Antimicrobial resistance and clinical outcome of Bacteroides bacteremia: findings of a multicenter prospective observational trial

Gas-forming abscess associated with prosthetic vascular graft infection caused by Bacteroides fragilis

INTRODUCTION

Prosthetic Vascular Graft Infection (PVGI) is a rare but serious complication of open surgical repair of abdominal aortic aneurysm. We report a case of gas-forming abscesses associated with PVGI caused by Bacteroides fragilis identified from the drainage fluid and blood cultures.

CASE PRESENTATION

A 67-year-old man with a complaint of worsening low back pain underwent an emergency open surgery due to abdominal aortic aneurysm. On postoperative day 18, an abdominal CT showed gas formation within the aneurysm. Gram staining of the drainage fluid revealed Gram-negative rods and 16S rRNA gene sequencing performed on the fluid identified B. fragilis, although the culture of the fluid was negative. PVGI caused by anaerobic bacteria such as Bacteroides spp. is relatively rare. The sensitivity of 16S rRNA gene sequencing for culture-negative specimens is generally low, but 16S rRNA sequencing-positive rate increases when a Gram stain of specimen is positive.

Effects of extended anaerobic antibiotic coverage on anaerobic bloodstream infection: A multisite retrospective study

OBJECTIVES

Routine clinical practice with extended anaerobic antibiotic coverage (EAC) has been recently reconsidered for several infections; however, its benefits remain unclear even in patients with anaerobic bacteremia (AB). Here, we aimed to elucidate the effects of EAC on AB prognosis.

METHODS

A multicenter retrospective observational study was conducted in patients with AB. Multivariate logistic regression analysis was performed to assess the effect of EAC on 30-day mortality. Inverse probability of treatment weighting analysis was performed to confirm the robustness of the findings.

RESULTS

In total, 483 patients were included, of whom 387 received EAC and 96 received limited anaerobic antibiotic coverage (LAC). Atypical foci of anaerobic infection, such as urinary tract infection and pneumonia, together with undetectable infection foci, comprised a larger proportion of infection foci in the LAC group than that in the EAC group (46.9% vs 30.5%). The 30-day mortality rates of the EAC and LAC groups were similar (12.5% and 14.2%, respectively; P = 0.664). Primary analysis revealed that EAC was not significantly associated with high mortality (odds ratio [OR], 1.42; 95% confidence interval [CI], 0.7-2.8), whereas source control significantly reduced this risk (OR, 0.28; 95% CI, 0.2-0.5). The sensitivity analysis results were consistent with those of the primary analyses.

CONCLUSION

This study demonstrated a less significant effect of initial EAC on AB compared with source control, particularly on AB with atypical infection foci. These findings would prompt reconsideration of the necessity of an initial EAC in several infections.

Comparison of clinical characteristics, risk factors, and outcomes of patients infected with Bacteroides fragilis group at a tertiary care hospital in central China between 2017 and March 2024

OBJECTIVES

This study aimed to explore the epidemiology, clinical presentation, and risk factors for treatment failure in patients infected with various Bacteroides fragilis group (BFG) species.

METHODS

We analyzed clinical and laboratory data from 178 patients infected with BFG who were admitted to our hospital between 2017 and 2024. We analyzed categorical data using Chi-square and Fisher exact tests, continuous variables using Student's t-tests or Mann-Whitney U-tests, and risk factors using multivariate logistic regression and Pearson's chi-squared tests.

RESULTS

Bacteroides fragilis (69.7 %) and Bacteroides thetaiotaomicron (16.9 %) were the most prevalent species among 178 BFG isolates. Most patients had polymicrobial infections, with the following pathogens isolated from concurrent samples: Escherichia coli, Klebsiella spp., and Enterococcus spp. Intra-abdominal sites were most frequently infected with BFG. Patients aged >50 years and those who had intravascular catheters were infected with more other Bacteroides species than B. fragilis. Admission to an ICU, respiratory, renal and cardiovascular diseases, and chest drainage were associated more often with B. thetaiotaomicron than with B. fragilis. Gastrointestinal diseases, tracheal intubation, and ICU admission were associated more frequently with treatment failure in patients infected with B. fragilis whereas solid cancers, renal disease, multiple organ dysfunction syndrome, and tracheal intubation were more likely to be associated with treatment failure in patients infected with other Bacteroides spp.

CONCLUSIONS

The most prevalent BFG species in the patients were B. fragilis and B. thetaiotaomicron. The demographic characteristics of the patients, underlying diseases, and risk factors for poor clinical outcomes clearly differed among species.

Bacteroides and related species: The keystone taxa of the human gut microbiota

Microbial communities play a significant role in maintaining ecosystems in a healthy homeostasis. Presently, in the human gastrointestinal tract, there are certain taxonomic groups of importance, though there is no single species that plays a keystone role. Bacteroides spp. are known to be major players in the maintenance of eubiosis in the human gastrointestinal tract. Here we review the critical role that Bacteroides play in the human gut, their potential pathogenic role outside of the gut, and their various methods of adapting to the environment, with a focus on data for B. fragilis and B. thetaiotaomicron. Bacteroides are anaerobic non-sporing Gram negative organisms that are also resistant to bile acids, generally thriving in the gut and having a beneficial relationship with the host. While they are generally commensal organisms, some Bacteroides spp. can be opportunistic pathogens in scenarios of GI disease, trauma, cancer, or GI surgery, and cause infection, most commonly intra-abdominal infection. B. fragilis can develop antimicrobial resistance through multiple mechanisms in large part due to its plasticity and fluid genome. Bacteroidota (formerly, Bacteroidetes) have a very broad metabolic potential in the GI microbiota and can rapidly adapt their carbohydrate metabolism to the available nutrients. Gastrointestinal Bacteroidota species produce short-chain fatty acids such as succinate, acetate, butyrate, and occasionally propionate, as the major end-products, which have wide-ranging and many beneficial influences on the host. Bacteroidota, via bile acid metabolism, also play a role in in colonization-resistance of other organisms, including Clostridioides difficile, and maintenance of gut integrity.

Antimicrobial susceptibility of Bacteroides fragilis group organisms in Hong Kong, 2020-2021

OBJECTIVES

This retrospective study analyzed the susceptibility levels of Bacteroides fragilis group (BFG) in a hospital-based laboratory where disk diffusion test (DDT) was routinely performed. Isolates non-susceptible to imipenem and metronidazole by DDT were further investigated using a gradient method.

METHODS

The DDT and MIC susceptibility data of clindamycin, metronidazole, moxifloxacin and imipenem obtained on Brucella blood agar for 1264 non-duplicated isolates during 2020-2021 were analyzed. Species identification was obtained by matrix-assisted laser desorption ionization time-of-flight mass spectrometry and 16S rRNA sequencing. Interpretative agreement of DDT results using the 2015 EUCAST tentative and 2021 CA-SFM breakpoints was compared against MIC as the reference.

RESULTS

The dataset included 604 B. fragilis (483 division I, 121 division II isolates), 415 non-fragilis Bacteroides, 177 Phocaeicola and 68 Parabacteroides. Susceptibility rates for clindamycin (22.1-62.1%) and moxifloxacin (59.9-80.9%) were low and many had no inhibition zones. At the EUCAST and CA-SFM breakpoints, 83.0 and 89.4% were imipenem-susceptible, and 89.6% and 97.4 were metronidazole-susceptible. MIC testing confirmed 11.4% and 2.8% isolates as imipenem-non-susceptible and metronidazole-resistant, respectively. Significant numbers of false-susceptibility and/or false-resistance results were observed at the CA-SFM breakpoint but not the EUCAST breakpoint. Higher rates of imipenem and/or metronidazole resistance were detected in B. fragilis division II, B. caccae, B. ovatus, B. salyersiae, B. stercoris and Parabacteroides. Co-resistance to imipenem and metronidazole was detected in 3 B. fragilis division II isolates.

