Genomic Analysis of 18th-Century Kazakh Individuals and Their Oral Microbiome

The Asian Central Steppe, consisting of current-day Kazakhstan and Russia, has acted as a highway for major migrations throughout history. Therefore, describing the genetic composition of past populations in Central Asia holds value to understanding human mobility in this pivotal region. In this study, we analyse paleogenomic data generated from five humans from Kuygenzhar, Kazakhstan. These individuals date to the early to mid-18th century, shortly after the Kazakh Khanate was founded, a union of nomadic tribes of Mongol Golden Horde and Turkic origins. Genomic analysis identifies that these individuals are admixed with varying proportions of East Asian ancestry, indicating a recent admixture event from East Asia. The high amounts of DNA from the anaerobic Gram-negative bacteria Tannerella forsythia, a periodontal pathogen, recovered from their teeth suggest they may have suffered from periodontitis disease. Genomic analysis of this bacterium identified recently evolved virulence and glycosylation genes including the presence of antibiotic resistance genes predating the antibiotic era. This study provides an integrated analysis of individuals with a diet mostly based on meat (mainly horse and lamb), milk, and dairy products and their oral microbiome.

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Antibiotic susceptibility profiles and frequency of resistance genes in clinical Shiga toxin-producing Escherichia coli isolates from Michigan over a 14-year period

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01189-21 ◽

2021 ◽

Author(s):

Sanjana Mukherjee ◽

Heather M. Blankenship ◽

Jose A. Rodrigues ◽

Rebekah E. Mosci ◽

James T. Rudrik ◽

...

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

Resistance Genes ◽

Shiga Toxin ◽

Antibiotic Susceptibility ◽

Genetic Relatedness ◽

Antibiotic Resistance Genes ◽

Genomic Analysis ◽

Mechanisms Of Resistance ◽

Susceptibility Profiles

Background: Shiga toxin-producing Escherichia coli (STEC) is an important foodborne pathogen that contributes to over 250,000 infections in the US each year. Because antibiotics are not recommended for STEC infections, resistance in STEC has not been widely researched despite an increased likelihood for the transfer of resistance gene from STEC to opportunistic pathogens residing within the same microbial community. Methods: Between 2001 and 2014, 969 STEC isolates were collected from Michigan patients. Serotyping and antibiotic susceptibility profiles to clinically relevant antibiotics were determined using disc diffusion, while epidemiological data was used to identify factors associated with resistance. Whole genome sequencing was used to examine genetic relatedness and identify genetic determinants and mechanisms of resistance in the non-O157 isolates. Results: Increasing frequencies of resistance to at least one antibiotic was observed over the 14 years (p=0.01). While the non-O157 serogroups were more commonly resistant than O157 (Odds Ratio: 2.4; 95% Confidence Interval:1.43-4.05), the frequency of ampicillin resistance among O157 isolates was significantly higher in Michigan compared to the national average (p=0.03). Genomic analysis of 321 non-O157 isolates uncovered 32 distinct antibiotic resistance genes (ARGs). Although mutations in genes encoding resistance to ciprofloxacin and ampicillin were detected in four isolates, most of the horizontally acquired ARGs conferred resistance to aminoglycosides, β-lactams, sulfonamides and/or tetracycline. Conclusions: This study provides insight into the mechanisms of resistance in a large collection of clinical non-O157 STEC isolates and demonstrates that antibiotic resistance among all STEC serogroups has increased over time, prompting the need for enhanced surveillance.

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1127. Genomic Analysis of Biofilm-Forming Enteroinvasive E. coli Emergent Pathogen

Open Forum Infectious Diseases ◽

10.1093/ofid/ofy210.960 ◽

2018 ◽

Vol 5 (suppl_1) ◽

pp. S337-S338

Author(s):

Oscar Gomez-Duarte ◽

Julio Guerra ◽

Ricky Ko

Keyword(s):

