The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny and Escherichia core genomic diversity

EnteroBase is an integrated software environment which supports the identification of global population structures within several bacterial genera that include pathogens. Here, we provide an overview on how EnteroBase works, what it can do, and its future prospects. EnteroBase has currently assembled more than 300,000 genomes from Illumina short reads from Salmonella, Escherichia, Yersinia, Clostridiodes, Helicobacter, Vibrio, and Moraxella, and genotyped those assemblies by core genome Multilocus Sequence Typing (cgMLST). Hierarchical clustering of cgMLST sequence types allows mapping a new bacterial strain to predefined population structures at multiple levels of resolution within a few hours after uploading its short reads. Case study 1 illustrates this process for local transmissions of Salmonella enterica serovar Agama between neighboring social groups of badgers and humans. EnteroBase also supports SNP calls from both genomic assemblies and after extraction from metagenomic sequences, as illustrated by case study 2 which summarizes the microevolution of Yersinia pestis over the last 5,000 years of pandemic plague. EnteroBase can also provide a global overview of the genomic diversity within an entire genus, as illustrated by case study 3 which presents a novel, global overview of the population structure of all of the species, subspecies and clades within Escherichia

Current landscape in the discovery of novel antibacterial agents

Background: Standard treatments against bacterial infections are becoming ineffective due to the rise of antibacterial resistance worldwide. Classical approaches to develop new antibacterial agents are not sufficient to fulfil the current pipeline, therefore new strategies are currently being devised in the field of antibacterial discovery. Objectives: The objective of this narrative review is to compile the most successful strategies for drug discovery within the antibacterial context that are currently being pursued. Sources: Peer-reviewed publications from the MEDLINE database with robust data addressing the discovery of new antibacterial agents in the current pipeline have been selected. Content: Several strategies to discover new antibacterials are described in this review: (i) derivatives of known antibacterial agents; the activity of a known antimicrobial agent can be improved through two strategies: (a) the modification of the original chemical structure of an antimicrobial agent to circumvent antibacterial resistance mechanisms and (b) the development of a compound that inhibits the mechanisms of resistance to an antibacterial agent; (ii) new antibacterial agents targeting new proteins; (iii) inhibitors of virulence factors; (iv) nanoparticles; (v) antimicrobial peptides and peptidomimetics; (vi) phage therapy and enzybiotics; and (vii) antisense oligonucleotides. Implications: This review intends to provide a positive message affirming that several different strategies to design new antibacterial agents are currently being developed, and we are therefore confident that in the near future some of the most promising approaches will come to fruition

Trends In Recurrent Clostridioides Difficile Infection In New Haven County

Background: Recurrent Clostridioides difficile infection (CDI) is a cause of increased burden on the healthcare system and factors associated with this disease merit understanding. This study aimed to determine the incidence rate and to describe the factors associated with recurrent CDI cases in New Haven County from 2015 to 2020. It also examined the trends in annual recurrent CDI cases across epidemiological classes. Methods: This study utilized data from a population-based surveillance program of the Healthcare-Associated Infectious Community Interface (HAIC) Program within the Connecticut Emerging Infectious Program (CT EIP) at Yale School of Public Health which served all residents of New Haven County. Annual incidence rates of CDI and recurrent CDI in aggregate and by epidemiological class were calculated. Logistic regression analysis was carried out to determine factors associated with recurrent CDI. Results: Among 7,023 CDI cases from 2015-2020, the incidence rate of CDI in 2015 and 2020 was 165.2 and 107.8 per 100,000 persons respectively (median=140.2/100,000 persons; IQR=25.6/100,000 persons). Overall, 12% of 4,301 CDI cases with complete chart reviews had recurrent CDI, which made up 13.6% of all HCFO-CDI, 14.1% of all CO-HCFA CDI, and 10.5% of all CA-CDI. Specifically, 18.1 and 16.9 per 100 persons in 2015 and 2020 respectively had recurrent CDI (median=11.3/100 persons; IQR=4.7/100 persons). There were a 37.3% and 2.3% increase in recurrent CDI among HCFO and CA cases respectively from 2019 to 2020. A significant proportion of those who had recurrent CDI were older (median age=70.0 years, IQR=23.0 years; median age of non-recurrent group=64.0 years, IQR=26.0 years, p\u3c0.001), female (recurrent of 66.0% vs non-recurrent of 61.3% p\u3c0.039), White race, non-Hispanic, and had healthcare-associated incident CDI. In the final multivariable model, there was a higher risk of recurrent CDI among individuals who had malignancies (OR, 1.51; 95% CI, 1.11-2.07), used nitrofurantoin (OR, 2.37; 95% CI, 1.23-4.58), or were of White race. Also, cases with incident CDI in 2017 (OR, 0.43; 95% CI, 0.26-0.73), 2018 (OR, 0.60; 95% CI, 0.37-0.97), and 2019 (OR, 0.50; 95% CI, 0.30-0.84) had lower risk of recurrent CDI when compared with incident CDI cases in 2015. Conclusions: There was a lowered risk of recurrent CDI over time (from 2015-2019) which may reflect effective measures in management of CDI. The loss of this pattern in 2020 with an increase in HCFO recurrent cases may reflect the impact of the COVID-19 pandemic in 2020. Older persons, White individuals, and those with malignancies are particularly vulnerable to recurrent CDI. Keywords: Chronic Disease Epidemiology, Thesis, Clostridioides difficile, CDI, recurrent CDI, recurrent Clostridioides difficil

