Changes in the antibiotic susceptibility of anaerobic bacteria from 2007-2009 to 2010-2012 based on the CLSI methodology

Emergence of Antibiotic-Resistant Porphyromonas gingivalis in United States Periodontitis Patients

Antibiotic resistance patterns of the major human periodontal pathogen Porphyromonas gingivalis were assessed over a 20-year period in the United States. Subgingival P. gingivalis was cultured pre-treatment from 2193 severe periodontitis patients during three time periods: 1999-2000 (936 patients), 2009-2010 (685 patients), and 2019-2020 (572 patients). The clinical isolates were tested for in vitro resistance to 4 mg/L for clindamycin and doxycycline, 8 mg/L for amoxicillin, and 16 mg/L for metronidazole, with a post hoc combination of data for metronidazole plus amoxicillin. Clindamycin-resistant P. gingivalis was significantly more prevalent in 2009-2010 (9.1% of patients) and 2019-2020 (9.3%; 15-fold increase) as compared to 1999-2000 (0.6%). P. gingivalis resistance to amoxicillin also significantly increased from 0.1% of patients in 1999-2000 to 1.3% in 2009-2010 and 2.8% (28-fold increase) in 2019-2020. P. gingivalis resistance to metronidazole, metronidazole plus amoxicillin, and doxycycline was low (≤0.5% prevalence), and statistically unchanged, over the 20-year period. These findings are the first to reveal marked increases over 20 years in clindamycin-resistant and amoxicillin-resistant P. gingivalis in United States periodontitis patients. Increased antibiotic resistance of P. gingivalis and other periodontitis-associated bacteria threatens the efficacy of periodontal antimicrobial chemotherapy.

Antibiotic Resistance Mediated by Escherichia coli in Kuwait Marine Environment as Revealed through Genomic Analysis

Antibiotic-resistance gene elements (ARGEs) such as antibiotic-resistance genes (ARGs), integrons, and plasmids are key to the spread of antimicrobial resistance (AMR) in marine environments. Kuwait's marine area is vulnerable to sewage contaminants introduced by numerous storm outlets and indiscriminate waste disposal near recreational beaches. Therefore, it has become a significant public health issue and warrants immediate investigation. Coliforms, especially Gram-negative Escherichia coli, have been regarded as significant indicators of recent fecal pollution and carriers of ARGEs. In this study, we applied a genome-based approach to identify ARGs' prevalence in E. coli isolated from mollusks and coastal water samples collected in a previous study. In addition, we investigated the plasmids and intl1 (class 1 integron) genes coupled with the ARGs, mediating their spread within the Kuwait marine area. Whole-genome sequencing (WGS) identified genes resistant to the drug classes of beta-lactams (blaCMY-150, blaCMY-42, blaCTX-M-15, blaDHA-1, blaMIR-1, blaOKP-B-15, blaOXA-1, blaOXA-48, blaTEM-1B, blaTEM-35), trimethoprim (dfrA14, dfrA15, dfrA16, dfrA1, dfrA5, dfrA7), fluroquinolone (oqxA, oqxB, qnrB38, qnrB4, qnrS1), aminoglycoside (aadA2, ant(3'')-Ia, aph(3'')-Ib, aph(3')-Ia, aph(6)-Id), fosfomycin (fosA7, fosA_6, fosA, fosB1), sulfonamide (sul1, sul2, sul3), tetracycline (tet-A, tet-B), and macrolide (mph-A). The MFS-type drug efflux gene mdf-A is also quite common in E. coli isolates (80%). The plasmid ColRNAI was also found to be prevalent in E. coli. The integron gene intI1 and gene cassettes (GC) were reported to be in 36% and 33%, respectively, of total E. coli isolates. A positive and significant (p < 0.001) correlation was observed between phenotypic AMR-intl1 (r = 0.311) and phenotypic AMR-GC (r = 0.188). These findings are useful for the surveillance of horizontal gene transfer of AMR in the marine environments of Kuwait.

Comparative evaluation of MALDI-TOF MS and 16S rRNA gene sequencing for the identification of clinically relevant anaerobic bacteria: critical evaluation of discrepant results

OBJECTIVES

The main study objective was to evaluate the correlation between matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and 16S rRNA gene sequencing results for the identification of anaerobes.

METHODS

A retrospective study was conducted of all anaerobic bacteria isolated from clinically significant specimens. MALDI-TOF (Bruker Byotyper) and 16S rRNA gene sequencing were performed in all strains. Identifications were considered correct when the concordance with gene sequencing was ≥99%.

RESULTS

The study included 364 isolates of anaerobic bacteria: 201 (55.2%) Gram-negative and 163 (44.8%) Gram-positive, mostly belonging to the genus Bacteroides. Isolates were largely obtained from blood cultures (128/35.4%) and intra-abdominal samples (116/32.1%). Overall, 87.3% of isolates were identified at species level using the version 9 database (89.5% of Gram-negative and 84.6% of Gram-positive anaerobic bacteria). All isolates belonging to the species B. fragilis sensu stricto were correctly identified by MALDI-TOF MS, but five cases of Phocaeicola (Bacteroides) dorei were misidentified as Phocaeicola (Bacteroides) vulgatus; all Prevotella isolates were correctly identified at the genus level, and most were correctly identified at the species level. Among Gram-positive anaerobes, 12 Anaerococcus species were not identified by MALDI-TOF MS, while six cases identified as Peptoniphilus indolicus were found to belong to other genera/species.

CONCLUSIONS

MALDI-TOF is a reliable technique for identifying most anaerobic bacteria, although the database needs frequent updating to identify rare, infrequent, and newly discovered species.