Virulence Factors ◽

Dna Sequences ◽

Horizontal Transfer ◽

Antibiotic Resistance Genes ◽

Genomic Analysis ◽

Coli Strain ◽

Virulence Plasmid ◽

E Coli ◽

Query Coverage

Abstract Background Enteroinvasive Escherichia coli (EIEC) are involved in dysenteric diarrhea among children in low- and middle-income countries. EIEC strains isolated in Colombia, South America were shown to form biofilms and to be invasive in vitro. The O96:H19 serotypes and biofilm formation (BF) are not common phenotypes among EIEC, and the role they may play in diarrhea is at present unknown. The main goal of this study was to identify virulence and BF genes from EIEC genomic data. We hypothesize that EIEC O96:H19 strain 52.1 originated from horizontal transfer of a Shigella-like virulence plasmid into a non-EIEC pathogenic E coli strain. Methods WGS was performed on the BF-EIEC 52.1 strain using NextGen Illumina and Pacific Biosciences (PacBio) platforms. Publically available genomes from other EIEC O96H19 and Shigella genomes previously published were analyzed using online available software and databases including NCBI, BLAST, Mauve, among others. This analysis was tailored to identify virulence factors from the virulence factor database (VFDB). BLASTn was used to determine identity and query coverage of genes encoding the Shigella virulence factors. EIEC and Shigella genomes were analyzed on a multiple genome alignment software (Mauve) to verify results from BLASTn and to determine pseudogenes. Results The genome of EIEC O96:H19 strain 52.1 was 5,193,449 bp in size, containing 5,050 coding DNA sequences (CDSs). O96:H19 strain 52.1 carries three plasmids, the invasion plasmid (pINV) contains all type 3 secretion system (TTSS) and TTSS effectors genes previously described for Shigella and EIEC O96:H19 CFSAN029787 Italian strain. Non-TTSS virulence genes were also identified, including: long polar fimbrial gene (IpfA), enterotoxin (senB), and antibiotic resistance genes. Conclusion The EIEC O96:H19 strain 52.1 genome carries TTSS genes within a virulence plasmid, protein effector genes, and enterotoxin genes known to be associated with EIEC virulence. The EIEC O96:H19 stain 52.1 is an emergent diarrheagenic pathogen likely derived from an E. coli O96:H19 strain that acquired a Shigella-like virulence plasmid by horizontal transfer. Disclosures All authors: No reported disclosures.

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Genomic analysis reveals high virulence and antibiotic resistance amongst phage susceptible Acinetobacter baumannii

Scientific Reports ◽

10.1038/s41598-020-73123-y ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Udomluk Leungtongkam ◽

Rapee Thummeepak ◽

Thawatchai Kitti ◽

Kannipa Tasanapak ◽

Jintana Wongwigkarn ◽

...

Keyword(s):

Antibiotic Resistance ◽

Acinetobacter Baumannii ◽

Biofilm Formation ◽

Antibiotic Resistance Genes ◽

Genomic Analysis ◽

Multidrug Resistant ◽

Copper Tolerance ◽

Virulence Determinants ◽

Genome Sequences ◽

High Virulence

Abstract In this study, we examined the association between antimicrobial resistance, CRISPR/Cas systems and virulence with phage susceptibility in Acinetobacter baumannii and investigated draft genomes of phage susceptible multidrug resistant A. baumannii strains from Thailand. We investigated 230 A. baumannii strains using 17 lytic A. baumannii phages and the phage susceptibility was 46.5% (107/230). Phage susceptibility was also associated with resistance to numerous antibiotics (p-value < 0.05). We also found association between biofilm formation and the presence of ompA gene among phage susceptible A. baumannii strains (p-value < 0.05). A. baumannii isolates carrying cas5 or combinations of two or three other cas genes, showed a significant increase in phage resistance. Whole-genome sequences of seven phage susceptible A. baumannii isolates revealed that six groups of antibiotic resistance genes were carried by all seven phage susceptible A. baumannii. All strains carried biofilm associated genes and two strains harbored complete prophages, acquired copper tolerance genes, and CRISPR-associated (cas) genes. In conclusion, our data exhibits an association between virulence determinants and biofilm formation among phage susceptible A. baumannii strains. These data help to understand the bacterial co-evolution with phages.

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Dysbiosis in the oral microbiomes of anti-CCP positive individuals at risk of developing rheumatoid arthritis

Annals of the Rheumatic Diseases ◽

10.1136/annrheumdis-2020-216972 ◽

2020 ◽

pp. annrheumdis-2020-216972

Author(s):

Zijian Cheng ◽

Thuy Do ◽

Kulveer Mankia ◽

Josephine Meade ◽

Laura Hunt ◽

...