Esculin hydrolysis negative and TcdA ‐only producing strains of clostridium (Clostridiodes) difficile from the environment in Western Australia

Background and Aims Clostridium (Clostridiodes) difficile clade 3 ribotype (RT) 023 strains that fail to produce black colonies on bioMérieux ChromID agar have been reported, as well as variant strains of C. difficile that produce only toxin A. We have recently isolated strains of C. difficile from the environment in Western Australia (WA) with similar characteristics. The objective of this study was to characterize these strains. It was hypothesized that a putative β-glucosidase gene was lacking in these strains of C. difficile, including RT 023, leading to white colonies. Methods and Results A total of 17 environmental isolates of C. difficile from garden soil and compost, and gardening shoe soles in Perth, WA, failed to produce black colonies on ChromID agar. MALDI-TOF MS analysis confirmed these strains as C. difficile. Four strains contained only a tcdA gene (A+B−CDT−) by PCR and were a novel RT (QX 597). All isolates were susceptible to all antimicrobials tested except one with low-level resistance to clindamycin (MIC = 8 mg/L). The four tcdA-positive strains were motile. All isolates contained neither bgl locus but only bgl K or a putative β-glucosidase gene by PCR. Whole-genome sequencing showed the 17 strains belonged to novel multi-locus sequence types 632, 848, 849, 850, 851, 852 and 853, part of the evolutionarily divergent clade C-III. Four isolates carried a full-length tcdA but not tcdB nor binary toxin genes. Conclusions ChromID C. difficile agar is used for the specific detection of C. difficile in the samples. To date, all strains except RT 023 strains from clinical samples hydrolyse esculin. This is the first report to provide insights into the identification of esculin hydrolysis negative and TcdA-only producing (A+B−CDT−) strains of C. difficile from environmental samples. Significance and Impact of the Study White colonies of C. difficile from environmental samples could be overlooked when using ChromID C. difficile agar, leading to false-negative results, however, whether these strains are truly pathogenic remains to be proven

Stuhlkulturausbeute und Prädiktoren für Stuhlkulturpositivität bei hospitalisierten erwachsenen Patienten mit Verdacht auf akute bakterielle Gastroenteritis

