Longitudinal dynamics of farmer and livestock nasal and faecal microbiomes and resistomes.

Globally, half a billion people are employed in animal agriculture and are directly exposed to the associated microorganisms. However, the extent to which such exposures affect resident human microbiomes is unclear. Here we conducted a longitudinal profiling of the nasal and faecal microbiomes of 66 dairy farmers and 166 dairy cows over a year-long period. We compare farmer microbiomes to those of 60 age-, sex- and ZIP code-matched people with no occupational exposures to farm animals (non-farmers). We show that farming is associated with microbiomes containing livestock-associated microbes; this is most apparent in the nasal bacterial community, with farmers harbouring a richer and more diverse nasal community than non-farmers. Similarly, in the gut microbial communities, we identify more shared microbial lineages between cows and farmers from the same farms. Additionally, we find that shared microbes are associated with antibiotic resistance genes. Overall, our study demonstrates the interconnectedness of human and animal microbiomes.

Antibiotic-resistant organisms establish reservoirs in new hospital built environments and are related to patient blood infection isolates.

Background: Healthcare-associated infections due to antibiotic-resistant organisms pose an acute and rising threat to critically ill and immunocompromised patients. To evaluate reservoirs of antibiotic-resistant organisms as a source of transmission to patients, we interrogated isolates from environmental surfaces, patient feces, and patient blood infections from an established and a newly built intensive care unit. Methods: We used selective culture to recover 829 antibiotic-resistant organisms from 1594 environmental and 72 patient fecal samples, in addition to 81 isolates from blood cultures. We conducted antibiotic susceptibility testing and short- and long-read whole genome sequencing on recovered isolates. Results: Antibiotic-resistant organism burden is highest in sink drains compared to other surfaces. Pseudomonas aeruginosa is the most frequently cultured organism from surfaces in both intensive care units. From whole genome sequencing, different lineages of P. aeruginosa dominate in each unit; one P. aeruginosa lineage of ST1894 is found in multiple sink drains in the new intensive care unit and 3.7% of blood isolates analyzed, suggesting movement of this clone between the environment and patients. Conclusions: These results highlight antibiotic-resistant organism reservoirs in hospital built environments as an important target for infection prevention in hospitalized patients.

Acute and persistent effects of commonly used antibiotics on the gut microbiome and resistome in healthy adults.

Antibiotics are deployed against bacterial pathogens, but their targeting of conserved microbial processes means they also collaterally perturb the commensal microbiome. To understand acute and persistent effects of antibiotics on the gut microbiota of healthy adult volunteers, we quantify microbiome dynamics before, during, and 6 months after exposure to 4 commonly used antibiotic regimens. We observe an acute decrease in species richness and culturable bacteria after antibiotics, with most healthy adult microbiomes returning to pre-treatment species richness after 2 months, but with an altered taxonomy, resistome, and metabolic output, as well as an increased antibiotic resistance burden. Azithromycin delays the recovery of species richness, resulting in greater compositional distance. A subset of volunteers experience a persistent reduction in microbiome diversity after antibiotics and share compositional similarities with patients hospitalized in intensive care units. These results improve our quantitative understanding of the impact of antibiotics on commensal microbiome dynamics, resilience, and recovery.

Manure Microbial Communities and Resistance Profiles Reconfigure after Transition to Manure Pits and Differ from Those in Fertilized Field Soil.

