10/2020] [Accepted: 06/11/2020] [Indexed: 11/30/2022]
Abstract
BACKGROUND The objective of this study was to identify sources and linkages among methicillin-resistant Staphylococcus aureus infections using whole-genome sequencing (WGS). METHODS A total of 56 samples were obtained from all patients with a confirmed MRSA infection over 6 months at University of Florida-Health Jacksonville. Samples were cultured and sequenced; data was analyzed on an automated cloud-based platform. Genetic Clusters were defined as <40 single nucleotide polymorphisms. Temporal Clusters were defined as ≥5 MRSA cases over 3 days. RESULTS We found 7 Genetic Clusters comprising 15 samples. Four Genetic Clusters contained patients with non-overlapping stays (3-10 weeks apart), 3 of which contained patients who shared the same Unit. We also found 5 Temporal Clusters comprising 23 samples, although none of the samples were genetically related. DISCUSSION Results showed that temporal clustering may be a poor indicator of genetic linkage. Shared epidemiological characteristics between patients in Genetic Clusters may point toward previously unidentified hospital sources. Repeated observation of related strains is also consistent with ongoing MRSA transmission within the surrounding high-risk community. CONCLUSIONS WGS is a valuable tool for hospital infection prevention and control.
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Affiliation(s)
| | | | | | | | | | - Yvette S McCarter
- Department of Pathology and Laboratory Medicine, UF Health Jacksonville, Jacksonville, FL
| | - Chad Neilsen
- Department of Infection Prevention & Control, UF Health Jacksonville, Jacksonville, FL
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11
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Illicit drug users, alcoholics, and psychiatric patients: Staphylococcus aureus and methicillin-resistant Staphylococcus aureus colonization on the border between community and healthcare settings. Infect Control Hosp Epidemiol 2020; 42:1544-1546. [PMID: 33261681 DOI: 10.1017/ice.2020.1330] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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12
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Popovich KJ. Intersection of HIV and community-associated methicillin-resistant Staphylococcus aureus. Future Virol 2020. [DOI: 10.2217/fvl-2019-0093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The epidemiology of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has evolved over the past approximately 20 years, with certain populations appearing to have disproportionate risk. Of concern is the potential worsening of S. aureus infections in light of the continued opioid crisis. This review will discuss how CA-MRSA has significantly impacted HIV-infected individuals and address additional factors and populations that are associated with increased risk for MRSA. It will review therapeutic options and infection control strategies as well as highlight how whole genome sequencing can be used to extend traditional epidemiologic analysis and ultimately, inform infection prevention efforts. Continued work identifying those at the highest risk for MRSA, what the best infection prevention settings are in community settings and how to effectively implement and target these strategies is needed. Ultimately, infection control efforts will likely need to extend beyond healthcare settings to effectively and sustainably reduce MRSA infections.
