The past, present and future of ancient bacterial DNA

Groundbreaking studies conducted in the mid-1980s demonstrated the possibility of sequencing ancient DNA (aDNA), which has allowed us to answer fundamental questions about the human past. Microbiologists were thus given a powerful tool to glimpse directly into inscrutable bacterial history, hitherto inaccessible due to a poor fossil record. Initially plagued by concerns regarding contamination, the field has grown alongside technical progress, with the advent of high-throughput sequencing being a breakthrough in sequence output and authentication. Albeit burdened with challenges unique to the analysis of bacteria, a growing number of viable sources for aDNA has opened multiple avenues of microbial research. Ancient pathogens have been extracted from bones, dental pulp, mummies and historical medical specimens and have answered focal historical questions such as identifying the aetiological agent of the black death as Yersinia pestis. Furthermore, ancient human microbiomes from fossilized faeces, mummies and dental plaque have shown shifts in human commensals through the Neolithic demographic transition and industrial revolution, whereas environmental isolates stemming from permafrost samples have revealed signs of ancient antimicrobial resistance. Culminating in an ever-growing repertoire of ancient genomes, the quickly expanding body of bacterial aDNA studies has also enabled comparisons of ancient genomes to their extant counterparts, illuminating the evolutionary history of bacteria. In this review we summarize the present avenues of research and contextualize them in the past of the field whilst also pointing towards questions still to be answered.

The combined antibacterial and anticancer properties of nano Ce-containing Mg-phosphate ceramic

AIM

This paper was mainly aimed at synthesis of Ce-containing nano-Mg-phosphate ceramic as a multifunctional material.

MATERIALS AND METHODS

Two ceramics based on Mg₃(PO₄)₂ and Ce_0.2Mg_2.8(PO₄)₂ formulas (MP and MP-C, respectively) were synthesized. The synthesized powders were characterized by XRD, TEM, Zeta potential, and FTIR. Also, their dissolution behavior was tested in Tris-HCl buffer solution. Moreover, the antimicrobial efficacy was evaluated against gram-positive bacteria (Bacillus sphaericus MTCC 511 &Staphylococcus aureus MTCC 87) and gram-negative bacteria (Enterobacter aerogenes MTCC 111 &Pseudomonas aeruginosa MTCC 1034) using dick diffusion assay and microdilution method. Furthermore, the cell viability test was performed for the ceramics on Vero cells (African green monkey kidney cells), and their antitumor activity was determined by PC3 cell line (prostatic cancer). Also, the cellular uptake was determined by the flow cytometry.

KEY FINDINGS

The results showed that the substitution of Mg by Ce decreased the particle size from 40 to 90 nm for MP sample to 2-10 nm for MP-C sample and increased the degradation rate. Both samples showed excellent antimicrobial activities. Moreover, MP demonstrated more cell viability than MP-C on Vero cells at high concentrations, whereas, MP-C showed more antitumor activity on PC3 cells than MP sample. Moreover, MP-C showed a higher cell uptake than MP due to its smaller size and more negative charge.

SIGNIFICANCE

Mg-phosphate ceramic can be used in this study successfully as a delivery system for cerium ions and showed a high antitumor activity, which makes it highly recommended as safe and effective cancer treatment materials.

Mechanisms of Immune Evasion and Bone Tissue Colonization That Make Staphylococcus aureus the Primary Pathogen in Osteomyelitis

PURPOSE OF REVIEW

Staphylococcus aureus is the primary pathogen responsible for osteomyelitis, which remains a major healthcare burden. To understand its dominance, here we review the unique pathogenic mechanisms utilized by S. aureus that enable it to cause incurable osteomyelitis.

RECENT FINDINGS

Using an arsenal of toxins and virulence proteins, S. aureus kills and usurps immune cells during infection, to produce non-neutralizing pathogenic antibodies that thwart adaptive immunity. S. aureus also has specific mechanisms for distinct biofilm formation on implants, necrotic bone tissue, bone marrow, and within the osteocyte lacuno-canicular networks (OLCN) of live bone. In vitro studies have also demonstrated potential for intracellular colonization of osteocytes, osteoblasts, and osteoclasts. S. aureus has evolved a multitude of virulence mechanisms to achieve life-long infection of the bone, most notably colonization of OLCN. Targeting S. aureus proteins involved in these pathways could provide new targets for antibiotics and immunotherapies.

