Bacteria and fungi in acute cholecystitis. A prospective study comparing next generation sequencing to culture

Adhesion of Klebsiella oxytoca to bladder or lung epithelial cells is promoted by the presence of other opportunistic pathogens

The intestinal and respiratory tracts of healthy individuals serve as habitats for a diverse array of microorganisms, among which Klebsiella oxytoca holds significance as a causative agent in numerous community- and hospital-acquired infections, often manifesting in polymicrobial contexts. In specific circumstances, K. oxytoca, alongside other constituents of the gut microbiota, undergoes translocation to distinct physiological niches. In these new environments, it engages in close interactions with other microbial community members. As this interaction may progress to co-infection where the virulence of involved pathogens may be promoted and enhance disease severity, we investigated how K. oxytoca affects the adhesion of commonly co-isolated bacteria and vice versa during co-incubation of different biotic and abiotic surfaces. Co-incubation was beneficial for the adhesion of at least one of the two co-cultured strains. K. oxytoca enhanced the adhesion of other enterobacteria strains to polystyrene and adhered more efficiently to bladder or lung epithelial cell lines in the presence of most enterobacteria strains and S. aureus. This effect was accompanied by bacterial coaggregation mediated by carbohydrate-protein interactions occurring between bacteria. These interactions occur only in sessile, but not planktonic populations, and depend on the features of the surface. The data are of particular importance for the risk assessment of the urinary and respiratory tract infections caused by K. oxytoca, including those device-associated. In this paper, we present the first report on K. oxytoca ability to acquire increased adhesive capacities on epithelial cells through interactions with common causal agents of urinary and respiratory tract infections.

Microbiological diagnosis of pleural infections: a comparative evaluation of a novel syndromic real-time PCR panel

Current microbial diagnostics for pleural infections are insufficient. Studies using 16S targeted next-generation sequencing report that only 10%-16% of bacteria present are cultured and that 50%-78% of pleural fluids containing relevant microbial DNA remain culture negative. As a rapid diagnostic alternative suitable for clinical laboratories, we wanted to explore a PCR-based approach. Based on the identification of key pathogens, we developed a syndromic PCR panel for community-acquired pleural infections (CAPIs). This was a pragmatic PCR panel, meaning that it was not designed for detecting all possibly involved bacterial species but for confirming the diagnosis of CAPI, and for detecting bacteria that might influence choice of antimicrobial treatment. We evaluated the PCR panel on 109 confirmed CAPIs previously characterized using culture and 16S targeted next-generation sequencing. The PCR secured the diagnosis of CAPI in 107/109 (98.2%) and detected all present pathogens in 69/109 (63.3%). Culture secured the diagnosis in 54/109 (49.5%) and detected all pathogens in 31/109 (28.4%). Corresponding results for 16S targeted next-generation sequencing were 109/109 (100%) and 98/109 (89.9%). For bacterial species included in the PCR panel, PCR had a sensitivity of 99.5% (184/185), culture of 21.6% (40/185), and 16S targeted next-generation sequencing of 92.4% (171/185). None of the bacterial species present not covered by the PCR panel were judged to impact antimicrobial therapy. A syndromic PCR panel represents a rapid and sensitive alternative to current diagnostic approaches for the microbiological diagnosis of CAPI.IMPORTANCEPleural empyema is a severe infection with high mortality and increasing incidence. Long hospital admissions and long courses of antimicrobial treatment drive healthcare and ecological costs. Current methods for microbiological diagnostics of pleural infections are inadequate. Recent studies using 16S targeted next-generation sequencing as a reference standard find culture to recover only 10%-16% of bacteria present and that 50%-78% of samples containing relevant bacterial DNA remain culture negative. To confirm the diagnosis of pleural infection and define optimal antimicrobial therapy while limiting unnecessary use of broad-spectrum antibiotics, there is a need for rapid and sensitive diagnostic approaches. PCR is a rapid method well suited for clinical laboratories. In this paper we show that a novel syndromic PCR panel can secure the diagnosis of pleural infection and detect all bacteria relevant for choice of antimicrobial treatment with a high sensitivity.

Microbiome analysis of bile from apparently healthy cats and cats with suspected hepatobiliary disease

BACKGROUND

Bacterial infection of bile is a common cause of hepatobiliary disease in cats. Whether bile harbors a core microbiota in health or in cases of suspected hepatobiliary disease in cats is unknown.

