Last data update: Jul 01, 2024. (Total: 47134 publications since 2009)
Records 1-9 (of 9 Records) |
Query Trace: McKee CD [original query] |
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Evaluation of the US COVID-19 Scenario Modeling Hub for informing pandemic response under uncertainty
Howerton E , Contamin L , Mullany LC , Qin M , Reich NG , Bents S , Borchering RK , Jung SM , Loo SL , Smith CP , Levander J , Kerr J , Espino J , van Panhuis WG , Hochheiser H , Galanti M , Yamana T , Pei S , Shaman J , Rainwater-Lovett K , Kinsey M , Tallaksen K , Wilson S , Shin L , Lemaitre JC , Kaminsky J , Hulse JD , Lee EC , McKee CD , Hill A , Karlen D , Chinazzi M , Davis JT , Mu K , Xiong X , Pastore YPiontti A , Vespignani A , Rosenstrom ET , Ivy JS , Mayorga ME , Swann JL , España G , Cavany S , Moore S , Perkins A , Hladish T , Pillai A , Ben Toh K , Longini I Jr , Chen S , Paul R , Janies D , Thill JC , Bouchnita A , Bi K , Lachmann M , Fox SJ , Meyers LA , Srivastava A , Porebski P , Venkatramanan S , Adiga A , Lewis B , Klahn B , Outten J , Hurt B , Chen J , Mortveit H , Wilson A , Marathe M , Hoops S , Bhattacharya P , Machi D , Cadwell BL , Healy JM , Slayton RB , Johansson MA , Biggerstaff M , Truelove S , Runge MC , Shea K , Viboud C , Lessler J . Nat Commun 2023 14 (1) 7260 Our ability to forecast epidemics far into the future is constrained by the many complexities of disease systems. Realistic longer-term projections may, however, be possible under well-defined scenarios that specify the future state of critical epidemic drivers. Since December 2020, the U.S. COVID-19 Scenario Modeling Hub (SMH) has convened multiple modeling teams to make months ahead projections of SARS-CoV-2 burden, totaling nearly 1.8 million national and state-level projections. Here, we find SMH performance varied widely as a function of both scenario validity and model calibration. We show scenarios remained close to reality for 22 weeks on average before the arrival of unanticipated SARS-CoV-2 variants invalidated key assumptions. An ensemble of participating models that preserved variation between models (using the linear opinion pool method) was consistently more reliable than any single model in periods of valid scenario assumptions, while projection interval coverage was near target levels. SMH projections were used to guide pandemic response, illustrating the value of collaborative hubs for longer-term scenario projections. |
Bats are key hosts in the radiation of mammal-associated Bartonella bacteria (preprint)
McKee CD , Bai Y , Webb CT , Kosoy MY . bioRxiv 2020 2020.04.03.024521 Bats are notorious reservoirs of several zoonotic diseases and may be uniquely tolerant of infection among mammals. Broad sampling has revealed the importance of bats in the diversification and spread of viruses and eukaryotes to other animal hosts. Vector-borne bacteria of the genus Bartonella are prevalent and diverse in mammals globally and recent surveys have revealed numerous Bartonella lineages in bats. We assembled a sequence database of Bartonella strains, consisting of nine genetic loci from 209 previously characterized lineages and 121 new cultured strains from bats, and used these data to perform the most comprehensive phylogenetic analysis of Bartonella to date. This analysis included estimation of divergence dates using a molecular clock and ancestral reconstruction of host associations and geography. We estimate that Bartonella began infecting mammals 62 million years ago near the Cretaceous-Paleogene boundary. Additionally, the radiation of particular Bartonella clades correlate strongly to the timing of diversification and biogeography of mammalian hosts. Bats were inferred to be the ancestral hosts of all mammal-associated Bartonella and appear to be responsible for the early geographic expansion of the genus. We conclude that bats have had a deep influence on the evolutionary radiation of Bartonella bacteria and their spread to other mammalian orders. These results support a ‘bat seeding’ hypothesis that could explain similar evolutionary patterns in other mammalian parasite taxa. Application of such phylogenetic tools as we have used to other taxa may reveal the general importance of bats in the ancient diversification of mammalian parasites.Significance statement Discovering the evolutionary history of infectious agents in animals is important for understanding the process of host adaptation and the origins of human diseases. To clarify the evolution of the Bartonella genus, which contains important human pathogens, we performed phylogenetic analysis on a broad diversity of Bartonella strains, including novel strains from bats. Our results indicate that Bartonella clades diversified along with their mammal hosts over millions of years. Bats appear to be especially important in the early radiation and geographic dispersal of Bartonella lineages. These patterns are consistent with research indicating a chiropteran origin of important human viruses and eukaryotic parasites, suggesting that bats may play a unique role as historical sources of infections to other hosts. |
Bats are key hosts in the radiation of mammal-associated Bartonella bacteria.