The microbial metagenome and bone tissue composition in mice with microbiome-induced reductions in bone strength

The genetic components of microbial species that inhabit the body are known collectively as the microbiome. Modifications to the microbiome have been implicated in disease processes throughout the body and have recently been shown to influence bone. Prior work has associated changes in the microbial taxonomy (phyla, class, species, etc.) in the gut with bone phenotypes but has provided limited information regarding mechanisms. With the goal of achieving a more mechanistic understanding of the effects of the microbiome on bone, we perform a metagenomic analysis of the gut microbiome that provides information on the functional capacity of the microbes (all microbial genes present) rather than only characterizing the microbial taxa. Male C57Bl/6 mice were subjected to disruption of the gut microbiota (ΔMicrobiome) using oral antibiotics (from 4 to 16 weeks of age) or remained untreated (n = 6-7/group). Disruption of the gut microbiome in this manner has been shown to lead to reductions in tissue mechanical properties and whole bone strength in adulthood with only minor changes in bone geometry and density. ΔMicrobiome led to modifications in the abundance of microbial genes responsible for the synthesis of the bacterial cell wall and capsule; bacterially synthesized carbohydrates; and bacterially synthesized vitamins (B and K) (p < 0.01). Follow up analysis focused on vitamin K, a factor that has previously been associated with bone health. The vitamin K content of the cecum, liver and kidneys was primarily microbe-derived forms of vitamin K (menaquinones) and was decreased by 32-66% in ∆Microbiome mice compared to untreated animals (p < 0.01). Bone mineral crystallinity determined using Raman spectroscopy was decreased in ∆Microbiome mice (p = 0.01). This study illustrates the use of metagenomic analysis to link the microbiome to bone phenotypes and provides preliminary findings implicating microbially synthesized vitamin-K as a regulator of bone matrix quality.

Impact of diagnostic bone biopsies on the management of non-vertebral osteomyelitis: A retrospective cohort study

Optimal antibiotic management of patients with osteomyelitis remains a challenge for many clinicians. Although image-guided bone biopsy (IGB) remains the gold standard, its role in confirming diagnosis and guiding antibiotic management is not clear in patients with non-vertebral osteomyelitis.To determine the diagnostic yield of IGB and its impact on antibiotic management in non-vertebral osteomyelitis.Retrospective cohort study.Urban academic medical center.Patients admitted for non-vertebral osteomyelitis who underwent image-guided bone biopsy.Primary outcomes were microbiologic and histopathological results. We evaluated the impact of IGB on clinician-initiated changes in antibiotic regimen before and after biopsy.We evaluated 203 bone biopsies in 185 patients with clinical suspicion of osteomyelitis. 79% of patient received antibiotics prior to biopsy. Bone cultures were positive in 28% and histopathology confirmed osteomyelitis in 29%, but concordance was poor. Furthermore, clinical suspicion of infection was much higher, given that 68% received empiric antibiotics. Leukocytosis was significantly associated with positive cultures in multivariate analysis. There was no statistically significant correlation between antibiotic management and bone culture results. When culture yielded an organism, empiric regimens were kept the same, broadened or narrowed with equal frequency; targeted regimens were chosen only in 4 cases. Despite negative cultures in 98/138 cases having received empiric treatment, antibiotics were discontinued in only 8 cases. Even when empiric treatment was not given, negative cultures did not dissuade clinicians from eventual antibiotic use in a significant number of cases (17/48). In 46/71 patients whose final regimen included vancomycin, there was no evidence of current or past infection with MRSA.In patients with non-vertebral osteomyelitis, the diagnostic yield of image-guided bone biopsy is low, and clinicians frequently make decisions regarding antibiotic management that are not aligned with culture results.

Candida auris Sternal Osteomyelitis in a Man from Kenya Visiting Australia, 2015

In Australia in 2015, Candida auris sternal osteomyelitis was diagnosed in a 65-year-old man with a history of intensive care treatment in Kenya in 2012 and without a history of cardiac surgery. The isolate was South Africa clade III. Clinicians should note that C. auris can cause low-grade disease years after colonization.

