Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories

Isolation, identification and virulence gene characterization of Aeromona dhakensis isolated from sea lion (Zalophus californianus)

Species of Aeromonas are ubiquitous pathogens of fish and aquatic animals and can infect humans and other animals through the food chain. However, there are few reports of marine mammalian infections. In 2020, a sea lion (Zalophus californianus) died acutely at an aquarium in Harbin, Heilongjiang Province, China. In order to explore the cause of death, we dissected the animal and observed pathological changes. Ogans were aseptically collected and used for bacterial isolation and culture. This revealed that the sea lion had died of sepsis caused by a bacterial infection. Isolated bacteria were investigated by morphology, biochemical phenotype and molecular identification, and this determined the pathogen as A. dhakensis. The isolate contained six virulence genes, hlyA, aerA, act, lafA, ela, fla, and was susceptible to most antibiotics. This is the first report of A. dhakensis associated with septicemia in pinnipeds and a description of its virulence and resistance profiles. Its presence in aquatic environments poses a potential threat to marine mammals.

CRISPR-Cas Systems in Gut Microbiome of Children with Autism Spectrum Disorders

The human gut microbiome is associated with various diseases, including autism spectrum disorders (ASD). Variations of the taxonomical composition in the gut microbiome of children with ASD have been observed repeatedly. However, features and parameters of the microbiome CRISPR-Cas systems in ASD have not been investigated yet. Here, we demonstrate such an analysis in order to describe the overall changes in the microbiome CRISPR-Cas systems during ASD as well as to reveal their potential to be used in diagnostics and therapy. For the systems identification, we used a combination of the publicly available tools suited for completed genomes with subsequent filtrations. In the considered data, the microbiomes of children with ASD contained fewer arrays per Gb of assembly than the control group, but the arrays included more spacers on average. CRISPR arrays from the microbiomes of children with ASD differed from the control group neither in the fractions of spacers with protospacers from known genomes, nor in the sets of known bacteriophages providing protospacers. Almost all bacterial protospacers of the gut microbiome systems for both children with ASD and the healthy ones were located in prophage islands, leaving no room for the systems to participate in the interspecies competition.

Potential influence of the microbiome environment in patients with biliary tract cancer and implications for therapy

Biliary tract cancers, including intra- and extra-hepatic cholangiocarcinoma as well as gallbladder cancer, are associated with poor prognosis and the majority of patients present with advanced-stage, non-resectable disease at diagnosis. Biliary tract cancer may develop through an accumulation of genetic and epigenetic alterations and can be influenced by microbial exposure. Furthermore, the liver and biliary tract are exposed to the gastrointestinal microbiome through the gut-liver axis. The availability of next-generation sequencing technology has led to an increase in studies investigating the relationship between microbiota and human disease. In particular, the interplay between the microbiome, the tumour micro-environment and response to systemic therapy is a prospering area of interest. Given the poor outcomes for patients with biliary tract cancer, this emerging field of research, through which new biomarkers may be identified, offers potential as a tool for early diagnosis, prognostication or even as a future therapeutic target. This review summarises the available evidence on the microbiome environment in patients with biliary tract cancer, including a discussion around confounding factors, implications for therapy and proposed future directions.

A New Strategy for Microbial Taxonomic Identification through Micro-Biosynthetic Gold Nanoparticles and Machine Learning

Microorganisms can serve as biological factories for the synthesis of inorganic nanomaterials that can become useful as nanocatalysts, energy-harvesting-storage components, antibacterial agents, and biomedical materials. Herein, the development of biosynthesis of inorganic nanomaterials into a simple, stable, and accurate strategy for distinguishing microorganisms from multiple classification levels (i.e., kingdom, order, genus, and species) without gene amplification, biochemical testing, or target recognition is reported. Gold nanoparticles (AuNPs) biosynthesized by different microorganisms differ in color of the solution, and their features can be characterized, including the particle size, the surface plasmon resonance (SPR) spectrum, and the surface potential. The inter-relation between the features of micro-biosynthetic AuNPs and the classification of microorganisms are exploited at different levels through machine learning to establish a taxonomic model. This model agrees well with traditional classification methods that offers a new strategy for microbial taxonomic identification. The underlying mechanism of this strategy is related to the biomolecules produced by different microorganisms including glucose, glutathione, and nicotinamide adenine dinucleotide phosphate-dependent reductase that regulate the features of micro-biosynthetic AuNPs. This work broadens the application of biosynthesis of inorganic materials through micro-biosynthetic AuNPs and machine learning, which holds great promise as a tool for biomedical research.

ARZIMM: A Novel Analytic Platform for the Inference of Microbial Interactions and Community Stability from Longitudinal Microbiome Study

Dynamic changes of microbiome communities may play important roles in human health and diseases. The recent rise in longitudinal microbiome studies calls for statistical methods that can model the temporal dynamic patterns and simultaneously quantify the microbial interactions and community stability. Here, we propose a novel autoregressive zero-inflated mixed-effects model (ARZIMM) to capture the sparse microbial interactions and estimate the community stability. ARZIMM employs a zero-inflated Poisson autoregressive model to model the excessive zero abundances and the non-zero abundances separately, a random effect to investigate the underlining dynamic pattern shared within the group, and a Lasso-type penalty to capture and estimate the sparse microbial interactions. Based on the estimated microbial interaction matrix, we further derive the estimate of community stability, and identify the core dynamic patterns through network inference. Through extensive simulation studies and real data analyses we evaluate ARZIMM in comparison with the other methods.

Effectiveness of a novel, non-intrusive, continuous-use air decontamination technology to reduce microbial contamination in clinical settings: A multi-centric study

BACKGROUND

Despite rigorous disinfection and fumigation, healthcare associated infection (HAI) remains a significant concern in health care settings. We have developed a novel airborne-microbicidal technology "ZeBox" which clears over 99.999% of airborne microbial load under controlled lab conditions [1].

AIM

To evaluate the clinical performance of ZeBox in reducing airborne and surface microbial load.

METHODS

The study was conducted in single bed and multi bed ICU of two hospitals. Airborne and surface microbial loads were sampled pre- and post-deployment of ZeBox at pre-determined sites. Statistical significance of the reduction was determined using Mann-Whitney's U test.

RESULTS

ZeBox brought statistically significant reduction of both airborne and surface bacterial and fungal load. In both hospital ICUs, airborne and surface bacterial load decreased by 90% and 75% on average respectively, providing a low bioburden zone of ∼10-15 feet diameter around the unit. The reduced microbial level was maintained during ZeBox's operation over several weeks. Most clinical bacterial isolates recovered from one of the hospitals were antibiotic resistant, highlighting ZeBox's ability to eliminate antimicrobial-resistant bacteria among others.

CONCLUSIONS

ZeBox significantly reduces airborne and surface microbial burden in clinical settings. It thereby serves an unmet need for reducing the incidence of HAI.

Phylogenetic analysis and antimicrobial susceptibility profile of uropathogens

The uropathogens is the main cause of urinary tract infection (UTI). The aim of the study was to isolate bacteria from urine samples of UTI patients and find out the susceptibility of isolated bacteria. Bacteria were identified using both conventional and molecular methods. Sanger sequence procedure used for 16S ribosomal RNA and phylogenetic analysis was performed using Molecular Evolutionary Genetics Analysis (MEGA-7) software. In this study, Escherichia coli, Klebsiella pneumonia, Staphylococcus were reported as 58, 28 and 14.0% respectively. Phylogenetic tree revealed that 99% of sample No. Ai (05) is closely related to E. coli to (NR 114042.1 E. coli strain NBRC 102203). Aii (23) is 99% similar to K. pneumoniae to (NR 117686.1 K. pneumonia strain DSM 30104) and 90% Bi (48) is closely linked to S. aureus to (NR 113956.1 S. aureus strain NBRC 100910). The antibiotic susceptibility of E. coli recorded highest resistance towards ampicillin (90%) and least resistant to ofloxacin (14%). Some of the other antibiotics such amoxicillin, ciprofloxacin, gentamicin, ceftazidime, cefuroxime and nitrofurantoin resistance were observed 86, 62, 24, 55, 48 and 35% respectively. The cefuroxime showed the highest antibiotic resistance against K. pneumoniae with 85% followed by amoxicillin, ciprofloxacin, gentamicin, ceftazidime, ampicillin and nitrofurantoin resulted in 60, 45, 67, 70, 75 and 30% respectively. The resistance of S. aureus against erythromycin, cefuroxime and ampicillin were found with 72%. The resistance against amoxicillin, gentamicin, ceftazidime and ceftriaxone found 57, 43, 43 and 15% respectively. Phylogenetic analysis shows that sequences are closely related with the reference sequences and E. coli is the dominant bacteria among UTI patients and is resistant to the commercially available antibiotics.