Recent Trends in Antimicrobial Resistance among Anaerobic Clinical Isolates

Anaerobic bacteria are normal inhabitants of the human commensal microbiota and play an important role in various human infections. Tedious and time-consuming, antibiotic susceptibility testing is not routinely performed in all clinical microbiology laboratories, despite the increase in antibiotic resistance among clinically relevant anaerobes since the 1990s. β-lactam and metronidazole are the key molecules in the management of anaerobic infections, to the detriment of clindamycin. β-lactam resistance is usually mediated by the production of β-lactamases. Metronidazole resistance remains uncommon, complex, and not fully elucidated, while metronidazole inactivation appears to be a key mechanism. The use of clindamycin, a broad-spectrum anti-anaerobic agent, is becoming problematic due to the increase in resistance rate in all anaerobic bacteria, mainly mediated by Erm-type rRNA methylases. Second-line anti-anaerobes are fluoroquinolones, tetracyclines, chloramphenicol, and linezolid. This review aims to describe the up-to-date evolution of antibiotic resistance, give an overview, and understand the main mechanisms of resistance in a wide range of anaerobes.

Anaerobic Gram-Negative Bacteria: Role as a Reservoir of Antibiotic Resistance

BACKGROUND

Anaerobic Gram-negative bacteria (AGNB) play a significant role as both pathogens and essential members of the human microbiota. Despite their clinical importance, there remains limited understanding regarding their antimicrobial resistance (AMR) patterns. This knowledge gap poses challenges in effectively managing AGNB-associated infections, as empirical treatment approaches may not adequately address the evolving resistance landscape. To bridge this research gap, we conducted a comprehensive study aimed at exploring the role of human AGNB as a reservoir of AMR. This can provide valuable insights for the prevention and management of anaerobic infections.

METHODS

We studied the prevalence of AMR and AMR determinants conferring resistance to metronidazole (nimE), imipenem (cfiA), piperacillin-tazobactam (cepA), cefoxitin (cfxA), clindamycin (ermF), chloramphenicol (cat) and mobile genetic elements (MGEs) such as cfiA^IS and IS1186 associated with the cfiA and nim gene expression. These parameters were studied in Bacteroides spp., Fusobacterium spp., Prevotella spp., Veillonella spp., Sutterella spp., and other clinical AGNB.

RESULTS

Resistance to metronidazole, clindamycin, imipenem, piperacillin-tazobactam, cefoxitin and chloramphenicol was 29%, 33.5%, 0.5%, 27.5%, 26.5% and 0%, respectively. The presence of resistance genes, viz., nim, ermF, cfiA, cepA, cfxA, was detected in 24%, 33.5%, 10%, 9.5%, 21.5% isolates, respectively. None of the tested isolates showed the presence of a cat gene and MGEs, viz., cfiA^IS and IS1186. The highest resistance to all antimicrobial agents was exhibited by Bacteroides spp. The association between resistant phenotypes and genotypes was complete in clindamycin, as all clindamycin-resistant isolates showed the presence of ermF gene, and none of the susceptible strains harbored this gene; similarly, all isolates were chloramphenicol-susceptible and also lacked the cat gene, whereas the association was low among imipenem and piperacillin-tazobactam. Metronidazole and imipenem resistance was seen to be dependent on insertion sequences for the expression of AMR genes. A constrained co-existence of cepA and cfiA gene in B. fragilis species was seen. Based on the absence and presence of the cfiA gene, we divided B. fragilis into two categories, Division I (72.6%) and Division II (27.3%), respectively.

CONCLUSION

AGNB acts as a reservoir of specific AMR genes, which may pose a threat to other anaerobes due to functional compatibility and acquisition of these genes. Thus, AST-complying standard guidelines must be performed periodically to monitor the local and institutional susceptibility trends, and rational therapeutic strategies must be adopted to direct empirical management.

The European committee on antimicrobial susceptibility testing disc diffusion susceptibility testing method for frequently isolated anaerobic bacteria

OBJECTIVES

Antimicrobial resistance in anaerobic bacteria is increasing and there is a link between inappropriate antimicrobial therapy and poor clinical outcome in the treatment of infections caused by anaerobic bacteria. Accurate and timely antimicrobial susceptibility testing of anaerobic bacteria is therefore of critical importance. The European Committee on Antimicrobial Susceptibility Testing (EUCAST) has recently described a disc diffusion susceptibility testing method for anaerobic bacteria using fastidious anaerobe agar (FAA) supplemented with 5% defibrinated horse blood (HB). This method was previously validated for Bacteroides spp. only. The aim of this study was to determine the suitability of FAA-HB for disc diffusion and also for frequently isolated anaerobic bacteria.

METHODS

Clinical isolates, including 54 Bacteroides/Phocaeicola/Parabacteroides spp., 49 Prevotella spp., 51 Fusobacterium necrophorum, 58 Clostridium perfringens, and 54 Cutibacterium acnes were evaluated against six antimicrobial agents. MICs were determined by agar dilution following Clinical and Laboratory Standards Institute methodology, modified to use FAA-HB as recommended by EUCAST, instead of supplemented Brucella agar, and disc diffusion was performed on FAA-HB following EUCAST methodology.

RESULTS

Results for quality control strains were reproducible, with 99.3% of zones within range. Disc diffusion by EUCAST methodology was able to distinguish between susceptible and resistant isolates of anaerobic bacteria for benzylpenicillin, piperacillin-tazobactam, meropenem, clindamycin, and metronidazole (98.7% correct categorization). No isolates resistant to vancomycin were tested, but zone diameters correctly categorized the susceptible isolates, and there was a logical relationship between MICs and inhibition zones.

DISCUSSION

The recently published EUCAST method for disc diffusion for anaerobic bacteria based on FAA-HB is a reproducible and accurate method for susceptibility testing of frequently isolated anaerobic bacteria.