Hintergrund. Die akute infektiöse Gastroenteritis (AIG) ist mit erheblicher Morbidität, Mortalität und sozioökonomischen Kosten verbunden. Die Stuhlkulturdiagnostik weist weltweit und regional unterschiedliche diagnostische Ausbeuten auf und deren undifferenzierter Einsatz ist mit erheblichen Kosten verbunden. In diesem Kontext mangelt es in Deutschland an belastbaren Daten. Hauptziel der vorliegenden Arbeit war es, die Ausbeute der Stuhlkulturdiagnostik zu bestimmen und eine Kostenanalyse vorzunehmen. Zudem wurden potentielle Prädiktoren für Stuhlkulturpositivität untersucht. Methoden. Zur Bestimmung der Ausbeute der Stuhlkulturdiagnostik wurden insgesamt 54.674 Stuhlkulturanforderungen ausgewertet. 189 Patienten mit einem positiven Stuhlkulturbefund wurden mit Patienten (n=588) mit einem negativen Stuhlkulturbefund verglichen. Ergebnisse. Die Stuhlkulturausbeute betrug 3,3% bei Patienten, bei denen die Stuhlkulturanforderung innerhalb von 3 Tagen nach Krankenhausaufnahme erfolgte (Number-needed-to-test (NNT=31, geschätzte Kosten ca. 930€ pro positive Stuhlkulturdiagnostik). Die Stuhlkulturausbeute bei Patienten, bei einer Liegedauer von >72 Stunden nach Krankenhausaufnahme betrug 0,65% (NNT=158, geschätzte Kosten ca. €4.740 pro positive Stuhlkultur). Eine Beschränkung der Stuhlkulturanforderungen auf <72 Stunden nach Krankenhausaufnahme hätte schätzungsweise zu einer Einsparung von €56.186 € pro Jahr geführt. Die am häufigsten isolierten Erreger waren Campylobacter spp. (60%) und Salmonella spp. (31%), gefolgt von Aeromonas spp (2,2%), Shigella spp. (5%) und Yersinia spp. (1,8%). Die univariate Analyse zeigte, dass Fieber (≥38°C), erhöhte Stuhlfrequenz (≥4 pro Tag), blutiger Diarrhö, Diarrhö von kurzer Dauer, niedriger Charlson Comorbidty Index, CCI, hohes CRP, Immunsuppression und Bauchschmerzen mit Stuhlkulturpositivität korrelierten. In der multivariaten Analyse zeigten sich Fieber, (OR 2,36, 95% CI:1,79-3,10, p=0,001), erhöhte Stuhlfrequenz (OR 1,38, 95% CI:1,04-1,82, p= 0,013), blutige Diarrhö (OR 0,45, 95% CI:0,20-0,95, p=0,038) und niedriger CCI (OR 0,85, 95% CI:0,78-0,94, p=0,002) als potentielle unabhängige Prädiktoren für Stuhlkulturpositivität. Unter Einbezug dieser Parameter zeigte eine ROC-Analyse eine gute Diskriminierungsfähigkeit (AUC 0,656, CI:0,610-0,702, p=0,001; Sensitivität=62%, Spezifizität=58%). Die Anwesenheit von Fieber erbrachte die größte Area Under the Curve, AUROC=0,698 (CI: 0,639-0,758, p=0,001), gefolgt von erhöhter Stuhlfrequenz, AUROC 0,582 (CI:0,519-0,645, p=0,012). Zusammenfassung. Die Stuhlkulturausbeute bei hospitalisierten Patienten mit Verdacht auf akute bakterielle GE ist niedrig. Eine Beschränkung der Stuhlkulturanforderung auf <3 Tage nach Krankenhausaufnahme würde zu Ersparnissen an Ressourcen führen. Die Kombination aus Fieber und erhöhter Stuhlfrequenz könnte als Entscheidungsgrundlage bei der Stuhlkulturanforderung im Kontext der akuten bakteriellen GE berücksichtigt werden.Background. Acute infectious gastroenteritis (AIG) is associated with substantial morbidity and mortality and huge socioeconomic costs. Stool culture (SC) studies are the mainstay in the diagnosis of AIG. However, low diagnostic yield and often-indiscriminate requests for SC studies contribute to increased healthcare costs. Robust data regarding SC yield and predictive factors for SC positivity are currently sparse for Germany. We therefore aimed to determine SC yield and associated costs as well as analyze patient factors in adult patients with suspected acute bacterial gastroenteritis. Methods. To determine SC yield, the results of SC requests (n=54,674) between 01 January, 2013 and December 31, 2020 were analyzed. For pathogen identification, positive stool culture results of 498 patients between January 01, 2013 and 31, December, 2020 were analyzed. To investigate patient factors that are associated with stool culture positivity, a cohort of 777 patients comprising those with positive SC results (n=189) and those with negative results (n=588) between January 01, 2014 and December 31, 2018 were analyzed for differences in regard to demographical, clinical and laboratory parameters. Univariate and multivariate analyses were undertaken to identify factors that are associated with SC positivity. Receiver Operating Curve (ROC) analyses were performed to explore patient factors that could hypothetically increase SC yield. Results. The SC yield for samples ≤3 days of admission was 3.3% (numberneeded- to-test, NNT=31, amounting to an estimated total cost of €930 per positive stool culture). SC positivity for samples obtained >72 hours after admission was 0.65% (number-needed to test=158, estimated cost per positive SC=€4,740 per). Limiting SC request to ≤3 days of hospital admission” would have led to estimated savings on average of €56,186 per year. Campylobacter spp. (60%) and Salmonella spp. (31%) were the most common enteric pathogens isolated, followed by Aeromonas ssp. (2.2%), Shigella spp. (5%) and Yersinia spp. (1.8%). In univariate analyses, younger age, fever, increased stool frequency (≥4 per day), bloody stools, a shorter duration of diarrhoea, a low Charlson Comorbidity Index, high CRP levels, immunosuppression and abdominal pain were associated with SC positivity. In multivariate analyses, a combination of fever (≥38°C; OR 2.36, 95 % CI: 1.79-3.10, p=0.001), increased stool frequency (≥4 per day; OR 1.38, 95 % CI:1.04-1.82, p=0.013), the absence of bloody stools (OR 0.45, 95 % CI:0.20-0.95, p=0.038), and a lower Charlson Comorbidity Index, CCI (OR 0.85, 95 % CI:0.78-0.94, p=0.002) were independently associated with SC positivity. A ROC analysis showed good diagnostic accuracy (AUC 0.656, CI:0.610- 0.702, p=0.001; sensitivity=62; specificity=58%. Fever yielded the largest area under the curve, AUROC=0.698 (CI: 0.639-0.758, p=0.001), followed by increased stool frequency, AUROC=0.582 (CI:0.519-0.645, p=0.012). Conclusions. The stool culture yield in hospitalized adult patients with suspected acute bacterial is low. Limiting the request for stool culture studies to ≤3 days of hospital admission could lead to significant resource savings. The inclusion of fever (≥38°C) and increased stool frequency (≥4 per day) in the clinical decision-making in suspected acute bacterial gastroenteritis could contribute to a discerning request for SC studies and could thus lead to containment of hospital costs