Multidrug-resistant bacteria isolated from surgical site of dogs, surgeon's hands and operating room in a veterinary teaching hospital in Brazil

Surgical environment can play as a source of multidrug-resistance organism, what can pose as a big threat to the patients and health care professionals. This study aimed to evaluate the prevalence and antimicrobial resistance profile of Gram-positive cocci (GPC) and Gram-negative bacilli (GNB) isolated from the surgical environment. All samples were collected during the intraoperative period of clean/clean-contaminated (G1) and contaminated (G2) surgery. A total of 150 samples were collected from the superficial surgical site in the beginning (n=30) and the end (n=30) of the procedure, surgeon's hands before (n=30) and after (n=30) antisepsis, and the surgical environment (n=30). MALDI-TOF MS and antimicrobial susceptibility testing by disk diffusion method were performed for species identification, and determination of the resistance profile. Sixty-eight isolates of GPC and 15 of GNB were obtained. Staphylococcus spp. were the most frequent species isolated from surgical site (55.26% [21/38]), surgeon's hands (46.15% [6/13]), and environment (56.67% [17/30]). GPC were mostly resistance to penicillin (85.71% [54/63]), and erythromycin (77.78% [49/63]), and GNB were mostly resistance to cefazolin (58.33% [7/12]), and azithromycin (58.33% [7/12]). High incidence of multidrug resistance was observed in coagulase-negative staphylococci (86.21% [25/29]), coagulase-positive staphylococci (86.67% [13/15]), Enterococcus spp. (68.42% [13/19]) and Gram-negative bacilli (60% [9/15]). The high rate of resistance of commensal bacteria found in our study is worrying. Coagulase-negative staphylococci are community pathogens related to nosocomial infections in human and veterinary hospitals, their presence in healthy patients and in veterinary professionals represent an important source of infection in the one health context. Continuous surveillance and application of antimicrobial stewardship programs are essential in the fight against this threat.

Single gene targeted nanopore sequencing enables simultaneous identification and antimicrobial resistance detection of sexually transmitted infections

OBJECTIVES

To develop a simple DNA sequencing test for simultaneous identification and antimicrobial resistance (AMR) detection of multiple sexually transmitted infections (STIs).

METHODS

Real-time PCR (qPCR) was initially performed to identify Neisseria gonorrhoeae (NG), Chlamydia trachomatis (CT), Mycoplasma genitalium (MG) and Trichomonas vaginalis (TV) infections among a total of 200 vulvo-vaginal swab samples from female sex workers in Ecuador. qPCR positive samples plus qPCR negative controls for these STIs were subjected to single gene targeted PCR MinION-nanopore sequencing using the smartphone operated MinIT.

RESULTS

Among 200 vulvo-vaginal swab samples 43 were qPCR positive for at least one of the STIs. Single gene targeted nanopore sequencing generally yielded higher pathogen specific read counts in qPCR positive samples than qPCR negative controls. Of the 26 CT, NG or MG infections identified by qPCR, 25 were clearly distinguishable from qPCR negative controls by read count. Discrimination of TV qPCR positives from qPCR negative controls was poorer as many had low pathogen loads (qPCR cycle threshold >35) which produced few specific reads. Real-time AMR profiling revealed that 3/3 NG samples identified had gyrA mutations associated with fluoroquinolone resistance, 2/10 of TV had mutations related to metronidazole resistance, while none of the MG samples possessed 23S rRNA gene mutations contributing to macrolide resistance.

CONCLUSIONS

Single gene targeted nanopore sequencing for diagnosing and simultaneously identifying key antimicrobial resistance markers for four common genital STIs shows promise. Further work to optimise accuracy, reduce costs and improve speed may allow sustainable approaches for managing STIs and emerging AMR in resource poor and laboratory limited settings.

Association Between Vaginal Gardnerella and Tubal Pregnancy in Women With Symptomatic Early Pregnancies in China: A Nested Case-Control Study

The early diagnosis and treatment of ectopic pregnancy (EP) remains a major challenge. Despite a known link between vaginal microbiota and female reproductive health, few studies have focused on the association between vaginal microbiota and pregnancy location. This nested case-control study aimed to characterize the vaginal microbiota in tubal pregnancy (TP) among symptomatic women in early pregnancy. Women with symptomatic early pregnancy of unknown location (PUL) were included in this study. 16S rDNA gene sequencing was performed to assess vaginal microbial diversity and relative abundance. Machine learning and multivariate logistic regression were also used to evaluate the association between Gardnerella and TP. The results indicate that the vaginal microbiome in TP was more diverse (Shannon, p < 0.05) and was different in composition to that of women with intrauterine pregnancy (IUP) (weighted Unifrac, R = 0.08, p = 0.01). The genus Gardnerella was significantly enriched in TP. The XGBoost analysis was able to classify Gardnerella-induced TP more reliably (AUC = 0.621). Moreover, after adjusting potential confounders, our results indicate a robust association between Gardnerella and TP (as a continuous variable, adjusted OR: 12.0, 95% CI: 2.1–67.4, p < 0.01; as a categorical variable (≥0.85%), and adjusted OR: 4.2, 95% CI: 2.0–8.8, p < 0.01). In conclusion, we found that higher virginal Gardnerella levels were associated with TP in women with symptomatic early pregnancy.

Microbial Contamination of Photographic and Cinematographic Materials in Archival Funds in the Czech Republic

In this study we investigated the microbial contamination of 126 samples of photographic and cinematographic materials from 10 archival funds in the Czech Republic. Microorganisms were isolated from the light-sensitive layer by swabbing it with a polyurethane sponge. Microbial isolates were identified by MALDI-TOF MS (bacteria) or by phenotype testing and microscopy (fungi). Bacterial contamination was more abundant and more diverse than fungal contamination, and both were significantly associated with archives. The most frequently isolated fungal genera were Cladosporium, Eurotium, Penicillium, Aspergillus and Alternaria. The most frequently isolated bacteria were Gram-positive genera such as Staphylococcus, Micrococcus, Kocuria, Streptococcus and Bacillus. This bacterial and fungal diversity suggests that air is the main vehicle of contamination. We also analysed the impact of the type of material used for the carrier (paper, baryta paper, cellulose acetate and nitrate or glass) or the light-sensitive layer (albumen, gelatine, collodion and other) on the level and diversity of microbial contamination. Carriers such as polyester and cellulose nitrate may have a negative impact on bacterial contamination, while paper and baryta paper may have a partially positive impact on both fungal and bacterial contamination.

MinION™ Nanopore Sequencing of Skin Microbiome 16S and 16S-23S rRNA Gene Amplicons

Human skin microbiome dysbiosis can have clinical consequences. Characterizing taxonomic composition of bacterial communities associated with skin disorders is important for dermatological advancement in both diagnosis and novel treatments. This study aims to analyze and improve the accuracy of taxonomic classification of skin bacteria with MinION™ nanopore sequencing using a defined skin mock community and a skin microbiome sample. We compared the Oxford Nanopore Technologies recommended procedures and concluded that their protocols highly bias the relative abundance of certain skin microbiome genera, most notably a large overrepresentation of Staphylococcus and underrepresentation of Cutibacterium and Corynebacterium. We demonstrated that changes in the amplification protocols improved the accuracy of the taxonomic classification for these three main skin bacterial genera. This study shows that MinION™ nanopore could be an efficient technology for full-length 16S rRNA sequencing; however, the analytical advantage is strongly influenced by the methodologies. The suggested alternatives in the sample processing improved characterization of a complex skin microbiome community using MinION™ nanopore sequencing.