Getting with the times: A review of peripartum infections and proposed modernized treatment regimens

This article provides a review of peripartum infections, including intra-amniotic infection, postpartum endometritis, and postabortal infections. We present a case of postabortal infection to frame the review. The microbiology, pathogenesis, risk factors, diagnosis, and treatment of peripartum infections are reviewed, and a critical appraisal of the literature and available guidelines is provided. There is a focus on discussing optimal antimicrobial therapy for treating these infections.

Antibiotic Resistance and Mechanisms of Pathogenic Bacteria in Tubo-Ovarian Abscess

A tubo-ovarian abscess (TOA) is a common type of inflammatory lump in clinical practice. TOA is an important, life-threatening disease, and it has become more common in recent years, posing a major health risk to women. Broad-spectrum antimicrobial agents are necessary to cover the most likely pathogens because the pathogens that cause TOA are polymicrobial. However, the response rate of antibiotic treatment is about 70%, whereas one-third of patients have poor clinical consequences and they require drainage or surgery. Rising antimicrobial resistance serves as a significant reason for the unsatisfactory medical outcomes. It is important to study the antibiotic resistance mechanism of TOA pathogens in solving the problems of multi-drug resistant strains. This paper focuses on the most common pathogenic bacteria isolated from TOA specimens and discusses the emerging trends and epidemiology of resistant Escherichia coli, Bacteroides fragilis, and gram-positive anaerobic cocci. Besides that, new methods that aim to solve the antibiotic resistance of related pathogens are discussed, such as CRISPR, nanoparticles, bacteriophages, antimicrobial peptides, and pathogen-specific monoclonal antibodies. Through this review, we hope to reveal the current situation of antibiotic resistance of common TOA pathogens, relevant mechanisms, and possible antibacterial strategies, providing references for the clinical treatment of drug-resistant pathogens.

Pharmacological potential of seaweed-associated heterotrophic Firmicutes

Seaweed-associated bacterial symbionts are sources of potential pharmacological properties. The present study resulted in the culture-dependent isolation of bioactive heterotrophs belonging to the bacterial phylum Firmicutes, which were dominated more than 30% of the 127 cultivable isolates, among which 23 of them showed potential antimicrobial activities against a wide range of pathogens. The symbionts isolated from the seaweed Sargassum wightii showed significant bioactivity. Those were characterised as Bacillus safensis MTCC13040, B. valismortis MTCC13041, B. velezensis MTCC13044, B. methylotrophicus MTCC13042, Oceanobacillus profundus MTCC13045, B. tequilensis MTCC13043, and B. altitudinis MTCC13046. The organic extracts of the studied isolates showed potential antimicrobial properties against methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococci (minimum inhibitory concentration 6.25-12.5 μg ml^-1 ). The organic extract of B. altitudinis MTCC13046 displayed significantly greater radical quenching ability (IC₉₀ 133 μg ml^-1 , p < 0.05) other than attenuating hydroxymethyl glutaryl coenzyme A reductase (IC₉₀ 10.21 μg ml^-1 , p < 0.05) and angiotensin converting enzyme-1 (IC₉₀ 498 μg ml^-1 , p < 0.05) relative to other studied heterotrophs. The organic extract of B. tequilensis MTCC13043 displayed significantly greater attenuation potential against pro-inflammatory 5-lipooxygenase (IC₉₀ 5.94 μg ml^-1 , p < 0.05) and dipeptidyl peptidase-4 (IC₉₀ 271 μg ml^-1 , p < 0.05). The seaweed-associated B. altitudinis MTCC13046 and B. tequilensis MTCC13043 could be used to develop promising pharmacological leads.

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.

Anaerobic bloodstream infections in Italy (ITANAEROBY): A 5-year retrospective nationwide survey

INTRODUCTION

A lack of updated data on the burden and profile of anaerobic bloodstream infections (ABIs) exists. We assessed the incidence of ABIs and trends in antimicrobial resistance in anaerobes isolated from blood in Italy.

MATERIAL AND METHODS

We conducted a retrospective study on 17 Italian hospitals (2016-2020). Anaerobes isolated from blood culture and their in vitro susceptibility profiles (EUCAST-interpreted) were registered and analyzed.

RESULTS

A total of 1960 ABIs were identified. The mean age of ABIs patients was 68.6 ± 18.5 years, 57.6% were males. The overall incidence rate of ABIs was 1.01 per 10.000 patient-days. Forty-seven% of ABIs occurred in medical wards, 17% in ICUs, 14% in surgical wards, 7% in hemato-oncology, 14% in outpatients. The three most common anti-anaerobic tested drugs were metronidazole (92%), clindamycin (89%) and amoxicillin/clavulanate (83%). The three most common isolated anaerobes were Bacteroides fragilis (n = 529), Cutibacterium acnes (n = 262) and Clostridium perfringens (n = 134). The lowest resistance rate (1.5%) was to carbapenems, whereas the highest rate (51%) was to penicillin. Clindamycin resistance was >20% for Bacteroides spp., Prevotella spp. and Clostridium spp. Metronidazole resistance was 9.2% after excluding C. acnes and Actinomyces spp. Bacteroides spp. showed an increased prevalence of clindamycin resistance through the study period: 19% in 2016, 33% in 2020 (p ≤ 0.001).

CONCLUSIONS

Our data provide a comprehensive overview of the epidemiology of ABIs in Italy, filling a gap that has existed since 1995. Caution is needed when clindamycin is used as empirical anti-anaerobic drug.