CONCLUSIONS

The data demonstrated emerging BFG resistance to several important anti-anaerobic antibiotics and highlights the importance of anaerobic susceptibility testing in clinical laboratories to guide therapy.

Distribution, Trends, and Antimicrobial Susceptibility of Bacteroides, Clostridium, Fusobacterium, and Prevotella Species Causing Bacteremia in Japan During 2011-2020: A Retrospective Observational Study Based on National Surveillance Data

Background

The increasing prevalence of anaerobic bacteremia is a major concern worldwide and requires longitudinal monitoring.

Methods

We present one of the largest and longest longitudinal studies on the prevalence and antimicrobial resistance of Bacteroides, Clostridium, Fusobacterium, and Prevotella spp. isolated from blood culture samples using national comprehensive surveillance data in Japan during 2011-2020 as part of the Japan Nosocomial Infections Surveillance.

Results

Data for 41 949 Bacteroides spp., 40 603 Clostridium spp., 7013 Fusobacterium spp., and 5428 Prevotella spp. isolates were obtained. The incidences of bacteremia caused by Bacteroides fragilis, Clostridium perfringens, and Fusobacterium nucleatum significantly increased during the period (P < .0001). Among the 20 species analyzed, 18 showed no significant changes in susceptibility over time, including B. fragilis, C perfringens, and F. nucleatum. However, resistance to clindamycin increased in B. thetaiotaomicron (P = .0312), and resistance to ampicillin increased in B. ovatus (P = .0008).

Conclusions

Our comprehensive national surveillance data analysis demonstrated a continuous increase in the incidence of anaerobic bacteremia, particularly in B. fragilis, C. perfringens, and F. nucleatum. This may be linked to the increasing number of colorectal cancer cases or advancing methods for species identification and susceptibility testing, requiring cautious interpretation. The discovery of an upsurge in anaerobic bacteremia and potential alterations in susceptibility highlights the necessity for more extensive studies in this field.

Prevalence of antimicrobial resistant genes in Bacteroides spp. isolated in Oita Prefecture, Japan

INTRODUCTION

Bacteroides spp. are the most common anaerobic bacteria isolated from the human gastrointestinal tract. Several resistant genes are present in Bacteroides spp. However, most studies have focused on the prevalence of the cfiA gene in Bacteroides fragilis alone. We assessed the susceptibility to antimicrobial agents and the prevalence of cepA, cfiA, cfxA, ermF, nim, and tetQ genes in Bacteroides strains isolated from clinical specimens in our hospital.

METHODS

We isolated 86 B. fragilis and 58 non-fragilis Bacteroides strains from human clinical specimens collected from January 2011 to November 2021. Resistance against piperacillin (PIPC), cefotaxime (CTX), cefepime (CFPM), meropenem (MEPM), clindamycin, and minocycline was determined.

RESULTS

The resistant rates of penicillins and cephalosporins in non-fragilis isolates were significantly higher than those in B. fragilis isolates. In B. fragilis isolates, the resistant rates of PIPC, CTX, and CFPM in cfxA-positive isolates were significantly higher than those in cfxA-negative isolates (71% vs. 16%, 77% vs. 19%, and 77% vs. 30%, respectively). Thirteen B. fragilis isolates harbored the cfiA gene, two of which were resistant to MEPM. Six of the 13 cfiA-positive B. fragilis isolates were heterogeneously resistant to MEPM.

CONCLUSION

It is important to evaluate the use of MEPM as empirical therapy for Bacteroides spp. infections, considering the emergence of carbapenem resistance during treatment, existence of MEPM-resistant strains, and heterogeneous resistance.

Korean Guidelines for Use of Antibiotics for Intra-abdominal Infections in Adults

The guidelines are intended to provide practical information for the correct use of antibiotics for intra-abdominal infections in Korea. With the aim of realizing evidence-based treatment, these guidelines for the use of antibiotics were written to help clinicians find answers to key clinical questions that arise in the course of patient care, using the latest research results based on systematic literature review. The guidelines were prepared in consideration of the data on the causative pathogens of intra-abdominal infections in Korea, the antibiotic susceptibility of the causative pathogens, and the antibiotics available in Korea.

Time for Some Group Therapy: Update on Identification, Antimicrobial Resistance, Taxonomy, and Clinical Significance of the Bacteroides fragilis Group

Bacteroides fragilis group (BFG) species are common members of the human microbiota that provide several benefits to healthy hosts, yet BFG are also the most common anaerobes isolated from human infections, including intra-abdominal infections, abscesses, and bloodstream infection. Compared to many other anaerobes associated with disease, members of the BFG are more likely to be resistant to commonly used antimicrobials, including penicillin (>90% resistant), carbapenems (2 to 20% resistant), and metronidazole (0.2 to 4% resistant). As a result, infection with BFG bacteria can be associated with poor clinical outcomes. Here, we discuss the role of BFG in human health and disease, proposed taxonomic reclassifications within the BFG, and updates in methods for species-level identification. The increasing availability of whole-genome sequencing (WGS) supports recent proposals that the BFG now span two families (Bacteroidaceae and "Tannerellaceae") and multiple genera (Bacteroides, Parabacteroides, and Phocaeicola) within the phylum Bacteroidota. While members of the BFG are often reported to "group" rather than "species" level in many clinical settings, new reports of species-specific trends in antimicrobial resistance profiles and improved resolution of identification tools support routine species-level reporting in clinical practice. Empirical therapy may not be adequate for treatment of serious infections with BFG, warranting susceptibility testing for serious infections. We summarize methods for antimicrobial susceptibility testing and resistance prediction for BFG, including broth microdilution, agar dilution, WGS, and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). We examine global trends in BFG antimicrobial resistance and review genomics of BFG, revealing insights into rapid activation and dissemination of numerous antimicrobial resistance mechanisms.

Development and Validation of a Novel Anaerobic Carbapenem Inactivation Method (Ana-CIM) for the Detection of Carbapenemase Production in Bacteroides fragilis

Antibiotic resistance, particularly to carbapenems, is of increasing concern in Bacteroides fragilis. Carbapenem resistance in B. fragilis is most often mediated by the activation of chromosomally encoded metallo-β-lactamase cfiA by the presence of an upstream insertion sequence (IS). While traditional phenotypic susceptibility methods and molecular tests to detect carbapenem resistance in B. fragilis exist, they are not available in most clinical microbiology laboratory settings. Here, we describe the development of the anaerobic carbapenem inactivation method (Ana-CIM) for predicting carbapenemase production in B. fragilis based off the principles of the well-established modified carbapenem inactivation method (mCIM) for Enterobacterales and Pseudomonas aeruginosa. We also present the clinical validation and reproducibility of the Ana-CIM at three clinical laboratory sites (with 60 clinical isolates, 45% ertapenem resistant). Compared to ertapenem susceptibility by Etest interpreted by CLSI M100 Ed30, the Ana-CIM accurately detected carbapenem resistance in B. fragilis with categorical agreement (CA) of 87% (52/60) and 0% (0/21) very major error (VME), 11% (4/36) major error (ME), and 7% (4/60) minor error (mE) rates across all sites. Additionally, the Ana-CIM demonstrated high reproducibility with 5 clinical and 3 quality control (QC) isolates tested in triplicate with 3 commercial Mueller-Hinton media across all sites, with 93% (604/648) of replicates within a 2-mm zone size of the mode for each isolate. We conclude that the Ana-CIM can be readily deployed in clinical laboratories at a low cost for detection of carbapenemase-mediated resistance in B. fragilis.

