Biology subjects

Hilty, M.

Publications and source records attributed to Hilty, M..

9 recordsLinked to original sources

bioRxiv2026

Shared species, strains and resistome between humans and pigs: A metagenomic analysis

Pig farming is one of the most intensive human-animal interfaces, and farm workers carry gut microbiotas that differ from those of non-farmers. Whether this overlap reflects genuine strain transmission or shared environmental exposure is unclear. Using shotgun metagenomics, we profiled the gut microbiomes of pigs at three growth stages (suckling, weaning, fattening), their farmers, and non-farmer controls, at species and strain resolution, and characterized the resistome in parallel. Farmers shared more species with pigs than controls, with Prevotellaceae the most consistently enriched family. Strain-level analysis of 137 shared species showed that most (71%) maintain host-specific sub-species clades. Strain sharing ran an order of magnitude below species sharing and was confined to early growth stages; its direction could not be determined. Pigs and farmers shared a farm-associated resistome signature, including the beta-lactamase cfxA4 and the methyltransferases ermF and cfrE. ermF and tet(X) were carried together on the same clonal Tn4351-family transposon, present in 86% of farmers and 80% of pigs but only 19% of controls. We found no evidence for transmission of mobile genetic elements between pigs and farmers; the shared resistome is best explained by carriage within shared gut taxa. Species sharing, strain transmission, and resistance gene carriage thus reflect different scales of microbial exchange at the livestock-human interface. Our results argue against ongoing strain or mobile genetic element transmission from handled animals: the shared species and resistome are best explained by shared environmental exposure and by carriage of resistance genes within shared gut taxa.

microbiology↗

bioRxiv2026

Tracking eco-evolutionary dynamics among lung pathobiome members from children with cystic fibrosis

Polymicrobial lung infections are common in individuals with cystic fibrosis (CF). Pathogen communities typically follow an ecological succession in which early colonizers such as Haemophilus influenzae and Staphylococcus aureus are later joined by Pseudomonas aeruginosa. Although adaptation to the lung environment is well described for single pathogens in adult people with CF, much less is known about the role of pathogen interactions and how changes in individual pathogens influence community dynamics at the early stages of disease. To address these questions, we combined genome sequencing with phenotypic screens and pathogen interaction assays using longitudinal clinical isolates (19 P. aeruginosa, 44 S. aureus, and 21 H. influenzae) collected from 23 children with CF (0-7.9 years of age) enrolled in the SCILD (Swiss CF Infant Lung Development) cohort. Our analysis revealed that early pathogen communities are characterized by a combination of strain turnover and persistence of isolates undergoing first steps of within-host evolution. Most notably, quorum-sensing-deficient P. aeruginosa variants repeatedly emerged, showing reduced protease production and diminished inhibition of S. aureus and H. influenzae. These changes indicate that P. aeruginosa becomes less antagonistic towards co-occurring pathogens, possibly promoting community stability. Together, our results show that ecological and evolutionary dynamics between pathobiome members may play an underappreciated role in shaping CF lung disease during early childhood.

evolutionary biology↗

bioRxiv2025

Megaplasmids associate with Escherichia coli and other Enterobacteriaceae

Humans and animals are ubiquitously colonized by Enterobacteriaceae, a bacterial family that contains both commensals and clinically significant pathogens. Here, we report Enterobacteriaceae megaplasmids of up to 1.58 Mbp in length in infant and adult guts, and other microbiomes. Of 19 complete plasmid genomes, one was reconstructed from an E. coli isolate; others were linked to species of Citrobacter and Enterobacter via analysis of genome modification patterns. The detection of related plasmids in different Enterobacteriaceae, conjugation machinery, and more diverse modified motifs in certain plasmids compared to hosts suggests that these elements are self-transmissible, with a broad host range. The plasmids encode multi-drug efflux systems and potential secreted effectors. Up to 208 tRNAs are encoded and include sequence variants that may counter tRNA-centric defense mechanisms. Overall, the vast megaplasmid coding capacity may broaden host range, increase competitiveness, control invasion by other elements, and counter programmed cell death.

microbiology↗

bioRxiv2023

Comparative genomic analysis reveals novel phylogenetically intermediate Streptococci with high phenotypic diversity in the human distal lung microbiota.