McKee CD , Bai Y , Webb CT , Kosoy MY . Infect Genet Evol 2021 89 104719 Bats are notorious reservoirs of several zoonotic diseases and may be uniquely tolerant of infection among mammals. Broad sampling has revealed the importance of bats in the diversification and spread of viruses and eukaryotes to other animal hosts. Vector-borne bacteria of the genus Bartonella are prevalent and diverse in mammals globally and recent surveys have revealed numerous Bartonella lineages in bats. We assembled a sequence database of Bartonella strains, consisting of nine genetic loci from 209 previously characterized Bartonella lineages and 121 new cultured isolates from bats, and used these data to perform a comprehensive phylogenetic analysis of the Bartonella genus. This analysis included estimation of divergence dates using a molecular clock and ancestral reconstruction of host associations and geography. We estimate that Bartonella began infecting mammals 62 million years ago near the Cretaceous-Paleogene boundary. Additionally, the radiation of particular Bartonella clades correlate strongly to the timing of diversification and biogeography of mammalian hosts. Bats were inferred to be the ancestral hosts of all mammal-associated Bartonella and appear to be responsible for the early geographic expansion of the genus. We conclude that bats have had a deep influence on the evolutionary radiation of Bartonella bacteria and their spread to other mammalian orders. These results support a 'bat seeding' hypothesis that could explain similar evolutionary patterns in other mammalian parasite taxa. Application of such phylogenetic tools as we have used to other taxa may reveal the general importance of bats in the ancient diversification of mammalian parasites. |
Host phylogeny, geographic overlap, and roost sharing shape parasite communities in European bats
McKee CD , Krawczyk AI , Sandor AD , Gorfol T , Foldvari M , Foldvari G , Dekeukeleire D , Haarsma AJ , Kosoy MY , Webb CT , Sprong H . Front Ecol Evol 2019 7 How multitrophic relationships between wildlife communities and their ectoparasitic vectors interact to shape the diversity of vector-borne microorganisms is poorly understood. Nested levels of dependence among microbes, vectors, and vertebrate hosts may have complicated effects on both microbial community assembly and evolution. We examined Bartonella sequences from European bats and their ectoparasites with a combination of network analysis, Bayesian phylogenetics, tip-association and cophylogeny tests, and linear regression to understand the ecological and evolutionary processes that shape parasite communities. We detected seven bat-ectoparasite-Bartonella communities that can be differentiated based on bat families and roosting patterns. Tips of the Bartonella tree were significantly clustered by host taxonomy and geography. We also found significant evidence of evolutionary congruence between bat host and Bartonella phylogenies, indicating that bacterial species have evolved to infect related bat species. Exploring these ecological and evolutionary associations further, we found that sharing of Bartonella species among bat hosts was strongly associated with host phylogenetic distance and roost sharing and less strongly with geographic range overlap. Ectoparasite sharing between hosts was strongly predicted by host phylogenetic distance, roost sharing, and geographic overlap but had no additive effect on Bartonella sharing. Finally, historical Bartonella host-switching was more frequent for closely related bats after accounting for sampling bias among bat species. This study helps to disentangle the complex ecology and evolution of Bartonella bacteria in bat species and their arthropod vectors. Our work provides insight into the important mechanisms that partition parasite communities among hosts, particularly the effect of host phylogeny and roost sharing, and could help to elucidate the evolutionary patterns of other diverse vector-borne microorganisms. |
Acquisition of Bartonella elizabethae by experimentally exposed oriental rat fleas (Xenopsylla cheopis; Siphonaptera, Pulicidae) and excretion of Bartonella DNA in flea feces