Infective Endocarditis Secondary to Bacteroides Thetaiotaomicron in a Patient With Uterine Smooth Muscle Tumor of Uncertain Malignant Potential: A Case Report and Review of the Literature

Bacteroides species are significant clinical pathogens with an associated mortality of more than 19% and are found in most anaerobic infections. Our report documents for the first time a case of infective endocarditis (IE) secondary to Bacteroides thetaiotaomicron (BT). We discuss the case of a 65-year-old female with a medical history of smooth muscle tumor of uncertain malignant potential (STUMP) who presented to the ED with lower quadrant pain. In the hospital, she was found to be in septic shock. A transthoracic echocardiogram showed large vegetation on the aortic valve with severe aortic regurgitation and a blood culture growing BT. We urge physicians to be alert to the fact that Gram-negative anaerobes like BT can cause IE.

In Vitro Efficacy of Antibiotic Combinations with Carbapenems and Other Agents against Anaerobic Bacteria

We investigated the in vitro efficacy of combinations of carbapenems with clindamycin (CLDM) and minocycline (MINO) against Bacteroides fragilis and Peptostreptococcus species. We selected the carbapenems imipenem, meropenem, panipenem, doripenem, and biapenem. To evaluate the antibiotic efficacy of these combination regimens, the fractional inhibitory concentration index (FICI) was calculated against clinical isolates. Consequently, combination regimens of each carbapenem with CLDM or MINO showed synergistic or additive effects against 83.3−100.0% and no antagonistic effects against P. anaerobius isolates. However, against the B. fragilis group (B. fragilis, B. thetaiotaomicron, and Parabacteroides distasonis), although the combination with other carbapenems and CLDM or MINO did not show remarkable synergistic effects, the combination regimen of IPM with CLDM or MINO indicated mainly additive antibiotic efficacies (FICIs: >0.5 to ≤1.0) to B. fragilis groups. Then, antagonistic effects were admitted in only 5.6% of B. fragilis groups. The effectiveness of antibiotic combination therapy against pathogenic anaerobes has remained unclear. Then, our results can provide new insights to explore the effective combination regimens against multidrug-resistant anaerobic bacteria as empirical and definitive therapies, while this study used only carbapenem susceptible isolates. Hence, further studies are needed to use highly antibiotic-resistant anaerobic isolates to carbapenems.

Correlation between antibiotic resistance and clinical outcome of anaerobic infections; mini-review

In anaerobic infections, the relationship between clinical failure and antibiotic resistance is difficult to demonstrate, especially in mixed anaerobic-aerobic infections. Single isolates of anaerobes in cases of bacteraemia revealed that treatment failures were due to inappropriate therapy. We review here cases, where the empiric treatment was unsuccessful due to resistance of anaerobic bacteria to the administered agents and where the change of the antibiotic allowed the patients to be cured. Many therapeutic failures could be linked to the lack of timely detection of resistance, including heteroresistance of the anaerobes. Disk diffusion or Etest methodology may be suitable, at least for rapidly growing anaerobes, to detect both resistance and heteroresistance to antibiotics widely used for empirical therapy.

UK Bacteroides species surveillance survey: Change in antimicrobial resistance over 16 years (2000-2016)

OBJECTIVES

To assess the differences in antimicrobial susceptibility of UK Bacteroides species across two distinct cohorts from 2000 to 2016.

METHODS

Strain identification was performed using matrix-assisted laser-desorption ionisation time of flight mass spectrometry (MALDI-TOF MS) or by partial 16S rRNA sequencing. Minimum inhibitory concentrations (MICs) were determined using agar dilution, following CLSI guidelines (CLSI, 2012; 2017).

RESULTS

224 isolates were included from 2000 to 168 from 2016. Bacteroides fragilis was the most common species, comprising 68% of the 2000 cohort, and 77% in 2016. For all antimicrobials tested, there was an overall increase in the rates of non-susceptible isolates between the cohorts.

CONCLUSIONS

The antibiogram of Bacteroides species in the UK is no longer predictable. Multi-drug resistant isolates although rare, are on the rise, and require testing to guide therapy. The monitoring and surveillance of resistance trends is imperative, as is the development of standardised, robust and accessible antimicrobial susceptibility testing methodology for clinical laboratories.

Rapid detection and surveillance of cfiA-positive Bacteroides fragilis using matrix-assisted laser desorption ionization time-of-flight mass spectrometry

OBJECTIVES

To perform surveillance of cfiA-positive Bacteroides fragilis using new subtyping software module, MALDI Biotyper Subtyping Module (MBT Subtyping Module), on MALDI-TOF MS system, and to evaluate the detection ability of the module.

METHODS

cfiA-positive strains were presumed using the module against B. fragilis isolated between 2006 and 2019. The cfiA gene was confirmed using PCR. In cfiA-positive B. fragilis, the insertion sequence (IS) elements were examined and the MBT STAR-BL assay was performed to examine meropenem hydrolysis activity.

RESULTS

Of the 396 B. fragilis strains included, the MBT Subtyping Module detected 33 presumptive cfiA-positive strains (8.3%), of which 32 harbored the cfiA gene. The sensitivity and specificity of the MBT Subtyping Module for detecting cfiA-positive B. fragilis were 100.0% and 99.7%, respectively. Of the 32 strains harboring the cfiA gene, seven strains possessed IS elements, which were thought to induce high cfiA expression. Meropenem hydrolysis was detected in all seven strains that were positive for both cfiA and IS elements, and they exhibited resistance to meropenem and imipenem. The overall non-susceptibility rates to meropenem and imipenem were 84.8% and 36.4%, respectively, in the 33 presumptive cfiA-positive strains.

CONCLUSION

The MBT Subtyping Module can detect cfiA-positive B. fragilis rapidly and accurately, supporting its use for surveillance of cfiA-positive B. fragilis in clinical settings.

Genotyping of multi drug resistant Bacteroides fragilis group of clinical isolates from mangalore, south India

INTRODUCTION

Bacteroides fragilis group, the most encountered anaerobic bacterium is emerging with resistance to antibiotics. This study explores the antibiogram and occurrence of resistance genes in isolates of B fragilis group from clinical samples.

METHOD

In this study the antimicrobial susceptibility test was done using commercially available E strip test and the results were recorded according to CLSI guidelines. Genotypic investigations were performed by conventional PCR to detect the target resistant genes.

RESULTS

Ceftriaxone, cefoxitin, clindamycin and imipenem were found to be the most resistant antimicrobials in E test method. Metronidazole has shown resistance in 7 strains in vitro while resistance nim genes were detected in 12 strains from 62 randomly selected isolates. Other resistance genes (cfiA, ermF and cepA) were expressed at 58%, 62.9% and 48.3% respectively, among these strains.

CONCLUSION

B fragilis group harbouring the resistant genes may not be fully expressed phenotypically. Hence, detection of these genes by PCR might be necessary for a pertinent conclusion.