Microbial differences between dental plaque and historic dental calculus are related to oral biofilm maturation stage

BACKGROUND

Dental calculus, calcified oral plaque biofilm, contains microbial and host biomolecules that can be used to study historic microbiome communities and host responses. Dental calculus does not typically accumulate as much today as historically, and clinical oral microbiome research studies focus primarily on living dental plaque biofilm. However, plaque and calculus reflect different conditions of the oral biofilm, and the differences in microbial characteristics between the sample types have not yet been systematically explored. Here, we compare the microbial profiles of modern dental plaque, modern dental calculus, and historic dental calculus to establish expected differences between these substrates.

RESULTS

Metagenomic data was generated from modern and historic calculus samples, and dental plaque metagenomic data was downloaded from the Human Microbiome Project. Microbial composition and functional profile were assessed. Metaproteomic data was obtained from a subset of historic calculus samples. Comparisons between microbial, protein, and metabolomic profiles revealed distinct taxonomic and metabolic functional profiles between plaque, modern calculus, and historic calculus, but not between calculus collected from healthy teeth and periodontal disease-affected teeth. Species co-exclusion was related to biofilm environment. Proteomic profiling revealed that healthy tooth samples contain low levels of bacterial virulence proteins and a robust innate immune response. Correlations between proteomic and metabolomic profiles suggest co-preservation of bacterial lipid membranes and membrane-associated proteins.

CONCLUSIONS

Overall, we find that there are systematic microbial differences between plaque and calculus related to biofilm physiology, and recognizing these differences is important for accurate data interpretation in studies comparing dental plaque and calculus.

Cretaceous dinosaur bone contains recent organic material and provides an environment conducive to microbial communities

Fossils were thought to lack original organic molecules, but chemical analyses show that some can survive. Dinosaur bone has been proposed to preserve collagen, osteocytes, and blood vessels. However, proteins and labile lipids are diagenetically unstable, and bone is a porous open system, allowing microbial/molecular flux. These 'soft tissues' have been reinterpreted as biofilms. Organic preservation versus contamination of dinosaur bone was examined by freshly excavating, with aseptic protocols, fossils and sedimentary matrix, and chemically/biologically analyzing them. Fossil 'soft tissues' differed from collagen chemically and structurally; while degradation would be expected, the patterns observed did not support this. 16S rRNA amplicon sequencing revealed that dinosaur bone hosted an abundant microbial community different from lesser abundant communities of surrounding sediment. Subsurface dinosaur bone is a relatively fertile habitat, attracting microbes that likely utilize inorganic nutrients and complicate identification of original organic material. There exists potential post-burial taphonomic roles for subsurface microorganisms.

Bacterial contamination rate and associated factors during bone and tendon allograft procurement from Spanish donors: exploring the contamination patterns

BACKGROUND

Allograft contamination during extraction represents a major limiting factor for tissue bank availability. Contamination rates remain persistently high independent of the hospital, country or year considered.

AIM

To analyse the factors associated with contamination of bone and tendon samples extracted from Spanish donors.

METHODS

Data for 1162 bone and tendon samples extracted from 102 donors between 2014 and 2017 were collected retrospectively from the hospital database. Descriptive statistics, potentially associated factors and correlation of contamination between samples extracted from different anatomical locations of the same donor were analysed.

FINDINGS

In total, 227 (19.54%) of the extracted samples [131 (18.49%) bone samples and 96 (20.92%) tendon samples] rendered positive cultures and were discarded. Male sex [odds ratio (OR) 2.023; P=0.019], extraction of >10 samples per donor (OR 1.997; P<0.001) and extraction time >240 min (OR 1.755; P=0.001) were factors independently associated with a higher contamination rate. Meanwhile, the tissue sample type 'bone-patellar tendon-bone' was associated with a significantly lower contamination rate (OR 0.446; P=0.001). Significant correlation between certain localization of contaminated samples and the concordance of bacterial species was also observed.

CONCLUSION

Factors related to the extraction procedure, such as total extraction time, extraction sequence, number of samples extracted and anatomical location of extracted samples, play a major role in allograft contamination. Further optimization of procedures, guided by the contamination patterns analysed in this study, should help to increase tissue bank availability.