Streptococci are one of the predominant and the most diverse genus in the human lung. Previously, we isolated human distal lung Streptococci from bronchoalvolear lavage fluid (BALF) as part of the human Lung Microbiota culture Collection (LuMiCol). Here, we performed whole genome sequencing, comparative phylogenomics and phenotypic characterization of six Streptococcal isolates representing the phylogenetic diversity of the genus in distal human lung. Here, we report five new species and one new subspecies including phylogenetic intermediates of commonly found Streptococci not limited to human lung. Pangenome analysis reveals gene content, evolutionary relationships, and metabolic functions shedding light on contribution of these Streptococci to lung microbial metabolism. Antimicrobial resistance gene analysis followed by MIC determination revealed macrolide, lincosamide and tetracycline resistance in lung Streptococci. We show the presence of capsular genes in lung streptococci both matching to the prototypical capsular genes (cps) and unique genes. Interestingly, the new Streptococcus isolate sp. nov. P2E5, genetically identical to the most prevalent Streptococcus in the human distal lung was revealed to be a phylogenetic intermediate between the S. mitis group and S. pneumoniae. It also harbors the pneumolysin (ply) gene and was found to have the serotype 21E. Finally, core genome phylogeny reveals that lung Streptococci the are evolutionary distinct from oral Streptococcal isolates in expanded Human Oral Microbiome Database (eHOMD). Hence, these findings we reveal new phylogenetically distinct Streptococcal species from the human distal lung microbiota and its genetic diversity and metabolism to understand the microbial ecology of human lung. ImportanceA healthy human distal lung harbour characteristic microbial communities mostly composed of oropharyngeal taxa, which are facultative or obligative anaerobes despite lung being the medium of oxygen intake. However, little is known about the genetic and functional diversity of these bacteria owing to the lack of resources including availability of primary lung isolate from human samples. Therefore, we have established a large bacterial collection that covers all major phyla by cultivating human bronchoalveolar lavage fluid (BALF) under various conditions. Streptococcus is the most prevalent and diverse genera in the human lung microbiota. Using genetic and biochemical approaches, we studied six diverse lung isolates from our collection representing the actual Streptococcal diversity and identify these as new species and subspecies. We hypothesize that learning about the phylogenetic genetic diversity, preferred metabolism and molecular structures of these Streptococci will provide with new insights on the understudied microbial ecosystem of the human lung.

microbiology↗

bioRxiv2023

Streptococcus pneumoniae serotype 33G: genetic, serological, and structural analysis of a new capsule type

Streptococcus pneumoniae (the pneumococcus) is a human pathogen responsible for a spectrum of diseases such as pneumonia, sepsis, and meningitis. The capsule is the major pneumococcal virulence factor and is encoded by the capsular polysaccharide (cps) locus, a recombination hot spot that has resulted in over 100 distinct capsular polysaccharide types (serotypes) identified to date. Recently, 33X (also known as 10X) was proposed as a putative novel serotype, but the capsule structure had not been elucidated. Here, we provide an in-depth investigation of 33X, demonstrating it is a new pneumococcal capsular serotype. In this study, we screened 12,850 nasopharyngeal swabs from both healthy children and pneumonia patients (adults and children) in Mongolia collected between 2015-2022. We identified 20 pneumococcal 33X isolates. Using whole genome sequencing, we found that the 33X cps locus is a chimera of genes from pneumococcal serogroups 35, 10 and 33, as well as other Streptococcal species. Serotyping of 33X pneumococci by the Quellung reaction revealed a unique serological profile, typing as both 10B and 33B. Competitive ELISAs confirmed that antibodies that were generated in mice directed against 33X were inhibited by 33X pneumococci but not 10B or 33B. Lastly, elucidation of the 33X capsule structure revealed that the polysaccharide is distinct from other serotypes, consisting of an O-acetylated hexasaccharide repeat unit of [->]5)-{beta}-Galf-(1[->]3)-{beta}-Glcp-(1[->]5)-{beta}-Galf 2Ac-(1[->]3)-{beta}-GalpNAc-(1[->]3)--Galp-(1[->]4)-Rib-ol-(5[->]P[->]. Therefore, 33X meets the requisite genetic, serological, and biochemical criteria to be designated as a new serotype, which we have named 33G. IMPORTANCEStreptococcus pneumoniae (the pneumococcus) is a bacterial pathogen with the greatest burden of disease in Asia and Africa. The pneumococcal capsular polysaccharide has biological relevance as a major virulence factor, as well as public health importance as it is the target for currently licensed vaccines. These vaccines have limited valency, covering up to 23 of the >100 known capsular types (serotypes) with higher valency vaccines in development. Here, we have characterized a new pneumococcal serotype, which we have named 33G. We detected serotype 33G in nasopharyngeal swabs (n=20) from children and adults hospitalized with pneumonia, as well as healthy children in Mongolia. We show that the genetic, serological, and biochemical properties of 33G differs from existing serotypes, satisfying the criteria to be designated as a new serotype. Future studies should focus on the geographical distribution of 33G and any changes in prevalence following vaccine introduction.

