Whole-Genome Sequencing (WGS) of Carbapenem-Resistant K. pneumoniae Isolated in Long-Term Care Facilities in the Northern Italian Region

K. pneumoniae (KPN) is one of the widest spread bacteria in which combined resistance to several antimicrobial groups is frequent. The most common β-lactamases found in K. pneumoniae are class A carbapenemases, both chromosomal-encoded (i.e., NMCA, IMI-1) and plasmid-encoded (i.e., GES-enzymes, IMI-2), VIM, IMP, NDM, OXA-48, and extended-spectrum β-lactamases (ESBLs) such as CTX-M enzymes. In the present study, a total of 68 carbapenem-resistant KPN were collected from twelve long-term care facilities (LTCFs) in the Northern Italian region. The whole-genome sequencing (WGS) of each KPN strain was determined using a MiSeq Illumina sequencing platform and analysed by a bacterial analysis pipeline (BAP) tool. The WGS analysis showed the prevalence of ST307, ST512, and ST37 as major lineages diffused among the twelve LTCFs. The other lineages found were: ST11, ST16, ST35, ST253, ST273, ST321, ST416, ST1519, ST2623, and ST3227. The blaKPC-2, blaKPC-3, blaKPC-9, blaSHV-11, blaSHV-28, blaCTX-M-15, blaOXA-1, blaOXA-9, blaOXA-23, qnrS1, qnrB19, qnrB66, aac(6′)-Ib-cr, and fosA were the resistance genes widespread in most LTCFs. In this study, we demonstrated the spreading of thirteen KPN lineages among the LTCFs. Additionally, KPC carbapenemases are the most widespread β-lactamase.

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Transmission Clusters of Methicillin-Resistant Staphylococcus Aureus in Long-Term Care Facilities Based on Whole-Genome Sequencing

Infection Control and Hospital Epidemiology ◽

10.1017/ice.2016.41 ◽

2016 ◽

Vol 37 (6) ◽

pp. 685-691 ◽

Cited By ~ 7

Author(s):

O. Colin Stine ◽

Shana Burrowes ◽

Sophia David ◽

J. Kristie Johnson ◽

Mary-Claire Roghmann

Keyword(s):

Staphylococcus Aureus ◽

Genome Sequencing ◽

Long Term Care ◽

Care Facility ◽

Whole Genome ◽

Term Care ◽

Long Term Care Facility ◽

Care Facilities ◽

Mrsa Colonization

OBJECTIVETo define how often methicillin-resistant Staphylococcus aureus (MRSA) is spread from resident to resident in long-term care facilities using whole-genome sequencingDESIGNProspective cohort studySETTINGA long-term care facilityPARTICIPANTSElderly residents in a long-term care facilityMETHODSCultures for MRSA were obtained weekly from multiple body sites from residents with known MRSA colonization over 12-week study periods. Simultaneously, cultures to detect MRSA acquisition were obtained weekly from 2 body sites in residents without known MRSA colonization. During the first 12-week cycle on a single unit, we sequenced 8 MRSA isolates per swab for 2 body sites from each of 6 residents. During the second 12-week cycle, we sequenced 30 MRSA isolates from 13 residents with known MRSA colonization and 3 residents who had acquired MRSA colonization.RESULTSMRSA isolates from the same swab showed little genetic variation between isolates with the exception of isolates from wounds. The genetic variation of isolates between body sites on an individual was greater than that within a single body site with the exception of 1 sample, which had 2 unrelated strains among the 8 isolates. In the second cycle, 10 of 16 residents colonized with MRSA (63%) shared 1 of 3 closely related strains. Of the 3 residents with newly acquired MRSA, 2 residents harbored isolates that were members of these clusters.CONCLUSIONSPoint prevalence surveys with whole-genome sequencing of MRSA isolates may detect resident-to-resident transmission more accurately than routine surveillance cultures for MRSA in long-term care facilities.Infect Control Hosp Epidemiol 2016;37:685–691

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A protracted iGAS outbreak in a long-term care facility 2014–2015: control measures and the use of whole-genome sequencing

Journal of Hospital Infection ◽

10.1016/j.jhin.2019.12.004 ◽

2020 ◽

Vol 105 (1) ◽

pp. 70-77

Author(s):

S. Degala ◽

R. Puleston ◽

R. Bates ◽

R. Borges-Stewart ◽

J. Coelho ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Long Term Care ◽

Care Facility ◽

Control Measures ◽

Whole Genome ◽

Term Care ◽

Term Care Facility ◽

Long Term Care Facility

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415. A Whole Genome Sequencing Analysis of a Multi-unit Long-term Care Facility COVID-19 Outbreak

Open Forum Infectious Diseases ◽

10.1093/ofid/ofab466.615 ◽

2021 ◽

Vol 8 (Supplement_1) ◽

pp. S308-S308

Author(s):

Ling Yuan Kong ◽

Leighanne Parkes ◽

Yves Longtin ◽

Christina Greenaway ◽

Jerry Zaharatos ◽

...