Genetic Relatedness, Antibiotic Resistance, and Effect of Silver Nanoparticle on Biofilm Formation by Clostridium perfringens Isolated from Chickens, Pigeons, Camels, and Human Consumers

In this study, we determined the prevalence and toxin types of antibiotic-resistant Clostridium perfringens in chicken, pigeons, camels, and humans. We investigated the inhibitory effects of AgNPs on biofilm formation ability of the isolates and the genetic relatedness of the isolates from various sources determined using RAPD-PCR. Fifty isolates were identified using PCR, and all the isolates were of type A. The cpe and cpb2 genes were detected in 12% and 56% of the isolates, respectively. The effect of AgNPs on biofilm production of six representative isolates indicated that at the highest concentration of AgNPs (100 µg/mL), the inhibition percentages were 80.8–82.8%. The RAPD-PCR patterns of the 50 C. perfringens isolates from various sources revealed 33 profiles and four clusters, and the discriminatory power of RAPD-PCR was high. Multidrug-resistant C. perfringens isolates are predominant in the study area. The inhibition of biofilm formation by C. perfringens isolates was dose-dependent, and RAPD-PCR is a promising method for studying the genetic relatedness between the isolates from various sources. This is the first report of AgNPs’ anti-biofilm activity against C. perfringens from chickens, pigeons, camels, and humans, to the best of our knowledge.

Patterns of bacterial culture and antimicrobial susceptibility test results for dogs with retrobulbar abscesses: 133 cases (2002-2019)

OBJECTIVE

To evaluate patterns of bacterial culture and antimicrobial susceptibility test results for dogs with retrobulbar abscesses and generate recommendations for empirical antimicrobial selection.

ANIMALS

133 dogs examined between 2002 and 2019.

PROCEDURES

Records were retrospectively reviewed to determine type of bacterial culture, number and type of bacterial isolates, antimicrobial susceptibility test results, concurrent and recent antimicrobial exposure, effect of culture results on antimicrobial regimen, and outcome.

RESULTS

Aerobic culture alone was performed in 37 dogs, and aerobic and anaerobic culture was performed in 96 dogs. Isolates were recovered from 96 dogs, with multiple isolates recovered from 54 (56%) of those dogs. Of the 69 dogs for which both aerobic and anaerobic culture was performed and at least 1 isolate was obtained, 34 (49%) had purely aerobic infections, 15 (22%) had mixed aerobic and anaerobic infections, and 20 (29%) had purely anaerobic infections. Pasteurella spp (n = 26), Streptococcus spp (20), and Escherichia coli (12) were the most common aerobic isolates. Bacteroides spp (n = 22), Actinomyces spp (10), and Fusobacterium (10) spp were the most common anaerobic isolates. Susceptibility test results led to changes in the antimicrobial regimen in 37 of 80 (46%) dogs. Of the 76 dogs for which outcome information was available, 78 (97%) recovered.

CLINICAL RELEVANCE

Multipathogen and anaerobic infections were common in dogs with retrobulbar abscesses. Susceptibility data supported the use of amoxicillin-clavulanate or a combination of clindamycin and enrofloxacin as first-line treatments. Additional study is needed to characterize anaerobic antimicrobial susceptibilities and to compare results of susceptibility testing with in vivo responses to antimicrobial administration.

In Vitro Activity of Gepotidacin Against Gram-negative and Gram-positive Anaerobes

Gepotidacin (formerly GSK2140944) is a first-in-class triazaacenaphthylene antibacterial currently in phase III clinical trials. When tested against Gram-negative (n = 333) and Gram-positive (n = 225) anaerobes by agar dilution, gepotidacin inhibited 90% of isolates at concentrations of 4 and 2 μg/mL, respectively. Given gepotidacin’s in vitro activity against the anaerobic isolates tested, further study is warranted to better understand the utility of gepotidacin in the treatment of infections caused by clinically relevant anaerobic organisms.

Bloodstream infection caused by Bacteroides caccae in a patient with renal hypertension: a case report

Bacteroides caccae is an anaerobic bacterium with a reportedly high isolation rate; however, it rarely causes bloodstream infections. Patients with hypertension are at increased risk of developing anaerobic bacterial infection. In this study, we report a case of bacteremia caused by B. caccae in a patient with renal hypertension and gastrointestinal hemorrhage. This study describes the clinical manifestations of bloodstream infection involving B. caccae to provide guidance for laboratory technicians and clinicians. A 42-year-old Chinese man was admitted for gastrointestinal hemorrhage and subsequently diagnosed with anaerobic blood infection. The pathogenic bacteria isolated from anaerobic blood culture bottles were identified as B. caccae by using an automatic bacterial identification instrument and mass spectrometry (MS). B. caccae is an intestinal opportunistic pathogen that can invade the intestinal mucosa and cause anaerobic bloodstream infection. Two or more sets of blood cultures and MS identification can greatly improve the positive detection rate of blood cultures of anaerobic bacteria. Furthermore, the increased drug resistance of anaerobic bacteria necessitates drug sensitivity tests for anaerobic bacteria in many hospitals. Thus, the early prevention and control of primary diseases with appropriate diagnoses and timely anti-infection therapies are necessary to reduce B. caccae bloodstream infection.

