Microbiome analysis reveals universal diagnostic biomarkers for colorectal cancer across populations and technologies

The gut microbial dysbiosis is a risk of colorectal cancer (CRC) and some bacteria have been reported as potential markers for CRC diagnosis. However, heterogeneity among studies with different populations and technologies lead to inconsistent results. Here, we investigated six metagenomic profiles of stool samples from healthy controls (HC), colorectal adenoma (CA) and CRC, and six and four genera were consistently altered between CRC and HC or CA across populations, respectively. In FengQ cohort, which composed with 61 HC, 47 CA, and 46 CRC samples, a random forest (RF) model composed of the six genera, denoted as signature-HC, distinguished CRC from HC with an area under the curve (AUC) of 0.84. Similarly, another RF model composed of the four universal genera, denoted as signature-CA, discriminated CRC from CA with an AUC of 0.73. These signatures were further validated in five metagenomic sequencing cohorts and six independent 16S rRNA gene sequencing cohorts. Interestingly, three genera overlapped in the two models (Porphyromonas, Parvimonas and Peptostreptococcus) were with very low abundance in HC and CA, but sharply increased in CRC. A concise RF model on the three genera distinguished CRC from HC or CA with AUC of 0.87 and 0.67, respectively. Functional gene family analysis revealed that Kyoto Encyclopedia of Genes and Genomes Orthogroups categories which were significantly correlated with markers in signature-HC and signature-CA were mapped into pathways related to lipopolysaccharide and sulfur metabolism, which might be vital risk factors of CRC development. Conclusively, our study identified universal bacterial markers across populations and technologies as potential aids in non-invasive diagnosis of CRC.

Culture on Selective Media and Amplicon-Based Sequencing of 16S rRNA from Spontaneous Brain Abscess-the View from the Diagnostic Laboratory

Forty-one stored samples from cases of spontaneous brain abscess were investigated to gain insight into the natural history, causative agents, and relevant laboratory diagnostics of a rare infection. Samples from a larger collection were selected based on retrospective analysis of patient records. All samples were subjected to amplicon sequencing of 16S rRNA gene fragments. Supplementary culture on selected media was performed as suggested by bioinformatics analysis. For three cases, no microorganism was disclosed, while Toxoplasma gondii, Aspergillus fumigatus, and various bacteria were the cause of 1, 2, and 35 cases, respectively. Bacterial infections were monomicrobial in 20 cases and polymicrobial in 15; the microorganisms of the latter cases were restricted to residents of cavum oris. Amplicon sequencing did not further enhance the importance of the Streptococcus anginosus group, which was involved in 17 cases, and the single primer set used may be suboptimal for amplification of Actinomyces and Nocardia. But, amplicon-based sequencing unquestionably expanded the number of polybacterial infections, with focus on the Fusobacterium nucleatum group, Parvimonas, and Porphyromonas. Culture on selective media confirmed the presence of F. nucleatum group bacteria, which attained a prominence in spontaneous brain abscess similar to the S. anginosus group. Metagenomics is a powerful tool to disclose the spectrum of agents in polymicrobial infections, but a reliable cutoff value for substantial detection is complex. Commercial media for isolation of F. nucleatum group bacteria from mixed infections are available, and these pathogens should be carefully characterized. Isolation of Parvimonas and Porphyromonas in polymicrobial infections has not been resolved. IMPORTANCE Polymicrobial brain abscess is a challenge to the clinical microbiology laboratory due to the aggregative nature of the dental and oral microbiota. Because polymicrobial infections may escape detection by conventional culture methods, directed therapy toward a single detected bacterium is problematic. Amplicon-based sequencing provides important clues to these infections, but only cultured microorganisms can be fully characterized, subjected to antimicrobial susceptibility testing, and formally named. By use of specific selective culture plates, we successfully isolated bacteria of the Fusobacterium nucleatum group, and these bacteria rose to the same prominence as the widely recognized pathogen, the Streptococcus anginosus group. Named and unnamed members of the Fusobacterium nucleatum group must be further investigated to gain insight into a rare but grave disease.

Native joint infections caused by Parvimonas micra

Parvimonas micra is an anaerobic, fastidious, gram positive organism commonly found in the oral cavity and gastrointestinal tract. It has been increasingly reported as the cause of septic arthritis of native joints, often times with delayed diagnosis leading to increased morbidity. Risk factors include immunosuppression, inflammation of the joint, and recent dental procedures or infections. It has been a historically difficult organism to culture. However, the development of and increasing use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) has led to increased identification of P. micra. Common antibiotic susceptibilities, as well as data regarding susceptibilities in specific situations, have been reported, but susceptibility testing is required in all cases. Common treatments include clindamycin, penicillin, and metronidazole for six to ten weeks.