Leprosy at the edge of Europe-Biomolecular, isotopic and osteoarchaeological findings from medieval Ireland

Relatively little is known of leprosy in Medieval Ireland; as an island located at the far west of Europe it has the potential to provide interesting insights in relation to the historical epidemiology of the disease. To this end the study focuses on five cases of probable leprosy identified in human skeletal remains excavated from inhumation burials. Three of the individuals derived from the cemetery of St Michael Le Pole, Golden Lane, Dublin, while single examples were also identified from Ardreigh, Co. Kildare, and St Patrick’s Church, Armoy, Co. Antrim. The individuals were radiocarbon dated and examined biomolecularly for evidence of either of the causative pathogens, M. leprae or M. lepromatosis. Oxygen and strontium isotopes were measured in tooth enamel and rib samples to determine where the individuals had spent their formative years and to ascertain if they had undertaken any recent migrations. We detected M. leprae DNA in the three Golden Lane cases but not in the probable cases from either Ardreigh Co. Kildare or Armoy, Co. Antrim. M. lepromatosis was not detected in any of the burals. DNA preservation was sufficiently robust to allow genotyping of M. leprae strains in two of the Golden Lane burials, SkCXCV (12-13^th century) and SkCCXXX (11-13^th century). These strains were found to belong on different lineages of the M. leprae phylogenetic tree, namely branches 3 and 2 respectively. Whole genome sequencing was also attempted on these two isolates with a view to gaining further information but poor genome coverage precluded phylogenetic analysis. Data from the biomolecular study was combined with osteological, isotopic and radiocarbon dating to provide a comprehensive and multidisciplinary study of the Irish cases. Strontium and oxygen isotopic analysis indicate that two of the individuals from Golden Lane (SkCXLVIII (10-11^th century) and SkCXCV) were of Scandinavian origin, while SkCCXXX may have spent his childhood in the north of Ireland or central Britain. We propose that the Vikings were responsible for introducing leprosy to Ireland. This work adds to our knowledge of the likely origins of leprosy in Medieval Ireland and will hopefully stimulate further research into the history and spread of this ancient disease across the world.

Development and biological evaluation of Ti6Al7Nb scaffold implants coated with gentamycin-saturated bacterial cellulose biomaterial

Herein we present an innovative method of coating the surface of Titanium-Aluminium-Niobium bone scaffold implants with bacterial cellulose (BC) polymer saturated with antibiotic. Customized Ti6Al7Nb scaffolds manufactured using Selective Laser Melting were immersed in a suspension of Komagataeibacter xylinus bacteria which displays an ability to produce a 3-dimensional structure of bio-cellulose polymer. The process of complete implant coating with BC took on average 7 days. Subsequently, the BC matrix was cleansed by means of alkaline lysis and saturated with gentamycin. Scanning electron microscopy revealed that BC adheres and penetrates into the implant scaffold structure. The viability and development of the cellular layer on BC micro-structure were visualized by means of confocal microscopy. The BC-coated implants displayed a significantly lower cytotoxicity against osteoblast and fibroblast cell cultures in vitro in comparison to non-coated implants. It was also noted that gentamycin released from BC-coated implants inhibited the growth of Staphylococcus aureus cultures in vitro, confirming the suitability of such implant modification for preventing hostile microbial colonization. As demonstrated using digital microscopy, the procedure used for implant coating and BC chemical cleansing did not flaw the biomaterial structure. The results presented herein are of high translational value with regard to future use of customized, BC-coated and antibiotic-saturated implants designed for use in orthopedic applications to speed up recovery and to reduce the risk of musculoskeletal infections.

Innate Immunity to Staphylococcus aureus: Evolving Paradigms in Soft Tissue and Invasive Infections

Staphylococcus aureus causes a wide range of diseases that together embody a significant public health burden. Aided by metabolic flexibility and a large virulence repertoire, S. aureus has the remarkable ability to hematogenously disseminate and infect various tissues, including skin, lung, heart, and bone, among others. The hallmark lesions of invasive staphylococcal infections, abscesses, simultaneously denote the powerful innate immune responses to tissue invasion as well as the ability of staphylococci to persist within these lesions. In this article, we review the innate immune responses to S. aureus during infection of skin and bone, which serve as paradigms for soft tissue and bone disease, respectively.

