@article{berman_goltsman_anderson_relman_callahan_2024, title={<i>Gardnerella</i> diversity and ecology in pregnancy and preterm birth}, volume={9}, ISSN={["2379-5077"]}, url={https://doi.org/10.1128/msystems.01339-23}, DOI={10.1128/msystems.01339-23}, abstractNote={ABSTRACT The vaginal microbiome has been linked to negative health outcomes including preterm birth. Specific taxa, including Gardnerella spp., have been identified as risk factors for these conditions. Historically, microbiome analysis methods have treated all Gardnerella spp. as one species, but the broad diversity of Gardnerella has become more apparent. We explore the diversity of Gardnerella clades and genomic species in the vaginal microbiome of pregnant women and their associations with microbiome composition and preterm birth. Relative abundance of Gardnerella clades and genomic species and other taxa was quantified in shotgun metagenomic sequencing data from three distinct cohorts of pregnant women. We also assessed the diversity and abundance of Gardnerella variants in 16S rRNA gene amplicon sequencing data from seven previously conducted studies in differing populations. Individual microbiomes often contained multiple Gardnerella variants, and the number of clades was associated with increased microbial load, or the ratio of non-human reads to human reads. Taxon co-occurrence patterns were largely consistent across Gardnerella clades and among cohorts. Some variants previously described as rare were prevalent in other cohorts, highlighting the importance of surveying a diverse set of populations to fully capture the diversity of Gardnerella . The diversity of Gardnerella both across populations and within individual vaginal microbiomes has long been unappreciated, as has been the intra-species diversity of many other members of the vaginal microbiome. The broad genomic diversity of Gardnerella has led to its reclassification as multiple species; here we demonstrate the diversity of Gardnerella found within and between vaginal microbiomes. IMPORTANCE The present study shows that single microbiomes can contain all currently known species of Gardnerella and that multiple similar species can exist within the same environment. Furthermore, surveys of demographically distinct populations suggest that some species appear more commonly in certain populations. Further studies in broad and diverse populations will be necessary to fully understand the ecological roles of each Gardnerella sp., how they can co-exist, and their distinct impacts on microbial communities, preterm birth, and other health outcomes.}, number={6}, journal={MSYSTEMS}, author={Berman, Hanna L. and Goltsman, Daniela S. Aliaga and Anderson, Megan and Relman, David A. and Callahan, Benjamin J.}, editor={Cope, Emily K.Editor}, year={2024}, month={Jun} }
 @article{monte_nethery_berman_keelara_lincopan_fedorka-cray_barrangou_landgraf_2022, title={Clustered Regularly Interspaced Short Palindromic Repeats Genotyping of Multidrug-Resistant Salmonella Heidelberg Strains Isolated From the Poultry Production Chain Across Brazil}, volume={13}, ISSN={["1664-302X"]}, DOI={10.3389/fmicb.2022.867278}, abstractNote={Salmonella enterica subsp. enterica serovar Heidelberg has been associated with a broad host range, such as poultry, dairy calves, swine, wild birds, environment, and humans. The continuous evolution of S. Heidelberg raises a public health concern since there is a global dispersal of lineages harboring a wide resistome and virulome on a global scale. Here, we characterized the resistome, phylogenetic structure and clustered regularly interspaced short palindromic repeats (CRISPR) array composition of 81 S. Heidelberg strains isolated from broiler farms (n = 16), transport and lairage (n = 5), slaughterhouse (n = 22), and retail market (n = 38) of the poultry production chain in Brazil, between 2015 and 2016 using high-resolution approaches including whole-genome sequencing (WGS) and WGS-derived CRISPR genotyping. More than 91% of the S. Heidelberg strains were multidrug-resistant. The total antimicrobial resistance (AMR) gene abundances did not vary significantly across regions and sources suggesting the widespread distribution of antibiotic-resistant strains from farm to market. The highest AMR gene abundance was observed for fosA7, aac(6′)-Iaa, sul2, tet(A), gyrA, and parC for 100% of the isolates, followed by 88.8% for blaCMY–2. The β-lactam resistance was essentially driven by the presence of the plasmid-mediated AmpC (pAmpC) blaCMY–2 gene, given the isolates which did not carry this gene were susceptible to cefoxitin (FOX). Most S. Heidelberg strains were classified within international lineages, which were phylogenetically nested with Salmonella strains from European countries; while CRISPR genotyping analysis revealed that the spacer content was overall highly conserved, but distributed into 13 distinct groups. In summary, our findings underscore the potential role of S. Heidelberg as a key pathogen disseminated from farm to fork in Brazil and reinforce the importance of CRISPR-based genotyping for salmonellae. Hence, we emphasized the need for continuous mitigation programs to monitor the dissemination of this high-priority pathogen.}, journal={FRONTIERS IN MICROBIOLOGY}, author={Monte, Daniel F. M. and Nethery, Matthew A. and Berman, Hanna and Keelara, Shivaramu and Lincopan, Nilton and Fedorka-Cray, Paula J. and Barrangou, Rodolphe and Landgraf, Mariza}, year={2022}, month={Jun} }
 @article{manvell_berman_callahan_breitschwerdt_swain_ferris_maggi_lashnits_2022, title={Identification of microbial taxa present in Ctenocephalides felis (cat flea) reveals widespread co-infection and associations with vector phylogeny}, volume={15}, ISSN={["1756-3305"]}, DOI={10.1186/s13071-022-05487-1}, abstractNote={Abstract
                Background
                Ctenocephalides felis, the cat flea, is the most common ectoparasite of cats and dogs worldwide. As a cause of flea allergy dermatitis and a vector for two genera of zoonotic pathogens (Bartonella and Rickettsia spp.), the effect of the C. felis microbiome on pathogen transmission and vector survival is of substantial medical importance to both human and veterinary medicine. The aim of this study was to assay the pathogenic and commensal eubacterial microbial communities of individual C. felis from multiple geographic locations and analyze these findings by location, qPCR pathogen prevalence, and flea genetic diversity.
              