In agricultural settings, microbes and antimicrobial resistance genes (ARGs) have the potential to be transferred across diverse environments and ecosystems. The consequences of these microbial transfers are unclear and understudied. On dairy farms, the storage of cow manure in manure pits and subsequent application to field soil as a fertilizer may facilitate the spread of the mammalian gut microbiome and its associated ARGs to the environment. To determine the extent of both taxonomic and resistance similarity during these transitions, we collected fresh manure, manure from pits, and field soil across 15 different dairy farms for three consecutive seasons. We used a combination of shotgun metagenomic sequencing and functional metagenomics to quantitatively interrogate taxonomic and ARG compositional variation on farms. We found that as the microbiome transitions from fresh dairy cow manure to manure pits, microbial taxonomic compositions and resistance profiles experience distinct restructuring, including decreases in alpha diversity and shifts in specific ARG abundances that potentially correspond to fresh manure going from a gut-structured community to an environment-structured community. Further, we did not find evidence of shared microbial community or a transfer of ARGs between manure and field soil microbiomes. Our results suggest that fresh manure experiences a compositional change in manure pits during storage and that the storage of manure in manure pits does not result in a depletion of ARGs. We did not find evidence of taxonomic or ARG restructuring of soil microbiota with the application of manure to field soils, as soil communities remained resilient to manure-induced perturbation.IMPORTANCE The addition of dairy cow manure-stored in manure pits-to field soil has the potential to introduce not only organic nutrients but also mammalian microbial communities and antimicrobial resistance genes (ARGs) to soil communities. Using shotgun sequencing paired with functional metagenomics, we showed that microbial community composition changed between fresh manure and manure pit samples with a decrease in gut-associated pathobionts, while ARG abundance and diversity remained high. However, field soil communities were distinct from those in manure in both microbial taxonomic and ARG composition. These results broaden our understanding of the transfer of microbial communities in agricultural settings and suggest that field soil microbial communities are resilient against the deposition of ARGs or microbial communities from manure.

Bacterial sepsis increases hippocampal fibrillar amyloid plaque load and neuroinflammation in a mouse model of Alzheimer's disease.

BACKGROUND: Sepsis, a leading cause for intensive care unit admissions, causes both an acute encephalopathy and chronic brain dysfunction in survivors. A history of sepsis is also a risk factor for future development of dementia symptoms. Similar neuropathologic changes are associated with the cognitive decline of sepsis and Alzheimer's disease (AD), including neuroinflammation, neuronal death, and synaptic loss. Amyloid plaque pathology is the earliest pathological hallmark of AD, appearing 10 to 20 years prior to cognitive decline, and is present in 30% of people over 65. As sepsis is also more common in older adults, we hypothesized that sepsis might exacerbate amyloid plaque deposition and plaque-related injury, promoting the progression of AD-related pathology. METHODS: We evaluated whether the brain's response to sepsis modulates AD-related neurodegenerative changes by driving amyloid deposition and neuroinflammation in mice. We induced polymicrobial sepsis by cecal ligation and puncture (CLP) in APP/PS1-21 mice, a model of AD-related ß-amyloidosis. We performed CLP or sham surgery at plaque onset (2 months of age) and examined pathology 2 months after CLP in surviving mice. RESULTS: Sepsis significantly increased fibrillar amyloid plaque formation in the hippocampus of APP/PS1-21 mice. Sepsis enhanced plaque-related astrocyte activation and complement C4b gene expression in the brain, both of which may play a role in modulating amyloid formation. CLP also caused large scale changes in the gut microbiome of APP/PS1 mice, which have been associated with a pro-amyloidogenic and neuroinflammatory state. CONCLUSIONS: Our results suggest that experimental sepsis can exacerbate amyloid plaque deposition and plaque-related inflammation, providing a potential mechanism for increased dementia in older sepsis survivors.

Genomic Characterization of Emerging Bacterial Uropathogen Neisseria meningitidis, Which Was Misidentified as Neisseria gonorrhoeae by Nucleic Acid Amplification Testing.