Historic Treponema pallidum genomes from Colonial Mexico retrieved from archaeological remains

Treponema pallidum infections occur worldwide causing, among other diseases, syphilis and yaws. In particular sexually transmitted syphilis is regarded as a re-emerging infectious disease with millions of new infections annually. Here we present three historic T. pallidum genomes (two from T. pallidum ssp. pallidum and one from T. pallidum ssp. pertenue) that have been reconstructed from skeletons recovered from the Convent of Santa Isabel in Mexico City, operational between the 17th and 19th century. Our analyses indicate that different T. pallidum subspecies caused similar diagnostic presentations that are normally associated with syphilis in infants, and potential evidence of a congenital infection of T. pallidum ssp. pertenue, the causative agent of yaws. This first reconstruction of T. pallidum genomes from archaeological material opens the possibility of studying its evolutionary history at a resolution previously assumed to be out of reach.

Gut Microbiota, Immune System, and Bone

The gut microbiota (GM) is the whole of commensal, symbiotic, and pathogenic microorganisms living in our intestine. The GM-host interactions contribute to the maturation of the host immune system, modulating its systemic response. It is well documented that GM can interact with non-enteral cells such as immune cells, dendritic cells, and hepatocytes, producing molecules such as short-chain fatty acids, indole derivatives, polyamines, and secondary bile acid. The receptors for some of these molecules are expressed on immune cells, and modulate the differentiation of T effector and regulatory cells: this is the reason why dysbiosis is correlated with several autoimmune, metabolic, and neurodegenerative diseases. Due to the close interplay between immune and bone cells, GM has a central role in maintaining bone health and influences bone turnover and density. GM can improve bone health also increasing calcium absorption and modulating the production of gut serotonin, a molecule that interacts with bone cells and has been suggested to act as a bone mass regulator. Thus, GM manipulation by consumption of antibiotics, changes in dietary habits, and the use of pre- and probiotics may affect bone health. This review summarizes evidences on the influence of GM on immune system and on bone turnover and density and how GM manipulation may influence bone health.

Osteomicrobiology: A New Cross-Disciplinary Research Field

The mutualistic interaction between the gut microbiota (GM) and its host profoundly shapes many aspects of our physiology. The composition and activity of the gut microbiota is modulated by environmental factors such as dietary habits and antibiotic treatments. In rodents, studies demonstrate that the GM is a crucial regulator of bone metabolism and that modulation of the GM composition by probiotic interventions can prevent castration-induced bone loss. Short-term colonization of germ-free mice with GM results in an activation of CD4+T cells, resulting in increased levels of pro-inflammatory cytokines in bone and thereby activation of osteoclastic bone resorption. Besides these immune-mediated effects on bone mass, the GM is involved in nutritional uptake and may, thereby, regulate overall body growth and bone sizes possibly mediated via altered IGF-I levels. We recently introduced a new term "osteomicrobiology" for the rapidly emerging research field of the role of the microbiota in bone health. This research field is aimed to bridge the gaps between bone physiology, gastroenterology, immunology, and microbiology. Future studies will determine if the GM is a novel therapeutic target for osteoporosis and if the GM composition might be used as a biomarker for fracture prediction.

Prebiotics, Bone and Mineral Metabolism

Increasing interest in functional foods has driven discovery in the area of bioactive compounds. Prebiotics are non-digestible carbohydrate compounds that, when consumed, elicit health benefits and aid in the prevention and treatment of chronic diseases. While prebiotics have been shown to improve a number of chronic, inflammatory conditions, growing evidence exists for prebiotic effects on calcium metabolism and bone health. These novel dietary fibers have been shown to increase calcium absorption in the lower intestines of both preclinical and human models. Rodent models have also been imperative for understanding prebiotic effects on bone mineral density and measures of skeletal strength. Although fewer data are available for humans, bone-related prebiotic effects exist across the lifecycle, suggesting benefits for attainment of peak bone mass during adolescence and minimized bone resorption among postmenopausal women. These effects are thought to occur through prebiotic-microbe interactions in the large intestine. Current prebiotic mechanisms for improved mineral absorption and skeletal health include alterations in gut microbiota composition, production of short-chain fatty acids, altered intestinal pH, biomarker modification, and immune system regulation. While the majority of available data support improved mineral bioavailability, emerging evidence suggests alternate microbial roles and the presence of an intricate gut-bone signaling axis. Overall, the current scientific literature supports prebiotic consumption as a cost-effective and sustainable approach for improved skeletal health and/or fracture prevention. The goal of this review is to discuss both foundational and recent research in the area of prebiotics, mineral metabolism, and bone health.