Keyword(s):

High Risk ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Long Term Care ◽

Care Facility ◽

Whole Genome ◽

Sequencing Analysis ◽

Term Care ◽

Phone Interview

Abstract Background The coronavirus disease (COVID-19) pandemic has affected residents in long-term care facilities (LTCF) significantly. Understanding transmission dynamics in this setting is crucial to control the spread of COVID-19 in this population. Using whole genome sequencing (WGS) of SARS-CoV-2, we aimed to delineate the points of introduction and transmission pathways in a large LTCF in Quebec, Canada. Methods Between 2020-10-28 and 2021-01-09, COVID-19 cases occurred in 102 residents and 111 HCW at a 387-bed LTCF; cases were distributed in 11 units on 6 floors. As part of outbreak analysis, SARS-CoV-2 isolates underwent WGS using the Oxford Nanopore Minion and the Artic V3 protocol. Lineage attribution and sequence types (ST, within 3 mutations) were assigned based on Pangolin classification and variant analysis. Epidemiologic data including date of positive PCR test, resident room number and HCW work location were collected. Self-reported high-risk exposures were collected by HCW questionnaire via phone interview after consent. Cases and their ST, geo-temporal relations and HCW-reported exposures were examined via network plots and geography-based epidemic curves to infer points of introduction and paths of transmission. Results Of 170 isolates available from 100/102 residents and 70/111 HCW, 130 (76.4%) were successfully sequenced. Phylogenetic analysis revealed 7 separate introductions to the LTCF. Grouping of ST by units was observed, with temporal appearance of ST supporting HCW introduction in 7/11 units. Proportion of phone interview completion was low at 35% (26/70). Few HCW recalled specific high-risk exposures. Recalled exposures supported by genetic linkage revealed potential between-unit introductions from HCW-to-HCW transmission at work and outside the workplace (e.g. carpooling). On one unit, a wandering resident was identified as a likely source of transmission to other residents (Figure 1). Network plot of cases clustered by geographic unit, colour-coded by sequence type. Circles represent residents; addition signs represent healthcare workers. Blue lines represent identified high-risk exposures. Node labels represent floor and unit identifiers; 2 units per floor. Conclusion We demonstrate the complex genomic epidemiology of a multi-unit LTCF outbreak, putting into evidence the importance of a multi-faceted approach to limit transmission. This analysis highlights the utility of using WGS to uncover unsuspected transmission routes, such as HCW contact outside work, which can prompt new infection control measures. Disclosures All Authors: No reported disclosures

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Environmental transmission of Clostridioides difficile ribotype 027 at a long-term care facility; an outbreak investigation guided by whole genome sequencing

Infection Control and Hospital Epidemiology ◽

10.1017/ice.2018.230 ◽

2018 ◽

Vol 39 (11) ◽

pp. 1322-1329 ◽

Cited By ~ 7

Author(s):

Bradley T. Endres ◽

Kierra M. Dotson ◽

Kelley Poblete ◽

Jacob McPherson ◽

Chris Lancaster ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Molecular Typing ◽