Cutibacterium acnes: An emerging pathogen in culture negative bacterial prosthetic valve infective endocarditis (IE)

Cutibacterium acnes (previously known as Propionibacterium) infections are reportedly increasing in patients with implanted foreign material. Though it is a rare cause of bacterial endocarditis, patients with implanted prosthetic valves and devices have potential increased risk. Cutibacterium species are an ubiquitous environmental surface contaminant and typically difficult to culture, in case of high suspicion for infective endocarditis extended duration incubation of blood or any tissue sample and 16S RNA sequencing of any tissue sample is helpful for a microbiological identification. We report a case of a 50 year old male with culture negative prosthetic valve endocarditis in which the pathogen was identified by molecular testing 16S RNA gene sequencing.

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Prosthetic valve endocarditis.

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Cutibacterium acnes.

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16S gene sequencing.

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Management challange for prostetic valve endocarditis.

Distribution Characteristics and Species Diversity of Bacteria in Hepatocellular Carcinoma Tissues

This study was to explore the differences in the distribution and species diversity of bacteria between hepatocellular carcinoma (HCC) tissues and normal liver tissues. 28 HCC patients treated with surgery were selected as the research objects (HCC group), and 19 healthy volunteers with normal physical examinations were included in the control group (Normal group). The tumor specimens were obtained by intraoperative and biopsy puncture, and a 16S ribosomal ribonucleic acid (rRNA) library was constructed. Based on the sequencing data obtained by the IlluminaHi Seq sequencing platform, the differences of bacteria in the liver tissues of the HCC group and the Normal group were analyzed at the level of phyla, family, and genus. The Ace, Chao1, and Shannon of the two groups were compared. The results showed that IlluminaHi Seq sequencing obtained a total of 11,714,659 valid sequences, with an average of 131,625 sequences per sample. The proportions of Bacteroidetes, Firmicutes, and Proteobacteria in HCC group and Normal group were 48.75% versus 34.16%, 37.44% versus 18.02%, and 10.85% versus 39.26%, respectively. The Bacteroidaceae, Prevotellaceae, Lachnospiraceae, and Ruminococcaceae accounted for 22.49%, 20.62%, 16.54%, and 19.93% in Normal group; while those in the HCC tissues accounted for 26.83%, 14.22%, 11.14%, and 13.18%, respectively. The dominant bacteria at the genus level in HCC group and Normal group were Bacteroides and Prevotella-9, with the proportions of 24.19% versus 26.04% and 14.19% versus 8.44%, respectively. The difference in operational taxonomic unit (OTU) numbers of HCC and Normal group were compared and analyzed, which were 1,266 and 1,082, respectively, and the number of common OTU in the two tissues was 875. The Ace in HCC tissue and normal liver tissue were 1063.8±66.79 and 1003.6±52.19, respectively. The Ace in HCC tissue was greater than that in normal liver tissue (P < 0.05). The Chao1 and Shannon in HCC tissue were 1022.9±67.74 and 5.4269±0.3608, respectively; while those in normal liver tissue were 1003.6±66.79 and 5.2842±0.9714, respectively. The Chao1 and Shannon in HCC tissues were much higher than those in Normal group (P < 0.05). It showed that there was no difference in the types of bacterial species in HCC tissues, but the proportions of their flora at the level of phyla, family, and genus changed greatly, which may be related to the occurrence of HCC. This study could provide a reference for the diagnosis and treatment of HCC.

Molecular identification and biological control of Ralstonia solanacearum from wilt of papaya by natural compounds and Bacillus subtilis: An integrated experimental and computational study

Ralstonia solanacearum is a harmful pathogen that causes severe wilt disease in several vegetables. In the present study, we identified R. solanacearum from wilt of papaya by 16S rRNA PCR amplification. Virulence ability of R. solanacearum was determined by amplification of approximately 1500 bp clear band of hrpB gene. Further, in-vitro seed germination assay showed that R. solanacearum reduced the germination rate up to 26.21%, 34% and 33.63% of cucumber, bottle guard and pumpkin seeds, respectively whereas shoot and root growth were also significantly decreased. Moreover, growth inhibition of R. solanacearum was recorded using antibacterial compound from medicinal plant and antagonistic B. subtilis. Petroleum ether root extract of Rauvolfia serpentina showed highest 22 ± 0.04 mm diameter of zone of inhibition where methanolic extract of Cymbopogon citratus and ethanolic extract of Lantana camara exhibited 20 ± 0.06 mm and 20 ± 0.01 mm zone of inhibition against R. solanacearum, respectively. In addition, bioactive compounds of B. subtilis inhibited R. solanacearum growth by generating 17 ± 0.09 mm zone of inhibition. To unveil the inhibition mechanism, we adopted chemical-protein interaction network and molecular docking approaches where we found that, rutin from C. citratus interacts with citrate (Si)-synthase and dihydrolipoyl dehydrogenase of R. solanacearum with binding affinity of -9.7 kcal/mol and -9.5 kcal/mol while quercetin from B. subtillis interacts with the essential protein F0F1 ATP synthase subunit alpha of the R. solancearum with binding affinity of -6.9 kcal/mol and inhibit the growth of R. solanacearum. Our study will give shed light on the development of eco-friendly biological control of wilt disease of papaya.

Identification of Bull Semen Microbiome by 16S Sequencing and Possible Relationships with Fertility

Reports on the use of 16S sequencing for the identification of bacteria in healthy animals are lacking. Bacterial contamination of bull semen can have a negative effect on the sperm quality. The aims of this study were threefold: to identify bacteria in the semen of healthy bulls using 16S sequencing; to investigate the differences in the bacterial community between individual bulls; and to establish if there was a relationship between the bacteria isolated and bull fertility. Semen from 18 bulls of known fertility was used for the DNA extraction and 16S sequencing; 107 bacterial genera were identified. The differences in the amplicon sequence variants (ASVs) and the numbers of genera between bulls were noted. Negative correlations (p < 0.05) between several bacterial genera with Curvibacter, Rikenellaceae RC9-gut-group and Dyella spp. were seen. Other negatively correlated bacteria were Cutibacterium, Ruminococcaceae UCG-005, Ruminococcaceae UCG-010 and Staphylococcus, all within the top 20 genera. Two genera, W5053 and Lawsonella, were enriched in bulls of low fertility; this is the first time that these bacteria have been reported in bull semen samples. The majority of the bacteria were environmental organisms or were species originating from the mucous membranes of animals and humans. The results of this study indicate that differences in the seminal microbiota of healthy bulls occur and might be correlated with fertility.

Nasopharyngeal bacterial and fungal microbiota in normal horses and horses with nasopharyngeal cicatrix syndrome

Background

The nasopharyngeal bacterial and fungal microbiota of normal horses and those with nasopharyngeal cicatrix syndrome (NCS) are unknown.

Hypotheses/Objectives

To describe the microbiota from nasopharyngeal washes of healthy horses and of horses acutely affected with NCS.

Animals

Twenty‐six horses acutely affected with NCS horses and 14 unaffected horses.

Methods

Prospective, observational cohort study. Horses were recruited by investigators through personal communications in central Texas. Bacterial (16s RNA) and fungal (internal transcribed spacer) microbiota from nasopharyngeal washes were evaluated. Polymerase chain reaction for detection of Pythium insidiosum was performed.

Results

Results indicated that 6 fungal genera (Alternaria, Bipolaris, Microascus, Spegazzinia, Paraconiothyrium, Claviceps) and 1 bacterial genera (Staphylococcus) were significantly different between affected and unaffected horses. The fungal genus Bipolaris had increased abundance in NCS affected horses and on NCS affected farms. Pythium insidiosum was absent in the nasopharyngeal wash of all horses, irrespective of health status.

Conclusion and Clinical Importance

Significant differences were identified in the fungal microbiota in horses affected with NCS and farms affected with NCS compared to those unaffected. Therefore, Bipolaris warrants further investigation.

A new approach to identifying pathogens, with particular regard to viruses, based on capillary electrophoresis and other analytical techniques

Fast determination, identification and characterization of pathogens is a significant challenge in many fields, from industry to medicine. Standard approaches (e.g., culture media and biochemical tests) are known to be very time-consuming and labor-intensive. Conversely, screening techniques demand a quick and low-cost grouping of microbial isolates, and current analysis call for broad reports of pathogens, involving the application of molecular, microscopy, and electromigration techniques, DNA fingerprinting and also MALDI-TOF methods. The present COVID-19 pandemic is a crisis that affects rich and poor countries alike. Detection of SARS-CoV-2 in patient samples is a critical tool for monitoring disease spread, guiding therapeutic decisions and devising social distancing protocols. The goal of this review is to present an innovative methodology based on preparative separation of pathogens by electromigration techniques in combination with simultaneous analysis of the proteome, lipidome, and genome using laser desorption/ionization analysis.