Antimicrobial susceptibility profiles of invasive isolates of anaerobic bacteria from a large Canadian reference laboratory: 2012-2019

Anaerobic bacteria can cause severe and life threatening infections. Susceptibility data are relatively limited on anaerobic organisms despite the clinical importance in guiding empiric treatment of infections. To determine antimicrobial susceptibility profiles of clinically significant anaerobic bacteria, isolates obtained from sterile sites submitted to Public Health Ontario Laboratory (2012-2019) were included in this study (N = 5712). Cefoxitin, clindamycin, metronidazole, meropenem, penicillin and piperacillin-tazobactam were tested using the gradient strip method with MICs interpreted based on Clinical and Laboratory Standards Institute guidelines. Bacteroides spp. (N = 958; 16.7%), Clostridium spp. (N = 798; 14.0%), Cutibacterium spp. (N =659; 11.5%) and Actinomyces spp. (N = 551; 7.0%) were the most commonly isolated genera. Bacteroides fragilis isolates were susceptible to cefoxitin (88.4%), clindamycin (68.4%), metronidazole (96.0%), meropenem (99.0%) and piperacillin-tazobactam (98.4%). Other Bacteroides spp. showed reduced susceptibility to several antimicrobials. Clostridium spp. isolates were susceptible to penicillin (69.7%), clindamycin (69.7%) and cefoxitin (76.3%); C. perfringens and C. ramosum showed distinct susceptibility profiles. Susceptibility rates among anaerobes remained relatively unchanged over 8 years with a few exceptions: C. perfringens susceptibility to clindamycin decreased from 91.3% to 60% (p = 0.03); Clostridium spp. susceptibility to penicillin similarly decreased from 82.1% to 65.9% (p = 0.03); Eggerthella spp. susceptibility to piperacillin-tazobactam decreased from 100% to 24.3% (p < 0.001); B. fragilis group susceptibility to cefoxitin decreased from 70.4% to 48.2% (p = 0.05); and Parabacteroides spp. susceptibility to piperacillin-tazobactam decreased from 100% to 25% (p = 0.01). Our findings underscore the need for ongoing surveillance and periodic monitoring of antimicrobial resistance in order to guide empiric therapy.

Antimicrobial susceptibility pattern of oral gram negative anaerobes from Indian subjects

OBJECTIVES

There is paucity of information on the antimicrobial susceptibility pattern of oral anaerobic bacteria. In this study, an attempt has been made to evaluate the antimicrobial susceptibility/resistance trend of oral Gram negative bacteria from Indian subjects.

METHODS

Minimum inhibitory concentrations (MIC) of 304 isolates against twelve different antibiotics were determined using gradient diffusion MIC strips. The organisms were isolated and identified based on phenotypic characteristics and included Porphyromonas gingivalis, Prevotella species, Tannerella forsythia, Fusobacterium nucleatum, Aggregatibacter actinomycetemcoitans, Eickenella corrodens and Capnocytophaga species. For each antimicrobial agent, MIC₅₀ and MIC₉₀ were calculated and expressed.

RESULTS

Resistance to azithromycin, clindamycin, and amoxicillin was observed in most of the anaerobic bacterial species studied. High degree of susceptibility was observed to amoxillin-clavulanic acid, doxycycline and moxifloxacin. A single strain of P. melaninogenica was resistant to moxifloxacin. The susceptibility pattern varied with cephalosporins among species. Ceftriaxone showed highest and cefazolin least efficacy among cephalosporins. All anaerobic bacteria tested were susceptible to metronidazole. Strains of T. forsythia were more resistant to several antibiotics than other anaerobic bacteria. All three species of capnophilic bacteria displayed high degree of resistance to metronidazole and significant resistance to amoxicillin, azithromycin, clindamycin, cefazolin and cefuroxime.

CONCLUSIONS

Amoxicillin-clavulanic acid, doxycycline, moxifloxacin and metronidazole appeared to be the most effective drugs against gram negative anaerobic bacteria. However, the MIC₅₀ and MIC₉₀ values against metronidazole were on the higher side of the normal indicating a potential for developing resistance.

Development of a EUCAST disk diffusion method for the susceptibility testing of rapidly growing anaerobic bacteria using Fastidious Anaerobe Agar (FAA): a development study using Bacteroides species

OBJECTIVES

Antimicrobial resistance among anaerobic bacteria is increasing, leading to a growing demand for inexpensive and reliable susceptibility testing methods. The aim of this study was to determine the suitability of Fastidious Anaerobe Agar (FAA) as a medium for disk diffusion for rapidly growing anaerobic bacteria.

METHODS

Reproducibility of zone diameters and quality of growth were tested using six quality control (QC) strains. We compared four anaerobic incubation systems, two incubation temperatures (35°C and 37°C), and FAA from four manufacturers. The effect of incubation for 16-20 hours instead of 24 hours was tested on ten randomly selected isolates of the Bacteroides fragilis group. The final method was tested on 170 clinical B. fragilis-group isolates and compared to agar dilution MICs.

RESULTS

After 24 hours' incubation, all QC strains demonstrated confluent growth. The different anaerobic incubation systems were equal regarding quality of growth and zone diameters. Incubation at 35°C resulted in slightly larger zones (1-2 mm) than at 37°C. Except for Acumedia FAA, the different manufacturers showed good agreement in zone diameters. All B. fragilis-group isolates displayed confluent growth after 16-20 hours. Metronidazole inhibition zones correlated well with the reference MICs. There was an area of poorer separation for meropenem and piperacillin-tazobactam between 19-27 and 14-23 mm respectively. Prolonged incubation (40-44 h) of clindamycin resulted in better separation and the area of overlap was reduced from 13 to 8 mm compared with 16-20 hours' incubation.

CONCLUSION

FAA is a suitable medium for disk diffusion of these rapidly growing anaerobic bacteria.

Diversity of antimicrobial resistance genes in Bacteroides and Parabacteroides strains isolated in Germany

OBJECTIVES

Bacteroides spp. are normal constituents of the human intestinal microflora, but they are also able to cause severe diseases. The aim of this study was to determine the diversity of antibiotic resistance genes found in phenotypically resistant Bacteroides and Parabacteroides strains.

METHODS

A total of 71 phenotypically resistant Bacteroides spp. from human clinical specimens were screened for the antibiotic resistance genes cfiA, tetQ, tetM, tet36, cepA, cfxA, nim, ermG, ermF, bexA, bla_VIM, bla_NDM, bla_KPC, bla_OXA-48 and bla_GES. The presence of these genes was compared with phenotypic resistance to ampicillin/sulbactam, cefoxitin, ceftolozane/tazobactam, piperacillin/tazobactam, imipenem, meropenem, meropenem/vaborbactam, clindamycin, moxifloxacin, tigecycline, eravacycline and metronidazole.

