Persistent Bacillus cereus Bacteremia in 3 Persons Who Inject Drugs, San Diego, California, USA

Everything but the Kitchen Sink: An Analysis of Bacterial and Chemical Contaminants Found in Syringe Residue From People Who Inject Drugs

Background

People who inject drugs (PWID) are at high risk of severe wounds, invasive infections, and overdoses. To date, there are few data on the bacterial and chemical contaminants PWID are exposed to when using illicitly manufactured fentanyls and stimulants.

Methods

Previously used injection drug use equipment was recovered in St Louis, Missouri, by harm reduction organizations over a 12-month period. Syringe residue was analyzed for bacterial contaminants by routine culturing followed by whole genome sequencing of single bacterial isolates. Chemical adulterants in syringe residue were identified by liquid chromatography-mass spectrometry.

Results

Bacteria were cultured from 58.75% of 160 syringes analyzed. Polymicrobial growth was common and was observed in 23.75% of samples. Bacillus cereus was the most common pathogen present and was observed in 20.6% of syringe residues, followed closely by Staphylococcus aureus at 18.8%. One hundred syringes underwent mass spectrometry, which demonstrated that chemical adulterants were common and included caffeine, diphenhydramine, lidocaine, quinine, and xylazine.

Conclusions

Analysis of syringe residue from discarded drug use equipment demonstrates both chemical and biological contaminants, including medically important pathogens and adulterants.

Surely you can't B. cereus: Bacillus cereus infection resulting in spontaneous pseudoaneurysm of a nonaccessed arteriovenous graft

Vascular graft infections are a well-described complication of loop arteriovenous grafts (AVGs) placed for hemodialysis access and are reported to occur in 0.5% to 6.0% of AVGs. The most common microorganisms implicated in these infections are the Staphylococcus species. We present a case of a chronically nonaccessed graft rupture caused by an indolent B. cereus colonization, which is usually a foodborne contaminant. The finding of this organism as the causal agent in an AVG infection warrants further research into the potential emergence of the Bacillus species as a contributing factor in the morbidity and mortality resulting from AVG infection.

The Distinguishing Bacterial Features From Active and Remission Stages of Ulcerative Colitis Revealed by Paired Fecal Metagenomes

Ulcerative colitis (UC) is a serious chronic intestinal inflammatory disease, with an increased incidence in recent years. The intestinal microbiota plays a key role in the pathogenesis of UC. However, there is no unified conclusion on how the intestinal microbiota changes. Most studies focus on the change between UC patients and healthy individuals, rather than the active and remission stage of the same patient. To minimize the influences of genetic differences, environmental and dietary factors, we studied the intestinal microbiota of paired fecal samples from 42 UC patients at the active and remission stages. We identified 175 species of microbes from 11 phyla and found no difference of the alpha and beta diversities between the active and remission stages. Paired t-test analysis revealed differential microbiota at levels of the phyla, class, order, family, genus, and species, including 13 species with differential abundance. For example, CAG-269 sp001916005, Eubacterium F sp003491505, Lachnospira sp000436475, et al. were downregulated in the remission, while the species of Parabacteroides distasonis, Prevotellamassilia sp900540885, CAG-495 sp001917125, et al. were upregulated in the remission. The 13 species can effectively distinguish the active and remission stages. Functional analysis showed that the sporulation and biosynthesis were downregulated, and the hydrogen peroxide catabolic process was upregulated in remission of UC. Our study suggests that the 13 species together may serve as a biomarker panel contributing to identify the active and remission stages of UC, which provides a valuable reference for the treatment of UC patients by FMT or other therapeutic methods.

Complete Genome Sequences of 24 Strains of Bacillus cereus Isolated from Nosocomial Infection and Bacteremia Cases in Japan

Bacillus cereus is mainly associated with foodborne illness but sometimes causes nosocomial infections. We previously reported that B. cereus strains of a specific sequence type, ST1420, were associated with nosocomial infection. Here, we determined the complete genome sequences of B. cereus strains isolated from nosocomial infection cases in Japanese hospitals.