Anti-inflammatory effects of purple sweet potato anthocyanin extract in DSS-induced colitis: modulation of commensal bacteria and attenuated bacterial intestinal infection

Purple sweet potato anthocyanins have been acknowledged for their beneficial effects on human inflammatory bowel diseases (IBD). Although the ability of anthocyanins in modulating the gut microbiota has been reported, the relationship between the bacteria modulated by anthocyanins and intestinal inflammation has not been fully elucidated. We aimed to ascertain whether the purple sweet potato anthocyanin extract (PSPAE) modulation of gut microbiota in the dextran sodium sulphate (DSS) induced chronic colitis mouse model could result in the maintenance of intestinal homeostasis and protection against bacterial intestinal inflammation. Chronic colitis was induced by adding DSS in drinking water while administering the mice with PSPAE via gavage (20 mg kg^-1). Effects on colon tissue damage, gut microbiota composition, tight junction protein, and cytokines were evaluated. PSPAE prevented the loss of Bifidobacterium and Lactobacillus and inhibited the increase of Gammaproteobacteria and Helicobacter upon DSS treatment. The non-pathogenic-dependent and pathogenic-dependent microenvironments were established upon treatment with broad-spectrum antibiotics. Both PSPAE treatment and non-pathogenic treatments modified the colonic expression of mouse tight junction proteins and maintained the architecture of the colon. However, the non-pathogenic treatment could not attenuate intestinal inflammation. Moreover, the pathogenic-dependent dysbiosis was exacerbated because of the increasing colonization of pathogens such as Helicobacter. The PSPAE exerted the modulation of gut microbiota to maintain the gut microbiome homeostasis in DSS-induced chronic colitis mice, which may help to propose a new treatment that combines efficacy and reduction of the possibility of bacterial intestinal infection.

Reprocessing 16S rRNA Gene Amplicon Sequencing Studies: (Meta)Data Issues, Robustness, and Reproducibility

High-throughput sequencing technology provides an efficient method for evaluating microbial ecology. Different bioinformatics pipelines can be used to convert 16S ribosomal RNA gene amplicon sequencing data into an operational taxonomic unit (OTU) table that is used to analyze microbial communities. It is important to assess the robustness of these pipelines, each with specific algorithms and/or parameters, and their influence on the outcome of statistical tests. Articles with publicly available datasets on the oral microbiome were searched for, and five datasets were retrieved. These were from studies on changes in microbiota related to smoking, oral cancer, caries, diabetes, or periodontitis. Next, the data was processed with four pipelines based on VSEARCH, USEARCH, mothur, and UNOISE3. OTU tables were rarefied, and differences in α-diversity and β-diversity were tested for different groups in a dataset. Finally, these results were checked for consistency among these example pipelines. Of articles that deposited data, only 57% made all sequencing and metadata available. When processing the datasets, issues were encountered, caused by read characteristics and differences between tools and their defaults in combination with a lack of detail in the methodology of the articles. In general, the four mainstream pipelines provided similar results, but importantly, P-values sometimes differed between pipelines beyond the significance threshold. Our results indicated that for published articles, the description of bioinformatics methods and data deposition should be improved, and regarding reproducibility, that analysis of multiple subsamples is required when using rarefying as library-size normalization method.

Evaluation of the antifungal activity of marine actinomycetes isolates against the phytopathogenic fungi Colletotrichum siamense KA: A preliminary study for new antifungal compound discovery

Marine actinomycetes are being explored to discover potential actinomycetes that produce antifungal compounds. In a previous study, marine actinomycetes isolates from the mangrove ecosystem were found to inhibit growth of the phytopathogenic fungi Colletotrichum siamense KA. In this study, the three of these isolates with the highest antagonistic activity—SM11, SM14, and SM15—were evaluated for their antifungal activity using antibiosis assay. The fermentation was performed in SCB:PDB medium (1:1) for 6, 9, and 12 days. The results showed that SM14 was the strongest potential isolate; it inhibited the growth of C. siamense KA on average up to 64.90% for 12 days on PDA filtrate medium. Molecular identification showed SM14 was closely related to Streptomyces sanyensis, but had differences in morphological and biochemical characteristics compared to SM11 or SM15. This indicated that the three isolates were different strains and may challenge further research on identifying and analyzing their antifungal compounds.

Periprosthetic Joint Infection Caused by Mycoplasma hominis, Diagnosed Using Metagenomic Sequencing

To our knowledge, the periprosthetic joint infection (PJI) caused by Mycoplasma hominis is a rare postoperative complication after total knee arthroplasty (TKA). Just a few cases associated with Mycoplasma hominis infection after TKA were reported all over the world currently. In view of the difficulty involved in isolating this microorganism, Mycoplasma hominis infection may be under-recognized and should be considered in culture-negative cases where the microbial etiology is not easily identified. Metagenomic sequencing is a new tool to identify pathogens undetected by conventional methods. In this report, we present a case where metagenomic sequencing was used to identify Mycoplasma hominis as a novel PJI pathogen after TKA in our hospital.

Coinfection of Clostridium perfringens and Escherichia coli in gas-producing perianal abscess diagnosed by 16S rDNA sequencing: a case report

BACKGROUND

Gas-producing perianal abscess raises the possibility of clostridial infection, with Clostridium perfringens being the most common causative agent, which is highly lethal if untreated timely. As the treatment of clostridial infections often differs from that of non-clostridial infections, which they may closely resemble, the importance of accurate pathogenic organism identification cannot be overemphasized. The 16S rDNA of bacteria is highly conserved within a species and among species of the same genus but demonstrates substantial variation between different species, thus making it a suitable genomic candidate for bacterial detection and identification.

CASE PRESENTATION

Here, we report the case of a 53-year-old patient who was admitted to the hospital for a gas-producing perianal abscess. The patient was managed with ceftizoxime and ornidazole and then received debridement and drainage at the lesion on the second day after admission. The bacterial cultures of the patient isolates from the debridement showed a coinfection of Escherichia coli and Enterococcus faecium. Although perianal redness and swelling subsided obviously after the surgery, the patient was febrile to 38.3℃ with his left upper thigh red and swollen, aggravated with tenderness and crepitus. Considering insufficient debridement and the risk of incorrect identification of pathogens, a second debridement and drainage were performed 4 days after the primary operation, and 16S rDNA sequencing of the isolates implicated Clostridium perfringens infection. Given the discrepancies in diagnostic results and the treatment outcomes, Enterococcus faecium was identified as sample contamination, and a diagnosis of coinfection of Clostridium perfringens and Escherichia coli in gas-producing perianal abscess was confirmed. The patient was then successfully treated with meropenem and vancomycin and was discharged at 27 days of admission.

CONCLUSIONS

This case represents the first report of coinfection of both clostridial and non-clostridial organisms in gas-producing perianal abscess and the first case reporting the use of 16S rDNA sequencing in the diagnosis of perianal abscess. Timely pathogen identification is critical for treating gas-producing perianal abscess and an antibiotic regimen covering both aerobic and anaerobic organisms is recommended before true pathogens are identified.

Comparative analysis of the serum microbiome of HIV infected individuals

HIV infects the CD4 cells which marks the suppression of our immune system. DNA from serum of healthy, treated and untreated HIV infected individuals was extracted. The DNA was subjected to 16S metagenomic sequencing and analyzed using QIIME2 pipeline. 16S sequencing analysis showed serum microbiome was dominated by Firmicutes, Proteobacteria, Bacteroidota and Actinobacteria. Treated HIV infection showed highest abundance of Firmicutes (66.40%) significantly higher than untreated HIV infection (35.88%) and control (41.89%). Bacilli was most abundant class in treated (63.59%) and second most abundant in untreated (34.53%) while control group showed highest abundance of class Gamma-proteobacteria (45.86%). Untreated HIV infection group showed Enterococcus (10.72%) and Streptococcus (6.599%) as the most abundant species. Untreated HIV infection showed significantly higher (p = 0.0039) species richness than treated and control groups. An altered serum microbiome of treated HIV infection and higher microbial abundance in serum of untreated HIV infection was observed.