The Versatility of Opportunistic Infections Caused by Gemella Isolates Is Supported by the Carriage of Virulence Factors From Multiple Origins

The molecular basis of the pathogenesis of the opportunistic invasive infections caused by isolates of the Gemella genus remains largely unknown. Moreover, inconsistencies in the current species assignation were detected after genome-level comparison of 16 public Gemella isolates. A literature search detected that, between the two most pathogenic species, Gemella morbillorum causes about twice the number of cases compared to Gemella haemolysans. These two species shared their mean diseases - sepsis and endocarditis - but differed in causing other syndromes. A number of well-known virulence factors were harbored by all species, such as a manganese transport/adhesin sharing 83% identity from oral endocarditis-causing streptococci. Likewise, all Gemellae carried the genes required for incorporating phosphorylcholine into their cell walls and encoded some choline-binding proteins. In contrast, other proteins were species-specific, which may justify the known epidemiological differences. G. haemolysans, but not G. morbillorum, harbor a gene cluster potentially encoding a polysaccharidic capsule. Species-specific surface determinants also included Rib and MucBP repeats, hemoglobin-binding NEAT domains, peptidases of C5a complement factor and domains that recognize extracellular matrix molecules exposed in damaged heart valves, such as collagen and fibronectin. Surface virulence determinants were associated with several taxonomically dispersed opportunistic genera of the oral microbiota, such as Granulicatella, Parvimonas, and Streptococcus, suggesting the existence of a horizontally transferrable gene reservoir in the oral environment, likely facilitated by close proximity in biofilms and ultimately linked to endocarditis. The identification of the Gemella virulence pool should be implemented in whole genome-based protocols to rationally predict the pathogenic potential in ongoing clinical infections caused by these poorly known bacterial pathogens.

Clinical and microbiological features of bacteraemia with Gram-positive anaerobic cocci: a population-based retrospective study

OBJECTIVES

Gram-positive, anaerobic cocci (GPAC) can cause infections in humans. Only a few cases of bacteraemia with GPAC have been reported. We describe the clinical and microbiological characteristics of GPAC bacteraemia.

METHODS

A retrospective population-based study of GPAC bacteraemia 2012-2016 in southern Sweden was performed. GPAC were identified using matrix-associated laser desorption ionization time-of-flight mass spectrometry or 16S rRNA gene sequencing. Etests were used to determine antibiotic susceptibilities. Data on patient and infection characteristics, treatment, and outcome were collected from the medical records.

RESULTS

A total of 226 episodes of GPAC bacteraemia in adults were studied; this corresponds to an annual incidence of 3.4 cases per 100,000 persons per year. The bacteria identified were Anaerococcus spp. (n = 43), Atopobium spp. (n = 7), Blautia spp. (n = 1), Finegoldia spp. (n = 15), Parvimonas spp. (n = 100), Peptoniphilus spp. (n = 52), Peptostreptococcus spp. (n = 2), and Ruminococcus spp. (n = 9) of which 200 isolates were identified to the species level. Resistance to imipenem and piperacillin was not identified, whereas resistance among the 229 isolates to penicillin was detected in four, to metronidazole in six, and clindamycin in 16 isolates. The median age of patients was 73 years (55-83, IQR), 57% were male and comorbidities were common. Fifty-one per cent of infections were polymicrobial. In 60% of cases a focus of infection was identified. Forty per cent of patients had either organ dysfunction or shock. The 30-day mortality was 11%, and nosocomial infections were over-represented among the deceased.

CONCLUSIONS

GPAC bacteraemia is much more common than previously reported. GPAC-bacteraemia is a condition with significant mortality mainly affecting elderly persons with comorbidities.

Acute septic arthritis of the knee: A rare case report of infection with Parvimonas micra after an intra-articular corticosteroid injection for osteoarthritis

Acute bacterial mono-articular septic arthritis affects most commonly the lower extremity joints in adult population and most commonly caused by Staphylococcus aureus. Various risk factors determine susceptibility to infection including host immunity, medical co-morbidity and joint structural abnormality and other organisms may be involved. Parvimonas micra (P. micra) is among the rare organisms that may be associated with atypical septic arthritis and primarily affects the native knee joint. Only 3 case reports in the literature have reported on pyogenic pyogenic joint infection caused by this organism. We hereby present our experience with a case of knee septic arthritis caused by P. micra in a patient with knee osteoarthritis following a recent intra-articular injection with corticosteroids. In susceptible patients, Intra-articular corticosteroid injection and crystal induced arthritis may propose a potential risk of contracting infection with P. micra.

Parvimonas micra: A rare cause of native joint septic arthritis

Parvimonas micra is a fastidious, anaerobic, gram positive coccus, which is found in normal human oral and gastrointestinal flora. It has also been known as Peptostreptococcus micros and Micromonas micros with its most recent re-classification in 2006. It has been described in association with hematogenous seeding of prosthetic joints [1,2]. Several cases of discitis and osteomyelitis have been described in association with dental procedures and periodontal disease often with a subacute presentation. However, cases of native joint septic arthritis are limited [3-5]. Per our literature review, there is one case of native knee septic arthritis described in 1999, with a prolonged time to diagnosis and treatment due to difficulty culturing P. micra. The previously reported patient experienced significant joint destruction and morbidity [6]. Advances in culture techniques and new methods of organism identification including MALDI-TOF and 16s rRNA sequencing have lead to increased identification of this organism, which may be a more frequent bone and joint pathogen than previously realized.