Neisseria meningitidis and Neisseria gonorrhoeae are pathogenic bacteria that can cause human infections. While N. meningitidis infections are associated with bacterial meningitis and bacteremia, a strain of N. meningitidis, isolated from the urogenital system, has recently been associated with urethritis. As this strain is becoming prominent as an emerging pathogen, it is essential to assess identification tools for N. meningitidis and N. gonorrhoeae urogenital isolates. Consecutive N. meningitidis isolates recovered from urogenital cultures of symptomatic patients with presumptive diagnoses of gonorrhea and a random selection of N. gonorrhoeae isolates recovered from the same population within the same time frame were characterized with routine identification systems, antimicrobial susceptibility testing, and whole-genome sequencing. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), multilocus sequence typing, 16S rRNA gene sequence, and average nucleotide identity methods accurately identified 95% (18/19) of N. meningitidis and N. gonorrhoeae isolates. With the Aptima Combo 2 CT/NG test, 30% (3/10) of N. meningitidis isolates were misidentified as N. gonorrhoeae, but no misidentifications were found with the Xpert CT/NG nucleic acid amplification test (NAAT). Phylogenetic core genome and single nucleotide polymorphism (SNP)-based grouping analyses showed that urogenital N. meningitidis isolates were highly related and phylogenetically distinct from N. gonorrhoeae and respiratory N. meningitidis isolates but similar to urogenital N. meningitidis isolates from patients with urethritis in the United States. Urogenital N. meningitidis isolates were predominantly azithromycin resistant, while N. gonorrhoeae isolates were azithromycin susceptible. These data indicate that urogenital isolates of N. meningitidis can cause false-positive detections with N. gonorrhoeae diagnostic assays. Misidentification of urogenital N. meningitidis isolates may confound public health-related activities for gonorrhea, and future studies are needed to understand the impact on clinical outcome of N. meningitidis urogenital infection.

Intraspecific Energetic Trade-Offs and Costs of Encephalization Vary from Interspecific Relationships in Three Species of Mormyrid Electric Fishes.

The evolution of increased encephalization comes with an energetic cost. Across species, this cost may be paid for by an increase in metabolic rate or by energetic trade-offs between the brain and other energy-expensive tissues. However, it remains unclear whether these solutions to deal with the energetic requirements of an enlarged brain are related to direct physiological constraints or other evolved co-adaptations. We studied the highly encephalized mormyrid fishes, which have extensive species diversity in relative brain size. We previously found a correlation between resting metabolic rate and relative brain size across species; however, it is unknown how this interspecific relationship evolved. To address this issue, we measured intraspecific variation in relative brain size, the sizes of other organs, metabolic rate, and hypoxia tolerance to determine if intraspecific relationships between brain size and organismal energetics are similar to interspecific relationships. We found that 3 species of mormyrids with varying degrees of encephalization had no intraspecific relationships between relative brain size and relative metabolic rate or relative sizes of other organs, and only 1 species had a relationship between relative brain size and hypoxia tolerance. These species-specific differences suggest that the interspecific relationship between metabolic rate and relative brain size is not the result of direct physiological constraints or strong stabilizing selection, but is instead due to other species level co-adaptations. We conclude that variation within species must be considered when determining the energetic costs and trade-offs underlying the evolution of extreme encephalization.

Genomic and Metagenomic Approaches for Predictive Surveillance of Emerging Pathogens and Antibiotic Resistance.

Antibiotic-resistant organisms (AROs) are a major concern to public health worldwide. While antibiotics have been naturally produced by environmental bacteria for millions of years, modern widespread use of antibiotics has enriched resistance mechanisms in human-impacted bacterial environments. Antibiotic resistance genes (ARGs) continue to emerge and spread rapidly. To combat the global threat of antibiotic resistance, researchers must develop methods to rapidly characterize AROs and ARGs, monitor their spread across space and time, and identify novel ARGs and resistance pathways. We review how high-throughput sequencing-based methods can be combined with classic culture-based assays to characterize, monitor, and track AROs and ARGs. Then, we evaluate genomic and metagenomic methods for identifying ARGs and biosynthetic pathways for novel antibiotics from genomic data sets. Together, these genomic analyses can improve surveillance and prediction of emerging resistance threats and accelerate the development of new antibiotic therapies to combat resistance.

Extreme Enlargement of the Cerebellum in a Clade of Teleost Fishes that Evolved a Novel Active Sensory System.