A Case of Persistent Bacillus cereus Bacteremia Responding to a Combination of Vancomycin and Gentamicin

A 56-year-old woman with a history of connective tissue disease developed fever, and Bacillus cereus (B. cereus) was detected in blood cultures. Therefore, treatment with vancomycin (VCM) was initiated. Since her blood cultures persistently detected B. cereus despite peripheral intravenous catheter replacement and VCM treatment, concomitant treatment with gentamicin (GM) was started. Blood cultures then became negative. Persistent B. cereus bacteremia responded to combination therapy with VCM and GM. This combination therapy may increase the risk of developing renal dysfunction, but the risk can be mitigated by appropriate therapeutic drug monitoring (TDM) and dose adjustments to achieve successful treatment.

Comparative analysis of Bacillus cereus group isolates' resistance using disk diffusion and broth microdilution and the correlation between antimicrobial resistance phenotypes and genotypes

Bacillus cereus group isolates (n = 85) were screened for phenotypic resistance to 18 antibiotics using broth microdilution and CLSI M45 Bacillus spp. breakpoints. The susceptibility to 9 out of 18 antibiotics was tested also using disk diffusion method and M100 Staphylococcus spp. breakpoints. Overall, a high prevalence of susceptibility to clinically relevant antibiotics was identified using broth microdilution. For most tested antibiotics, a poor correlation was found between zones of inhibition and minimum inhibitory concentrations. Using the broth microdilution results as a reference for comparison, we identified high error rates and low categorical agreement between results produced using disk diffusion and broth microdilution for the seven tested antibiotics with defined breakpoints. This suggests that disk diffusion should be avoided for AST of B. cereus group isolates. Further, we detected antimicrobial resistance genes with ARIBA and ABRIcate to calculate the sensitivity and specificity for predicting phenotypic resistance determined using broth microdilution based on the presence of detected antimicrobial resistance genes (ARGs). ARGs with poor sensitivity and high specificity included rph (rifampicin, 0%, 93%), mph (erythromycin, 0%, 99%), bla1 (penicillin, 29%, 100), and blaZ (penicillin, 56%, 100%). Compared to penicillin, bla1 and blaZ had lower specificity for the prediction of ampicillin resistance. Overall, none of the ARGs had both high sensitivity and specificity, suggesting the need for further study of the mechanisms underlying phenotypic antimicrobial resistance in the B. cereus group. IMPORTANCE Bacillus cereus group includes human pathogens that can cause severe infections requiring antibiotic treatment. Screening of environmental and food isolates for antimicrobial resistance can provide insight into what antibiotics may be more effective therapeutic options based on the lower prevalence of resistance. Currently, the comparison of antimicrobial susceptibility testing results using the disk diffusion method is complicated by the fact that many previous studies have used Staphylococcus spp. breakpoints to interpret their results. In this study, we compared the results of disk diffusion interpreted using the Staphylococcus spp. breakpoints against the results of broth microdilution interpreted using Bacillus spp. breakpoints. We demonstrated that the disk diffusion method does not produce reliable results for B. cereus group isolates and should therefore be avoided. This study also provides new insight into poor associations between the presence of antimicrobial resistance genes and resistance phenotypes for the B. cereus group.

Differences in the sequence of PlcR transcriptional regulator binding site affect sphingomyelinase production in Bacillus cereus

Bacillus cereus is an opportunistic pathogen that often causes severe infections such as bacteremia, with sphingomyelinase (SMase) being a crucial virulence factor. Although many strains of B. cereus carry the SMase gene, they are classified as SMase-producing and non-producing strains. The reason for different SMase production among B. cereus strains remains unknown. In this study, we investigated the relationship between SMase and the PlcR transcriptional regulation system to clarify the mechanism leading to varied SMase production among B. cereus strains. We analyzed the sequence of the PlcR box, which is a transcriptional regulator binding site, located at the promoter region of SMase and phosphatidylcholine-specific phospholipase C. Based on differences in the PlcR box sequences, we classified the B. cereus strains into three groups (I, II, and III). SMase expression and activity were hardly detected in Group III strains. In Group I strains, SMase activity and its expression were maximal at the onset of the stationary phase and decreased during the stationary phase, whereas those were maintained during the stationary phase in Group II stains. On injection of B. cereus strains into mice or incubation with macrophages for phagocytosis assay, the SMase-producing Group I and II strains showed higher pathogenicity than Group III strains. These findings suggest that PlcR box sequence in B. cereus affects the production of SMase, which may provide important clinical information for the detection of highly pathogenic B. cereus strains. This article is protected by copyright. All rights reserved.