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Affiliation(s)
- Kyle J Popovich
- Associate Professor, Section of Infectious Diseases, Rush University Medical Center, 600 South Paulina St. Suite 143, Chicago, IL 60612, USA
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13
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Mody L, Foxman B, Bradley S, McNamara S, Lansing B, Gibson K, Cassone M, Armbruster C, Mantey J, Min L. Longitudinal Assessment of Multidrug-Resistant Organisms in Newly Admitted Nursing Facility Patients: Implications for an Evolving Population. Clin Infect Dis 2019; 67:837-844. [PMID: 29635360 DOI: 10.1093/cid/ciy194] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 03/29/2018] [Indexed: 01/25/2023] Open
Abstract
Background The spread of multidrug-resistant organisms (MDROs) is a global concern, and much about transmission in healthcare systems remains unknown. To reduce hospital stays, nursing facilities (NFs) have increasingly assumed care of post-acute populations. We estimate the prevalence of MDRO colonization in NF patients on enrollment and discharge to community settings, risk factors for colonization, and rates of acquiring MDROs during the stay. Methods We conducted a prospective, longitudinal cohort study of newly admitted patients in 6 NFs in southeast Michigan using active microbial surveillance of multiple anatomic sites sampled at enrollment, days 14 and 30, and monthly thereafter for up to 6 months. Results We enrolled 651 patients and collected 7526 samples over 1629 visits, with an average of 29 days of follow-up per participant. Nearly all participants were admitted for post-acute care (95%). More than half (56.8%) were colonized with MDROs at enrollment: methicillin-resistant Staphylococcus aureus (MRSA), 16.1%; vancomycin-resistant enterococci (VRE), 33.2%; and resistant gram-negative bacilli (R-GNB), 32.0%. Risk factors for colonization at enrollment included prolonged hospitalization (>14 days), functional disability, antibiotic use, or device use. Rates per 1000 patient-days of acquiring a new MDRO were MRSA, 3.4; VRE, 8.2; and R-GNB, 13.6. MDRO colonization at discharge was similar to that at enrollment (56.4%): MRSA, 18.4%; VRE, 30.3%; and R-GNB, 33.6%. Conclusions Short-stay NF patients exhibit a high prevalence of MDROs near the time of admission, as well as at discharge, and may serve as a reservoir for spread in other healthcare settings. Future interventions to reduce MDROs should specifically target this population.
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Affiliation(s)
- Lona Mody
- Department of Internal Medicine, Division of Geriatric and Palliative Medicine, University of Michigan Medical School.,Geriatrics Research Education and Clinical Center, Veterans Affairs Ann Arbor Healthcare System
| | - Betsy Foxman
- Department of Epidemiology, University of Michigan School of Public Health
| | - Suzanne Bradley
- Infectious Diseases Section, Veterans Affairs Ann Arbor Healthcare System.,Internal Medicine, Division of Infectious Diseases, University of Michigan Medical School, Ann Arbor
| | - Sara McNamara
- Department of Internal Medicine, Division of Geriatric and Palliative Medicine, University of Michigan Medical School
| | - Bonnie Lansing
- Department of Internal Medicine, Division of Geriatric and Palliative Medicine, University of Michigan Medical School
| | - Kristen Gibson
- Department of Internal Medicine, Division of Geriatric and Palliative Medicine, University of Michigan Medical School
| | - Marco Cassone
- Department of Internal Medicine, Division of Geriatric and Palliative Medicine, University of Michigan Medical School
| | - Chelsie Armbruster
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor
| | - Julia Mantey
- Department of Internal Medicine, Division of Geriatric and Palliative Medicine, University of Michigan Medical School
| | - Lillian Min
- Department of Internal Medicine, Division of Geriatric and Palliative Medicine, University of Michigan Medical School.,Geriatrics Research Education and Clinical Center, Veterans Affairs Ann Arbor Healthcare System
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14
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Redmond SN, MacInnis BM, Bopp S, Bei AK, Ndiaye D, Hartl DL, Wirth DF, Volkman SK, Neafsey DE. De Novo Mutations Resolve Disease Transmission Pathways in Clonal Malaria. Mol Biol Evol 2019; 35:1678-1689. [PMID: 29722884 PMCID: PMC5995194 DOI: 10.1093/molbev/msy059] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Detecting de novo mutations in viral and bacterial pathogens enables researchers to reconstruct detailed networks of disease transmission and is a key technique in genomic epidemiology. However, these techniques have not yet been applied to the malaria parasite, Plasmodium falciparum, in which a larger genome, slower generation times, and a complex life cycle make them difficult to implement. Here, we demonstrate the viability of de novo mutation studies in P. falciparum for the first time. Using a combination of sequencing, library preparation, and genotyping methods that have been optimized for accuracy in low-complexity genomic regions, we have detected de novo mutations that distinguish nominally identical parasites from clonal lineages. Despite its slower evolutionary rate compared with bacterial or viral species, de novo mutation can be detected in P. falciparum across timescales of just 1–2 years and evolutionary rates in low-complexity regions of the genome can be up to twice that detected in the rest of the genome. The increased mutation rate allows the identification of separate clade expansions that cannot be found using previous genomic epidemiology approaches and could be a crucial tool for mapping residual transmission patterns in disease elimination campaigns and reintroduction scenarios.