Keyword(s):

Rheumatoid Arthritis ◽

At Risk ◽

Risk Group ◽

Orthologous Gene ◽

Oral Microbiome ◽

Periodontal Pathogen ◽

P Value ◽

Illumina Hiseq ◽

Early Ra ◽

Taxonomic Profile

ObjectivesAn increased prevalence of periodontitis and perturbation of the oral microbiome has been identified in patients with rheumatoid arthritis (RA). The periodontal pathogen Porphyromonas gingivalis may cause local citrullination of proteins, potentially triggering anti-citrullinated protein antibody production. However, it is not known if oral dysbiosis precedes the onset of clinical arthritis. This study comprehensively characterised the oral microbiome in anti-cyclic citrullinated peptide (anti-CCP) positive at-risk individuals without clinical synovitis (CCP+at risk).MethodsSubgingival plaque was collected from periodontally healthy and diseased sites in 48 CCP+at risk, 26 early RA and 32 asymptomatic healthy control (HC) individuals. DNA libraries were sequenced on the Illumina HiSeq 3000 platform. Taxonomic profile and functional capability of the subgingival microbiome were compared between groups.ResultsAt periodontally healthy sites, CCP+at risk individuals had significantly lower microbial richness compared with HC and early RA groups (p=0.004 and 0.021). Microbial community alterations were found at phylum, genus and species levels. A large proportion of the community differed significantly in membership (523 species; 35.6%) and structure (575 species; 39.1%) comparing CCP+at risk and HC groups. Certain core species, including P. gingivalis, had higher relative abundance in the CCP+at risk group. Seventeen clusters of orthologous gene functional units were significantly over-represented in the CCP+at risk group compared with HC (adjusted p value <0.05).ConclusionAnti-CCP positive at-risk individuals have dysbiotic subgingival microbiomes and increased abundance of P. gingivalis compared with controls. This supports the hypothesis that the oral microbiome and specifically P. gingivalis are important in RA initiation.

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Comprehensive Genome Analysis of Carbapenem-Resistant Strains of Raoultella Species, an Emerging Multidrug-Resistant Bacterium in Hospitals

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01367-19 ◽

2019 ◽

Vol 63 (12) ◽

Cited By ~ 1

Author(s):

Xiao Yu ◽

Beiwen Zheng ◽

Jing Zhang ◽

Hao Xu ◽

Tingting Xiao ◽

...

Keyword(s):

Antibiotic Resistance ◽

Antibiotic Resistance Genes ◽

Genomic Analysis ◽

Multidrug Resistant ◽

Control Measures ◽

Carbapenem Resistant ◽

Multidrug Resistant Bacterium ◽

The World ◽

Resistant Strains

ABSTRACT We report the characterization of six carbapenem-resistant Raoultella spp. (CRRS) in our hospital and a genomic analysis of 58 publicly available isolates. CRRS isolates are sporadically identified around the world, and different transposons carrying carbapenemases were the resistant mechanisms. Mobile genetic elements play an important role in acquiring antibiotic resistance genes from the hospital. An improved understanding of these transposon and targeted control measures will be very valuable to prevent CRRS dissemination.

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Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp

10.1101/319723 ◽

2018 ◽

Cited By ~ 1

Author(s):

Olga O Bochkareva ◽

Elena V Moroz ◽

Iakov I Davydov ◽

Mikhail S Gelfand

Keyword(s):

Phase Variation ◽

Genomic Analysis ◽

Genomic Islands ◽

Chromosome Rearrangements ◽

Integrated Analysis ◽

Ecological Niches ◽

Genes Encoding ◽

Variation Mechanism ◽

Membrane Components ◽

Large Groups

AbstractBackgroundThe genus Burkholderia consists of species that occupy remarkably diverse ecological niches. Its best known members are important pathogens, B. mallei and B. pseudomallei, which cause glanders and melioidosis, respectively. Burkholderia genomes are unusual due to their multichromosomal organization.ResultsWe performed integrated genomic analysis of 127 Burkholderia strains. The pan-genome is open with the saturation to be reached between 86,000 and 88,000 genes. The reconstructed rearrangements indicate a strong avoidance of intra-replichore inversions that is likely caused by selection against the transfer of large groups of genes between the leading and the lagging strands. Translocated genes also tend to retain their position in the leading or the lagging strand, and this selection is stronger for large syntenies. Integrated reconstruction of chromosome rearrangements in the context of strains phylogeny reveals parallel rearrangements that may indicate inversion-based phase variation and integration of new genomic islands. In particular, we detected parallel inversions in the second chromosomes of B. pseudomallei with breakpoints formed by genes encoding membrane components of multidrug resistance complex, that may be linked to a phase variation mechanism. Two genomic islands, spreading horizontally between chromosomes, were detected in the B. cepacia group.ConclusionsThis study demonstrates the power of integrated analysis of pan-genomes, chromosome rearrangements, and selection regimes. Non-random inversion patterns indicate selective pressure, inversions are particularly frequent in a recent pathogen B. mallei, and, together with periods of positive selection at other branches, may indicate adaptation to new niches. One such adaptation could be a possible phase variation mechanism in B. pseudomallei.