The effects of dairy and dairy derivatives on the gut microbiota: a systematic literature review

The effects of dairy and dairy-derived products on the human gut microbiota remains understudied. A systematic literature search was conducted using Medline, CINAHL, Embase, Scopus, and PubMed databases with the aim of collating evidence on the intakes of all types of dairy and their effects on the gut microbiota in adults. Risk of bias was assessed using the Cochrane risk-of-bias tool.The search resulted in 6,592 studies, of which eight randomized controlled trials (RCTs) met pre-determined eligibility criteria for inclusion, consisting of a total of 468 participants. Seven studies assessed the effect of type of dairy (milk, yogurt, and kefir) and dairy derivatives (whey and casein) on the gut microbiota, and one study assessed the effect of the quantity of dairy (high dairy vs low dairy). Three studies showed that dairy types consumed (milk, yogurt, and kefir) increased the abundance of beneficial genera Lactobacillus and Bifidobacterium. One study showed that yogurt reduced the abundance of Bacteroides fragilis, a pathogenic strain. Whey and casein isolates and the quantity of dairy consumed did not prompt changes to the gut microbiota composition. All but one study reported no changes to bacterial diversity in response to dairy interventions and one study reported reduction in bacterial diversity in response to milk intake.In conclusion, the results of this review suggest that dairy products such as milk, yogurt, and kefir may modulate the gut microbiota composition in favor to the host. However, the broader health implications of these findings remain unclear and warrant further studies.

A phase conversion headspace technique for the determination of anti-anaerobic activity of drug candidate based on the metabolic acidity change in culture medium

Screening for anti-anaerobic drug candidates is still challenging although the anaerobic bacteria are important sources for human infections, because the method for anti-anaerobic activity testing is not readily available with low-cost and -expertise. We report a novel method for the determination of the anti-anaerobic activity of drug candidates by automated headspace-gas chromatography (HS-GC). Anaerobic bacteria were inoculated in an anaerobic atmosphere or rapidly using sterile syringe in an air-tight manner, and incubated with and without drugs for 48 h. The metabolic acidities of the cultured media were used as an indicator of cell activities and measured as end-products in place by HS-GC after being completely converted to CO₂ with sodium bicarbonate. The present method is precise (relative standard deviation is below 5%) and validated by excellent agreements with a reference method on the determinations of the inhibition rates (root-mean-square error = 10%, n = 48) and half maximal inhibitory concentrations (R² = 0.996, n = 8) of both pure drug compounds and plant extracts. Advantageously, the present method is sensitive in response to cell activity, safe with regard to cross contamination, and suitable for routine screening of diversified drug candidates for anti-anaerobic activity.

Antimicrobial susceptibility and prevalence of resistance genes in Bacteroides fragilis isolated from blood culture bottles in two tertiary care hospitals in Japan

The in vitro susceptibilities of Bacteroides fragilis to antimicrobial agents, especially to carbapenem, are a major concern in the treatment of patients with bloodstream infections. In this study, 50 isolates of B. fragilis were obtained from positive blood bottles from 2014 to 2019 in Saitama, Japan. Their susceptibility to ampicillin/sulbactam was reduced to 70.0% compared with a previous report, whereas they were still sufficiently susceptible to piperacillin/tazobactam (94.0%). Five cfiA-positive isolates (5/50, 10.0%) were identified that were resistant to doripenem and meropenem, and two of them carried an insertion sequence located upstream of the cfiA-coding region. In particular, imipenem should be considered as a first-line carbapenem for the empirical treatment of B. fragilis infection because only insertion sequence and cfiA double-positive strains showed resistance to imipenem. Thirty-six percent of the isolates had a reduced minimum inhibitory concentration for moxifloxacin. In addition, metronidazole should still be considered as an active agent for B. fragilis because all isolates were susceptible to this antibiotic and the prevalence of the nim gene was low in Japan.

Rapid identification of bloodstream bacterial and fungal pathogens and their antibiotic resistance determinants from positively flagged blood cultures using the BioFire FilmArray blood culture identification panel

BACKGROUND/PURPOSE

Rapid and accurate identification of pathogens and their antibiotic resistance directly from flagged blood cultures can aid clinicians in optimizing early antibiotic treatment and improve the clinical outcomes, especially in settings associated with high rates of bloodstream infection caused by vancomycin-resistant Enterococci (VRE) and carbapenem-resistant Enterobacteriaceae (CRE). We compared the results of the BioFire FilmArray Blood Culture Identification (BCID) panel with those of conventional methods for identifying the pathogens and their antibiotic susceptibility status.

METHODS

In total, 100 randomly selected positive blood cultures (BACTEC Plus Aerobic/F bottles or BACTEC Anaerobic Lytic/10 bottles) were analyzed. The pathogen detection efficiency of FilmArray BCID panel was compared with that of conventional method using MALDI-TOF MS system (Bruker MALDI Biotyper) and susceptibility testing by the Vitek 2 system. The sequencing analysis of antibiotic resistance genes was performed for discrepant results obtained from MALDI Biotyper and Vitek 2.

RESULTS

Among the 100 positively flagged blood cultures, 94% of FilmArray BCID panel results were consistent with the MALDI Biotyper results. All five VRE isolates positive for vanA/vanB genes, 10 of 12 Staphylococcus species positive for mecA gene, and only one Klebsiella pneumoniae isolate positive for K. pneumoniae carbapenemase gene (bla_KPC) detected in the FilmArray BCID panel were also concordant with results by the results by conventional susceptibility testing/molecular confirmation.

CONCLUSIONS

The FilmArray BCID panel results not only demonstrated good correlation with conventional blood culture identification and susceptibility results but also provided results rapidly, especially for the early detection of MRSA, VRE and bla_KPC-mediated CRE.

Anaerobic blood culture positivity at a University Hospital in Hungary: A 5-year comparative retrospective study

Anaerobic bacteremia (AB) is usually detected in about 0.5-13% of positive blood cultures. The aim of this study was to determine prevalence of anaerobic bacteremia over a 5-year period (2013-2017), to identify current trends at our University Hospital and to compare the results to those in a similar study (2005-2009) in the same region. During the study period, an average of 23,274 ± 2,756 blood cultures were received per year. Out of the positive blood cultures, 3.3-3.6% (n = 423) yielded anaerobic bacteria, representing 3.5-3.8 anaerobic isolates/1000 blood culture bottles (including both aerobic and anaerobic bottles) per year for hospitalized patients. Mean age of affected patients was 70-73 years (range: 18-102 years) with a male-to-female ratio: 0.60. Most isolated anaerobes were Cutibacterium spp. (54.0 ± 8.5%; n = 247), while among anaerobes other than Cutibacterium spp., Bacteroides and Parabacteroides and Clostridium spp. were the most prevalent. Blood culture time-to-positivity (TTP) for clinically relevant bacteria was 31.4 ± 23.4 h, while for Cutibacterium spp., TTP values were 112.9 ± 37.2 h (p < 0.0001). In conclusion, the prevalence of anaerobic bacteremia should be determined on institutional basis.

Utility of anaerobic bottles for the diagnosis of bloodstream infections

BACKGROUND

Obligate anaerobes usually account for less than 10% of bacteria recovered from blood cultures (BC). The relevance of routine use of the anaerobic bottle is under debate. The aim of this study was to evaluate the utility of anaerobic bottles for the diagnosis of bloodstream infections (BSI).

METHODS

We conducted a 6-month, retrospective, monocentric study in a tertiary hospital. All positive BC were grouped into a single episode of bacteremia when drawn within 7 consecutive days. Bacteremia were classified into contaminants and BSI. Charts of patients with BSI due to obligate anaerobes were studied.

RESULTS

A total of 19,739 blood cultures were collected, 2341 of which (11.9%) were positive. Anaerobic bottles were positive in 1528 (65.3%) of all positive BC but were positive alone (aerobic bottles negative) in 369 (15.8%). Overall 1081 episodes of bacteremia were identified, of which 209 (19.3%) had positive anaerobic bottles alone. The majority 126/209 (60.3%) were contaminants and 83 (39.7%) were BSI. BSI due to facultative anaerobes, obligate aerobes and obligate anaerobes were identified in 67 (80.7%), 3 (3.6%) and 13 (15.7%) of these 83 episodes, respectively. BSI due to obligate anaerobic bacteria were reported in 9 patients with gastro-intestinal disease, in 3 with febrile neutropenia and in 1 burned patient.