RESULTS

tetQ was the most frequently detected gene, followed by cfiA, ermF, cfxA, ermG, cepA, nim and bexA. None of the strains were positive for tetM, tet36, bla_VIM, bla_NDM, bla_KPC, bla_OXA-48 or bla_GES. Resistance to the tested β-lactams was mainly linked to the presence of the cfiA gene. Clindamycin resistance correlated with the presence of the genes ermG and ermF. The bexA gene was found in six strains, but only two of them were resistant to moxifloxacin. Tigecycline and eravacycline showed good activities despite the frequent occurrence of tetQ. The nim gene was detected in six isolates, five of which were resistant to metronidazole.

CONCLUSION

The findings of our study support the general belief that antimicrobial resistance within Bacteroides should be taken into consideration. This underlines the necessity of reliable routine antimicrobial susceptibility test methods for anaerobic bacteria and the implementation of antimicrobial surveillance programmes worldwide.

Anaerobic resistance: should we be worried?

PURPOSE OF REVIEW

Anaerobic bacteria are implicated in a broad range of infections and can cause significant morbidity and mortality. As such, development of antimicrobial resistance (AMR) increases the risk of worse clinical outcomes and death.

RECENT FINDINGS

Anaerobe AMR is highly variable according to region and species included in the survey. The overall trend is to increasing resistance, particularly in Europe and Asia, and in the Bacteroides fragilis group and Clostridium sp. Conversely, with the decline in RT027, resistance in Clostridiodes difficile is decreasing. Resistance to moxifloxacin and clindamycin has reached 30-50%, whereas prevalence of metronidazole and carbapenem resistance is generally low. Infections due to multidrug anaerobes have been increasingly reported, with clinical studies demonstrating adverse clinical outcomes, including higher mortality, with anaerobic resistance or inappropriate therapy. The role of antimicrobial stewardship in the setting of increasing anaerobe resistance is yet to be fully elucidated.

SUMMARY

These findings highlight the importance of continuous surveillance in monitoring emerging trends in anaerobe AMR. Mean inhibitory concentrations should be reported due to variable susceptibility breakpoints and for detection of isolates with reduced susceptibility. At a local level, the clinical microbiology laboratory has a key role in identifying and undertaking susceptibility testing to inform individual patient management, develop local antibiograms and liaise with antimicrobial stewardship teams. A greater understanding of the clinical impact of anaerobic resistance and the role of antimicrobial stewardship in preventing resistance is required.

Bacteroides Fragilis Vertebral Osteomyelitis and Discitis: "Back" to Susceptibility Testing

Genetic testing of anaerobic isolates can be important for proper antimicrobial stewardship to identify the appropriate narrow-spectrum treatment for a polymicrobial infection.

Eggerthella lenta Bloodstream Infections Are Associated With Increased Mortality Following Empiric Piperacillin-Tazobactam (TZP) Monotherapy: A Population-based Cohort Study

Background

Eggerthella lenta is a anaerobic gram-positive bacilli associated with polymicrobial intraabdominal infections. Recently, E. lenta was recognized as an important cause of anaerobic bloodstream infections (BSIs) associated with high mortality. Eggerthella lenta has been reported to have high minimal inhibitory concentrations (MICs) to piperacillin-tazobactam (TZP), a broad-spectrum antibiotic with anaerobic coverage commonly used in multiple centers for empiric treatment of abdominal sepsis.

Methods

We describe a retrospective population-based analysis of invasive E. lenta infections from 2009 through 2015. A logistic regression analysis for 30-day mortality risk factors was conducted.

Results

We identified 107 E. lenta infections, 95 (89%) were BSIs, 11 (10%) skin and soft tissue infections, and 1 intraabdominal abscess. Polymicrobial infections were found in 40%; 72% of isolates were from a gastrointestinal source, most commonly appendicitis (33%) of which two-thirds were perforated. TZP MIC50 and MIC90 for E. lenta isolates were 32 μg/mL and 64 μg/mL, respectively. The overall 30-day mortality for BSI was 23% and was independently associated with empiric TZP monotherapy (odds ratio [OR], 4.4; 95% confidence interval [CI], 1.2-16; P = .02) and intensive care unit stay (OR, 6.2; 95% CI, 1.4-27.3; P = .01). Thirty-day mortality rates were significantly influenced by the use of different TZP MIC breakpoints.

Conclusions

Our results demonstrate the increased recognition of E. lenta as an anaerobic opportunistic pathogen and highlight the need for improved empiric antimicrobial guidelines and TZP MIC breakpoints with better correlation to clinical outcomes to guide appropriate management of invasive E. lenta infections.

Streamlined Genetic Manipulation of Diverse Bacteroides and Parabacteroides Isolates from the Human Gut Microbiota

We have entered an era when studies of the gut microbiota are transitioning from basic questions of composition and host effects to understanding the microbial molecules that underlie compositional shifts and mediate health and disease processes. The importance of the gut Bacteroidales to human health and disease and their potential as a source of engineered live biotherapeutics make these bacteria of particular interest for in-depth mechanistic study. However, there are still barriers to the genetic analysis of diverse Bacteroidales strains, limiting our ability to study important host and community phenotypes identified in these strains. Here, we have overcome many of these obstacles by constructing a series of vectors that allow easy genetic manipulation in diverse gut Bacteroides and Parabacteroides strains. These constructs fill a critical need and allow streamlined allelic replacement in diverse gut Bacteroidales, including the growing number of multiantibiotic-resistant strains present in the modern-day human intestine.