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Affiliation(s)
- Seth N Redmond
- Broad Institute of MIT and Harvard, Cambridge, MA.,Harvard T.H. Chan School of Public Health, Boston, MA
| | - Bronwyn M MacInnis
- Broad Institute of MIT and Harvard, Cambridge, MA.,Harvard T.H. Chan School of Public Health, Boston, MA
| | - Selina Bopp
- Broad Institute of MIT and Harvard, Cambridge, MA.,Harvard T.H. Chan School of Public Health, Boston, MA
| | - Amy K Bei
- Harvard T.H. Chan School of Public Health, Boston, MA.,Department of Parasitology, Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar, Senegal
| | - Daouda Ndiaye
- Harvard T.H. Chan School of Public Health, Boston, MA.,Department of Parasitology, Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar, Senegal
| | - Daniel L Hartl
- Broad Institute of MIT and Harvard, Cambridge, MA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA
| | - Dyann F Wirth
- Broad Institute of MIT and Harvard, Cambridge, MA.,Harvard T.H. Chan School of Public Health, Boston, MA
| | - Sarah K Volkman
- Broad Institute of MIT and Harvard, Cambridge, MA.,Harvard T.H. Chan School of Public Health, Boston, MA.,Department of Nursing, School of Nursing and Health Sciences, Simmons College, Boston, MA, 02115
| | - Daniel E Neafsey
- Broad Institute of MIT and Harvard, Cambridge, MA.,Harvard T.H. Chan School of Public Health, Boston, MA
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15
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Millar EV, Rice GK, Schlett CD, Elassal EM, Cer RZ, Frey KG, Hamilton T, Ellis MW, Tribble DR, Bishop-Lilly KA, Bennett JW. Genomic epidemiology of MRSA infection and colonization isolates among military trainees with skin and soft tissue infection. Infection 2019; 47:729-737. [DOI: 10.1007/s15010-019-01282-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/12/2019] [Indexed: 10/27/2022]
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16
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Lee GC, Dallas SD, Wang Y, Olsen RJ, Lawson KA, Wilson J, Frei CR. Emerging multidrug resistance in community-associated Staphylococcus aureus involved in skin and soft tissue infections and nasal colonization. J Antimicrob Chemother 2018; 72:2461-2468. [PMID: 28859442 DOI: 10.1093/jac/dkx200] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 05/12/2017] [Indexed: 12/21/2022] Open
Abstract
Background Staphylococcus aureus is a major pathogen causing significant morbidity and mortality worldwide. The emergence of MDR S. aureus strains in the community setting has major implications in disease management. However, data regarding the occurrence and patterns of MDR community-associated S. aureus sub-clones is limited. Objectives To use whole-genome sequences to describe the diversity and distribution of resistance mechanisms among community-associated S. aureus isolates. Methods S. aureus isolates from skin and soft tissue infections (SSTIs) and nasal colonization were collected from patients within 10 primary care clinics from 2007 to 2015. The Illumina Miseq platform was used to determine the genome sequences for 144 S. aureus isolates. Phylogenetic and bioinformatics analyses were performed using in silico tools. The resistome was assembled and compared with the phenotypically derived antibiogram. Results Approximately one-third of S. aureus isolates in the South Texas primary care setting were MDR. A higher proportion of SSTI isolates were MDR in comparison with nasal colonization isolates. Individuals with MDR S. aureus SSTIs were more likely to be African American and obese. Furthermore, S. aureus populations are able to acquire and lose antimicrobial resistance genes. USA300 strains were differentiated by a stable chromosomal mutation in gyrA conferring quinolone resistance. The resistomes were highly predictive of antimicrobial resistance phenotypes. Conclusions These findings highlight the high prevalence and epidemiological factors associated with MDR S. aureus strains in the community setting and demonstrate the utility of next-generation sequencing to potentially quicken antimicrobial resistance detection and surveillance for targeted interventions.