                Methods
                16S Next Generation Sequencing (NGS) was utilized to sequence the microbiome of fleas collected from free-roaming cats, and the cox1 gene was used for flea phylogenetic analysis. NGS data were analyzed for 168 individual fleas from seven locations within the US and UK. Given inconsistency in the genera historically reported to constitute the C. felis microbiome, we utilized the decontam prevalence method followed by literature review to separate contaminants from true microbiome members.
              
                Results
                NGS identified a single dominant and cosmopolitan amplicon sequence variant (ASV) from Rickettsia and Wolbachia while identifying one dominant Bartonella clarridgeiae and one dominant Bartonella henselae/Bartonella koehlerae ASV. Multiple less common ASVs from these genera were detected within restricted geographical ranges. Co-detection of two or more genera (Bartonella, Rickettsia, and/or Wolbachia) or multiple ASVs from a single genus in a single flea was common. Achromobacter, Peptoniphilus, and Rhodococcus were identified as additional candidate members of the C. felis microbiome on the basis of decontam analysis and literature review. Ctenocephalides felis phylogenetic diversity as assessed by the cox1 gene fell within currently characterized clades while identifying seven novel haplotypes. NGS sensitivity and specificity for Bartonella and Rickettsia spp. DNA detection were compared to targeted qPCR.
              
                Conclusions
                Our findings confirm the widespread coinfection of fleas with multiple bacterial genera and strains, proposing three additional microbiome members. The presence of minor Bartonella, Rickettsia, and Wolbachia ASVs was found to vary by location and flea haplotype. These findings have important implications for flea-borne pathogen transmission and control.
              