OBJECTIVES

Establish if gallbladder bile in apparently healthy cats harbors a core microbiota composed of bacterial taxa common to many individuals. Compare results of bile cytology, bile culture, and 16S rRNA gene amplicon sequencing in apparently healthy cats and cats with suspected hepatobiliary disease.

ANIMALS

Forty-three client-owned cats with suspected hepatobiliary disease and 17 control cats.

METHODS

Bile was collected by ultrasound guided cholecystocentesis (cats with suspected hepatobiliary disease) or laparotomy after euthanasia (controls). Bile samples underwent cytologic examination, aerobic and anaerobic culture, and DNA was extracted for 16S rRNA gene amplification and sequencing.

RESULTS

Microbiome sequencing did not identify a core microbiota in control cats or cats having bile sampled because of clinical suspicion for hepatobiliary disease. Microbiome profiles from control cats were indistinguishable from profiles obtained from sampling instruments and reagents that were not exposed to bile (technical controls). Bacterial taxa that could not be explained by contamination or off-target amplification were identified only in samples from cats with bactibilia and positive bile culture results for Escherichia coli. In several E. coli positive samples, microbiome sequencing also identified a small number of potentially co-infecting bacterial genera not identified by culture.

CONCLUSIONS AND CLINICAL IMPORTANCE

Cat bile does not harbor a core microbiota. Uncultured bacteria may contribute to pathogenesis of hepatobiliary disease in cats with bile E. coli infection.

Identification and characterization of pancreatic infections in severe and critical acute pancreatitis patients using 16S rRNA gene next generation sequencing

Objectives

This study aimed to identify the bacterial composition in the pancreatic fluid of severe and critical acute pancreatitis (SAP and CAP) patients.

Methods

A total of 78 pancreatic fluid samples were collected from 56 SAP and CAP patients and analyze using aerobic culture and 16S rRNA gene next-generation sequencing. The clinical data of the patients were obtained from the electronic medical records.

Results

Among the total 78 samples, 16S rRNA gene NGS identified a total of 660 bacterial taxa, belonging to 216 species in 123 genera. The dominant aerobic bacteria included Klebsiella pneumoniae, Acinetobacter baumannii, and Enterococcus faecium, while the dominant anaerobic bacteria included Bacteroides, Dialister invisus, and Olsenella uli. As compared to aerobic culturing, 95.96% (95/99) of the aerobic cultured bacteria were detected using the 16S rRNA gene NGS.

Conclusion

The pancreatic infections in SAP and CAP patients might originate not only from the gut but also from the oral cavity and airways as well as related environments. Dynamic analysis of bacterial profile and abundance showed that some bacteria with low abundance might become the main pathogenic bacteria. There were no significant differences in the bacterial diversity between SAP and CAP.

Fungal infections and the fungal microbiome in hepatobiliary disorders

Liver and biliary diseases affect more than a billion people worldwide, with high associated morbidity and mortality. The impact of the intestinal bacterial microbiome on liver diseases has been well established. However, the fungal microbiome, or mycobiome, has been overlooked for a long time. Recently, several studies have shed light on the role of the mycobiome in the development and progression of hepatobiliary diseases. In particular, the fungal genus Candida has been found to be involved in the pathogenesis of multiple hepatobiliary conditions. Herein, we compare colonisation and infection, describe mycobiome findings in the healthy state and across the various hepatobiliary conditions, and point toward communalities. We detail how quantitation of immune responses to fungal antigens can be employed to predict disease severity, e.g. using antibodies to Saccharomyces cerevisiae or specific anti-Candida albicans antibodies. We also show how fungal products (e.g. beta-glucans, candidalysin) activate the host's immune system to exacerbate liver and biliary diseases. Finally, we describe how the gut mycobiome can be modulated to ameliorate hepatobiliary conditions.

Microorganisms isolated from the bile of the patients who have undergone cholecystectomy and their antibiotic resistance pattern: multicenter prospective study

BACKGROUND

Gallbladder and biliary tract infections are diseases with high mortality rates if they are not treated properly. Microbiological evaluation of perioperatively collected samples both ensures proper treatment of patients and guides empirical treatment due to the determination of microorganism susceptibility.