Clinical Characteristics of Actinomyces viscosus Bacteremia

Background and Objectives: Actinomyces species are part of the normal flora of humans and rarely cause disease. It is an uncommon cause of disease in humans. The clinical features of actinomycosis have been described, and various anatomical sites (such as face, bones and joints, respiratory tract, genitourinary tract, digestive tract, central nervous system, skin, and soft tissue structures) can be affected. It is not easy to identify actinomycosis because it sometimes mimics cancer due to under-recognition. As new diagnostic methods have been applied, Actinomyces can now more easily be identified at the species level. Recent studies have also highlighted differences among Actinomyces species. We report a case of Actinomyces viscosus bacteremia with cutaneous actinomycosis. Materials and Methods: A 66 years old male developed fever for a day with progressive right lower-leg erythematous swelling. Blood culture isolates yielded Actinomyces species, which was identified as Actinomyces viscosus by sequencing of the 16S rRNA gene. In addition, we searched for the term Actinomyces or actinomycosis cross-referenced with bacteremia or "blood culture" or "blood stream" from January 2010 to July 2020. The infectious diseases caused by species of A. viscosus from January 1977 to July 2020 were also reviewed. Results: The patient recovered well after intravenous ampicillin treatment. Poor oral hygiene was confirmed by dental examination. There were no disease relapses during the following period. Most cases of actinomycosis can be treated with penicillin. However, clinical alertness, risk factor evaluation, and identification of Actinomyces species can prevent inappropriate antibiotic or intervention. We also compiled a total of 18 cases of Actinomyces bacteremia after conducting an online database search. Conclusions: In summary, we describe a case of fever and progressive cellulitis. Actinomyces species was isolated from blood culture, which was further identified as Actinomyces viscosus by 16S rRNA sequencing. The cellulitis improved after pathogen-directed antibiotics. Evaluation of risk factors in patients with Actinomyces bacteremia and further identification of the Actinomyces species are recommended for successful treatment.

Conjunctival Sac Microbiome in Infectious Conjunctivitis

Acute bacterial conjunctival infections are common, and this study identified the conjunctival bacterial community in infectious conjunctivitis cases seen at the outpatient clinic of Khanh Hoa General Hospital in Nha Trang, Vietnam from October 2016 through December 2017. Conjunctival swabs were collected and tested using conventional culture, PCR, and 16S ribosomal RNA sequencing. The study included 47 randomly selected patients. More than 98% of all DNA reads represented five bacterial phyla. Three of these phyla constituted 92% of all sequences (Firmicutes (35%), Actinobacteria (31%), and Proteobacteria (26%)). At the genus level, there were 12 common genera that constituted about 61% of all sequence reads. Seven of those genera were common (Streptococcus (10%), Cutibacterium (10%), Staphylococcus (7%), Nocardioides (7%), Corynebacterium 1 (5%), Anoxybacillus (5%), and Acinetobacter (5%)), which encompassed 49% of all reads. As for diversity analysis, there was no difference on PERMANOVA analysis (unweighted UniFrac) for sex (p = 0.087), chemosis (p = 0.064), and unclassified eyedrops (p = 0.431). There was a significant difference in cases with bilateral conjunctivitis (p = 0.017) and for using antibiotics (p = 0.020). Of the predominant phyla, Firmicutes had the highest abundance in bacterial conjunctivitis in this study. Pseudomonas as a resident commensal microbiota may have an important role in the prevention of infection.

The Ocular Microbiome Is Altered by Sampling Modality and Age

Background

Studies of the ocular microbiome have used a variety of sampling techniques, but no study has directly compared different sampling methods applied to the same eyes to one another or to a reference standard of corneal epithelial biopsy. We addressed this lack by comparing the microbiome from three conjunctival swabs with those of corneal epithelial biopsy.

Methods

Twelve eyes (11 patients) were swabbed by calcium alginate swab, cotton-tipped applicator, and Weck-Cel cellulose sponge before a corneal epithelial biopsy (48 samples). We then performed 16S rRNA gene sequencing and universal 16S rRNA gene real-time polymerase chain reaction. Negative/blank controls were used to eliminate contaminants. An analysis was performed to examine the concordance of the three swab types to corneal epithelial biopsy. The effect of patient age on the ocular microbiome as determined by epithelial biopsy was also examined.

Results

The ocular microbiome from corneal epithelial biopsies consisted of 31 genera with a relative abundance of 1% or more, including Weisella, Corynebacterium, and Pseudomonas. Of the three swab types, Weck-Cel differed the most from corneal biopsies based on beta-diversity analysis. Cotton swabs were unable to capture the Bacteroides population seen on epithelial biopsy. Therefore, calcium alginate swabs seemed to be the closest to epithelial biopsies. Older patients (≥65 years old) had higher alpha diversity (P < 0.05) than younger patients. Differential abundance testing showed that there were 18 genera that were differentially abundant between the two age groups, including Streptococcus and eight members of the Proteobacteria phylum.

Conclusions

We demonstrate that ocular sampling method and patient age can greatly affect the outcome of sequencing-based analysis of the ocular microbiome.

Translational Relevance

By understanding the impact of different sampling methods on the results obtained from the ocular surface microbiome, future research on the topic will be more reproducible, leading to a better understanding of ocular surface microbiome in health and disease.

Clinical Relevance of the Microbiome in Odontogenic Abscesses

Simple Summary

Odontogenic infections are very common. The course of disease ranges from mild to severe and sometimes even life-threatening infections. Optimal therapy is based on rapid abscess incision and, especially in severe cases, on adjuvant antibiotic therapy that ideally targets the culprit bacteria. In order to identify these bacteria, clinicians usually perform cultural analysis from smears of pus and aim for antibiotic susceptibility testing. In recent years, using new molecular methods, it has become possible to carry out a much more detailed analysis of the bacterial colonization of different parts of the human body by determining a microbiome. In our study, we have, for the first time, compared such a microbiome of odontogenic abscesses with cultural bacterial determination carried out in the clinical routine of a university hospital. The key finding of the study is not only that considerably more bacteria can be detected in the abscess in this way but also that easily cultivated bacteria dominate over the actual fastidious pathogenic bacteria. Thus, routine clinical culture probably only provides a distorted picture of reality and should be supplemented by molecular methods in the future.

Abstract

Odontogenic abscesses are usually caused by bacteria of the oral microbiome. However, the diagnostic culture of these bacteria is often prone to errors and sometimes fails completely due to the fastidiousness of the relevant bacterial species. The question arises whether additional pathogen diagnostics using molecular methods provide additional benefits for diagnostics and therapy. Experimental 16S rRNA gene analysis with next-generation sequencing (NGS) and bioinformatics was used to identify the microbiome of the pus in patients with severe odontogenic infections and was compared to the result of standard diagnostic culture. The pus microbiome was determined in 48 hospitalized patients with a severe odontogenic abscess in addition to standard cultural pathogen detection. Cultural detection was possible in 41 (85.42%) of 48 patients, while a pus-microbiome could be determined in all cases. The microbiomes showed polymicrobial infections in 46 (95.83%) cases, while the picture of a mono-infection occurred only twice (4.17%). In most cases, a predominantly anaerobic spectrum with an abundance of bacteria was found in the pus-microbiome, while culture detected mainly Streptococcus, Staphylococcus, and Prevotella spp. The determination of the microbiome of odontogenic abscesses clearly shows a higher number of bacteria and a significantly higher proportion of anaerobes than classical cultural methods. The 16S rRNA gene analysis detects considerably more bacteria than conventional cultural methods, even in culture-negative samples. Molecular methods should be implemented as standards in medical microbiology diagnostics, particularly for the detection of polymicrobial infections with a predominance of anaerobic bacteria.