Studies of the gut microbiota have dramatically increased in recent years as the importance of this microbial ecosystem to human health and disease is better appreciated. The Bacteroidales are the most abundant order of bacteria in the healthy human gut and induce both health-promoting and disease-promoting effects. There are more than 55 species of gut Bacteroidales with extensive intraspecies genetic diversity, especially in regions involved in the synthesis of molecules that interact with other bacteria, the host, and the diet. This property necessitates the study of diverse species and strains. In recent years, the genetic toolkit to study these bacteria has greatly expanded, but we still lack a facile system for creating deletion mutants and allelic replacements in diverse strains, especially with the rapid increase in resistance to the two antibiotics used for genetic manipulation. Here, we present a new versatile and highly efficient vector suite that allows the creation of allelic deletions and replacements in multiresistant strains of Bacteroides and Parabacteroides using a gain-of-function system based on polysaccharide utilization. These vectors also allow for easy counterselection independent of creating a mutant background strain, using a toxin from a type VI secretion system of Bacteroides fragilis. Toxin production during counterselection is induced with one of two different molecules, providing flexibility based on strain phenotypes. This family of vectors greatly facilitates functional genetic analyses and extends the range of gut Bacteroidales strains that can be genetically modified to include multiresistant strains that are currently genetically intractable with existing genetic tools.

Obligate anaerobes are abundant in human necrotizing soft tissue infection samples - a metagenomics analysis

Necrotizing soft tissue infections (NSTIs) are associated with high morbidity and mortality and are increasing in incidence. Proper identification of the microbial causes of NSTIs is a crucial step in diagnosis and treatment, but the majority of data collected are culture based, which is biased against fastidious organisms, including obligate anaerobes. The goal of this study was to address this gap in knowledge by characterizing NSTI microbial communities through molecular diagnostics. We performed 16S rRNA sequencing on human NSTI samples and identified five genera most commonly found in NSTIs (Prevotella, Bacteroides, Peptoniphilus, Porphyromonas, and Enterococcus). We found that a >70% contribution of obligate anaerobes to the bacterial population distribution was associated with NSTI mortality, and that NSTI samples, from both survivors and non-survivors, had an increased relative abundance of gram negative bacteria compared to those of abscess patients. Based on our data, we conclude that obligate anaerobes are abundant in NSTIs and a high relative abundance of anaerobes is associated with a worse outcome. We recommend increasing anaerobe antibiotic coverage during the treatment of NSTIs even when anaerobes are not found by traditional clinical microbiology methods, and especially when there is a clinical suspicion for anaerobe involvement.

Antimicrobial susceptibility and clinical findings of significant anaerobic bacteria in southern Spain

The objectives of this study were to report on the antimicrobial susceptibility of 276 clinically significant anaerobic bacteria belonging to the major genera isolated between May 2017 and November 2018 in a tertiary hospital in Granada (Spain) and to describe key clinical features of the patients. Species identification was performed by MALDI-TOF MS. Antimicrobial susceptibility tests were performed against penicillin, amoxicillin-clavulanic, imipenem, meropenem, moxifloxacin, clindamycin, metronidazole, vancomycin, and piperacillin-tazobactam using the gradient diffusion technique and EUCAST breakpoints (except for moxifloxacin). The most frequent anaerobes were Bacteroides (29.7%; n = 82), Clostridioides difficile (15.9%, n = 44), Prevotella (10.8%, n = 30), and Propionibacterium (10.7%, n = 25). Metronidazole was not universally active against all genera tested, and some isolates showed resistance to this drug. Almost all tested anaerobes were susceptible to carbapenems and amoxicillin-clavulanate except for Clostridioides difficile (resistance rate of 94%) and Bacteroides (19%), respectively. High overall resistance rates to clindamycin were observed, especially for genera Finegoldia (54%), Bacteroides (49%), and Prevotella (40%). Resistance rates to carbapenems and amoxicillin-clavulanate were very low for the majority of tested genera but were high for Clostridioides difficile and Bacteroides spp., respectively. Resistance to clindamycin was very high, especially for Bacteroides, Finegoldia magna, Prevotella and Peptoniphilus. Routine antimicrobial susceptibility testing for anaerobes contributes information on the global situation and allows empirical therapies to be selected in accordance with local data on resistant strains.

The prevalence of plasmid-coded cpe enterotoxin, β2 toxin, tpeL toxin, and tetracycline resistance in Clostridium perfringens strains isolated from different sources

Clostridium perfringens, an anaerobic, spore-forming bacterium, causes infections in humans and animals by producing several toxins encoded by genes found either on the chromosomes or on diverse plasmids. The plasmids may code for more than one toxin gene or antimicrobial-resistance gene. In this study, the prevalence of the β2, cpe and tpeL toxin genes and the tetA(P), tetB(P) and tetM tetracycline-resistance genes, in 56 strains of C. perfringens type A isolated from diseased domestic animals and 15 strains isolated from chickens, was compared with that in 74 strains isolated from other sources. The frequency of chromosome-associated cpe enterotoxin genes was higher in strains not isolated from diseased domestic animals; however, plasmid-associated cpe genes were found in strains from some animal sources more than others. Enterotoxin production was detected in some strains that had chromosomal or plasmid cpe genes, but not in all. The percentages of strains carrying β2 toxin genes among chicken, swine, human patient and soil isolates were higher than those among bovine, canine and food isolates. The incidence of the tpeL toxin gene was lower than that of the β2 gene. Phenotypic resistance to tetracycline was found in more than 50% of the porcine, bovine, and canine isolates, which carried a wide range of plasmids of 2-100 kb size, most of which had the tcpH clostridial transfer gene. PCR amplified tetA(P) and tetB(P) genes from most isolates from diseased animals. Some strains that carried <40 kb plasmids and had the tcpH gene also had one or more toxin genes or tetracycline-resistance gene. This study shows that the prevalence of plasmid-borne toxins and antimicrobial resistance genes varied among C. perfringens strains isolated from different sources. Plasmids of smaller size than those previously reported in strains of C. perfringens type A may also harbor toxin genes and antimicrobial-resistance genes.