AIMS

This study aimed to isolate the microorganisms in bile cultures from patients who underwent cholecystectomy and to determine sensitivity results of these microorganisms.

METHODS

This study was a multi-center and prospective design, included 360 patients, and was performed between 2019 and 2020. Culture results of bile taken during cholecystectomy were evaluated.

RESULTS

Bacterial growth was found in the bile cultures of 84 out of 360 (23.3%) patients. Patients were divided into two groups according to whether they had risk factors for resistant microorganisms or not. While Escherichia coli (n = 11, 13%), Enterococcus spp. (n = 8, 9.5%), and Enterobacter spp. (n = 4, 4.7%) were detected most frequently in patients without risk. Staphylococcus spp. (n = 17, 20.2%), Enterococcus spp. (n = 16, 19%), and E. coli (n = 8, 9.5%) were the most frequently found microorganism at-risk patients. In multivariate analysis, bile culture positivity was found higher in patients who had history of biliary disease (p = 0.004), operation performed concurrently with a cholecystectomy (p = 0.035), and high rate of polymorphonuclear leukocytes (PNL) in total leukocyte count (p = 0.001).

CONCLUSIONS

Our study shows that when starting empirical antibiotic treatment for bile ducts, whether patients are at risk for the development of resistant bacterial infection should be evaluated after which antibiotic selection should be made accordingly.

Targeted Metagenomic Sequencing-Based Approach Applied to 2,146 Tissue and Body Fluid Samples in Routine Clinical Practice

BACKGROUND

The yield of next generation sequencing (NGS) added to a Sanger sequencing-based 16S ribosomal RNA (rRNA) gene PCR assay was evaluated in clinical practice for diagnosis of bacterial infection.

METHODS

PCR targeting the V1 to V3 regions of the 16S rRNA gene was performed, with amplified DNA submitted to Sanger sequencing and/or NGS (Illumina MiSeq), or reported as negative, depending on cycle threshold (Ct) value. 2,146 normally sterile tissues or body fluids were tested between August 2020 and March 2021. Clinical sensitivity was assessed in 579 subjects from whom clinical data was available.

RESULTS

Compared to Sanger sequencing alone (400 positive tests), positivity increased by 87% by adding NGS (347 added positive tests). Clinical sensitivity of the assay incorporating NGS was 53%, higher than culture (42%, p<0.001), with an impact on clinical decision-making in 14% of infected cases. Clinical sensitivity in the subgroup receiving antibiotics at sampling was 41% for culture and 63% for the sequencing assay (p<0.001).

CONCLUSION

Adding NGS to Sanger sequencing of the PCR-amplified 16S rRNA gene substantially improved test positivity. In the patient population studied, the assay was more sensitive than culture, and especially so in patients who had received antibiotic therapy.

Microbial Diversity and Contribution to the Formation of Volatile Compounds during Fine-Flavor Cacao Bean Fermentation

Cacao demand is continuously increasing, and variations in cacao prices have been associated with the aroma of fermented cacao beans. However, the role of microorganisms in the formation of volatile-aroma compounds during fermentation remains unclear. Microbial diversity in Nacional × Trinitario cacao was characterized during spontaneous fermentation by using culture-based methods and next-generation sequencing (NGS) of DNA amplicons. Cacao beans that were spontaneously fermented for 0, 24, 48, 72 and 96 h were UV-sterilized prior to the inoculation of the microbial isolates obtained by the culture-based methods. The volatile formation in inoculated cacao beans was evaluated by GC-MS. The species isolated during fermentation included yeast, such as Saccharomyces cerevisiae and Candida metapsilosis; lactic acid bacteria (LAB), such as Limosilactobacillus fermentum and Liquorilactobacillus nagelii; acetic acid bacteria (AAB), such as Acetobacter pasteurianus, Acetobacter ghanensis and Acetobacter syzygii, as well as other species, such as Bacillus subtilis and Bacillus amyloliquefaciens. Additionally, NGS revealed an abundance of environmental microorganisms, including Escherichia spp., Pantoea spp., Staphylococcus spp., Botrytis spp., Tetrapisispora spp. and Pichia spp., among others. During the lab-scale fermentation, the inoculation of S. cerevisiae mostly yielded alcohols, while LAB and AAB produced volatiles associated with floral, almond and fruity notes throughout the fermentation, but AAB also produced acetic acid with a sour aroma. Similarly, the inoculation of C. metapsilosis and Bacillus spp. in 96 h fermented cacao beans yielded esters with floral aromas. This is the first report describing the role of microorganisms in volatile formation during fine-flavor cacao fermentation.