Current understanding and management of clostridioides difficile infection: an overview

Clostridiodes difficile infection (CDI) is a major cause of healthcare-associated infections worldwide, with a significant morbidity and mortality. The incidence of this infection has been increasing in recent years, particularly among elderly patients and those with comorbidities. The pathogenesis of CDI involves the disruption of the gut microbiota, followed by the production of toxins that lead to colonic inflammation and tissue damage. The clinical presentation varies from mild diarrhea to severe pseudomembranous colitis, toxic megacolon, and sepsis. The diagnosis of CDI is based on the presence of clinical symptoms, laboratory testing, and imaging studies. The treatment of CDI involves antimicrobial therapy, supportive care, and infection control measures. Recently, there have been significant developments in the management of CDI, including the use of fidaxomicin, fecal microbiota transplantation (FMT), and monoclonal antibodies. This manuscript reviews the epidemiology, pathogenesis, clinical presentation, diagnosis and updated guidelines for the management of CDI

Successful Experience of Fecal Transplantation in a Patient with Severe Pseudomembranous Colitis

Introduction. At the present time there is increase the number of patients diagnosed with pseudomembranous colitis due to Clostridiodes difficile, respectively it significantly increases the frequency of hospitalizations, the length of hospital stay and the cost of treatment. Approved drug methods for correcting a  pathological condition are not always able to lead to recovery after the first use, repeated and prolonged courses of therapy are often required, especially with recurrent Clostridiodes difficile. An alternative way of treatment is fecal microbiota transplantation from a donor. Nowadays, fecal microbiota transplantation is included in national clinical guidelines in several countries in Europe, the USA and Australia. In Russia this method has not been registered, however, there are some publications about its successful application in gastrointestinal diseases, oncohematology, and some autoimmune diseases. Aim. To show the result of successful treatment of severe pseudomembranous colitis after a single fecal microbiota transplantation.Material and methods. Outpatient treatment of an acute respiratory infection with a broad-spectrum antibacterial drug caused the development of severe pseudomembranous colitis in a young patient. Standard courses of metronidazole and vancomycin were unsuccessful. Transplantation of fecal microbiota from a donor was performed via ileocolonoscopy.Results. A single fecal microbiota transplantation contributed to the patient’s complete recovery, short term  rehabilitation and the absence of recurrence of Clostridiodes difficile within two years. Conclusions. Evidence-based medicine has shown the high efficiency of fecal microbiota transplantation. In Russia a legislative basis is needed for including fecal microbiota transplantation in clinical guidelines for the treatment of severe Clostridiodes difficile resistant to standard therapy