CONCLUSIONS

Anaerobic bottles contributed to the diagnosis of a significant number of episodes of bacteremia. Isolated bacteria were mostly contaminants and non-obligate anaerobic pathogens. Rare BSI due to obligate anaerobes were reported mainly in patients with gastro-intestinal disorders and during febrile neutropenia.

Microbial Metabolism Modulates Antibiotic Susceptibility within the Murine Gut Microbiome

Although antibiotics disturb the structure of the gut microbiota, factors that modulate these perturbations are poorly understood. Bacterial metabolism is an important regulator of susceptibility in vitro and likely plays a large role within the host. We applied a metagenomic and metatranscriptomic approach to link antibiotic-induced taxonomic and transcriptional responses within the murine microbiome. We found that antibiotics significantly alter the expression of key metabolic pathways at the whole-community and single-species levels. Notably, Bacteroides thetaiotaomicron, which blooms in response to amoxicillin, upregulated polysaccharide utilization. In vitro, we found that the sensitivity of this bacterium to amoxicillin was elevated by glucose and reduced by polysaccharides. Accordingly, we observed that dietary composition affected the abundance and expansion of B. thetaiotaomicron, as well as the extent of microbiome disruption with amoxicillin. Our work indicates that the metabolic environment of the microbiome plays a role in the response of this community to antibiotics.

Bacteroides fragilis requires the ferrous-iron transporter FeoAB and the CobN-like proteins BtuS1 and BtuS2 for assimilation of iron released from heme

The intestinal commensal and opportunistic anaerobic pathogen Bacteroides fragilis has an essential requirement for both heme and free iron to support growth in extraintestinal infections. In the absence of free iron, B. fragilis can utilize heme as the sole source of iron. However, the mechanisms to remove iron from heme are not completely understood. In this study, we show that the inner membrane ferrous iron transporter ∆feoAB mutant strain is no longer able to grow with heme as the sole source of iron. Genetic complementation with the feoAB gene operon completely restored growth. Our data indicate that iron is removed from heme in the periplasmic space, and the released iron is transported by the FeoAB system. Interestingly, when B. fragilis utilizes iron from heme, it releases heme-derived porphyrins by a dechelatase activity which is upregulated under low iron conditions. This is supported by the findings showing that formation of heme-derived porphyrins in the ∆feoAB mutant and the parent strain increased 30-fold and fivefold (respectively) under low iron conditions compared to iron replete conditions. Moreover, the btuS1 btuS2 double-mutant strain (lacking the predicted periplasmic, membrane anchored CobN-like proteins) also showed growth defect with heme as the sole source of iron, suggesting that BtuS1 and BtuS2 are involved in heme-iron assimilation. Though the dechelatase mechanism remains uncharacterized, assays performed in bacterial crude extracts show that BtuS1 and BtuS2 affect the regulation of the dechelatase-specific activities in an iron-dependent manner. These findings suggest that the mechanism to extract iron from heme in Bacteroides requires a group of proteins, which spans the periplasmic space to make iron available for cellular functions.

Sample preparation method influences direct identification of anaerobic bacteria from positive blood culture bottles using MALDI-TOF MS

Rapid detection and identification of anaerobic bacteria from blood is important to adjust antimicrobial therapy by including antibiotics with activity against anaerobic bacteria. Limited data is available about direct identification of anaerobes from positive blood culture bottles using MALDI-TOF mass spectrometry (MS). In this study, we evaluated the performance of two sample preparation protocols for direct identification of anaerobes from positive blood culture bottles, the MALDI Sepsityper kit (Sepsityper) and the in-house saponin (saponin) method. Additionally, we compared two blood culture bottle types designed to support the growth of anaerobic bacteria, the BacT/ALERT-FN Plus (FN Plus) and the BACTEC-Lytic (Lytic), and their influence on direct identification. A selection of 30 anaerobe strains belonging to 22 different anaerobic species (11 reference strains and 19 clinical isolates) were inoculated to 2 blood culture bottle types in duplicate. In total, 120 bottles were inoculated and 99.2% (n = 119) signalled growth within 5 days of incubation. The Sepsityper method correctly identified 56.3% (n = 67) of anaerobes, while the saponin method correctly identified 84.9% (n = 101) of anaerobes with at least log(score) ≥1.6 (low confidence correct identification), (p < 0.001). Gram negative anaerobes were better identified with the saponin method (100% vs. 46.5%; p < 0.001), while Gram positive anaerobes were better identified with the Sepsityper method (70.8% vs. 62.5%; p = 0.454). Average log(score) values among only those isolates that were correctly identified simultaneously by both sample preparation methods were 2.119 and 2.029 in favour of the Sepsityper method, (p = 0.019). The inoculated bottle type didn't influence the performance of the two sample preparation methods. We confirmed that direct identification from positive blood culture bottles with MALDI-TOF MS is reliable for anaerobic bacteria. However, the results are influenced by the sample preparation method used.

Antimicrobial Susceptibility Testing of Bacteria of Veterinary Origin

Antimicrobial susceptibility testing is an essential tool to the veterinarian for selecting the most appropriate agent for treatment of bacterial diseases of animals. The availability of well-defined methods that incorporate the necessary quality controls coupled to clinical outcome data is foundational in providing relevant test results for clinical decisions. Since 1993, the Clinical Laboratory and Standards Institute (CLSI) Subcommittee on Veterinary Antimicrobial Susceptibility Testing (VAST) has developed specific test methods and interpretive criteria for veterinary pathogens. This information has allowed for veterinarians to more effectively treat animal diseases thereby protecting both animal welfare and human food security. Moreover, the availability of standardized test methods for veterinary pathogens has allowed for the development of antimicrobial surveillance programs to detect the emergence of resistance among veterinary pathogens. Future work by the VAST and other groups will be critical to expanding the current test methods and interpretive criteria to more pathogen-antibacterial combinations, as well as, the incorporation of genomic information for routine antimicrobial susceptibility testing in the veterinary diagnostic laboratory.

Implementation of the new VIRTUO blood culture system: evaluation and comparison to the 3D system using simulated blood cultures

PURPOSE

To evaluate the performances of the newly approved BacT/ALERT VIRTUO blood culture system for the recovery of bloodstream pathogens and compare it to the BacT/ALERT 3D system.

METHODS

Simulated blood cultures of eight clinically relevant microorganisms were used: Bacteroides fragilis (ATCC 25285), Escherichia coli (ATCC 25922), Haemophilus influenzae (ATCC 49247), Pseudomonas aeruginosa (ATCC 27853), Enterococcus faecalis (ATCC 29212), Staphylococcus aureus (ATCC 29213), Streptococcus pneumoniae (ATCC 49619) and Candida krusei (ATCC 6258). Criteria for comparison were culture positivity and time to detection (TTD). The effects of delayed entry on recovery and TTD were also evaluated.

RESULTS

The VIRTUO exhibited around 3 h faster detection time compared to the 3D system. (p < 0.01) for aerobic and facultative microorganisms. The difference in TTD was greatest for the B. fragilis, with a median difference of 46.67 h. The anaerobic bottle of the VIRTUO (FN Plus) did not support the growth of obligate aerobes, whereas the 3D did so. Delayed entry (studied with an E. Coli isolate) had no effect on the recovery rate but proportionally reduced TTD.

CONCLUSIONS

The VIRTUO performed better than the 3D in terms of TTD and hands-on-time. FN Plus vial appears to be more efficient than the SN bottle in the recovery of anaerobes.

Identification and Antimicrobial Susceptibility Testing of Anaerobic Bacteria: Rubik's Cube of Clinical Microbiology?