Syphilitic Spinal Disease: An Old Nemesis Revisited. A Case Series and Review of Literature

ABSTRACT

Syphilitic spinal disease is a rare condition caused by the spirochete Treponema pallidum, either from direct spirochete involvement of the cord or as a consequence of indirect spirochete involvement of the meninges, blood vessels, or the vertebral column. After the introduction of penicillin therapy in the 1940s, it has become an increasingly rare condition. We report 3 challenging cases of syphilitic spinal disease presenting as myelopathy-1 with an extra-axial gumma of tertiary syphilis causing cord compression and 2 with tabes dorsalis complicated by tabetic spinal neuroarthropathy-each presenting a diagnostic dilemma to their treating physicians. We also review the literature for updates on modern investigative modalities and discuss pitfalls physicians need to avoid to arrive at the diagnosis.

Eggerthella lenta Bacteremia in a Middle-Aged Healthy Man with Acute Hepatic Abscess: Case Report and Literature Review, 1970-2020

Eggerthella lenta (E. lenta) is a rare but significant human emerging pathogen. Infections caused by it are rare and little-known, both on clinical and therapeutical aspects, in spite of new emergence of bacteria isolation and identification techniques. In this article, we report a case involving a previously healthy 52-year-old man suffering from a newly diagnosed hepatic abscess who developed E. lenta bacteremia, which was treated successfully using empirical therapy with ertapenem and teicoplanin. To the best of our knowledge, this is the first documented report of E. lenta bacteremia related specifically to liver abscess. Cases related to this bacterial species are infrequent and sporadic; thus, we reviewed English literature on E. lenta infection in PubMed/MEDLINE in the last 50 years. A total of 31 sporadic cases were identified. The majority of patients were male (71%), had an average age of 54.3 years and presented predisposing conditions, such as digestive system trouble (45.2%), immunocompromised state (25.8%) or risk factors (22.6%). Two of the cases had more than one predisposing factors. Fever was common (93.5%). Average days to diagnosis of them were 6.8 days. MALDI-TOF MS is emerging as a fast and useful tool in the identification of it. Teicoplanin, vancomycin, amoxicillin-clavulanate, metronidazole, clindamycin, cefoxitin, chloramphenicol, and carbapenems appear to be the most used antibiotic treatment options. The purpose of this review is to increase awareness about the clinical infections caused by E. lenta.

Pharmacological inhibition of MELK restricts ferroptosis and the inflammatory response in colitis and colitis-propelled carcinogenesis

INTRODUCTION

Inflammatory bowel disease (IBD), including ulcerative colitis (UC) and Crohn's disease (CD), is a group of chronic recurrent and incurable gastrointestinal diseases with an unknown etiology that leads to a high risk of developing colitis-associated colorectal cancer (CRC).

OBJECTIVES

In this study, we measured the expression characteristics of MELK in IBD and CRC tissues and explored the regulatory effect of OTSSP167 (a MELK-selective inhibitor) on the mice models of colitis and colitis-associated carcinogenesis and analyzed the specific molecular mechanisms.

METHODS

DSS-induced colitis and colitis-associated carcinogenesis (CAC) model were treated with MELK inhibitor OTSSP167 then the fight against effect of OTSSP167 in the clinical symptoms of colitis and CAC was measured. In addition, underlying mechanism of OTSSP167 treatment in vitro and vivo including anti-ferroptosis and anti-inflammatory response effect was further explored.

RESULTS

We found that pharmacological inhibition of MELK was indicated to significantly alleviate the inflammatory response in mice with colitis, reduce intestinal damage, and effectively inhibit the occurrence and progression of colitis-propelled carcinogenesis, which was closely related to the regulation of gut microbial composition, and OTSSP167-mediated fecal microbiota transplantation effectively alleviated DSS-induced colitis. In addition, OTSSP167 treatment obviously inhibited ferroptosis in the intestinal tissue and suppressed macrophage infiltration and M1 polarization, which reduced the secretion of pro-inflammatory factors. Further exploration of the molecular mechanism revealed that OTSSP167 inhibited AKT/IKK/P65 and ERK/IKK/P65 signaling cascades both in vivo and in vitro, which may help alleviate intestinal inflammation and control the occurrence of cancer.

CONCLUSION

Our findings lay a theoretical foundation for the use of OTSSP167 as a treatment for IBD and its inhibition of the occurrence of colitis-associated carcinogenesis; additionally, MELK may be a potentially effective target molecule, thus providing more options for clinical treatment.

Streptomyces xanthii sp. nov. and Streptomyces roseirectus sp. nov. isolated from a Chinese medicinal plant

Two strains of Actinobacteria, designated CRXT-Y-14^T and CRXT-G-22^T, were isolated from the healthy leaves and seeds, respectively, of a medicinal plant Xanthium sibiricum. Their taxonomic positions were determined using a polyphasic approach. Strain CRXT-Y-14^T produced flexuous chains of smooth-surfaced spores. Strain CRXT-G-22^T produced straight chains of smooth-surfaced spores. Their morphological features were consistent with the diagnostic characteristics of members of the genus Streptomyces. The results of 16S rRNA gene sequence analyses indicated two strains represented members of the genus Streptomyces. CRXT-Y-14^T shared 99.3, 98.9, 98.8 % sequence similarities to Streptomyces atriruber NRRL B-24165^T, Streptomyces avermitilis MA-4680^T and Streptomyces davaonensis JCM 4913^T, respectively. Whilst CRXT-G-22^T exhibited highest similarity to Streptomyces acidiscabies ATCC 49003^T (98.9 %). The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that the closest phylogenetic neighbours of strains CRXT-Y-14^T and CRXT-G-22^T were S. atriruber NRRL B-24165^T and S. acidiscabies ATCC 49003^T, respectively. The phylogenomic analyses further confirmed the relative relationship between strain CRXT-G-22^T and S. acidiscabies ATCC 49003^T, but indicated that CRXT-Y-14^T could represent a novel species of the genus Streptomyce. However, the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between CRXT-Y-14^T and strain CRXT-G-22^T, between CRXT-Y-14^T and S. atriruber NRRL B-24165^T, and between CRXT-G-22^T and S. acidiscabies ATCC 49003^T were 85.4 and 23.2 %, 85.8 and 23.9 % and 89.1 and 34.1 %, respectively, far below the 95~96 and 70 % cut-off points recommended for delineating species. Furthermore, these two novel isolates were distinctly differentiated from their relatives in the genus Streptomyces with respect to phenotypic and chemotaxonomic characteristics. On the basis of these data, CRXT-Y-14^T and CRXT-G-22^T clearly represent two novel species within the genus Streptomyces, for which the names Streptomyces xanthii sp. nov. (type strain CRXT-Y-14^T = MCCC 1K04966^T= JCM 34527^T) and Streptomyces roseirectus sp. nov. (type CRXT-G-22^T = MCCC 1K04979^T= JCM 34565^T) are proposed.

Proposal of Streptomyces aureorectus (ex Taig et al. 1969) Taig and Solovieva 1986 as a later heterotypic synonym of Streptomyces calvus Backus et al. 1957 (Approved Lists 1980) on the basis of a polyphasic taxonomic approach

As two separate genomic species, Streptomyces calvus and Streptomyces aureorectus were approved in 1980 and 1986, respectively. However, recently, it has been found that the average nucleotide identity and digital DNA-DNA hybridization values between S. calvus JCM 4326^T and S. aureorectus DSM 41692^T were 99.19 and 92.70 %, respectively, much higher than 95-96 and 70  % cut-off points proposed and the generally accepted species boundaries. These data indicated that they should be classified as the same genomic species. Furthermore, this result was also supported by a comprehensive comparison of phenotypic, chemotaxonomic and physio-biochemical characteristics between the two type strains. All these data indicated that S. calvus and S. aureorectus had the same taxonomic position. In accordance with the principle of priority, it is proposed that S. aureorectus is a later heterotypic synonyms of S. calvus.

Bacterial Endocarditis Caused by Actinomyces oris: First Reported Case and Literature Review

Actinomyces species are gram-positive, facultative anaerobic bacilli. Infection caused by Actinomyces species is usually limited to cervicofacial, thoracic, and abdominopelvic regions. Infective endocarditis due to Actinomyces species is extremely rare with only 30 reported cases since 1939. We report a case of Actinomyces oris endocarditis in a 14-year-old boy who had a 2-week history of dyspnea on exertion without other constitutional signs. Transthoracic echocardiography was suggestive of perforation of the right coronary cusp of aortic valve. No organisms were isolated from blood cultures. The patient underwent surgical valve repair due to deteriorated cardiac function. Valve tissue culture did not initially identify the organism. However, the terminal subculture in a thioglycolate broth grew gram-positive bacilli. The matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) was compatible with Actinomyces oris. After 6 weeks of intravenous ampicillin, the patient remained well with improved cardiac function. We reviewed all reported cases of infective endocarditis caused by Actinomyces species, commenting on clinical characteristics and factors associated with unfavorable outcomes in infective endocarditis due to Actinomyces species. Although infective endocarditis caused by Actinomyces spp is rare, it could be considered in a case of culture-negative endocarditis since the clinical features might be indistinguishable from other bacterial endocarditis. Additionally, MALDI-TOF MS is a useful diagnostic tool for the identification of Actinomyces spp to improve the accuracy of diagnosis.