Long Term Care ◽

Care Facility ◽

Whole Genome ◽

Term Care ◽

Long Term Care Facility ◽

Ribotype 027

AbstractObjectiveThis article describes a CDI outbreak in a long-term care (LTC) facility that used molecular typing techniques and whole-genome sequencing to identify widespread dissemination of the clonal strain in the environment which was successfully removed after terminal cleaning.SettingThis study was conducted in a long-term care facility in Texas.MethodsA recently hospitalized LTC patient was diagnosed with CDI followed shortly thereafter by 7 subsequent CDI cases. A stool specimen was obtained from each patient for culturing and typing. An environmental point-prevalence study of the facility was conducted before and after terminal cleaning of the facility to assess environmental contamination. Cultured isolates were typed using ribotyping, multilocus variant analysis, and whole-genome sequencing.ResultsStool samples were available for 5 of 8 patients; of these specimens, 4 grew toxigenic C. difficile ribotype 027. Of 50 environmental swab samples collected throughout the facility prior to the facility-wide terminal cleaning, 19 (38%) grew toxigenic C. difficile (most commonly ribotype 027, 79%). The terminal cleaning was effective at reducing C. difficile spores in the environment and at eradicating the ribotype 027 strain (P<.001). Using multilocus variance analysis and whole-genome sequencing, clinical and environmental strains were highly related and, in some cases, were identical.ConclusionUsing molecular typing techniques, we demonstrated reduced environmental contamination with toxigenic C. difficile and the eradication of a ribotype 027 clone. These techniques may help direct infection control efforts and decrease the burden of CDI in the healthcare system.

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Active surveillance for carbapenem-resistant Enterobacteriaceae, vancomycin-resistant enterococci and toxigenic Clostridium difficile among patients transferred from long-term care facilities in Korea

Journal of Hospital Infection ◽

10.1016/j.jhin.2018.02.017 ◽

2018 ◽

Vol 99 (4) ◽

pp. 487-491 ◽

Cited By ~ 4

Author(s):

J-H. Hwang ◽

J.S. Park ◽

E. Lee ◽

J.Y. Bae ◽

K-H. Song ◽

...

Keyword(s):

Clostridium Difficile ◽

Active Surveillance ◽

Long Term Care ◽

Term Care ◽

Carbapenem Resistant ◽

Vancomycin Resistant Enterococci ◽

Care Facilities ◽

Vancomycin Resistant ◽

Carbapenem Resistant Enterobacteriaceae

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Establishment of a Statewide Network for Carbapenem-Resistant Enterobacteriaceae Prevention in a Low-Incidence Region

Infection Control and Hospital Epidemiology ◽

10.1086/675605 ◽

2014 ◽

Vol 35 (4) ◽

pp. 356-361 ◽

Cited By ~ 15

Author(s):

Christopher D. Pfeiffer ◽

Margaret C. Cunningham ◽

Tasha Poissant ◽

Jon P. Furuno ◽

John M. Townes ◽

...

Keyword(s):

Acute Care ◽

Infection Prevention ◽

Long Term Care ◽

Term Care ◽

Carbapenem Resistant ◽

Care Facilities ◽

Low Incidence ◽

Acute Care Facilities ◽

Carbapenem Resistant Enterobacteriaceae

Objective.To establish a statewide network to detect, control, and prevent the spread of carbapenem-resistant Enterobacteriaceae (CRE) in a region with a low incidence of CRE infection.Design.Implementation of the Drug Resistant Organism Prevention and Coordinated Regional Epidemiology (DROP-CRE) Network.Setting and Participants.Oregon infection prevention and microbiology laboratory personnel, including 48 microbiology laboratories, 62 acute care facilities, and 140 long-term care facilities.Methods.The DROP-CRE working group, comprising representatives from academic institutions and public health, convened an interdisciplinary advisory committee to assist with planning and implementation of CRE epidemiology and control efforts. The working group established a statewide CRE definition and surveillance plan; increased the state laboratory capacity to perform the modified Hodge test and polymerase chain reaction for carbapenemases in real time; and administered surveys that assessed the needs and capabilities of Oregon infection prevention and laboratory personnel. Results of these inquiries informed CRE education and the response plan.Results.Of 60 CRE reported from November 2010 through April 2013, only 3 were identified as carbapenemase producers; the cases were not linked, and no secondary transmission was found. Microbiology laboratories, acute care facilities, and long-term care facilities reported lacking carbapenemase testing capability, reliable interfacility communication, and CRE awareness, respectively. Survey findings informed the creation of the Oregon CRE Toolkit, a state-specific CRE guide booklet.Conclusions.A regional epidemiology surveillance and response network has been implemented in Oregon in advance of widespread CRE transmission. Prospective surveillance will determine whether this collaborative approach will be successful at forestalling the emergence of this important healthcare-associated pathogen.

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Carbapenem-Resistant Enterobacterales in Long-Term Care Facilities: A Global and Narrative Review

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2021.601968 ◽

2021 ◽

Vol 11 ◽

Author(s):

Hsin-Yu Chen ◽

Shio-Shin Jean ◽

Yu-Lin Lee ◽

Min-Chi Lu ◽

Wen-Chien Ko ◽

...