Anaerobic bacteria have pivotal roles in the microbiota of humans and they are significant infectious agents involved in many pathological processes, both in immunocompetent and immunocompromised individuals. Their isolation, cultivation and correct identification differs significantly from the workup of aerobic species, although the use of new technologies (e.g., matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, whole genome sequencing) changed anaerobic diagnostics dramatically. In the past, antimicrobial susceptibility of these microorganisms showed predictable patterns and empirical therapy could be safely administered but recently a steady and clear increase in the resistance for several important drugs (β-lactams, clindamycin) has been observed worldwide. For this reason, antimicrobial susceptibility testing of anaerobic isolates for surveillance purposes or otherwise is of paramount importance but the availability of these testing methods is usually limited. In this present review, our aim was to give an overview of the methods currently available for the identification (using phenotypic characteristics, biochemical testing, gas-liquid chromatography, MALDI-TOF MS and WGS) and antimicrobial susceptibility testing (agar dilution, broth microdilution, disk diffusion, gradient tests, automated systems, phenotypic and molecular resistance detection techniques) of anaerobes, when should these methods be used and what are the recent developments in resistance patterns of anaerobic bacteria.

Genetic identification and antimicrobial susceptibility of clinically isolated anaerobic bacteria: A prospective multicenter surveillance study in Japan

This prospective multicenter surveillance study was designed to provide antimicrobial susceptibility profiles of clinical anaerobic bacteria with genetic species identification in Japan. In 2014, a total of 526 non-duplicate clinical anaerobic isolates were collected from 11 acute-care hospitals in the Kyoto and Shiga regions of Japan. Genetic identification was performed using 16S rRNA sequencing. Minimum inhibitory concentrations were determined in the central laboratory and were interpreted using the CLSI criteria. Genetic analysis provided species-level identification for 496 isolates (83 species in 40 genera) and genus-level identification for 21 isolates (13 genera). Among these 517 isolates, the most frequent anaerobes were Bacteroides spp. (n = 207), Prevotella spp. (n = 43), Clostridium spp. (n = 40), and Peptoniphilus spp. (n = 40). B. fragilis was the most common species (n = 107) and showed 91.6%-97.2% susceptibility to β-lactam/β-lactamase inhibitor combinations (BLBLIs; ampicillin-sulbactam, amoxicillin-clavulanate, and piperacillin-tazobactam) and carbapenems (imipenem and meropenem) as well as 100% susceptibility to metronidazole. Gram-negative anaerobes were highly susceptible to metronidazole (99.0%) followed by BLBLIs and carbapenems (>90% each). BLBLIs or carbapenems also retained activity against Gram-positive anaerobes (99.5%-100%) except Clostridioides difficile. All isolates were susceptible to combinations of metronidazole with BLBLIs or carbapenems. Thus, BLBLIs or carbapenems are first choices for empirical therapy of anaerobic infections in Japan, and these antimicrobials in combination with metronidazole should be reserved for very severe infections and targeted therapy.

Prevalence of antimicrobial resistance and the cfiA resistance gene in Danish Bacteroides fragilis group isolates since 1973

OBJECTIVES

The purpose of this study was to determine the prevalence of resistance and the cfiA carbapenemase-producing gene in historical Bacteroides fragilis group isolates.

METHODS

Danish clinical B. fragilis group isolates (n = 444) from 1973 to 2015 were identified with Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF MS) on the Biotyper platform. Antimicrobial resistance was determined using a disk diffusion screening method and commercial antibiotic gradient strips. Division I (cfiA-negative) and division II (cfiA-positive) B. fragilis strains were differentiated using MALDI-TOF MS and real-time polymerase chain reaction (PCR).

RESULTS

From 1973-1980 to 2010-2015 the prevalence of antimicrobial resistance rose from 0% to 21.2%, 2.5%, and 1% for clindamycin, meropenem, and metronidazole, respectively. MALDI-TOF MS and real-time PCR identified 16 of 266 (6.0%) B. fragilis strains as division II, of which 4 strains, isolated between 2010 and 2015, were resistant to meropenem.

CONCLUSIONS

Substantial increases in resistance were found throughout this study. This supports the general perception that antimicrobial resistance in the B. fragilis group has been established in the recent decades in Europe. Resistance to meropenem, facilitated by expression of the cfiA resistance gene, seems to be increasing; therefore, it is imperative to monitor the occurrence of this gene, e.g. using MALDI-TOF MS.

Clinical and Microbiologic Characteristics of Early-onset Sepsis Among Very Low Birth Weight Infants: Opportunities for Antibiotic Stewardship

BACKGROUND

Most very low birth weight (VLBW, birth weight <1500 g) infants receive empiric antibiotics for risk of early-onset sepsis (EOS). The objective of this study was to determine the characteristics of VLBW infants with culture-confirmed EOS at a single center during 25 years and to identify opportunities for antibiotic stewardship.

METHODS

Retrospective cohort study includes VLBW infants admitted from 1990 to 2015. EOS was defined as isolation of a pathogen in blood or cerebrospinal fluid culture obtained at <72 hours of age. Clinical and microbiologic characteristics of EOS case infants were obtained by review of medical, laboratory and administrative records. Blood culture, antibiotic initiation and maternal discharge code data were available for all VLBW infants born between 1999 and 2013.

RESULT

One-hundred nine EOS cases (20.5/1000 VLBW births) occurred during the study period. Preterm labor, preterm rupture of membranes and/or the obstetrical diagnosis of chorioamnionitis were present in 106/109 cases (97%). Obligate anaerobic organisms accounted for 16% of cases. Time to culture positivity was 36 hours for 88% and 48 hours for 98% of cases. From 1999 to 2013, 97% of VLBW infants were evaluated for EOS and 90% administered empiric antibiotics; 22% of these infants were born by cesarean section to mothers with preeclampsia and without preterm labor or chorioamnionitis and had a 12-fold lower incidence of EOS compared with the remaining infants.

CONCLUSION

Decisions to initiate and discontinue empiric antibiotics among VLBW infants can be informed by the delivery characteristics of infected infants and by local microbiologic data.

Antimicrobial resistance in the Bacteroides fragilis group in faecal samples from patients receiving broad-spectrum antibiotics

Members of the Bacteroides fragilis group are opportunistic pathogens and cause severe infections including bacteraemia. As increased levels of antimicrobial resistance in B. fragilis group bacteria can be detected years after administration of specific antibiotics, monitoring antimicrobial susceptibility in the gut microbiota could be important. The objectives of this study were to 1) investigate the distribution of species and the occurrence of reduced antimicrobial susceptibility in the B. fragilis group from patients treated at departments with a high level of antibiotic use, 2) to determine the prevalence of the carbapenem resistance gene cfiA in B. fragilis in this patient group, and 3) to determine the association between previous antibiotic treatment and reduced susceptibility to clindamycin, meropenem, metronidazole, and piperacillin-tazobactam. Consecutive faecal samples (n = 197) were collected from patients at the departments of haematology, oncology, and infectious diseases at Odense University Hospital, Denmark. Three colonies from each sample were identified by Matrix Assisted Lazer Desorption Ionization Time of Flight Mass Spectrometry and isolates were screened for resistance to clindamycin, meropenem, metronidazole, and piperacillin-tazobactam. B. fragilis isolates were tested for the cfiA metallo-beta-lactamase gene. Fisher's Exact test was used to test for correlation between antimicrobial exposure and reduced susceptibility. A total of 359 isolates were tested for reduced susceptibility. Of these 28%, 5%, <1%, and 11% were intermediate susceptible or resistant to clindamycin, meropenem, metronidazole, and piperacillin-tazobactam respectively. Three metronidazole resistant Bacteroides spp. were isolated. The proportion of B. fragilis belonging to division II (cfiA+) was 5.3%. Previous exposure to meropenem was associated with reduced susceptibility to meropenem (p= 0.001). In conclusion, antimicrobial resistance is prevalent and the distribution of species appears to be affected in the B. fragilis group from patients receiving broad-spectrum antibiotics, with meropenem exposure being associated with meropenem resistance.