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Affiliation(s)
- Grace C Lee
- College of Pharmacy, The University of Texas at Austin, San Antonio, TX, USA.,Pharmacotherapy Education and Research Center, School of Medicine, The University of Texas Health Science Center, San Antonio, TX, USA
| | - Steven D Dallas
- Department of Clinical Laboratory Sciences, School of Health Professions, University of Texas Health Science Center, San Antonio, TX, USA
| | - Yufeng Wang
- Department of Biology, The University of Texas San Antonio, San Antonio, TX, USA
| | - Randall J Olsen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital and Research Institute, Houston, TX, USA
| | - Kenneth A Lawson
- College of Pharmacy, The University of Texas at Austin, San Antonio, TX, USA
| | - James Wilson
- College of Pharmacy, The University of Texas at Austin, San Antonio, TX, USA
| | - Christopher R Frei
- College of Pharmacy, The University of Texas at Austin, San Antonio, TX, USA.,Pharmacotherapy Education and Research Center, School of Medicine, The University of Texas Health Science Center, San Antonio, TX, USA
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17
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Huang YC, Chen CJ, Kuo CC, Lu MC. Emergence, transmission and phylogeny of meticillin-resistant Staphylococcus aureus sequence type 8 (USA300) in Taiwan. J Hosp Infect 2018; 100:355-358. [PMID: 29475012 DOI: 10.1016/j.jhin.2018.02.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 02/14/2018] [Indexed: 11/30/2022]
Abstract
Twenty-seven (0.51%) USA300 isolates were identified from a pool of 5308 meticillin-resistant Staphylococcus aureus (MRSA) isolates collected in Taiwan between 1995 and October 2015, including 12 infecting isolates from 10 patients. The first two isolates were identified in 2005, and 23 isolates have been collected since 2010. Phylogenetic analysis revealed that all the local isolates were closely related to those in North America, and there was a clade consisting of 13 local isolates from 10 patients. MRSA USA300 existed in Taiwan in 2005 or earlier, with increasing identification since 2010. Local transmission of USA300 has occurred in Taiwan after importation from North America.
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Affiliation(s)
- Y-C Huang
- Division of Paediatric Infectious Diseases, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Chang Gung University College of Medicine, Taoyuan, Taiwan.
| | - C-J Chen
- Division of Paediatric Infectious Diseases, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - C-C Kuo
- Division of Paediatric Infectious Diseases, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - M-C Lu
- Department of Medicine, China Medical University Hospital, Taichung, Taiwan; Department of Microbiology and Immunology, School of Medicine, China Medical University, Taichung, Taiwan
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18
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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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19
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Popovich KJ, Snitkin ES, Hota B, Green SJ, Pirani A, Aroutcheva A, Weinstein RA. Genomic and Epidemiological Evidence for Community Origins of Hospital-Onset Methicillin-Resistant Staphylococcus aureus Bloodstream Infections. J Infect Dis 2017; 215:1640-1647. [PMID: 28486667 DOI: 10.1093/infdis/jiw647] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 12/23/2016] [Indexed: 12/12/2022] Open
Abstract
Background We examined whether disparities existed in hospital-onset (HO) Staphylococcus aureus bloodstream infections (BSIs) and used whole-genome sequencing (WGS) to identify factors associated with USA300 transmission networks. Methods We evaluated HO methicillin-susceptible S. aureus (MSSA) and HO methicillin-resistant S. aureus (MRSA) BSIs for 2009-2013 at 2 hospitals and used an adjusted incidence for modeling. WGS and phylogenetic analyses were performed on a sample of USA300 BSI isolates. Epidemiologic data were analyzed in the context of phylogenetic reconstructions. Results On multivariate analysis, male sex, African-American race, and non-Hispanic white race/ethnicity were significantly associated with HO-MRSA BSIs whereas Hispanic ethnicity was negatively associated (rate ratio, 0.41; P = .002). Intermixing of community-onset and HO-USA300 strains on the phylogenetic tree indicates that these strains derive from a common pool. African-American race was the only factor associated with genomic clustering of isolates. Conclusions In a multicenter assessment of HO-S. aureus BSIs, African-American race was significantly associated with HO-MRSA but not MSSA BSIs. There appears to be a nexus of USA300 community and hospital transmission networks, with a community factor being the primary driver. Our data suggest that HO-USA300 BSIs likely are due to colonizing strains acquired in the community before hospitalization. Therefore, prevention efforts may need to extend to the community for maximal benefit.
