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

Overview of Anaerobic infections in children and their treatment

Anaerobic bacteria can cause many infections in children. Because they predominant in the normal human skin and mucous membranes bacterial flora, they are often associated with bacterial infections that originate from these sites. They are difficult to isolate from infectious sites, and are frequently missed. Anaerobic infections can occur in all body sites, including the central nervous system, oral cavity, head and neck, chest, abdomen, pelvis, skin, and soft tissues. Anaerobes colonize the newborn after birth and have been isolated in several types of neonatal infections. These include cellulitis of the site of fetal monitoring, neonatal aspiration pneumonia, bacteremia, conjunctivitis, omphalitis, and infant botulism. Management of anaerobic infection is challenging because of the the slow growth of these bacteria, by their polymicrobial nature and by the growing antimicrobial resistance of anaerobic. Antimicrobial therapy may be the only treatment required, and may also be an adjunct to a surgical approach. Polymicrobial aerobic-anaerobic infection generally requires delivering antimicrobial therapy effective against all pathogens. The antibiotics with the greatest activity against anaerobes include carbapenems, beta-lactam/beta-lactamase inhibitor combinations, metronidazole, and chloramphenicol. Antimicrobial resistance is growing among anaerobic bacteria. The major increased in resistance have been reported with clindamycin, cephamycins, and moxifloxacin against Bacteroides fragilis group and related strains. Resistance patterns vary between different geographic areas and medical facilities.

Antimicrobial resistance surveillance of Bacteroides fragilis isolated from blood cultures, Europe, 2022 (ReSuBacfrag)

BACKGROUND

Bacteroides fragilis is the most frequent cause of anaerobic bacteraemia. Although recent data suggest a rise in antimicrobial resistance (AMR) of this and other anaerobic bacteria, surveillance remains limited due to a lack of both data availability and comparability. However, a newly introduced standardised method for antimicrobial susceptibility testing (AST) of anaerobic bacteria has made larger scale surveillance possible for the first time.

AIM

To investigate phenotypic AMR of Bacteroides fragilis isolates from bacteraemia across Europe in 2022.

METHODS

In a multicentre approach, clinical microbiology laboratories in Europe were invited to contribute results of AST for Bacteroides fragilis blood culture isolates (including only the first isolate per patient and year). AST of a selection of four antibiotics was performed locally by participating laboratories in a prospective or retrospective manner, using the new EUCAST disc diffusion method on fastidious anaerobe agar (FAA-HB).

RESULTS

A total of 16 European countries reported antimicrobial susceptibilities in 449 unique isolates of Bacteroides fragilis from blood cultures in 2022. Clindamycin demonstrated the highest resistance rates (20.9%, range 0 - 63.6%), followed by piperacillin-tazobactam (11.1%, 0 - 54.5%), meropenem (13.4%, 0 - 45.5%), and metronidazole (1.8%, 0 - 20.0%), all with wide variation between countries.

CONCLUSION

Considering that the mean resistance rates across Europe were higher than expected for three of the four anti-anaerobic antibiotics under surveillance, both local AST of clinically relevant isolates of Bacteroides fragilis and continued surveillance on an international level is warranted.

Anaerobes in diabetic foot infections: pathophysiology, epidemiology, virulence, and management

SUMMARYDiabetic foot infections (DFI) are a public health problem worldwide. DFI are polymicrobial, biofilm-associated infections involving complex bacterial communities organized in functional equivalent pathogroups, all including anaerobes. Indeed, multiple pathophysiological factors favor the growth of anaerobes in this context. However, the prevalence, role, and contribution of anaerobes in wound evolution remain poorly characterized due to their challenging detection. Studies based on culture reviewed herein showed a weighted average of 17% of patients with anaerobes. Comparatively, the weighted average of patients with anaerobes identified by 16S rRNA gene sequencing was 83.8%. Culture largely underestimated not only the presence but also the diversity of anaerobes compared with cultivation-independent approaches but both methods showed that anaerobic Gram-negative bacilli and Gram-positive cocci were the most commonly identified in DFI. Anaerobes were more present in deeper lesions, and their detection was associated with fever, malodorous lesions, and ulcer depth and duration. More specifically, initial abundance of Peptoniphilus spp. was associated with ulcer-impaired healing, Fusobacterium spp. detection was significantly correlated with the duration of DFI, and the presence of Bacteroides spp. was significantly associated with amputation. Antimicrobial resistance of anaerobes in DFI remains slightly studied and warrants more consideration in the context of increasing resistance of the most frequently identified anaerobes in DFI. The high rate of patients with DFI-involving anaerobes, the increased knowledge on the species identified, their virulence factors, and their potential role in wound evolution support recommendations combining debridement and antibiotic therapy effective on anaerobes in moderate and severe DFI.