                Graphical Abstract
                
              }, number={1}, journal={PARASITES & VECTORS}, author={Manvell, Charlotte and Berman, Hanna and Callahan, Benjamin and Breitschwerdt, Edward and Swain, William and Ferris, Kelli and Maggi, Ricardo and Lashnits, Erin}, year={2022}, month={Oct} }
 @article{monte_lincopan_berman_cerdeira_keelara_thakur_fedorka-cray_landgraf_2019, title={Genomic Features of High-Priority Salmonella enterica Serovars Circulating in the Food Production Chain, Brazil, 2000-2016}, volume={9}, ISSN={["2045-2322"]}, DOI={10.1038/s41598-019-45838-0}, abstractNote={AbstractMultidrug-resistant (MDR) Salmonella enterica has been deemed a high-priority pathogen by the World Health Organization. Two hundred and sixty-four Salmonella enterica isolates recovered over a 16-year period (2000 to 2016) from the poultry and swine production chains, in Brazil, were investigated by whole-genome sequencing (WGS). Most international lineages belonging to 28 serovars, including, S. enterica serovars S. Schwarzengrund ST96, S. Typhimurium ST19, S. Minnesota ST548, S. Infantis ST32, S. Heidelberg ST15, S. Newport ST45, S. Brandenburg ST65 and S. Kentucky ST198 displayed MDR and virulent genetic backgrounds. In this regard, resistome analysis revealed presence of qnrE1 (identified for the first time in S. Typhimurium from food chain), qnrB19, qnrS1, blaCTX-M-8, blaCTX-M-2 and blaCMY-2 genes, as well as gyrA mutations; whereas ColpVC, IncHI2A, IncHI2, IncFIA, Incl1, IncA/C2, IncR, IncX1 and po111 plasmids were detected. In addition, phylogenetic analysis revealed multiple independent lineages such as S. enterica serovars S. Infantis, S. Schwarzengrund, S. Minnesota, S. Kentucky and S. Brandenburg. In brief, ocurrence and persistence of international lineages of S. enterica serovars in food production chain is supported by conserved genomes and wide virulome and resistome.}, journal={SCIENTIFIC REPORTS}, author={Monte, Daniel F. . and Lincopan, Nilton and Berman, Hanna and Cerdeira, Louise and Keelara, Shivaramu and Thakur, Siddhartha and Fedorka-Cray, Paula J. and Landgraf, Mariza}, year={2019}, month={Jul} }
 @article{martinetti_caughron_berman_andre_sokolowski_wiley_naassila_2019, title={The Behavioral Economics of Alcohol Demand in French and American University Students}, volume={43}, ISSN={["1530-0277"]}, DOI={10.1111/acer.13954}, abstractNote={BackgroundBehavioral economic approaches have revealed several characteristics of alcohol demand (e.g., intensity, elasticity, and essential value) in university students; however, these approaches have not yet examined alcohol demand among students outside of the United States. The current study examined alcohol demand among student samples in the United States and France using a hypothetical alcohol purchase task (APT) and a novel APT Choice task, in which nonalcoholic beverages were concurrently available at a fixed low price.MethodsParticipants at each site (United States, n = 132; France, n = 132) were asked to complete an Internet‐based survey including the APT, APT Choice, Alcohol Use Disorders Identification Test, Daily Drinking Questionnaire, and Drinking Motives Questionnaire‐Revised Short Form. Group demand functions were produced for each of the 2 samples in both country‐specific and standardized drink units, and the exponential demand equation was fitted to each of the APT and APT Choice demand curves. Slope analyses were performed on the Non‐Alcoholic Cross‐Price demand to assess substitutability.ResultsAPT data revealed that in both samples, alcohol price and consumption were inversely related and demand measures were significantly associated with other alcohol measures. In addition, the availability of a nonalcoholic alternative reduced alcohol demand in both samples, with evidence of substitutability revealed by increases in cross‐price consumption.ConclusionsLow‐cost alcohol is associated with increased alcohol consumption in both French and U.S. university students, and concurrent availability of a nonalcoholic beverage within the APT both reduces alcohol demand and demonstrates behavioral economic substitutability. These findings will inform future studies investigating behavioral and environmental factors underlying transcultural differences and specific prevention efforts.}, number={3}, journal={ALCOHOLISM-CLINICAL AND EXPERIMENTAL RESEARCH}, author={Martinetti, Margaret P. and Caughron, Rebecca L. and Berman, Hanna L. and Andre, Judith and Sokolowski, Michel B. C. and Wiley, Shaun and Naassila, Mickael}, year={2019}, month={Mar}, pages={531–544} }