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Affiliation(s)
- Kyle J Popovich
- Division of Infectious Diseases, Rush University Medical Center/Stroger Hospital of Cook County, Chicago, Illinois
| | - Evan S Snitkin
- Department of Microbiology and Immunology, Division of Infectious Diseases, University of Michigan, Ann Arbor
| | - Bala Hota
- Division of Infectious Diseases, Rush University Medical Center/Stroger Hospital of Cook County, Chicago, Illinois
| | - Stefan J Green
- Department of Microbiology and Immunology, University of Illinois at Chicago, Research Resources Center
| | - Ali Pirani
- Department of Microbiology and Immunology, University of Illinois at Chicago, Research Resources Center
| | - Alla Aroutcheva
- Division of Infectious Diseases, Rush University Medical Center/Stroger Hospital of Cook County, Chicago, Illinois
| | - Robert A Weinstein
- Division of Infectious Diseases, Rush University Medical Center/Stroger Hospital of Cook County, Chicago, Illinois
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20
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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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21
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Popovich KJ, Snitkin ES. Whole Genome Sequencing-Implications for Infection Prevention and Outbreak Investigations. Curr Infect Dis Rep 2017; 19:15. [PMID: 28281083 DOI: 10.1007/s11908-017-0570-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
PURPOSE OF REVIEW Whole genome sequencing (WGS) is a laboratory method that has emerged as a promising tool for epidemiologic investigations. RECENT FINDINGS Genomic epidemiology approaches have been utilized in outbreak settings, community settings, within acute care hospitals, and across healthcare facilities to better understand transmission and spread of potential pathogens. These studies have highlighted how essential robust epidemiologic data is in these analyses as well as how results can be translated into clinical practice and infection control and prevention. Existing studies have highlighted both the promise and challenges of using WGS as an epidemiologic tool in a community and healthcare setting and across a region. Costs for performing and interpreting WGS analyses are decreasing, and availability of and experience with WGS analyses in healthcare epidemiology are increasing. With these favorable trends, this laboratory method soon could emerge as the gold standard for epidemiologic evaluations.
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Affiliation(s)
- Kyle J Popovich
- Department of Internal Medicine, University Infectious Diseases, Rush University Medical Center, Stroger Hospital of Cook County, 600 South Paulina, Suite 143, Chicago, IL, 60612, USA.
| | - Evan S Snitkin
- Department of Microbiology and Immunology, Department of Medicine, Division of Infectious Diseases, Center for Microbial Systems, University of Michigan, 1520D MSRB I, 1150 W. Medical Center Dr., Ann Arbor, MI, 48109-5680, USA
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22
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Azarian T, Daum RS, Petty LA, Steinbeck JL, Yin Z, Nolan D, Boyle-Vavra S, Hanage WP, Salemi M, David MZ. Intrahost Evolution of Methicillin-Resistant Staphylococcus aureus USA300 Among Individuals With Reoccurring Skin and Soft-Tissue Infections. J Infect Dis 2016; 214:895-905. [PMID: 27288537 DOI: 10.1093/infdis/jiw242] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 05/31/2016] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Methicillin-resistant Staphylococcus aureus (MRSA) USA300 is the leading cause of MRSA infections in the United States and has caused an epidemic of skin and soft-tissue infections. Recurrent infections with USA300 MRSA are common, yet intrahost evolution during persistence on an individual has not been studied. This gap hinders the ability to clinically manage recurrent infections and reconstruct transmission networks. METHODS To characterize bacterial intrahost evolution, we examined the clinical courses of 4 subjects with 3-6 recurrent USA300 MRSA infections, using patient clinical data, including antibiotic exposure history, and whole-genome sequencing and phylogenetic analysis of all available MRSA isolates (n = 29). RESULTS Among sequential isolates, we found variability in diversity, accumulation of mutations, and mobile genetic elements. Selection for antimicrobial-resistant populations was observed through both an increase in the number of plasmids conferring multidrug resistance and strain replacement by a resistant population. Two of 4 subjects had strain replacement with a genetically distinct USA300 MRSA population. DISCUSSIONS During a 5-year period in 4 subjects, we identified development of antimicrobial resistance, intrahost evolution, and strain replacement among isolates from patients with recurrent MRSA infections. This calls into question the efficacy of decolonization to prevent recurrent infections and highlights the adaptive potential of USA300 and the need for effective sampling.