McKee CD , Osikowicz LM , Schwedhelm TR , Maes SE , Enscore RE , Gage KL , Kosoy MY . J Med Entomol 2018 55 (5) 1292-1298 Few studies have been able to provide experimental evidence of the ability of fleas to maintain rodent-associated Bartonella infections and excrete these bacteria. These data are important for understanding the transmission cycles and prevalence of these bacteria in hosts and vectors. We used an artificial feeding approach to expose groups of the oriental rat flea (Xenopsylla cheopis Rothschild; Siphonaptera, Pulicidae) to rat blood inoculated with varying concentrations of Bartonella elizabethae Daly (Bartonellaceae: Rhizobiales). Flea populations were maintained by membrane feeding on pathogen-free bloodmeals for up to 13 d post infection. Individual fleas and pools of flea feces were tested for the presence of Bartonella DNA using molecular methods (quantitative and conventional polymerase chain reaction [PCR]). The threshold number of Bartonellae required in the infectious bloodmeal for fleas to be detected as positive was 106 colony-forming units per milliliter (CFU/ml). Individual fleas were capable of harboring infections for at least 13 d post infection and continuously excreted Bartonella DNA in their feces over the same period. This experiment demonstrated that X. cheopis are capable of acquiring and excreting B. elizabethae over several days. These results will guide future work to model and understand the role of X. cheopis in the natural transmission cycle of rodent-borne Bartonella species. Future experiments using this artificial feeding approach will be useful for examining the horizontal transmission of B. elizabethae or other rodent-associated Bartonella species to naive hosts and for determining the viability of excreted bacteria. |
Survey of parasitic bacteria in bat bugs, Colorado
McKee CD , Osikowicz LM , Schwedhelm TR , Bai Y , Castle KT , Kosoy MY . J Med Entomol 2018 55 (1) 237-241 Bat bugs (Cimex adjunctus Barber) (Hemiptera: Cimicidae) collected from big brown bats (Eptesicus fuscus Palisot de Beauvoir) in Colorado, United States were assessed for the presence of Bartonella, Brucella, and Yersinia spp. using molecular techniques. No evidence of Brucella or Yersinia infection was found in the 55 specimens collected; however, 4/55 (7.3%) of the specimens were positive for Bartonella DNA. Multi-locus characterization of Bartonella DNA shows that sequences in bat bugs are phylogenetically related to other Bartonella isolates and sequences from European bats. |
Diversity and phylogenetic relationships among Bartonella strains from Thai bats.
McKee CD , Kosoy MY , Bai Y , Osikowicz LM , Franka R , Gilbert AT , Boonmar S , Rupprecht CE , Peruski LF . PLoS One 2017 12 (7) e0181696 Bartonellae are phylogenetically diverse, intracellular bacteria commonly found in mammals. Previous studies have demonstrated that bats have a high prevalence and diversity of Bartonella infections globally. Isolates (n = 42) were obtained from five bat species in four provinces of Thailand and analyzed using sequences of the citrate synthase gene (gltA). Sequences clustered into seven distinct genogroups; four of these genogroups displayed similarity with Bartonella spp. sequences from other bats in Southeast Asia, Africa, and Eastern Europe. Thirty of the isolates representing these seven genogroups were further characterized by sequencing four additional loci (ftsZ, nuoG, rpoB, and ITS) to clarify their evolutionary relationships with other Bartonella species and to assess patterns of diversity among strains. Among the seven genogroups, there were differences in the number of sequence variants, ranging from 1-5, and the amount of nucleotide divergence, ranging from 0.035-3.9%. Overall, these seven genogroups meet the criteria for distinction as novel Bartonella species, with sequence divergence among genogroups ranging from 6.4-15.8%. Evidence of intra- and intercontinental phylogenetic relationships and instances of homologous recombination among Bartonella genogroups in related bat species were found in Thai bats. |
Phylogenetic and geographic patterns of bartonella host shifts among bat species.