Diagnosing hospital bacteraemia in the framework of predictive, preventive and personalised medicine using electronic health records and machine learning classifiers

Background

The bacteraemia prediction is relevant because sepsis is one of the most important causes of morbidity and mortality. Bacteraemia prognosis primarily depends on a rapid diagnosis. The bacteraemia prediction would shorten up to 6 days the diagnosis, and, in conjunction with individual patient variables, should be considered to start the early administration of personalised antibiotic treatment and medical services, the election of specific diagnostic techniques and the determination of additional treatments, such as surgery, that would prevent subsequent complications. Machine learning techniques could help physicians make these informed decisions by predicting bacteraemia using the data already available in electronic hospital records.

Objective

This study presents the application of machine learning techniques to these records to predict the blood culture's outcome, which would reduce the lag in starting a personalised antibiotic treatment and the medical costs associated with erroneous treatments due to conservative assumptions about blood culture outcomes.

Methods

Six supervised classifiers were created using three machine learning techniques, Support Vector Machine, Random Forest and K-Nearest Neighbours, on the electronic health records of hospital patients. The best approach to handle missing data was chosen and, for each machine learning technique, two classification models were created: the first uses the features known at the time of blood extraction, whereas the second uses four extra features revealed during the blood culture.

Results

The six classifiers were trained and tested using a dataset of 4357 patients with 117 features per patient. The models obtain predictions that, for the best case, are up to a state-of-the-art accuracy of 85.9%, a sensitivity of 87.4% and an AUC of 0.93.

Conclusions

Our results provide cutting-edge metrics of interest in predictive medical models with values that exceed the medical practice threshold and previous results in the literature using classical modelling techniques in specific types of bacteraemia. Additionally, the consistency of results is reasserted because the three classifiers' importance ranking shows similar features that coincide with those that physicians use in their manual heuristics. Therefore, the efficacy of these machine learning techniques confirms their viability to assist in the aims of predictive and personalised medicine once the disease presents bacteraemia-compatible symptoms and to assist in improving the healthcare economy.

Every breath you take: Impacts of environmental dust exposure on intestinal barrier function-from the gut-lung axis to COVID-19

As countries continue to industrialize, major cities experience diminished air quality, whereas rural populations also experience poor air quality from sources such as agricultural operations. These exposures to environmental pollution from both rural and populated/industrialized sources have adverse effects on human health. Although respiratory diseases (e.g., asthma and chronic obstructive pulmonary disease) are the most commonly reported following long-term exposure to particulate matter and hazardous chemicals, gastrointestinal complications have also been associated with the increased risk of lung disease from inhalation of polluted air. The interconnectedness of these organ systems has offered valuable insights into the roles of the immune system and the micro/mycobiota as mediators of communication between the lung and the gut during disease states. A topical example of this relationship is provided by reports of multiple gastrointestinal symptoms in patients with coronavirus disease 2019 (COVID-19), whereas the rapid transmission and increased risk of COVID-19 has been linked to poor air quality and high levels of particulate matter. In this review, we focus on the mechanistic effects of environmental pollution on disease progression with special emphasis on the gut-lung axis.

Skin and Soft Tissue Infections in Persons Who Inject Drugs

Persons who inject drugs are at high risk for skin and soft tissue infections. Infections range from simple abscesses and uncomplicated cellulitis to life-threatening and limb-threatening infections. These infections are predominantly caused by gram-positive organisms with Staphylococcus aureus, Streptococcus pyogenes, and other streptococcal species being most common. Although antimicrobial therapy has an important role in treatment of these infections, surgical incision, drainage, and debridement of devitalized tissue are primary. Strategies that decrease the frequency of injection drug use, needle sharing, use of contaminated equipment, and other risk behaviors may be effective in preventing these infections in persons who inject drugs.