Evaluation of CHROMagar™-Serratia agar, a new chromogenic medium for the detection and isolation of Serratia marcescens

A comparative analysis of the performance of the new selective chromogenic CHROMagar™-Serratia culture medium for detection and isolation of Serratia marcescens was undertaken. A total of 134 clinical isolates (95 S. marcescens with and without carbapenemase production and 39 non-S. marcescens isolates) and 96 epidemiological samples (46 rectal swabs and 50 from environmental surfaces) were studied. Diagnostic values when compared with CHROMagar™-Orientation medium were 96.8% sensitivity, 100% specificity, 100% positive predictive value and 88.5% negative predictive value. In conclusion, CHROMagar™-Serratia shows an excellent ability for differentiation of S. marcescens among clinical isolates and in environmental samples.

Technological tools and strategies for culturing human gut microbiota in engineered in vitro models

The gut microbiota directly impacts the pathophysiology of different human body districts. Consequently, microbiota investigation is an hot topic of research and its in vitro culture has gained extreme interest in different fields. However, the high sensitivity of microbiota to external stimuli, such as sampling procedure, and the physicochemical complexity of the gut environment make its in vitro culture a challenging task. New engineered microfluidic gut-on-a-chip devices have the potential to model some important features of the intestinal structure, but they are usually unable to sustain culture of microbiota over an extended period of time. The integration of gut-on-a-chip devices with bioreactors for continuous bacterial culture would lead to fast advances in the study of microbiota-host crosstalk. In this review, we summarize the main technologies for the continuous culture of microbiota as upstream systems to be coupled with microfluidic devices to study bacteria-host cells communication. The engineering of integrated microfluidic platforms, capable of sustaining both anaerobic and aerobic cultures, would be the starting point to unveil complex biological phenomena proper of the microbiota-host crosstalks, paving to way to multiple research and technological applications.

Development and evaluation of a nanopore 16S rRNA gene sequencing service for same day targeted treatment of bacterial respiratory infection in the intensive care unit

OBJECTIVES

Assess the feasibility and impact of nanopore-based 16S rRNA gene sequencing (Np16S) service on antibiotic treatment for acute severe pneumonia on the intensive care unit (ICU).

METHODS

Speciation and sequencing accuracy of Np16S on isolates with bioinformatics pipeline optimisation, followed by technical evaluation including quality checks and clinical-reporting criteria analysing stored respiratory samples using single-sample flow cells. Pilot service comparing Np16S results with all routine respiratory tests and impact on same-day antimicrobial prescribing.

RESULTS

Np16S correctly identified 140/167 (84%) isolates after 1h sequencing and passed quality control criteria including reproducibility and limit-of-detection. Sequencing of 108 stored respiratory samples showed concordance with routine culture in 80.5% of cases and established technical and clinical reporting criteria. A 10-week same-day pilot Np16S service analysed 45 samples from 37 patients with suspected community (n=15) or hospital acquired (n=30) pneumonia. Np16S showed concordance compared with all routine culture or molecular tests for 27 (82%) of 33 positive samples. It identified the causative pathogen in 32/33 (97%) samples and contributed to antimicrobial treatment changes for 30 patients (67%).

CONCLUSIONS

This study demonstrates feasibility of providing a routine same-day nanopore sequencing service that makes a significant contribution to early antibiotic prescribing for bacterial pneumonia in the ICU.

Nanopore 16S Amplicon Sequencing Enhances the Understanding of Pathogens in Medically Intractable Diabetic Foot Infections

Diabetic foot infections (DFIs) cause substantial morbidity and mortality. The mainstay of the treatment is empiric antibiotics and surgical debridement in severe cases. In this study, we performed nanopore 16S rDNA sequencing from the debridement specimens of DFIs. Fifty-four surgical debridement specimens obtained from 45 patients with medically intractable DFI were included. The 16S rDNA PCR was performed on each specimen, and Nanopore sequencing was performed for up to 3 h. The reads were aligned to the BLAST database, and the results were compared with conventional culture studies. The 16S sequencing results revealed that the majority of the DFIs (44 of 54, 81.5%) were polymicrobial infections. All bacteria isolated by conventional culture studies were detected by 16S sequencing. Several anaerobes (Prevotella, Finegoldia, Anaerococcus, Bacteroides) were commonly identified by 16S sequencing but were frequently missed by culture studies. In many cases, certain bacteria only revealed by the 16S sequencing were more abundant than the bacteria isolated by the culture studies. In conclusion, nanopore 16S sequencing was capable of pathogen identification in DFIs and has many advantages over conventional culture studies. Nanopore 16S sequencing enables a comprehensive understanding of the bacteria involved in DFIs.

A Bioinformatics Whole-Genome Sequencing Workflow for Clinical Mycobacterium tuberculosis Complex Isolate Analysis, Validated Using a Reference Collection Extensively Characterized with Conventional Methods and In Silico Approaches

The use of whole-genome sequencing (WGS) for routine typing of bacterial isolates has increased substantially in recent years. For Mycobacterium tuberculosis (MTB), in particular, WGS has the benefit of drastically reducing the time required to generate results compared to most conventional phenotypic methods. Consequently, a multitude of solutions for analyzing WGS MTB data have been developed, but their successful integration in clinical and national reference laboratories is hindered by the requirement for their validation, for which a consensus framework is still largely absent. We developed a bioinformatics workflow for (Illumina) WGS-based routine typing of MTB complex (MTBC) member isolates allowing complete characterization, including (sub)species confirmation and identification (16S, csb/RD, hsp65), single nucleotide polymorphism (SNP)-based antimicrobial resistance (AMR) prediction, and pathogen typing (spoligotyping, SNP barcoding, and core genome multilocus sequence typing). Workflow performance was validated on a per-assay basis using a collection of 238 in-house-sequenced MTBC isolates, extensively characterized with conventional molecular biology-based approaches supplemented with public data. For SNP-based AMR prediction, results from molecular genotyping methods were supplemented with in silico modified data sets, allowing us to greatly increase the set of evaluated mutations. The workflow demonstrated very high performance with performance metrics of >99% for all assays, except for spoligotyping, where sensitivity dropped to ∼90%. The validation framework for our WGS-based bioinformatics workflow can aid in the standardization of bioinformatics tools by the MTB community and other SNP-based applications regardless of the targeted pathogen(s). The bioinformatics workflow is available for academic and nonprofit use through the Galaxy instance of our institute at https://galaxy.sciensano.be.

Antibacterial Effects of Disulfiram in Helicobacter pylori

Background

Helicobacter pylori infection poses a risk of the occurrence of gastrointestinal diseases, such as gastric cancer. Its incidence rate is significantly reduced by eradication, and thereby, eradication therapy is generally performed. Disulfiram is an oral prescription drug mainly used for the treatment of alcohol dependence. In recent years, reports have been made on its anticancer and antibacterial effects, and thus, it has recently become an interesting subject. This study aimed to examine the antibacterial activity of disulfiram, investigate the presence or absence of its antibacterial activity on H. pylori, and determine whether it could be a new bactericidal drug against drug-resistant H. pylori.

Materials and Methods

Drug-sensitive strains of H. pylori and amoxicillin-resistant, clarithromycin-resistant, and metronidazole-resistant strains were used, and a growth inhibition test of H. pylori using disulfiram was performed. Furthermore, the expression of urease, vacuolating cytotoxin A (VacA), and CagA, the virulence proteins of H. pylori, was quantitatively analyzed using the Western blotting method. In addition, for H. pylori used in this study, the 16SrDNA sequence, a ribosomal gene involved in protein production, was analyzed to examine the presence or absence of gene mutation.