Evaluation of the routine antimicrobial susceptibility testing results of clinically significant anaerobic bacteria in a Slovenian tertiary-care hospital in 2015

The aim of our study was to determined antimicrobial susceptibility profiles of 2673 clinically significant anaerobic bacteria belonging to the major genera, isolated in 2015 in a large tertiary-care hospital in Slovenia. The species identification was performed by MALDI-TOF mass spectrometry. Antimicrobial susceptibility was determined immediately at the isolation of the strains against: penicillin, co-amoxiclav, imipenem, clindamycin and metronidazole, using gradient diffusion methodology and EUCAST breakpoints. The most frequent anaerobes were Bacteroides fragilis group with 31% (n = 817), Gram positive anaerobic cocci (GPACs) with 22% (n = 589), Prevotella with 14% (n = 313) and Propionibacterium with 8% (n = 225). Metronidazole has retained full activity (100%) against all groups of anaerobic bacteria intrinsically susceptible to it. Co-amoxiclav and imipenem were active against most tested anaerobes with zero or low resistance rates. However, observed resistance to co-amoxiclav (8%) and imipenem (1%) is worrying especially among B. fragilis group isolates. High overall resistance (23%) to clindamycin was detected in our study and was highest among the genera Prevotella, Bacteroides, Parabacteroides, GPACs and Clostridium. Routine testing of antimicrobial susceptibility of clinically relevant anaerobic bacteria is feasible and provides good surveillance data.

Antimicrobial susceptibility of Bacteroides fragilis group organisms in Hong Kong by the tentative EUCAST disc diffusion method

This study used a recently developed EUCAST disc diffusion method to measure the susceptibility of 741 B. fragilis group isolates to six antibiotics. Isolates nonsusceptible to imipenem and metronidazole by the disc method were further investigated by E-test. Species identification was obtained by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS), PCR assays and 16S rRNA sequencing. The most common species were B. fragilis (n = 424, including 81 division II and 343 division I isolates), B. thetaiotaomicron (n = 111), B. ovatus (n = 53) and B. vulgatus (n = 46). Overall, metronidazole following by imipenem and amoxicillin-clavulanate are the most active agents with over 90% of all the isolates being susceptible at the tentative disc breakpoints. Susceptibility rates for moxifloxacin (69.5%), piperacillin-tazobactam (58.2%) and clindamycin (37.2%) were much lower. Metronidazole is the only agent active against >90% of B. fragilis, non-fragilis Bacteroides and Parabacteroides isolates. With the exception of B. fragilis division II, imipenem was active against 88.0%-98.3% of isolates of the other species. Susceptibility rates for clindamycin (14.4%-54.3%) and moxifloxacin (33.3%-80.6%) were low across all species and many isolates had no inhibition zone around the discs. E-test testing confirmed 8.2% (61/741) and 1.6% (12/741) isolates as nonsusceptible to imipenem and metronidazole, respectively with B. fragilis and B. thetaoiotaomicron accounting for a large share of the observed resistance to both agents. Two imipenem-resistant and one metronidazole-resistant B. dorei were misidentified as B. vulgatus by MALDI-TOF MS. These data highlights the importance anaerobic susceptibility testing in clinical laboratories to guide therapy.

Performance of two blood culture systems to detect anaerobic bacteria. Is there any difference?

We studied the performance characteristics of two blood culture (BC) bottles/systems, (i) BacT/ALERT-FN Plus/3D (bioMérieux, Marcy l'Étoile, France) and (ii) BACTEC-Lytic/9000 (Becton Dickinson, Sparks, USA) for detection of growth and time-to-positivity (TTP) against a balanced and diverse collection of anaerobic bacterial strains (n = 48) that included reference strains (n = 19) and clinical isolates (n = 29) of 32 species (15 Gram-negative and 17 Gram-positive). Standard suspension of bacteria was inoculated to each bottle in duplicates and incubated in the corresponding system. Overall, 62.5% (n = 30) of strains were detected by both BC bottle types. Comparing the two, 70.8% (n = 34) and 79.2% (n = 38) of strains were detected by BacT/ALERT-FN Plus and BACTEC-Lytic bottles, respectively (p = 0.38). Among Gram-negative anaerobes (n = 25) the detection rate was 76.0% (n = 19) vs. 92.0% (n = 23) (p = 0.22), respectively. Among Gram-positive anaerobes (n = 23) the detection rate was 65.2% (n = 15) in both bottles (p = 1). The average TTP per bottle was calculated only for the strains detected by both systems (n = 30) and was 40.85 h and 28.08 h for BacT/ALERT-FN Plus and BACTEC-Lytic, respectively (p < 0.001). The mean difference was 12.76 h (95% CI: 6.21-19-31 h). Six anaerobic strains were not detected by any system, including Gram-negative Porphyromonas gingivalis, and five Gram-positive strains: Finegoldia magna, Peptostreptococcus anaerobius, Propionibacterium acnes, Clostridium novyi and Clostridium clostridioforme. Furthermore, Eggerthella lenta and Prevotella bivia were detected only by BacT/ALERT-FN Plus, while Prevotella disiens and Prevotella intermedia were detected only by BACTEC-Lytic bottles. There were no major differences in detection rate among clinical and reference strains. Anaerobic bacteria represent a minority of BC isolates, however, far from ideal detection rate was observed in this study for both tested bottle/system combinations. Nevertheless, in those cases where both gave positive signal, BACTEC-Lytic was superior to BacT/ALERT FN Plus with 12.76 h shorter mean TTP. Improvements of media in blood culture bottles available for detection of anaerobes are warranted.

Clinical characteristics and antimicrobial susceptibilities of anaerobic bacteremia in an acute care hospital

This study investigated the clinical features of anaerobic bacteraemia in an acute-care hospital, and evaluated the antimicrobial susceptibility of these isolates to commonly available antibiotics. Microbiological and epidemiological data from 2009 to 2011were extracted from the laboratory information system and electronic medical records. One hundred and eleven unique patient episodes consisting of 116 anaerobic isolates were selected for clinical review and antibiotic susceptibility testing. Susceptibilities to amoxicillin-clavulanate, clindamycin, imipenem, metronidazole, moxifloxacin, penicillin and piperacillin-tazobactam were performed using Etest strips with categorical interpretations according to current CLSI breakpoints. Metronidazole-resistant and carbapenem-resistant anaerobic Gram-negative bacilli were screened for the nim and cfiA genes. Clinical data was obtained retrospectively from electronic medical records. During the 3 year period, Bacteroides fragilis group (41%), Clostridium species (14%), Propionibacterium species (9%) and Fusobacterium species (6%) were the most commonly isolated anaerobes. Patients with anaerobic bacteraemia that were included in the study were predominantly above 60 years of age, with community-acquired infections. The most commonly used empiric antibiotic therapies were beta-lactam/beta-lactamase inhibitor combinations (44%) and metronidazole (10%). The crude mortality was 25%, and appropriate initial antibiotic therapy was not significantly associated with improved survival. Intra-abdominal infections (39%) and soft-tissue infections (33%) accounted for nearly three-quarters of all bacteraemia. Antibiotics with the best anaerobic activity were imipenem, piperacillin-tazobactam, amoxicillin-clavulanate and metronidazole, with in-vitro susceptibility rates of 95%, 95%, 94% and 92% respectively. Susceptibilities to penicillin (31%), clindamycin (60%) and moxifloxacin (84%) were more variable. Two multidrug-resistant isolates of Bacteroides species were positive for nim and cfiA genes respectively, while another two imipenem-resistant Fusobacterium species were negative for cfiA genes. This study demonstrated that anaerobic bacteraemia in our patient population was predominantly associated with intra-abdominal and soft-tissue infections. Overall antibiotic resistance was high for penicillin and clindamycin, and the presence of emerging resistance to carbapenems and metronidazole warrants further monitoring.