Characterization of Bacillus cereus in Dairy Products in China

Bacillus cereus is a common and ubiquitous foodborne pathogen with an increasing prevalence rate in dairy products in China. High and unmet demands for such products, particularly milk, raise the risk of B. cereus associated contamination. The presence of B. cereus and its virulence factors in dairy products may cause food poisoning and other illnesses. Thus, this review first summarizes the epidemiological characteristics and analytical assays of B. cereus from dairy products in China, providing insights into the implementation of intervention strategies. In addition, the recent achievements on the cytotoxicity and mechanisms of B. cereus are also presented to shed light on the therapeutic options for B. cereus associated infections.

A case of Bacillus cereus bacteremia in a COVID-19 patient treated with steroids

This report describes a case of Bacillus cereus bacteremia in a COVID-19 patient with prior inhalational steroid use and inpatient steroid treatment for COVID-19 pulmonary symptoms. The case herein is intended to illustrate an uncommon presentation of B. cereus bacteremia and highlight the increased likelihood for the occurrence of this bacteremia in patients with COVID-19 and concomitant steroid use.

The cereus matter of Bacillus endophthalmitis

Bacillus cereus (B. cereus) endophthalmitis is a devastating intraocular infection primarily associated with post-traumatic injuries. The majority of these infections result in substantial vision loss, if not loss of the eye itself, within 12-48 h. Multifactorial mechanisms that lead to the innate intraocular inflammatory response during this disease include the combination of robust bacterial replication, migration of the organism throughout the eye, and toxin production by the organism. Therefore, the window of therapeutic intervention in B. cereus endophthalmitis is quite narrow compared to that of other pathogens which cause this disease. Understanding the interaction of bacterial and host factors is critical in understanding the disease and formulating more rational therapeutics for salvaging vision. In this review, we will discuss clinical and research findings related to B. cereus endophthalmitis in terms of the organism's virulence and inflammogenic potential, and strategies for improving of current therapeutic regimens for this blinding disease.

Novel Sequence Type in Bacillus cereus Strains Associated with Nosocomial Infections and Bacteremia, Japan

This sequence type was dominant in isolates from bacteremia patients in 3 hospitals.

Bacillus cereus is associated with foodborne illnesses characterized by vomiting and diarrhea. Although some B. cereus strains that cause severe extraintestinal infections and nosocomial infections are recognized as serious public health threats in healthcare settings, the genetic backgrounds of B. cereus strains causing such infections remain unknown. By conducting pulsed-field gel electrophoresis and multilocus sequence typing, we found that a novel sequence type (ST), newly registered as ST1420, was the dominant ST isolated from the cases of nosocomial infections that occurred in 3 locations in Japan in 2006, 2013, and 2016. Phylogenetic analysis showed that ST1420 strains belonged to the Cereus III lineage, which is much closer to the Anthracis lineage than to other Cereus lineages. Our results suggest that ST1420 is a prevalent ST in B. cereus strains that have caused recent nosocomial infections in Japan.

Comparative genomic survey of Bacillus cereus sensu stricto isolates from the dairy production chain in Brazil

The genomes of 262 Bacillus cereus isolates were analyzed including 69 isolates sampled from equipment, raw milk and dairy products from Brazil. The population structure of isolates showed strains belonging to known phylogenetic groups II, III, IV, V and VI. Almost all the isolates obtained from dairy products belonged to group III. Investigation of specific alleles revealed high numbers of isolates carrying toxin-associated genes including cytK (53.62%), hblA (59.42%), hblC (44.93%), hblD (53.62%), nheA (84.06%), nheB (89.86%) and nheC (84.06%) with isolates belonging to groups IV and V having significant higher prevalence of hblACD and group IV of CytK genes. Strains from dairy products had significantly lower prevalence of CytK and hblACD genes compared to isolates from equipment and raw milk/bulk tanks. Genes related to sucrose metabolism were detected at higher frequency in isolates obtained from raw milk compared to strains from equipment and utensils. The population genomic analysis demonstrated the diversity of strains and variability of putative function among B. cereus group isolates in Brazilian dairy production, with large numbers of strains potentially able to cause foodborne illness. This detailed information will contribute to targeted interventions to reduce milk contamination and spoilage associated with B. cereus in Brazil.