Clinical impact of bloodstream infection on acute cholecystitis indicated for emergency cholecystectomy

BACKGROUND

The significance of blood culture for acute cholecystitis remains unclear.

METHODS

A retrospective cohort study was conducted on patients who underwent emergency cholecystectomy at Hyogo Prefectural Amagasaki General Medical Center to examine the clinical impact of bloodstream infection (BSI), focusing on the association of BSI with bactibilia and severity grade based on the Tokyo guidelines 2018 (TG18).

RESULTS

Among 177 patients included in the study, 32 had positive and 145 had negative BSI. Significant differences were observed between the positive and negative BSI in terms of age, body mass index (BMI), the American Society of Anesthesiologists physical status (ASA-PS) and TG18 severity score. The odds ratios of BSI for patients aged ≥72 years, with a BMI of ≤21.8, an ASA-PS of ≥3E, and grade III acute cholecystitis were 3.45, 3.23, 2.43 and 4.51, respectively. In the multivariate analysis, lower BMI and grade III were significantly associated with BSI with odds ratios of 2.53 (95% confidence interval: 1.07-6.21, P = .037) and 3.03 (95% confidence interval: 1.02-8.82, P = .041). Bacterial species that could not be isolated in the bile culture alone were identified in blood culture on 10 (38.5%) of 26 patients.

CONCLUSIONS

Bloodstream infection is associated with grade III acute cholecystitis. Blood culture enables the identification of bacteria that cannot be isolated in bile culture. Blood culture should be obtained for patients with grade III acute cholecystitis who undergo emergency cholecystectomy.

Biliary infection; distribution of species and antibiogram study

Background

Biliary infections like cholecystitis and cholangitis are common and could be life threatening if treated inappropriate. Prescribing antibiotics is the key to control such infections. Occurrence of bacterial resistance to antibiotics is highly probable and should be continuously monitored. This study aimed to re-evaluate bacterial species distribution and their interaction to antibiotics in biliary infections.

Method

Total 2288 patients who were diagnosed as whether acute or chronic cholecystitis with/without concurrent cholangitis enrolled in this cohort study. All were candidate for cholecystectomy operation. In the theatre a sterile bile sample was aspirated from the gallbladder as early as the organ was exposed. Analysis was performed on culture and antibiogram results.

Results

Finally 492 (21.5%) microorganism growth was seen in all culture environments. Bacterial colonization was most common in cholangitis (63.8%) which followed by acute (26%) and chronic (10.9%) cholecystitis respectively (p = 0.001). Escherichia coli (58%) and Klebsiella species (12.2%) were mostly isolated pathogens. Antibiogram study illustrated bacterial sensitivity of gram-negative pathogens to imipenem (100%), amikacin (98.1%), and gentamicin (90.4%) which in gram-positive bacterial species was 100% to imipenem, vancomycin, rifampcin, and clindamycin.

Conclusion

Cephalosporins as an empirical treatment for biliary infections is not suitable. Aminoglycosides including amikacin and gentamycin are costly beneficial as the first line for empirical antibiotic therapy in selected patients because of their good bacterial sensitivity and low expenses. Imipenem should remain for multidrug resistance species.

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Distribution of bacterial species in biliary infection has not obviously changed in recent decades.

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Relative resistance of biliary germ to current advised antibiotic is flashed.

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Aminoglycoside more widely covers biliary germ than cephalosporin does in selected patient.

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Revision of current antibiotic guide for biliary infection to prevent antibiotic resistance is needed.