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Affiliation(s)
- Taj Azarian
- Center for Communicable Disease Dynamics, Department of Epidemiology, T. H. Chan School of Public Health, Harvard University, Boston, Massachusetts
| | | | | | | | | | - David Nolan
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine Emerging Pathogens Institute, University of Florida, Gainesville
| | | | - W P Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, T. H. Chan School of Public Health, Harvard University, Boston, Massachusetts
| | - Marco Salemi
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine Emerging Pathogens Institute, University of Florida, Gainesville
| | - Michael Z David
- Department of Pediatrics Department of Medicine, University of Chicago, Illinois
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23
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Toleman MS, Reuter S, Coll F, Harrison EM, Blane B, Brown NM, Török ME, Parkhill J, Peacock SJ. Systematic Surveillance Detects Multiple Silent Introductions and Household Transmission of Methicillin-Resistant Staphylococcus aureus USA300 in the East of England. J Infect Dis 2016; 214:447-53. [PMID: 27122590 PMCID: PMC4936647 DOI: 10.1093/infdis/jiw166] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 04/14/2016] [Indexed: 11/25/2022] Open
Abstract
Background. The spread of USA300 methicillin-resistant Staphylococcus aureus (MRSA) across the United States resulted in an epidemic of infections. In Europe, only sporadic cases or small clusters of USA300 infections are described, and its prevalence in England is unknown. We conducted prospective surveillance for USA300 in the east of England. Methods. We undertook a 12-month prospective observational cohort study of all individuals with MRSA isolated from community and hospital samples submitted to a microbiology laboratory. At least 1 MRSA isolate from each individual underwent whole-genome sequencing. USA300 was identified on the basis of sequence analysis, and phylogenetic comparisons were made between these and USA300 genomes from the United States. Results. Between April 2012 and April 2013, we sequenced 2283 MRSA isolates (detected during carriage screening and in clinical samples) from 1465 individuals. USA300 was isolated from 24 cases (1.6%). Ten cases (42%) had skin and soft tissue infection, and 2 cases had invasive disease. Phylogenetic analyses identified multiple introductions and household transmission of USA300. Conclusions. Use of a diagnostic laboratory as a sentinel for surveillance has identified repeated introductions of USA300 in eastern England in 2012–2013, with evidence for limited transmission. Our results show how systematic surveillance could provide an early warning of strain emergence and dissemination.
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Affiliation(s)
- Michelle S Toleman
- University of Cambridge Wellcome Trust Sanger Institute Cambridge University Hospitals NHS Foundation Trust
| | | | | | | | | | - Nicholas M Brown
- Cambridge University Hospitals NHS Foundation Trust Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge
| | - M Estée Török
- University of Cambridge Cambridge University Hospitals NHS Foundation Trust Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge
| | | | - Sharon J Peacock
- University of Cambridge Wellcome Trust Sanger Institute Cambridge University Hospitals NHS Foundation Trust London School of Hygiene and Tropical Medicine, United Kingdom
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