microbiology↗

bioRxiv2023

In Vitro Antibacterial Activity of Dinuclear Thiolato-Bridged Ruthenium(II)-Arene Compounds

The antibacterial activity of 22 thiolato-bridged dinuclear ruthenium(II)-arene compounds was assessed in vitro against Escherichia coli, Streptococcus pneumoniae and Staphylococcus aureus. None of the compounds efficiently inhibited the growth of the three E. coli strains tested and only compound 5 exhibited a medium activity against this bacterium (MIC (minimum inhibitory concentration) of 25 M). However, a significant antibacterial activity was observed against S. pneumoniae, with MIC values ranging from 1.3 to 2.6 M for compounds 1-3, 5 and 6. Similarly, compounds 2, 5-7 and 20-22 had MIC values ranging from 2.5 to 5 M against S. aureus. The tested diruthenium compounds have a bactericidal effect significantly faster than that of penicillin. Fluorescence microscopy assays performed on S. aureus using the BODIPY-tagged diruthenium complex 15 showed that this type of metal compound enter the bacteria and do not accumulate in the cell wall of gram-positive bacteria. Cellular internalization was further confirmed by inductively coupled plasma mass spectrometry (ICP-MS) experiments. The nature of the substituents anchored on the bridging thiols and the compounds molecular weight appear to significantly influence the antibacterial activity. Thus, if overall a decrease of the bactericidal effect with the increase of compounds molecular weight is observed, however the complexes bearing larger benzo-fused lactam substituents had low MIC values. This first antibacterial activity screening demonstrated that the thiolato-diruthenium compounds exhibit promising activity against S. aureus and S. pneumoniae and deserve to be considered for further studies.

pharmacology and toxicology↗

bioRxiv2022

Developing and optimizing a personalized probiotic treatment regime for nasal endogenous Staphylococcus aureus decolonization

AbstractDespite the increasing burden of antibiotic resistance and persistence, current approaches to eradicate nasal pathobionts such as Staphylococcus aureus and Streptococcus pneumoniae are based on the use of antibacterial agents. An alternative approach is the artificial inoculation of commensal bacteria, i.e., probiotic treatment, which is supported by the increasing evidence for commensal-mediated inhibition of pathogens. To systematically investigate the potential and the limitations of this approach, we developed a quantitative framework simulating the dynamics of the nasal bacterial microbiome by combining mathematical modeling with longitudinal microbiota data. By inferring the microbial interaction parameters using 16S rRNA amplicon sequencing data and simulating the nasal microbial dynamics of patients colonized with S. aureus, we compared the decolonization performance of probiotic and antibiotic treatments under different assumptions on patients bacterial community composition and susceptibility profile. To further compare the robustness of these treatments, we simulated a S. aureus challenge following each treatment and quantified the recolonization probability. Eventually, using nasal swabs of adults colonized with S. aureus, we confirmed that after antibiotic treatment, recolonization of S. aureus was inhibited in samples treated with a probiotic mixture compared to the non-treated control. Our results suggest that probiotic treatment clearly outperforms antibiotics in terms of decolonization performance, recolonization robustness, and leads to less collateral reduction of the microbiome diversity. Moreover, we find that recolonization robustness is highest in those patients that were not initially colonized by Dolosigranulum pigrum. Thus, probiotic treatment may provide a promising alternative to combat antibiotic resistance, with the additional advantage of personalized treatment options via using the patients own metagenomic data to tailor the intervention. The combination of an in silico framework with in vitro confirmatory experiments using clinical samples reported in this work is an important step forward to further investigate this alternative in clinical trials. ImportanceThe development of new antimicrobial agents is declining while antibiotic resistance is rising, which is particularly concerning for upper respiratory tract pathogens S. pneumoniae and S. aureus. Combating such resistant infections will only become more challenging unless alternative treatment strategies are explored. Despite the accumulating evidence on using commensal bacteria for pathobiont decolonization, it is still not commonly practiced. To investigate the potential of commensal-mediated inhibition of pathogens systematically, we developed a quantitative framework describing the dynamics of the nasal microbiome by merging mathematical modeling and metagenomic data. We show that probiotic treatment outperforms antibiotics regarding decolonization performance and recolonization robustness while preserving the microbiome diversity with the additional advantage of personalized treatment options via using the patients own microbiota data. Moreover, we validated the approach by using nasal swabs from adults with nasal S. aureus colonization, demonstrating that probiotic treatment prevents recolonization with S. aureus in vitro. The framework developed in this work is an important step forward for the translation of experimental and clinical data into mainstream clinical practice in a systematic and controlled manner.