Diagnostic approaches, aetiological agents and their associations with short-term survival and laminitis in horses with acute diarrhoea admitted to referral institutions

Background: An international description of the diagnostic approaches used in different institutions to diagnose acute equine diarrhoea and the pathogens detected is lacking. Objectives: To describe the diagnostic approach, aetiological agents, outcome, and development of laminitis for diarrhoeic horses worldwide. Study design: Multicentre retrospective case series. Methods: Information from horses with acute diarrhoea presenting to participating institutions between 2016 and 2020, including diagnostic approaches, pathogens detected and their associations with outcomes, were compared between institutions or geographic regions. Results: One thousand four hundred and thirty‐eight horses from 26 participating institutions from 4 continents were included. Overall, aetiological testing was limited (44% for Salmonella spp., 42% for Neorickettsia risticii [only North America], 40% for Clostridiodes difficile, and 29% for ECoV); however, 13% (81/633) of horses tested positive for Salmonella, 13% (35/262) for N. risticii, 9% (37/422) for ECoV, and 5% (27/578) for C. difficile. C. difficile positive cases had greater odds of non‐survival than horses negative for C. difficile (OR: 2.69, 95%CI: 1.23–5.91). In addition, horses that were positive for N. risticii had greater odds of developing laminitis than negative horses (OR: 2.76, 95%CI: 1.12–6.81; p = 0.029). Main limitations: Due to the study's retrospective nature, there are missing data. Conclusions: This study highlighted limited diagnostic investigations in cases of acute equine diarrhoea. Detection rates of pathogens are similar to previous reports. Non‐survival and development of laminitis are related to certain detected pathogens

Effect of Tanshinone IIA on gut microbiome in diabetes-induced cognitive impairment

Diabetes-induced cognitive impairment (DCI) presents a major public health risk among the aging population. Previous clinical attempts on known therapeutic targets for DCI, such as depleted insulin secretion, insulin resistance, and hyperglycaemia have delivered poor patient outcomes. However, recent evidence has demonstrated that the gut microbiome plays an important role in DCI by modulating cognitive function through the gut–brain crosstalk. The bioactive compound tanshinone IIA (TAN) has shown to improve cognitive and memory function in diabetes mellitus models, though the pharmacological actions are not fully understood. This study aims to investigate the effect and underlying mechanism of TAN in attenuating DCI in relation to regulating the gut microbiome. Metagenomic sequencing analyses were performed on a group of control rats, rats with diabetes induced by a high-fat/high-glucose diet (HFD) and streptozotocin (STZ) (model group) and TAN-treated diabetic rats (TAN group). Cognitive and memory function were assessed by the Morris water maze test, histopathological assessment of brain tissues, and immunoblotting of neurological biomarkers. The fasting blood glucose (FBG) level was monitored throughout the experiments. The levels of serum lipopolysaccharide (LPS) and tumor necrosis factor-α (TNF-α) were measured by enzyme-linked immunoassays to reflect the circulatory inflammation level. The morphology of the colon barrier was observed by histopathological staining. Our study confirmed that TAN reduced the FBG level and improved the cognitive and memory function against HFD- and STZ-induced diabetes. TAN protected the endothelial tight junction in the hippocampus and colon, regulated neuronal biomarkers, and lowered the serum levels of LPS and TNF-α. TAN corrected the reduced abundance of Bacteroidetes in diabetic rats. At the species level, TAN regulated the abundance of B. dorei, Lachnoclostridium sp. YL32 and Clostridiodes difficile. TAN modulated the lipid metabolism and biosynthesis of fatty acids in related pathways as the main functional components. TAN significantly restored the reduced levels of isobutyric acid and butyric acid. Our results supported the use of TAN as a promising therapeutic agent for DCI, in which the underlying mechanism may be associated with gut microbiome regulation