Results

Disulfiram suppressed the growth of 7 out of 12 H. pylori strains at 1 µg/mL, and no correlation was observed between their susceptibility/resistance to current eradication antimicrobial drugs and disulfiram resistance. Disulfiram reduced the expression levels of urease, VacA, and CagA proteins. H. pylori, which showed resistance to disulfiram, tended to have fewer gene deletions/insertions in the 16S rDNA sequence; however, no specific mutation was detected.

Conclusion

Disulfiram has a bactericidal effect on H. pylori at low concentrations, suggesting that it can be used as a supplement for current H. pylori eradication drugs.

Microbial diagnosis of endophthalmitis using nanopore amplicon sequencing

OBJECTIVES

We investigated whether nanopore amplicon sequencing of aqueous humor was capable of rapid pathogen identification in infectious endophthalmitis.

METHODS

5 cases of culture-positive bacterial endophthalmitis and 3 cases of fungal endophthalmitis (1 culture-positive and 2 presumed) were included. DNA was extracted from the aqueous humor and vitreous specimen, and PCR of bacterial rDNA (16S) and fungal rDNA (ITS1 and D1/2/3) was performed. Then, nanopore amplicon sequencing was performed for 2 h. The results of amplicon sequencing were compared to those of conventional culture studies.

RESULTS

In all cases, pathogens were identified by amplicon sequencing of aqueous humor specimens. In 3 cases of bacterial endophthalmitis, the identified microbes were confirmed by culture studies of both aqueous humor and vitreous specimens. In 2 cases of bacterial and 1 case of fungal endophthalmitis, the identified pathogens were confirmed only by culture studies of vitreous specimens. In all cases, amplicon sequencing identified pathogen in a shorter turnaround time than culture studies. In 2 cases with negative culture results, amplicon sequencing of aqueous humor identified fungal pathogens.

CONCLUSIONS

Our data demonstrates the potential of amplicon nanopore sequencing using aqueous humor to enable rapid, sensitive and less invasive microbial diagnosis of endophthalmitis.

Application of MALDI-TOF MS Profiling Coupled With Functionalized Magnetic Enrichment for Rapid Identification of Pathogens in a Patient With Open Fracture

Posttraumatic infections can occur in orthopedic trauma patients, especially in open fractures. Rapid and accurate identification of pathogens in orthopedic trauma is important for clinical diagnosis and antimicrobial treatment. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been successfully used for first-line identification of pathogens grown on culture plates. However, for direct analysis of liquid clinical specimens, pre-purification of the sample is necessary. Herein, we investigated the feasibility of coupling Fc-MBL@Fe₃O₄ enrichment with MALDI-TOF MS profiling in the identification of pathogens in liquid-cultured samples. This method is successfully used for the identification of pathogens in a patient with an open-leg fracture obtained at sea. Pathogens were enriched by Fc-MBL@Fe₃O₄ from briefly pre-cultured liquid media and identified by MALDI-TOF MS. We identified an opportunistic pathogen, Vibrio alginolyticus, which is uncommon in clinical orthopedic trauma infection but exists widely in the sea. Therefore, combining Fc-MBL@Fe₃O₄ enrichment and MALDI-TOF MS profiling has great potential for direct identification of microbes in clinical samples.

Defining the burden of febrile illness in rural South and Southeast Asia: an open letter to announce the launch of the Rural Febrile Illness project

In rural areas of South and Southeast Asia malaria is declining but febrile illnesses still account for substantial morbidity and mortality. Village health workers (VHWs) are often the first point of contact with the formal health system, and for patients with febrile illnesses they can provide early diagnosis and treatment of malaria. However, for the majority of febrile patients, VHWs lack the training, support and resources to provide further care. Consequently, treatable bacterial illnesses are missed, antibiotics are overused and poorly targeted, and patient attendance wanes along with declining malaria. This Open Letter announces the start of a new initiative, the Rural Febrile Illness (RFI) project, the first in a series of projects to be implemented as part of the South and Southeast Asian Community-based Trials Network (SEACTN) research programme. This multi-country, multi-site project will begin in Bangladesh, Cambodia, Lao PDR, and Myanmar and will define the epidemiological baseline of febrile illness in five remote and underserved areas of Asia where malaria endemicity is declining and access to health services is limited. The RFI project aims to determine the incidence, causes and outcomes of febrile illness; understand the opportunities, barriers and appetite for adjustment of the role of VHWs to include management of non-malarial febrile illnesses; and establish a network of community healthcare providers and facilities capable of implementing interventions designed to triage, diagnose and treat patients presenting with febrile illnesses within these communities in the future.

A Cell Membrane Fluorogenic Probe for Gram-Positive Bacteria Imaging and Real-Time Tracking of Bacterial Viability

Bacterial infections are a global healthcare problem, resulting in serious clinical morbidities and mortality. Real-time monitoring of live bacteria by fluorescent imaging technology has potential in diagnosis of bacterial infections, elucidating antimicrobial agents' mode of action, assessing drug toxicity, and examining bacterial antimicrobial resistance. In this work, a naphthalimide-derived fluorescent probe ZTRS-BP was developed for wash-free Gram-positive bacteria imaging. The probe aggregated in aqueous solutions and exhibited aggregation-caused fluorescence quenching (ACQ). The interaction with Gram-positive bacteria cell walls would selectively disaggregate the probe and the liberated probes were dispersed on the outside of the bacteria cell walls to achieve surface fluorescence imaging. There were no such interactions with Gram-negative bacteria, which indicates that selective binding and imaging of Gram-positive bacteria was achieved. The binding of zinc ions by ZTRS-BP can enhance the fluorescent signals on the bacterial surface by inhibiting the process of photoinduced electron transfer. ZTRS-BP-Zn(II) complex was an excellent dye to discriminate mixed Gram-positive and Gram-negative bacteria. Also, live and dead bacteria can be differentially imaged by ZTRS-BP-Zn(II). Furthermore, ZTRS-BP-Zn(II) was used for real-time monitoring bacteria viability such as B. cereus treated with antibiotic vancomycin.

Nanopore sequencing and its application to the study of microbial communities

Since its introduction, nanopore sequencing has enhanced our ability to study complex microbial samples through the possibility to sequence long reads in real time using inexpensive and portable technologies. The use of long reads has allowed to address several previously unsolved issues in the field, such as the resolution of complex genomic structures, and facilitated the access to metagenome assembled genomes (MAGs). Furthermore, the low cost and portability of platforms together with the development of rapid protocols and analysis pipelines have featured nanopore technology as an attractive and ever-growing tool for real-time in-field sequencing for environmental microbial analysis. This review provides an up-to-date summary of the experimental protocols and bioinformatic tools for the study of microbial communities using nanopore sequencing, highlighting the most important and recent research in the field with a major focus on infectious diseases. An overview of the main approaches including targeted and shotgun approaches, metatranscriptomics, epigenomics, and epitranscriptomics is provided, together with an outlook to the major challenges and perspectives over the use of this technology for microbial studies.

The Changing Face of the Family Enterobacteriaceae (Order: "Enterobacterales"): New Members, Taxonomic Issues, Geographic Expansion, and New Diseases and Disease Syndromes

The family Enterobacteriaceae has undergone significant morphogenetic changes in its more than 85-year history, particularly during the past 2 decades (2000 to 2020). The development and introduction of new and novel molecular methods coupled with innovative laboratory techniques have led to many advances. We now know that the global range of enterobacteria is much more expansive than previously recognized, as they play important roles in the environment in vegetative processes and through widespread environmental distribution through insect vectors. In humans, many new species have been described, some associated with specific disease processes. Some established species are now observed in new infectious disease settings and syndromes. The results of molecular taxonomic and phylogenetics studies suggest that the current family Enterobacteriaceae should possibly be divided into seven or more separate families. The logarithmic explosion in the number of enterobacterial species described brings into question the relevancy, need, and mechanisms to potentially identify these taxa. This review covers the progression, transformation, and morphogenesis of the family from the seminal Centers for Disease Control and Prevention publication (J. J. Farmer III, B. R. Davis, F. W. Hickman-Brenner, A. McWhorter, et al., J Clin Microbiol 21:46-76, 1985, https://doi.org/10.1128/JCM.21.1.46-76.1985) to the present.