Antimicrobial Susceptibility Patterns of Anaerobic Bacterial Clinical Isolates From 2014 to 2016, Including Recently Named or Renamed Species

BACKGROUND

Anaerobic bacterial resistance trends may vary across regions or institutions. Regional susceptibility patterns are pivotal in the empirical treatment of anaerobic infections. We determined the antimicrobial resistance patterns of clinically important anaerobic bacteria, including recently named or renamed anaerobes.

METHODS

A total of 521 non-duplicated clinical isolates of anaerobic bacteria were collected from a tertiary-care hospital in Korea between 2014 and 2016. Anaerobes were isolated from blood, body fluids, and abscess specimens. Each isolate was identified by conventional methods and by Bruker biotyper mass spectrometry (Bruker Daltonics, Leipzig, Germany) or VITEK matrix-assisted laser desorption ionization time-of-flight mass spectrometry (bioMérieux, Marcy-l'Étoile, France). Antimicrobial susceptibility was tested using the agar dilution method according to the CLSI guidelines. The following antimicrobials were tested: piperacillin-tazobactam, cefoxitin, cefotetan, imipenem, meropenem, clindamycin, moxifloxacin, chloramphenicol, tetracycline, and metronidazole.

RESULTS

Most Bacteroides fragilis isolates were susceptible to piperacillin-tazobactam, imipenem, and meropenem. The non-fragilis Bacteroides group (including B. intestinalis, B. nordii, B. pyogenes, B. stercoris, B. salyersiae, and B. cellulosilyticus) was resistant to meropenem (14%) and cefotetan (71%), and Parabacteroides distasonis was resistant to imipenem (11%) and cefotetan (95%). Overall, the Prevotella and Fusobacterium isolates were more susceptible to antimicrobial agents than the B. fragilis group isolates. Anaerobic gram-positive cocci exhibited various resistance rates to tetracycline (6-86%). Clostridioides difficile was highly resistant to penicillin, cefoxitin, imipenem, clindamycin, and moxifloxacin.

CONCLUSIONS

Piperacillin-tazobactam, cefoxitin, and carbapenems are highly active β-lactam agents against most anaerobes, including recently named or renamed species.

Clinical efficacy of 12-h metronidazole dosing regimens in patients with anaerobic or mixed anaerobic infections

Traditional metronidazole dosing regimens utilize an every 8 h dosing strategy to treat anaerobic and mixed anaerobic infections. However, pharmacokinetic data demonstrate that the half-life of metronidazole is 8-12 h and blood levels at 12 h exceed the in vitro minimum inhibitory concentration (MIC) for most anaerobic infections. The primary objective of this study was to evaluate the frequency of clinical cure among patients who received metronidazole every 12 h compared with those who received an every 8 h frequency. Secondary endpoints included duration of antibiotics, hospital length of stay, escalation of antibiotic therapy, microbiologic cure, and mortality.

METHODS

This retrospective, single-center, pre-post intervention study of 200 patients between June 2014 to July 2016.

RESULTS

No significant differences in clinical cure for every 12 h versus every 8 h metronidazole dosing regimens (85% for both groups, p = 1.00) were found. There were no differences in any of the secondary endpoints, with a mean duration of antibiotic therapy being 5.9 versus 5.8 days and a hospital length of stay averaging 8.1 versus 6.7 days for the 12- and 8-h dosing groups, respectively (p > 0.05).

DISCUSSION

Findings validate pharmacokinetic data suggesting that an extended metronidazole dosing interval effectively treats anaerobic infections.

In vitro activity of tigecycline and comparators against a European collection of anaerobes collected as part of the Tigecycline Evaluation and Surveillance Trial (T.E.S.T.) 2010-2016

The Tigecycline Evaluation and Surveillance Trial (T.E.S.T.) is a global program that aims to monitor the in vitro antimicrobial activities of current therapeutic agents against clinical isolates. This study presents surveillance data for Gram-positive and Gram-negative anaerobic isolates (N = 7008) collected from nine European countries between 2010 and 2016. Presented in this study are antimicrobial susceptibility data, according to the European Committee for Antimicrobial Susceptibility Testing (EUCAST) breakpoints, and minimum inhibitory concentration (MIC) distributions. The antimicrobial agents tested were cefoxitin (Gram-negative isolates only), clindamycin, meropenem, metronidazole, penicillin (Gram-positive isolates only), piperacillin-tazobactam and tigecycline. Among all Gram-positive and Gram-negative anaerobes, the lowest rates of resistance were to meropenem and metronidazole (0.0%-1.7% and 0.0%-1.9%, respectively). High rates of resistance were reported to clindamycin, in particular among isolates of the Bacteroides fragilis group (22.1%-48.1%) and Prevotella spp. (10.9%-32.2%). The majority of MIC distributions were unimodal, with the exception of clindamycin, which were mostly bimodal. Fifty percent of Gram-negative isolates gave tigecycline MICs between 0.06 and 1 mg/L, and 50% of Gram-positive isolates exhibited tigecycline MICs between 0.06 and 0.25 mg/L. The findings of this study suggest that the majority of anaerobic isolates were susceptible to meropenem and metronidazole, and that tigecycline remained active, but clindamycin resistance is a cause for concern in Europe. Surveillance studies, such as T.E.S.T., provide information on changes in the susceptibility of clinically important pathogens to commonly prescribed antimicrobial agents, and can highlight problems of antimicrobial resistance that need to be addressed.

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.