Antimicrobial susceptibility profile of clinically relevant Bacteroides, Phocaeicola, Parabacteroides and Prevotella species, isolated by eight laboratories in the Netherlands

OBJECTIVES

Recently, reports on antimicrobial-resistant Bacteroides and Prevotella isolates have increased in the Netherlands. This urged the need for a surveillance study on the antimicrobial susceptibility profile of Bacteroides, Phocaeicola, Parabacteroides and Prevotella isolates consecutively isolated from human clinical specimens at eight different Dutch laboratories.

METHODS

Each laboratory collected 20-25 Bacteroides (including Phocaeicola and Parabacteroides) and 10-15 Prevotella isolates for 3 months. At the national reference laboratory, the MICs of amoxicillin, amoxicillin/clavulanic acid, piperacillin/tazobactam, meropenem, imipenem, metronidazole, clindamycin, tetracycline and moxifloxacin were determined using agar dilution. Isolates with a high MIC of metronidazole or a carbapenem, or harbouring cfiA, were subjected to WGS.

RESULTS

Bacteroides thetaiotaomicron/faecis isolates had the highest MIC90 values, whereas Bacteroides fragilis had the lowest MIC90 values for amoxicillin/clavulanic acid, piperacillin/tazobactam, meropenem, imipenem and moxifloxacin. The antimicrobial profiles of the different Prevotella species were similar, except for amoxicillin, for which the MIC50 ranged from 0.125 to 16 mg/L for Prevotella bivia and Prevotella buccae, respectively. Three isolates with high metronidazole MICs were sequenced, of which one Bacteroides thetaiotaomicron isolate harboured a plasmid-located nimE gene and a Prevotella melaninogenica isolate harboured a nimA gene chromosomally.Five Bacteroides isolates harboured a cfiA gene and three had an IS element upstream, resulting in high MICs of carbapenems. The other two isolates harboured no IS element upstream of the cfiA gene and had low MICs of carbapenems.

CONCLUSIONS

Variations in resistance between species were observed. To combat emerging resistance in anaerobes, monitoring resistance and conducting surveillance are essential.

Fifty years devoted to anaerobes: historical, lessons, and highlights

Renew interest and enthusiasm for anaerobes stem from both technological improvements (culture media, production of an adequate anaerobic atmosphere, identification methods) and greater awareness on the part of clinicians. Anaerobic infections were historically treated empirically, targeting the species known to be involved in each type of infection. Prevotella, fusobacteria, and Gram-positive cocci (GPAC) were considered responsible for infections above the diaphragm whereas for intra-abdominal infections, Bacteroides of the fragilis group (BFG), GPAC and clostridia were predominantly implicated. The antibiotic susceptibility of anaerobes was only taken into consideration by the clinician in the event of treatment failure or when faced with infections by multidrug-resistant bacteria (MDR). The evolution of antibiotic resistance together with clinical failures due to the absence of detection of hetero-resistant clones has resulted in a greater need for accessible antibiotic susceptibility testing (AST) and disc diffusion method. Improved isolation and identification of anaerobes, along with the availability of accessible and robust methods for performing AST, will ensure that treatment, whether empirical or guided by an antibiogram, will lead to better outcomes for anaerobic infections.

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.

First large-scale study of antimicrobial susceptibility data, and genetic resistance determinants, in Fusobacterium necrophorum highlighting the importance of continuing focused susceptibility trend surveillance

OBJECTIVES

The objective of the study was to explore antimicrobial resistance gene determinant, and phenotypic antibiotic susceptibility, data for Fusobacterium necrophorum from a collection of UK strains. Antimicrobial resistance genes detected in publicly available assembled whole genome sequences were investigated for comparison.

METHODS

Three hundred and eighty five F. necrophorum strains (1982-2019) were revived from cryovials (Prolab). Subsequent to sequencing (Illumina) and quality checking, 374 whole genomes were available for analysis. Genomes were interrogated, using BioNumerics (bioMérieux; v 8.1), for the presence of known antimicrobial resistance genes (ARGs). Agar dilution susceptibility results for 313 F. necrophorum isolates (2016-2021) were also examined.