Brains, and the distinct regions that make up brains, vary widely in size across vertebrates [1, 2]. Two prominent hypotheses have been proposed to explain brain region scaling evolution. The mosaic hypothesis proposes that changes in the relative sizes of particular brain regions are the result of selection acting independently on those regions [2, 3]. The concerted hypothesis proposes that the brain evolves as a coordinated structure due to developmental constraints [4]. These hypotheses have been widely debated [3-7], and recent studies suggest a combination of the two best describes vertebrate brain region scaling [8-10]. However, no study has addressed how the mosaic and concerted models relate to the evolution of novel behavioral phenotypes. We addressed this question using African mormyroid fishes. The mormyroids have evolved a novel active electrosensory system and are well known for having extreme encephalization [11] and a large cerebellum [2, 12], which is cited as a possible example of mosaic evolution [2]. We found that compared to outgroups without active electrosensing, mormyroids experienced mosaic increases in the sizes of the cerebellum and hindbrain, and mosaic decreases in the sizes of the telencephalon, optic tectum, and olfactory bulb. However, the evolution of extreme encephalization within mormyroids was associated with concerted changes in the sizes of all brain regions. This suggests that mosaic evolutionary change in the regional composition of the brain is most likely to occur alongside the evolution of novel behavioral functions, but not with the evolution of extreme encephalization.

The costs of a big brain: extreme encephalization results in higher energetic demand and reduced hypoxia tolerance in weakly electric African fishes.

A large brain can offer several cognitive advantages. However, brain tissue has an especially high metabolic rate. Thus, evolving an enlarged brain requires either a decrease in other energetic requirements, or an increase in overall energy consumption. Previous studies have found conflicting evidence for these hypotheses, leaving the metabolic costs and constraints in the evolution of increased encephalization unclear. Mormyrid electric fishes have extreme encephalization comparable to that of primates. Here, we show that brain size varies widely among mormyrid species, and that there is little evidence for a trade-off with organ size, but instead a correlation between brain size and resting oxygen consumption rate. Additionally, we show that increased brain size correlates with decreased hypoxia tolerance. Our data thus provide a non-mammalian example of extreme encephalization that is accommodated by an increase in overall energy consumption. Previous studies have found energetic trade-offs with variation in brain size in taxa that have not experienced extreme encephalization comparable with that of primates and mormyrids. Therefore, we suggest that energetic trade-offs can only explain the evolution of moderate increases in brain size, and that the energetic requirements of extreme encephalization may necessitate increased overall energy investment.

Independent evolution of visual and electrosensory specializations in different lineages of mormyrid electric fishes.

African mormyrid fishes are by far the most diverse group of osteoglossomorph (bony tongue) fishes. Mormyrids communicate using pulses of electricity, and they process electric communication signals in the midbrain exterolateral nucleus (EL). In its ancestral form, the EL is relatively small and homogenous. In two different lineages, however, the EL expanded in size and increased in cytological complexity. This evolutionary change established the perceptual ability to distinguish variation in electric pulse waveform, which plays an important role in species recognition and mate choice. However, the sensory basis of social behavior in species with a small, homogenous EL remains unknown. Using published species descriptions, we found that species in one of these lineages have relatively large eyes. Using sectioned brains, we measured the volume of a major visual region, the optic tectum (OT), and found that this same lineage also has an enlarged OT. We also found that eye size and OT size are highly correlated across species. Phylogenetic analysis suggests that a reduced visual system evolved with the origins of an active electrosense, and that this one particular lineage secondarily evolved an enlarged visual system. Behavioral tests revealed that this enlargement of the visual system established increased visual acuity. Thus, our findings demonstrate that different lineages of mormyrids have evolved visual or electrosensory specializations, but that no lineages have specialized in both. This sensory divergence likely reflects fundamentally different ecologies and suggests that vision may play an especially important role in the social behavior of mormyrids that cannot detect variation in electric signal waveform. Our findings provide an example of evolutionary change in multiple sensory systems among closely related species that lays a foundation for relating ecological adaptation to evolutionary change in multisensory perception and social behavior.