Emphysematous Cholecystitis Secondary to Fusobacterium nucleatum

Fusobacterium nucleatum may be implicated in cases of emphysematous cholecystitis (EC) and carries a high mortality risk, especially in individuals with heart disease, renal insufficiency, and underlying malignancy. Fusobacterium infections are rarely detected in the setting of cholecystitis possibly due to the difficulty with properly culturing the bacteria. We describe a case of a patient with EC in whom blood cultures were positive for growth of F. nucleatum in one of two samples. The patient was treated with empiric antibiotic therapy consisting of metronidazole and cefepime. In patients with EC and negative cultures, it is possible that they may have an undetected infection with fusobacteria, which carries a high mortality risk. As such, clinicians should maintain a high degree of suspicion of obligate anaerobic infection in patients who have negative blood culture for growth in the setting of EC and consider continuation of adequate antimicrobial coverage.

Managing Contamination and Diverse Bacterial Loads in 16S rRNA Deep Sequencing of Clinical Samples: Implications of the Law of Small Numbers

In this article, we investigate patterns of microbial DNA contamination in targeted 16S rRNA amplicon sequencing (16S deep sequencing) and demonstrate how this can be used to filter background bacterial DNA in diagnostic microbiology. We also investigate the importance of sequencing depth. We first determined the patterns of contamination by performing repeat 16S deep sequencing of negative and positive extraction controls. This process identified a few bacterial species dominating across all replicates but also a high intersample variability among low abundance contaminant species in replicates split before PCR amplification. Replicates split after PCR amplification yielded almost identical sequencing results. On the basis of these observations, we suggest using the abundance of the most dominant contaminant species to define a threshold in each clinical sample from where identifications with lower abundances possibly represent contamination. We evaluated this approach by sequencing of a diluted, staggered mock community and of bile samples from 41 patients with acute cholangitis and noninfectious bile duct stenosis. All clinical samples were sequenced twice using different sequencing depths. We were able to demonstrate the following: (i) The high intersample variability between sequencing replicates is caused by events occurring before or during the PCR amplification step. (ii) Knowledge about the most dominant contaminant species can be used to establish sample-specific cutoffs for reliable identifications. (iii) Below the level of the most abundant contaminant, it rapidly becomes very demanding to reliably discriminate between background and true findings. (iv) Adequate sequencing depth can be claimed only when the analysis also picks up background contamination.

A Series of Haemophilus parainfluenzae Surgical Infections and Review of the Literature

Background: Haemophilus parainfluenzae (HPI) is a rare and underreported pathogen. Haemophilus parainfluenzae causes respiratory, soft tissue, and central nervous system (CNS) infections, and endocarditis. Little data on HPI surgical infections are available, especially for intra-abdominal infections (IAI). Patients and Methods: Haemophilus parainfluenzae isolates were recovered from patients treated at a rural hospital during a two-year period. Isolation and identification of the pathogen was done according to standard guidelines. A literature review with regard to HPI IAI was done. Results: A total of 273 HPI isolates were analyzed, 15 patients had double isolates; HPI was commonly part of a mixed infection. Respiratory tract infections accounted for 64.8%, ear-nose-throat (ENT)/eye infections for 17.9%, genital/urologic infections for 3%, blood stream infections for 1% of cases and 13.2% of HPI isolates involved surgical infections. Thirty-four patients (36 isolates) had HPI surgical infections including 28 skin/soft tissue infections, two bone infections, two perirectal abscesses, one infected hemodialysis catheter, and three IAIs including perforated appendicitis, perforated diverticulitis, and a pelvic abscess 10 days after laparoscopic appendectomy. All three IAIs were mixed infections and successfully managed with percutaneous drainage and antibiotic therapy. More than 90% of HPI isolates in our hospital tested negative for β-lactamase production. A literature review revealed 32 reported cases of HPI IAI including biliary infections (12), peritonitis (9), liver abscess (7), and IA abscess (4) with the majority being monomicrobial; treatment included antibiotic agents and surgery/intervention in most cases. Outcomes were generally favorable. Conclusions: Our study confirms data from the literature that HPI is capable of causing a variety of severe surgical infections. More research with regard to this pathogen is warranted.

The Bacteriology of Acute Cholecystitis: Comparison of Bile Cultures and Clinical Outcomes in Diabetic and Non-Diabetic Patients

BACKGROUND

Acute cholecystitis is one of the most common acute surgical diseases. Diabetic patients have been shown to have an increased risk for gallbladder disease, but the correlation between the severity of gallstone disease and diabetes is still debated. The aim of this study is to examine the possible difference in the disease process between patients with diabetes mellitus (DM) and those without.

