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. 2022 Aug 24;226(2):332-341.
doi: 10.1093/infdis/jiac058.

Invasive Pneumococcal Disease Clusters Disproportionally Impact Persons Experiencing Homelessness, Injecting Drug Users, and the Western United States

Bernard Beall  1   2 , Sopio Chochua  3 , Zhongya Li  4 , Theresa Tran  4 , Jasmine Varghese  4 , Lesley McGee  3 , Yuan Li  3 , Benjamin J Metcalf  3
Affiliations

Invasive Pneumococcal Disease Clusters Disproportionally Impact Persons Experiencing Homelessness, Injecting Drug Users, and the Western United States

Bernard Beall et al. J Infect Dis. .

Abstract

Background: Invasive pneumococcal disease (IPD) isolates forming genomic clusters can reflect rapid disease transmission between vulnerable individuals.

Methods: We performed whole genome sequencing of 2820 IPD isolates recovered during 2019 through Centers for Disease Control and Prevention's Active Bacterial Core surveillance to provide strain information (serotypes, resistance, genotypes), and 2778 of these genomes were analyzed to detect highly related genomic clusters.

Results: Isolates from persons experiencing homelessness (PEH) were more often within genomic clusters than those from persons not experiencing homelessness (PNEH) (105/198 [53.0%] vs 592/2551 [23.2%]; P < .001). The 4 western sites accounted for 33.4% (929/2778) of isolates subjected to cluster analysis yet accounted for 48.7% (343/705) of clustering isolates (P < .001) and 75.8% (150/198) of isolates recovered from PEH (P < .001). Serotypes most frequent among PEH were (in rank order) 12F, 4, 3, 9N, 8, 20, and 22F, all of which were among the 10 serotypes exhibiting the highest proportions of clustering isolates among all cases. These serotypes accounted for 44.9% (1265/2820) of all IPD cases and are included within available vaccines.

Conclusions: We identified serotype-specific and geographic differences in IPD transmission. We show the vulnerability of PEH within different regions to rapidly spreading IPD transmission networks representing several pneumococcal serotypes included in available vaccines.

Keywords: adult transmission; genomic clustering; invasive pneumococcal disease.

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Conflict of interest statement

Potential conflicts of interest. All authors: No reported conflicts of interest.

All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed.

Figures

Figure 1.
Figure 1.
Distribution of Active Bacterial Core surveillance serotypes during 2019 for 2820 total isolates. Residence status (people not experiencing homelessness [PNEH], people experiencing homelessness [PEH], and unknown residency) are indicated. Percentages of clustering isolates from all cases (black dots) and from PEH (red dots) are indicated. Only isolates of known residence status were used to determine percentage of clustering from PEH alone.
Figure 2.
Figure 2.
A, Total Active Bacterial Core surveillance (ABCs) invasive pneumococcal disease (IPD) isolates per state during 2019, subdivided by residence status. Percentages of total cluster isolates from all cases and from people experiencing homelessness (PEH) are indicated. Department of Housing and Urban Development (HUD) estimates for PEH are provided where possible above each column. A range is provided for Tennessee based upon HUD estimates and overlapping ABCs counties [13]. B, Year 2019 distributions and proportion of total isolates from PEH per state, subdivided by serotype. C, Clustering isolates recovered from PEH within individual ABCs sites, subdivided by serotype. Within each site is indicated the percentages of isolates from PEH, from all clustering isolates, and of total isolates. D, Distributions of all clustering isolates within individual ABCs sites. The proportion of clustering isolates to total isolates is indicated.
Figure 3.
Figure 3.
A, Core phylogeny of serotype 3 Active Bacterial Core surveillance (ABCs) isolates (427 of the 432 characterized). There are 17 339 variable positions depicted in the phylogeny. Legends for this and all other phylogenies depicted employ the same scheme as follows: Clustering isolates are color coded according to state. Isolates from people experiencing homelessness (PEH), injecting drug users (IDUs), individuals from long-term care facilities (LTCFs), and individuals <5 years of age are indicated. The 2 adjacent parentheses indicate a cluster of 2 cases within the same LTCF as indicated in text. The phylogeny separates recently described clade 2 sequence type (ST) 180 indicated in square shape (phylogeny in agreement with penicillin binding protein (PBP) types identical to or related to 1a-2/2b-0/2x-2) from clade 1 [20]. There are only 7 non-CC180 outliers within the surveillance isolates that are depicted extending far outward. A cluster of 4 penicillin-nonsusceptible clade 1 isolates is indicated. B, Core phylogeny of serotype 22F ABCs isolates (266 of the 273 characterized). There are 14 825 variable positions depicted in the phylogeny. Clustering isolates are color coded according to state. Isolates from PEH, IDUs, individuals from LTCFs, and individuals <5 years of age are indicated. All isolates are within CC433 except for the 11 extending far outward. State abbreviations: CA, California; CO, Colorado; CT, Connecticut; GA, Georgia; MD, Maryland; MN, Minnesota; NY, New York; OR, Oregon; TN, Tennessee.
Figure 4.
Figure 4.
A, Core phylogeny of serotype 12F Active Bacterial Core surveillance (ABCs) isolates (all 102 characterized). The phylogeny is based upon 13 763 variable positions. All isolates are within CC220/218 except for the 5 extending far outward. B, Core phylogeny of serotype 4 ABCs isolates (all 75 characterized). The phylogeny is based upon 11 002 variable positions. There are 2 main clonal complexes depicted. C, Core phylogeny of serotype 20 ABCs isolates (all 98 characterized). The phylogeny is based upon 12 850 variable positions. There are 3 main clonal complexes depicted. Abbreviations: CA, California; CO, Colorado; CT, Connecticut; GA, Georgia; IDU, injecting drug user; LTCF, long-term care facility; MD, Maryland; MN, Minnesota; NY, New York; OR, Oregon; PEH, people experiencing homelessness; ST, sequence type; TN, Tennessee.
Figure 5.
Figure 5.
A, Core phylogeny of serotype 8 Active Bacterial Core surveillance (ABCs) isolates (125 of the 129 characterized). The phylogeny is based upon 14 795 variable positions. There are 3 main clonal complexes depicted. B, Core phylogeny of serotype 7F ABCs isolates (all 17 characterized). The phylogeny is based upon 3314 variable positions. All isolates were sequence type 191. C, Core phylogeny of serotype 28A ABCs isolates (all 17 characterized). The phylogeny is based upon 3153 variable positions. There is a single broad clonal complex depicted. Abbreviations: CA, California; CO, Colorado; CT, Connecticut; GA, Georgia; IDU, injecting drug user; LTCF, long-term care facility; MD, Maryland; MN, Minnesota; NY, New York; OR, Oregon; PEH, people experiencing homelessness; ST, sequence type; TN, Tennessee.
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