Trends in antimicrobial resistance among Bacteroides species and Parabacteroides species in the United States from 2010-2012 with comparison to 2008-2009

The susceptibility trends for Bacteroides fragilis and related species against various antibiotics were determined using data from 3 years of surveillance (2010-2012) on 779 isolates referred by 7 medical centers. The antibiotic test panel included imipenem, ertapenem, meropenem, ampicillin-sulbactam, piperacillin-tazobactam, cefoxitin, clindamycin, moxifloxacin, tigecycline, linezolid, chloramphenicol and . MICs were determined using the agar dilution CLSI reference method. Carbapenem resistance remained low (range 1.1%-2.5%) and unchanged from 2008 to 9 through 2010-2012. Resistance also remained low to the beta-lactam/beta-lactamase inhibitor combinations (1.1%-4.4%). While resistance to clindamycin and moxifloxacin remained high; rates were lower for B. fragilis in 2010-12 (24% and 19% respectively) compared to the earlier time frame of 2008-9 (29% and 35% respectively for the earlier time frame). There were notable species and resistance associations which have been demonstrated previously. No resistance to metronidazole or chloramphenicol resistance was seen. These data demonstrate the continued variability in resistance among Bacteroides and Parabacteroides species, but do demonstrate that carbapenems and beta-lactam/beta-lactamase inhibitor combinations remain very active throughout the United States.

Selected Topics in Anaerobic Bacteriology

Alteration in the host microbiome at skin and mucosal surfaces plays a role in the function of the immune system, and may predispose immunocompromised patients to infection. Because obligate anaerobes are the predominant type of bacteria present in humans at skin and mucosal surfaces, immunocompromised patients are at increased risk for serious invasive infection due to anaerobes. Laboratory approaches to the diagnosis of anaerobe infections that occur due to pyogenic, polymicrobial, or toxin-producing organisms are described. The clinical interpretation and limitations of anaerobe recovery from specimens, anaerobe-identification procedures, and antibiotic-susceptibility testing are outlined. Bacteriotherapy following analysis of disruption of the host microbiome has been effective for treatment of refractory or recurrent Clostridium difficile infection, and may become feasible for other conditions in the future.

Anaerobic Bacteremia: Impact of Inappropriate Therapy on Mortality

BACKGROUND

Investigation on incidence and mortality of anaerobic bacteremia (AB) is clinically relevant in spite of its infrequent occurrence and not often explored, which report varies according to period and institutions. Therefore, it is necessary to analyze the incidence and risk factors related to mortality and assess clinical outcomes of AB in current aspect.

MATERIALS AND METHODS

Characteristics of AB patients and anaerobic bacteria from blood culture at a university hospital in 2012 were reviewed retrospectively. The correlation between risk factors and 28-day patient mortality was analyzed.

RESULTS

A total of 70 non-duplicated anaerobic bacteria were isolated from blood of 70 bacteremia patients in 2012. The history of cardiovascular disease as host's risk factor was statistically significant (P = 0.0344) in univariate and multivariate analysis. Although the inappropriate therapy was not statistically significant in univariate and multivariate analysis, the survival rate of bacteremia was significantly worse in patients who had inappropriate therapy compared with those underwent appropriate therapy (hazard ratio, 5.4; 95% confidence interval, 1.7-6.9; P = 0.004). The most frequently isolated organism was Bacteroides fragilis (32 isolates, 46%), followed by Bacteroides thetaiotaomicron (10, 14%), and non-perfringens Clostridium (7, 10%).

CONCLUSION

The incidence of AB in 2012 was 2.3% (number of AB patients per 100 positive blood culture patients) and the mortality rate in patients with clinically significant AB was 21.4%. In addition, AB was frequently noted in patients having malignancy and the survival rate of AB was significantly worse in patients who received inappropriate therapy compared with those underwent appropriate therapy.

Clinical characteristics associated with mortality of patients with anaerobic bacteremia

The presence of anaerobes in the blood stream is known to be associated with a higher rate of mortality. However, few prognostic risk factor analyses examining whether a patient's background characteristics are associated with the prognosis have been reported. We performed a retrospective case-controlled study to assess the prognostic factors associated with death from anaerobic bacteremia. Seventy-four patients with anaerobic bacteremia were treated between January 2005 and December 2014 at Aichi Medical University Hospital. The clinical information included drug susceptibility was used for analysis of prognostic factors for 30-day mortality. Multivariate logistic analyses revealed an association between the 30-day mortality rate and malignancy (OR: 3.64, 95% CI: 1.08-12.31) and clindamycin resistance (OR: 7.93, 95% CI: 2.33-27.94). The result of Kaplan-Meier analysis of mortality showed that the 30-day survival rate was 83% in clindamycin susceptible and 38.1% in clindamycin resistant anaerobes causing bacteremia. The result of log-rank test also showed that susceptibility to clindamycin affected mortality (P < 0.001). Our results indicated that malignancy and clindamycin susceptibility could be used to identify subgroups of patients with anaerobic bacteremia with a higher risk of 30-day mortality. The results of this study are important for the early and appropriate management of patients with anaerobic bacteremia.

The Performance of the Four Anaerobic Blood Culture Bottles BacT/ALERT-FN, -FN Plus, BACTEC-Plus and -Lytic in Detection of Anaerobic Bacteria and Identification by Direct MALDI-TOF MS

Detection and identification of anaerobic bacteria in blood cultures (BC) is a well-recognized challenge in clinical microbiology. We studied 100 clinical anaerobic BC isolates to evaluate the performance of BacT/ALERT-FN, -FN Plus (BioMérieux), BACTEC-Plus and -Lytic (Becton Dickinson BioSciences) BC bottles in detection and time to detection (TTD) of anaerobic bacteria. BACTEC Lytic had higher detection rate (94/100, 94%) than BacT/ALERT FN Plus (80/100, 80%) (p<0.01) in the studied material. There was no significant difference in detection of anaerobic bacteria among the remaining bottle types. The 67 anaerobic bacteria that signalled positive in all four bottle types were analyzed to compare the time to detection (TTD) and isolates were directly identified by MALDI-TOF MS. There was a significant difference in TTD among the four bottle types (p<0.0001). The shortest median TTD was 18 h in BACTEC Lytic followed by BacT/ALERT FN (23.5 h), BACTEC Plus (27 h) and finally BacT/ALERT FN Plus (38 h) bottles. In contrast, MALDI-TOF MS performed similarly in all bottle types with accurate identification in 51/67 (76%) BacT/ALERT FN, 51/67 (76%) BacT/ALERT FN Plus, 53/67 (79%) BACTEC Plus and 50/67 (75%) BACTEC Lytic bottles. In conclusion, BACTEC Lytic bottles have significantly better detection rates and shorter TTD compared to the three other bottle types. The anaerobic BC bottles are equally suitable for direct MALDI-TOF MS for rapid and reliable identification of common anaerobic bacteria. Further clinical studies are warranted to investigate the performance of anaerobic BC bottles in detection of anaerobic bacteria and identification by direct MALDI-TOF MS.