Keyword(s):

United States ◽

Mechanical Ventilation ◽

Long Term Care ◽

The United States ◽

Sequence Type ◽

Health Concern ◽

Term Care ◽

Carbapenem Resistant ◽

Care Facilities

The emergence of carbapenem-resistant Enterobacterales (CRE) has become a major public health concern. Moreover, its colonization among residents of long-term care facilities (LTCFs) is associated with subsequent infections and mortality. To further explore the various aspects concerning CRE in LTCFs, we conducted a literature review on CRE colonization and/or infections in long-term care facilities. The prevalence and incidence of CRE acquisition among residents of LTCFs, especially in California, central Italy, Spain, Japan, and Taiwan, were determined. There was a significant predominance of CRE in LTCFs, especially in high-acuity LTCFs with mechanical ventilation, and thus may serve as outbreak centers. The prevalence rate of CRE in LTCFs was significantly higher than that in acute care settings and the community, which indicated that LTCFs are a vital reservoir for CRE. The detailed species and genomic analyses of CRE among LTCFs reported that Klebsiella pneumoniae is the primary species in the LTCFs in the United States, Spain, and Taiwan. KPC-2-containing K. pneumoniae strains with sequence type 258 is the most common sequence type of KPC-producing K. pneumoniae in the LTCFs in the United States. IMP-11- and IMP-6-producing CRE were commonly reported among LTCFs in Japan. OXA-48 was the predominant carbapenemase among LTCFs in Spain. Multiple risk factors associated with the increased risk for CRE acquisition in LTCFs were found, such as comorbidities, immunosuppressive status, dependent functional status, usage of gastrointestinal devices or indwelling catheters, mechanical ventilation, prior antibiotic exposures, and previous culture reports. A high CRE acquisition rate and prolonged CRE carriage duration after colonization were found among residents in LTCFs. Moreover, the patients from LTCFs who were colonized or infected with CRE had poor clinical outcomes, with a mortality rate of up to 75% in infected patients. Infection prevention and control measures to reduce CRE in LTCFs is important, and could possibly be controlled via active surveillance, contact precautions, cohort staffing, daily chlorhexidine bathing, healthcare-worker education, and hand-hygiene adherence.

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Invasive pneumococcal strain distributions and isolate clusters associated with persons experiencing homelessness during 2018

Clinical Infectious Diseases ◽

10.1093/cid/ciaa1680 ◽

2020 ◽

Author(s):

Benjamin J Metcalf ◽

Sopio Chochua ◽

Hollis Walker ◽

Theresa Tran ◽

Zhongya Li ◽

...

Keyword(s):

Pneumococcal Disease ◽

Long Term Care ◽

Whole Genome Sequence ◽

Whole Genome ◽

Term Care ◽

Pneumococcal Strain ◽

Care Facilities ◽

The Usa ◽

Common Serotypes

Abstract Objectives We aimed to characterize invasive pneumococcal disease (IPD) isolates collected from multistate surveillance in the USA during 2018 and examine within-serotype propensities of isolates to form related clusters. Methods We predicted strain features using whole genome sequence obtained from 2885 IPD isolates obtained through the Center for Disease Control and Prevention’s Active Bacterial Core surveillance (ABCs) that has a surveillance population of approximately 34.5 million individuals distributed among 10 states. Phylogenetic analysis was provided for serotypes accounting for >27 isolates. Results Thirteen-valent conjugate vaccine (PCV13) serotypes together with 6C accounted for 23/105 (21.9%) of isolates from children aged <5 years and 820/2780 (29.5%) isolates from those aged >5 years. The most common serotypes from adult IPD isolates were serotypes 3 (413/2780, 14.9%), 22F (291/2780, 10.5%) and 9N (191/2780, 6.9%). Among children IPD isolates, serotypes 15BC (18/105, 17.1%), 3 (11/105, 10.5%) and 33F (10/105, 9.5%) were most common. Serotypes 4, 12F, 20, and 7F had the highest proportions of isolates that formed related clusters together with highest proportions of isolates from persons experiencing homelessness (PEH). Among 84 isolates from long-term care facilities, two instances of highly related isolate pairs from co-residents were identified. Conclusions Non-PCV13 serotypes accounted for more than 70% of IPD in ABCs, however PCV13 serotype 3 is the most common IPD serotype overall. Serotypes most common among PEH were more often associated with temporally related clusters identified both among PEH and among persons not reportedly experiencing homelessness.

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