PATIENTS AND METHODS

A retrospective study was conducted of all patients who underwent percutaneous cholecystostomy between 2005 and 2015 at Emek Medical Center, Afula, Israel. Demographic and medical history including data on bile and blood culture results, antimicrobial susceptibility, and clinical outcomes were retrieved from patient files.

RESULTS

The cohort included 272 patients. Mean age was 68 years old, 50.74% were male and 43.75% had diabetes mellitus. Bile cultures were obtained from 252 (92.64%) patients and were positive in 134 (53.2%) patients. In 11 patients (4%) two pathogens were isolated. Blood cultures obtained from 231 patients and were positive in 35 (15.2%). Escherichia coli was the most common isolate, and was seen in 22.3% of positive bile cultures and 40% of blood cultures. Although diabetic patients had significantly more positive bile cultures, the severity of the disease, according to the Tokyo guidelines, was not higher.

CONCLUSIONS

Acute cholecystitis was neither more severe nor had significant difference in bacteriological properties when comparing diabetic patients to non-diabetic ones.

The Prevalence and Clinical Significance of Anaerobic Bacteria in Major Liver Resection

(1) Background: Anaerobic infections in hepatobiliary surgery have rarely been addressed. Whereas infectious complications during the perioperative phase of liver resections are common, there are very limited data on the prevalence and clinical role of anaerobes in this context. Given the risk of contaminated bile in liver resections, the goal of our study was to investigate the prevalence and outcome of anaerobic infections in major hepatectomies. (2) Methods: We retrospectively analyzed the charts of 245 consecutive major hepatectomies that were performed at the department of General, Visceral, and Transplantation Surgery of the University Hospital of Tuebingen between July 2017 and August 2020. All microbiological cultures were screened for the prevalence of anaerobic bacteria and the patients' clinical characteristics and outcomes were evaluated. (3) Results: Of the 245 patients, 13 patients suffered from anaerobic infections. Seven had positive cultures from the biliary tract during the primary procedure, while six had positive culture results from samples obtained during the management of complications. Risk factors for anaerobic infections were preoperative biliary stenting (p = 0.002) and bile leaks (p = 0.009). All of these infections had to be treated by intervention and adjunct antibiotic treatment with broad spectrum antibiotics. (4) Conclusions: Anaerobic infections are rare in liver resections. Certain risk factors trigger the antibiotic coverage of anaerobes.

Clinical Presentation and Incidence of Anaerobic Bacteria in Surgically Treated Biliary Tract Infections and Cholecystitis

(1) Background: Cholecystitis and cholangitis are among the most common diseases treated by general surgery. Gallstones lead to inflammation and bacterial infection of the biliary tract. Biliary infections can lead to live threatening bacteremia and liver abscesses. The true role of anaerobes remains unclear. (2) Methods: We retrospectively analyzed bacterial cultures from biliary samples obtained from bile ducts and gallbladders at our tertiary care center. Patient characteristics and clinical outcomes were analyzed. (3) Results: In our database of 1719 patients, 365 patients had microbial testing, of which 42 grew anaerobic bacteria. Anaerobes were more frequently cultured in patients with hepatic abscesses and gallbladder perforation. These patients were older and had more comorbidities than the control group. The overall outcomes of all patients were favorable and the resistance rate to commonly used antibiotics remained low. (4) Conclusions: Anaerobes in biliary tract infections appear to be underdiagnosed and more prevalent in the elderly with advanced disease. Due to low antibiotic resistance, the combination of source control and adjunct anti-infective treatment leads to favorable outcomes.

Minority report: the intestinal mycobiota in systemic infections

Compared to bacteria, fungi often exhibit a lower abundance and a higher temporal volatility in the intestinal microbiota. Analysis of fungi in the microbiota (mycobiota) faces technical limitations with tools that were originally developed for analyzing bacteria. Dysbiotic states of the intestinal mycobiota, often associated with disruption of the healthy bacterial microbiota, are characterized by overgrowth (domination) of specific fungal taxa and loss of diversity. Intestinal domination by Candida species has been shown to be a major source of Candida bloodstream infections. Fungal dysbiosis is also linked to the development and treatment response in non-fungal infections, for example Clostridioides difficile colitis and HIV. Further research is needed to define the contribution of intestinal mycobiota to human fungal and non-fungal infections.