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

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

Microorganisms ◽

10.3390/microorganisms9091985 ◽

2021 ◽

Vol 9 (9) ◽

pp. 1985

Author(s):

Alessandra Piccirilli ◽

Sabrina Cherubini ◽

Anna Azzini ◽

Evelina Tacconelli ◽

Giuliana Lo Cascio ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Long Term Care ◽

Whole Genome ◽

Italian Region ◽

Term Care ◽

Sequencing Platform ◽

Carbapenem Resistant ◽

Care Facilities

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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