McKee CD , Hayman DT , Kosoy MY , Webb CT . Infect Genet Evol 2016 44 382-394 The influence of factors contributing to parasite diversity in individual hosts and communities are increasingly studied, but there has been less focus on the dominant processes leading to parasite diversification. Using bartonella infections in bats as a model system, we explored the influence of three processes that can contribute to bartonella diversification and lineage formation: (1) spatial correlation in the invasion and transmission of bartonella among bats (phylogeography); (2) divergent adaptation of bartonellae to bat hosts and arthropod vectors; and (3) evolutionary codivergence between bats and bartonellae. Using a combination of global fit techniques and ancestral state reconstruction, we found that codivergence appears to be the dominant process leading to diversification of bartonella in bats, with lineages of bartonellae corresponding to separate bat suborders, superfamilies, and families. Furthermore, we estimated the rates at which bartonellae shift bat hosts across taxonomic scales (suborders, superfamilies, and families) and found that transition rates decrease with increasing taxonomic distance, providing support for a mechanism that can contribute to the observed evolutionary congruence between bats and their associated bartonellae. While bartonella diversification is associated with host sympatry, the influence of this factor is minor compared to the influence of codivergence and there is a clear indication that some bartonella lineages span multiple regions, particularly between Africa and Southeast Asia. Divergent adaptation of bartonellae to bat hosts and arthropod vectors is apparent and can dilute the overall pattern of codivergence, however its importance in the formation of Bartonella lineages in bats is small relative to codivergence. We argue that exploring all three of these processes yields a more complete understanding of bat-bartonella relationships and the evolution of the genus Bartonella, generally. Application of these methods to other infectious bacteria and viruses could uncover common processes that lead to parasite diversification and the formation of host-parasite relationships. |
Classification of Bartonella strains associated with straw-colored fruit bats (Eidolon helvum) across Africa using a multi-locus sequence typing platform.
Bai Y , Hayman DT , McKee CD , Kosoy MY . PLoS Negl Trop Dis 2015 9 (1) e0003478 Bartonellae are facultative intracellular bacteria and are highly adapted to their mammalian host cell niches. Straw-colored fruit bats (Eidolon helvum) are commonly infected with several bartonella strains. To elucidate the genetic diversity of these bartonella strains, we analyzed 79 bartonella isolates from straw-colored fruit bats in seven countries across Africa (Cameroon, Annobon island of Equatorial Guinea, Ghana, Kenya, Nigeria, Tanzania, and Uganda) using a multi-locus sequencing typing (MLST) approach based on nucleotide sequences of eight loci (ftsZ, gltA, nuoG, ribC, rpoB, ssrA, ITS, and 16S rRNA). The analysis of each locus but ribC demonstrated clustering of the isolates into six genogroups (E1 - E5 and Ew), while ribC was absent in the isolates belonging to the genogroup Ew. In general, grouping of all isolates by each locus was mutually supportive; however, nuoG, gltA, and rpoB showed some incongruity with other loci in several strains, suggesting a possibility of recombination events, which were confirmed by network analyses and recombination/mutation rate ratio (r/m) estimations. The MLST scheme revealed 45 unique sequence types (ST1 - 45) among the analyzed bartonella isolates. Phylogenetic analysis of concatenated sequences supported the discrimination of six phylogenetic lineages (E1 - E5 and Ew) corresponding to separate and unique Bartonella species. One of the defined lineages, Ew, consisted of only two STs (ST1 and ST2), and comprised more than one-quarter of the analyzed isolates, while other lineages contained higher numbers of STs with a smaller number of isolates belonging to each lineage. The low number of allelic polymorphisms of isolates belonging to Ew suggests a more recent origin for this species. Our findings suggest that at least six Bartonella species are associated with straw-colored fruit bats, and that distinct STs can be found across the distribution of this bat species, including in populations of bats which are genetically distinct. |
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