Effects of Fermented Milk Products on Bone

Fermented milk products like yogurt or soft cheese provide calcium, phosphorus, and protein. All these nutrients influence bone growth and bone loss. In addition, fermented milk products may contain prebiotics like inulin which may be added to yogurt, and provide probiotics which are capable of modifying intestinal calcium absorption and/or bone metabolism. On the other hand, yogurt consumption may ensure a more regular ingestion of milk products and higher compliance, because of various flavors and sweetness. Bone mass accrual, bone homeostasis, and attenuation of sex hormone deficiency-induced bone loss seem to benefit from calcium, protein, pre-, or probiotics ingestion, which may modify gut microbiota composition and metabolism. Fermented milk products might also represent a marker of lifestyle promoting healthy bone health.

Impact of Fluoroscopically Guided Bone Biopsy on Antibiotic Management of Osteomyelitis in the Lower Extremity

This study evaluated the impact of fluoroscopically guided percutaneous bone biopsy on altering antibiotic regimens in lower extremity osteomyelitis. Eighty-eight patients who received fluoroscopically guided bone biopsies were identified. There was bacterial growth in 28% of bone biopsies overall. The rate of positive culture was decreased in patients started on empiric antibiotics before biopsy (23%) compare with patients without empiric antibiotics (44%). Antibiotic regimens were changed in 24% of patients overall in response to culture data. The majority of positive biopsy cultures (76%) but minority of negative biopsy cultures (3%) resulted in a change to antibiotic regimens. The impact of percutaneous bone biopsy on antibiotic management of adult patients with osteomyelitis diagnosed by magnetic resonance imaging is modest and is decreased in patients previously started on antibiotics. Despite its modest impact, bone biopsy results can provide useful information in antibiotic management, especially when positive (Journal of Surgical Orthopaedic Advances 27(4):277-280, 2018).

Bone responses in health and infectious diseases: A focus on osteoblasts

Historically, bone was thought to be immunologically inactive with the sole function of supporting locomotion and ensuring stromaness functions as a major lymphoid organ. However, a myriad of pathogens (bacteria such as staphylococcus as well as viruses including alphaviruses, HIV or HCV) can invade the bone. These pathogens can cause apoptosis, autophagy and necrosis of osteoblasts and lead to lymphopenia and immune paralysis. There are now several detailed studies on how osteoblasts contribute to innate immune and inflammatory responses; indeed, osteoblasts in concert with resident macrophages can engage an armory of defense mechanisms capable of detecting and controlling pathogen evasion mechanisms. Osteoblasts can express the so-called pattern recognition receptors such as TOLL-like receptors involved in the detection for example of lipids and unique sugars (polysaccharides and polyriboses) expressed by bacteria or viruses (e.g. LPS and RNA respectively). Activated osteoblasts can produce interferon type I, cytokines, chemokines and interferon-stimulated proteins through autocrine and paracrine mechanisms to control for viral replication and to promote phagocytosis or lysis of bacteria for example by defensins. Uncontrolled and sustained innate immune activation of infected osteoblasts will also lead to an imbalance in the production of osteoclastogenic factors such as RANKL and osteoprotegerin involved in bone repair.

Comprehensive analysis of microorganisms accompanying human archaeological remains

Metagenome analysis has become a common source of information about microbial communities that occupy a wide range of niches, including archaeological specimens. It has been shown that the vast majority of DNA extracted from ancient samples come from bacteria (presumably modern contaminants). However, characterization of microbial DNA accompanying human remains has never been done systematically for a wide range of different samples. We used metagenomic approaches to perform comparative analyses of microorganism communities present in 161 archaeological human remains. DNA samples were isolated from the teeth of human skeletons dated from 100 AD to 1200 AD. The skeletons were collected from 7 archaeological sites in Central Europe and stored under different conditions. The majority of identified microbes were ubiquitous environmental bacteria that most likely contaminated the host remains not long ago. We observed that the composition of microbial communities was sample-specific and not correlated with its temporal or geographical origin. Additionally, traces of bacteria and archaea typical for human oral/gut flora, as well as potential pathogens, were identified in two-thirds of the samples. The genetic material of human-related species, in contrast to the environmental species that accounted for the majority of identified bacteria, displayed DNA damage patterns comparable with endogenous human ancient DNA, which suggested that these microbes might have accompanied the individual before death. Our study showed that the microbiome observed in an individual sample is not reliant on the method or duration of sample storage. Moreover, shallow sequencing of DNA extracted from ancient specimens and subsequent bioinformatics analysis allowed both the identification of ancient microbial species, including potential pathogens, and their differentiation from contemporary species that colonized human remains more recently.