RESULTS

The phenotypic data for the 313 contemporary strains demonstrated potential resistance to penicillin in three isolates, using EUCAST v 11.0 breakpoints, and 73 (23%) strains using v 13.0 analysis. All strains were susceptible to multiple agents using v 11.0 guidance other than clindamycin (n = 2). Employing v 13.0 breakpoints, metronidazole (n = 3) and meropenem (n = 13) resistance were also detected. The tet(O), tet(M), tet(40), aph(3')-III, ant(6)-la and bla_OXA-85 ARGs were present in publicly available genomes. tet(M), tet(32), erm(A) and erm(B) were found within the UK strains, with correspondingly raised clindamycin and tetracycline minimum inhibitory concentrations.

CONCLUSIONS

Susceptibility to antibiotics recommended for the treatment of F. necrophorum infections should not be assumed. With evidence of potential ARG transmission from oral bacteria, and the detection of a transposon-mediated beta-lactamase resistance determinant in F. necrophorum, surveillance of both phenotypic and genotypic antimicrobial susceptibility trends must continue, and increase.

Characterization of mobile genetic elements in multidrug-resistant Bacteroides fragilis isolates from different hospitals in the Netherlands

OBJECTIVES

Five human clinical multidrug-resistant (MDR) Bacteroides fragilis isolates, including resistance to meropenem and metronidazole, were recovered at different hospitals in the Netherlands between 2014 and 2020 and sent to the anaerobic reference laboratory for full characterization.

METHODS

Isolates were recovered from a variety of clinical specimens from patients with unrelated backgrounds. Long- and short-read sequencing was performed, followed by a hybrid assembly to study the presence of mobile genetic elements (MGEs) and antimicrobial resistance genes (ARGs).

RESULTS

A cfxA gene was present on a transposon (Tn) similar to Tn4555 in two isolates. In two isolates a novel Tn was present with the cfxA gene. Four isolates harbored a nimE gene, located on a pBFS01_2 plasmid. One isolate contained a novel plasmid carrying a nimA gene with IS1168. The tetQ gene was present on novel conjugative transposons (CTns) belonging to the CTnDOT family. Two isolates harbored a novel plasmid with tetQ. Other ARGs in these isolates, but not on an MGE, were: cfiA, ermF, mef(EN2), and sul2. ARGs harboured differed between isolates and corresponded with the observed phenotypic resistance.

CONCLUSIONS

Novel CTns, Tns, and plasmids were encountered in the five MDR B. fragilis isolates, complementing our knowledge on MDR and horizontal gene transfer in anaerobic bacteria.

Population pharmacokinetics of levornidazole in healthy subjects and patients, and sequential dosing regimen proposal using pharmacokinetic/pharmacodynamic analysis

Although sequential treatment with levornidazole has been used for anaerobic infection in clinical practice, there is no evidence-based dosing regimen. This study aimed to evaluate the pharmacokinetics (PK) of levornidazole in healthy subjects and patients, and to propose an evidence-based sequential dosing regimen by pharmacokinetic/pharmacodynamic (PK/PD) analysis. A population PK model was built using the data of 116 Chinese subjects, including 88 healthy young subjects, 12 healthy elderly subjects, and 16 patients with intra-abdominal anaerobic infection. PK/PD analysis was performed combining the minimum inhibitory concentration (MIC) values of levornidazole against 375 anaerobic strains. Four sequential dosing regimens (500 mg q12h, 1000 mg loading dose followed by 500 mg q12h, 750 mg q24h, and 1000 mg q24h) were evaluated in terms of cumulative fraction of response (CFR) and probability of target attainment (PTA) by Monte Carlo simulation. The concentration data of levornidazole and its active metabolites were described adequately by two- and one-compartment models, respectively. Body weight was identified as a significant covariate of levornidazole clearance. Simulations showed that satisfactory PTA (>90%) was achieved for the four dosing regimens when MIC ≤1 mg/L. Considering the simulation results, patients' safety and compliance, levornidazole 750 mg intravenous infusion q24h for 2 days followed by 750 mg oral dose q24h for 5 days was optimal for Bacteroides spp. with an identified MIC ≤1 mg/L.

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.

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.

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.