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Case Report: Metagenomics Next-Generation Sequencing Can Help Define the Best Therapeutic Strategy for Brain Abscesses Caused by Oral Pathogens

Frontiers in Medicine ◽

10.3389/fmed.2021.644130 ◽

2021 ◽

Vol 8 ◽

Author(s):

Zhonghui Ma ◽

Su Yan ◽

Haoxin Dong ◽

Huifen Wang ◽

Yonggang Luo ◽

...

Keyword(s):

Next Generation Sequencing ◽

Brain Abscess ◽

Genomic Analysis ◽

Critical Factor ◽

Oral Microbiome ◽

Next Generation ◽

Gram Staining ◽

Brain Abscesses ◽

Generation Sequencing

Brain abscesses are associated with an increased long-term risk of new seizures and increased mortality within several years after infection. Common microorganisms that cause brain abscesses include bacteria, fungi, and mycoplasma. We report a 75-year-old man with a brain abscess caused by Prevotella denticola, an oral pathogen. Based on the clinical condition, we suspected that the patient had a blood-borne brain abscess, and he received antibiotics and systemic supportive treatment. The patient developed shock for the second time after negative Gram-staining results. Metagenomics next-generation sequencing showed one strain from the oral microbiome, confirming our hypothesis, and targeted antibiotic treatment was administered quickly. Thus, we report a case in which genomic analysis was the critical factor in determining the best antimicrobial therapy for administration.

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Comprehensive genomic analysis reveals virulence factors and antibiotic resistance genes in Pantoea agglomerans KM1, a potential opportunistic pathogen

10.1101/2020.09.15.297663 ◽

2020 ◽

Author(s):

Robin B. Guevarra ◽

Stefan Magez ◽

Eveline Peeters ◽

Mi Sook Chung ◽

Kyung Hyun Kim ◽

...

Keyword(s):

Antibiotic Resistance ◽

Virulence Factors ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Genomic Analysis ◽

Pantoea Agglomerans ◽

Whole Genome ◽

Tnf Α ◽

Wide Range ◽

Depth Analysis

AbstractPantoea agglomerans is a Gram-negative aerobic bacillus causing a wide range of opportunistic infections in humans including septicemia, pneumonia, septic arthritis, wound infections and meningitis. To date, the determinants of virulence, antibiotic resistance, metabolic features conferring survival and host-associated pathogenic potential of this bacterium remain largely underexplored. In this study, we sequenced and assembled the whole-genome of P. agglomerans KM1 isolated from kimchi in South Korea. The genome contained one circular chromosome of 4,039,945 bp, 3 mega plasmids, and 2 prophages. The phage-derived genes encoded integrase, lysozyme and terminase. Six CRISPR loci were identified within the bacterial chromosome. Further in-depth analysis showed that the genome contained 13 antibiotic resistance genes conferring resistance to clinically important antibiotics such as penicillin G, bacitracin, rifampicin, vancomycin, and fosfomycin. Genes involved in adaptations to environmental stress were also identified which included factors providing resistance to osmotic lysis, oxidative stress, as well as heat and cold shock. The genomic analysis of virulence factors led to identification of a type VI secretion system, hemolysin, filamentous hemagglutinin, and genes involved in iron uptake and sequestration. Finally, the data provided here show that, the KM1 isolate exerted strong immunostimulatory properties on RAW 264.7 macrophages in vitro. Stimulated cells produced Nitric Oxide (NO) and pro-inflammatory cytokines TNF-α, IL-6 and the anti-inflammatory cytokine IL-10. The upstream signaling for production of TNF-α, IL-6, IL-10, and NO depended on TLR4 and TLR1/2. While production of TNF-α, IL-6 and NO involved solely activation of the NF-κB, IL-10 secretion was largely dependent on NF-κB and to a lesser extent on MAPK Kinases. Taken together, the analysis of the whole-genome and immunostimulatory properties provided in-depth characterization of the P. agglomerans KM1 isolate shedding a new light on determinants of virulence that drive its interactions with the environment, other microorganisms and eukaryotic hosts.