The Cause of Death of a Child in the 18th Century Solved by Bone Microbiome Typing Using Laser Microdissection and Next Generation Sequencing

The history of medicine abounds in cases of mysterious deaths, especially by infectious diseases, which were probably unresolved because of the lack of knowledge and of appropriate technology. The aim of this study was to exploit contemporary technologies to try to identify the cause of death of a young boy who died from a putative “infection” at the end of the 18th century, and for whom an extraordinarily well-preserved minute bone fragment was available. After confirming the nature of the sample, we used laser microdissection to select the most “informative” area to be examined. Tissue genotyping indicated male gender, thereby confirming the notary’s report. 16S ribosomal RNA sequencing showed that Proteobacteria and Actinobacteria were more abundant than Firmicutes and Bacteroidetes, and that Pseudomonas was the most abundant bacterial genus in the Pseudomonadaceae family. These data suggest that the patient most likely died from Pseudomonas osteomyelitis. This case is an example of how new technological approaches, like laser microdissection and next-generation sequencing, can resolve ancient cases of uncertain etiopathology. Lastly, medical samples may contain a wealth of information that may not be accessible until more sophisticated technology becomes available. Therefore, one may envisage the possibility of systematically storing medical samples for evaluation by future generations.

Diagnostic value of sinus tract culture versus intraoperative bone culture in patients with chronic osteomyelitis

To compare the organisms isolated from the sinus tract culture and intraoperative bone culture in patients with chronic osteomyelitis. This cross sectional prospective study was conducted from February 2015 to March 2016. Ninety consecutive patients were enrolled in study (n=90). Inclusion criteria were patients with either sex, any age, chronic osteomyelitis having discharging sinus. Sample from sinus tracts and bone were taken through standardized aseptic technique and organism were cultured. There were 62 males and 28 females, male to female ratio 3:1, mean age was 40 years. 23 patients had primary osteomyelitis and 67 had secondary osteomyelitis. 68 patients had orthopaedic implant infections. In 61/90 (67%) patients the same organism was isolated on both sinus tract and intraoperative cultures.In our scenario we found that within the limitations of this study, there was a high ratio of agreement between the sinus tract and intraoperative cultures. We conclude that if used judiciously, sinus tract cultures can yield accurate results in the majority of cases.

[The microbiological study of purulent focus of inflammation in patients with chronic osteomyelitis of long bones]

The article presents analysis of results of microbiological study of pathologic samples from fistula and surgical wounds of 155 patients with chronic osteomyelitis of long bones in the period of exacerbation of disease during 2014-2015. In totality, 126 samples from fistula and 95 samples from wounds were analyzed. Correspondingly, 164 and 102 strains of bacteria were separated. The microbial contamination of fistula and wounds was established. The species composition of microflora was analyzed. It is established that in the analyzed groups the main agent still continues to be staphylococcus and priority pathogen Staphylococcus aureus differing slightly in rate of occurrence and coefficient of resistance. MRSA was separated up to 5.6% more often from surgical wounds than from fistula. The highest detection rate of strains S. aureus and MRSA falls on 2009-2010. In 2015, the lowest detection rate of S. aureus was marked with relatively high rate of detection of MRSA. The disk diffusion D-test was applied to determine resistance of inducible type to Clindamycin of 17 strains of S. aureus resistant to Erythromycin and sensitive to Clindamycin. The inducible resistance to Clindamycin for strains from surgery pounds made up to 62.5% that is three times higher than in case of strains separated from fistula. The important role in development of chronic of osteomyelitis of long bones is played by Gram-negative microorganisms (E. coli, Enterobacter, P. aeruginosa, etc.). The rate of detection of these microorganisms in surgery wounds makes up to 22.5% and 17.1% in fistula.