Bacillus cereus group: genetic aspects related to food safety and dairy processing

ABSTRACT: Bacillus cereus group includes not pathogenic and high pathogenic species. They are considered as a risk to public health due to foodborne diseases and as an important cause of economic losses to industries due to production of spoilage enzymes. Some researches have been performed in order to assess the possible factors that contribute to put public health into risk because of consumption of food contaminated with viable cells or toxins which have complex mechanisms of production. The control of these bacteria in food is difficult because they are resistant to several processes used in industries. Thus, in this way, this review focused on highlighting the risk due to toxins production by bacteria from B. cereus group in food and the consequences for food safety and dairy industries.

Deposition of Bacteria and Bacterial Spores by Bathroom Hot-Air Hand Dryers

Hot-air hand dryers in multiple men's and women's bathrooms in three basic science research areas in an academic health center were screened for their deposition on plates of (i) total bacteria, some of which were identified, and (ii) a kanamycin-resistant Bacillus subtilis strain, PS533, spores of which are produced in large amounts in one basic science research laboratory. Plates exposed to hand dryer air for 30 s averaged 18 to 60 colonies/plate; but interior hand dryer nozzle surfaces had minimal bacterial levels, plates exposed to bathroom air for 2 min with hand dryers off averaged ≤1 colony, and plates exposed to bathroom air moved by a small fan for 20 min had averages of 15 and 12 colonies/plate in two buildings tested. Retrofitting hand dryers with HEPA filters reduced bacterial deposition by hand dryers ∼4-fold, and potential human pathogens were recovered from plates exposed to hand dryer air whether or not a HEPA filter was present and from bathroom air moved by a small fan. Spore-forming colonies, identified as B. subtilis PS533, averaged ∼2.5 to 5% of bacteria deposited by hand dryers throughout the basic research areas examined regardless of distance from the spore-forming laboratory, and these were almost certainly deposited as spores. Comparable results were obtained when bathroom air was sampled for spores. These results indicate that many kinds of bacteria, including potential pathogens and spores, can be deposited on hands exposed to bathroom hand dryers and that spores could be dispersed throughout buildings and deposited on hands by hand dryers.IMPORTANCE While there is evidence that bathroom hand dryers can disperse bacteria from hands or deposit bacteria on surfaces, including recently washed hands, there is less information on (i) the organisms dispersed by hand dryers, (ii) whether hand dryers provide a reservoir of bacteria or simply blow large amounts of bacterially contaminated air, and (iii) whether bacterial spores are deposited on surfaces by hand dryers. Consequently, this study has implications for the control of opportunistic bacterial pathogens and spores in public environments including health care settings. Within a large building, potentially pathogenic bacteria, including bacterial spores, may travel between rooms, and subsequent bacterial/spore deposition by hand dryers is a possible mechanism for spread of infectious bacteria, including spores of potential pathogens if present.

Introducing the sporobiota and sporobiome

Unrelated spore-forming bacteria share unique characteristics stemming from the presence of highly resistant endospores, leading to similar challenges in health and disease. These characteristics are related to the presence of these highly transmissible spores, which are commonly spread within the environment and are implicated in host-to-host transmission. In humans, spore-forming bacteria contribute to a variety of pathological processes that share similar characteristics, including persistence, chronicity, relapses and the maintenance of the resistome. We first outline the necessity of characterizing the totality of the spore-forming bacteria as the sporobiota based on their unique common characteristics. We further propose that the collection of all genes of spore-forming bacteria be known as the sporobiome. Such differentiation is critical for exploring the cross-talk between the sporobiota and other members of the gut microbiota, and will allow for a better understanding of the implications of the sporobiota and sporobiome in a variety of pathologies and the spread of antibiotic resistance.