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Oral Microbiome and Preterm Birth: Correlation or Coincidence? A Narrative Review

Open Access Macedonian Journal of Medical Sciences ◽

10.3889/oamjms.2020.4444 ◽

2020 ◽

Vol 8 (F) ◽

pp. 123-132

Author(s):

Biagio Rapone ◽

Elisabetta Ferrara ◽

Nicola Montemurro ◽

Ilaria Converti ◽

Matteo Loverro ◽

...

Keyword(s):

Preterm Birth ◽

Oral Bacteria ◽

Oral Microbiome ◽

Periodontal Pathogen ◽

Oral Microbiota ◽

Periodontal Pathogens ◽

Medline Search ◽

Phylogenetic Community Structure ◽

Inflammatory Status ◽

Periodontal Infection

BACKGROUND: Physiological changes that occur during pregnancy involve, as a natural consequence, also modifications of oral microbiome. However, the addition with microbial imbalance due to pre-existing periodontal infection might impair a pathological alteration in the phylogenetic community structure and composition in the oral cavity, exacerbating an inflammatory status, and becoming a potential risk factor for preterm birth. From the empirical findings about the relationship between periodontal pathogens and systemic diseases, a clear interest focused on the potential impact of some periodontal pathogens on the preterm birth risk has emerged. AIM: Exploration of the potential interdependence existing between dysbiosis of oral microbiome and changes in maternal-fetal barrier in premature rupture of membranes. MATERIALS AND METHODS: In accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, a Medline search was performed for studies focusing on oral microbioma and its association with pre-term birth, and completed by additional hand searching. Two reviewers independently selected studies and extracted data. The search was restricted to only reports written in English. RESULTS: The electronic search produced 66 items. Six duplicates were found. Among the collected studies, 56 were discarded because they met the exclusion criteria. The articles and reports in our review showed a connection between preterm birth and altered oral microbiome, suggesting a potential key role of Fusobacterium nucleatum, a notable periodontal pathogen involved in several pathological periodontal conditions, in increasing the risk of premature birth. CONCLUSIONS: Since F. nucleatum is frequently associated with preterm birth, it is coherent to hypothesize a potential role for the oral microbiota for preterm birth risk. Further studies should be carried out to determine the changes of the oral microflora in pregnancy and to provide comprehensive knowledge of the diversity of oral bacteria involved in preterm birth.

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A roadmap to mammalian oral microbiome evolution with dental calculus

10.1101/596791 ◽

2019 ◽

Cited By ~ 1

Author(s):

Jaelle C. Brealey ◽

Henrique G. Leitão ◽

Tom van der Valk ◽

Wenbo Xu ◽

Katia Bougiouri ◽

...

Keyword(s):

Antibiotic Production ◽

Antibiotic Resistance Genes ◽

Oral Microbiome ◽

Oral Disease ◽

Dental Calculus ◽

Wild Mammals ◽

Host Diet ◽

Host Genetic ◽

Genetic Profiles ◽

The Impact

AbstractAnimals and their associated microbiomes share a long evolutionary history, influenced by a complex interplay between extrinsic environmental and intrinsic host factors. However, we know little about microbiome responses to long-lasting environmental and host-centred processes, which require studying microbiome changes through time. Here, we apply a temporal metagenomics approach to dental calculus, the calcified oral microbial biofilm. We establish dental calculus as a valuable tool for the study of host microbiome evolution by characterising the taxonomic and functional composition of the oral microbiome in a variety of wild mammals. We detect oral pathogens in individuals with evidence of oral disease, assemble near-complete bacterial genomes from historical specimens, characterise antibiotic resistance genes even before the advent of industrial antibiotic production, reconstruct components of the host diet and recover host genetic profiles. Our work demonstrates how dental calculus can be used in the future to study the evolution of oral microbiomes and pathogens, and the impact of anthropogenic changes on wildlife and the environment.

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