microbiology↗

bioRxiv2022

The baseline immunological and hygienic status of pigs impact disease severity of African swine fever

African Swine Fever virus (ASFV) is a large double-enveloped DNA virus of the Asfarviridae family that causes a lethal hemorrhagic disease in domestic pigs and wild boars. Since 2007, a highly virulent genotype II strain has emerged and spread in Europe and South-East Asia, where millions of animals succumbed to the disease. Field- and laboratory-attenuated strains of ASFV cause highly variable clinical disease severity and survival, and mechanisms remain unclear. We hypothesized that the immunological and hygienic status of pigs is a determinant of ASF disease course. Here we compared the immunological profile at baseline and in response to ASFV infection in specific pathogen-free (SPF) and farm-raised Large White domestic pigs. At steady state, SPF pigs showed lower white blood cell counts and a lower basal inflammatory and antiviral transcriptomic profile compared to farm pigs associated with profound differences in gut microbiome composition. After inoculation with a highly virulent ASFV genotype II strain (Armenia 2008), severe clinical signs, viremia and pro-inflammatory cytokines appeared sooner in SPF pigs, indicating a reduced capacity to control early virus replication. In contrast, during infection with an attenuated field isolate (Estonia 2014), SPF pigs presented a milder and shorter clinical disease with full recovery, whereas farm pigs presented severe protracted disease with 50% lethality. Interestingly, farm pigs showed higher production of inflammatory cytokines, whereas SPF pigs produced more anti-inflammatory IL-1ra early after infection, and presented a stronger expansion of leukocytes in the recovery phase. Altogether, our data indicate that the hygiene-dependent innate immune status has a double-edge sword impact on immune responses in ASF pathogenesis. While the higher baseline innate immune activity helps the host in reducing initial virus replication, it promotes immunopathological cytokine responses, and delays lymphocyte proliferation after infection with an attenuated strain. Such effects should be considered for live vaccine development and vigilance.

microbiology↗

bioRxiv2020

Population structure and transmission of Mycobacterium bovis in Ethiopia

Bovine tuberculosis (bTB) is endemic in cattle in Ethiopia, a country that hosts the largest national cattle herd in Africa. The intensive dairy sector, most of which is peri-urban, has the highest prevalence of disease. Previous studies in Ethiopia have demonstrated that the main cause is Mycobacterium bovis (M. bovis), which has been investigated using conventional molecular tools including deletion typing, spoligotyping and Mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR). Here we use whole genome sequencing (WGS) to examine the population structure of M. bovis in Ethiopia. A total of 134 M. bovis isolates were sequenced including 128 genomes from 85 mainly dairy cattle and six genomes isolated from humans, originating from 12 study sites across Ethiopia. These genomes provided a good representation of the previously described population structure of M. bovis, based on spoligotyping and demonstrated that the population is dominated by the clonal complexes African 2 (Af2) and European 3 (Eu3). A range of within-host diversity was observed amongst the isolates and evidence was found for both short- and long-distance transmission. Detailed analysis of available genomes from the Eu3 clonal complex combined with previously published genomes revealed two distinct introductions of this clonal complex into Ethiopia between 1950 and 1987, likely from Europe. This work is important to help better understand bTB transmission in cattle in Ethiopia and can potentially inform national strategies for bTB control in Ethiopia and beyond.

genomics↗