Recent evolution of antibiotic resistance in the anaerobes as compared to previous decades

Diagnostic and epidemiological landscape of anaerobic bacteria in Europe, 2020-2023 (ANAEuROBE)

INTRODUCTION

Despite being implicated in a wide spectrum of community- and healthcare-acquired infections, anaerobes have not yet been incorporated into systematic surveillance programs in Europe.

METHODS

We conducted a multicentre retrospective observational study analysing all anaerobic strains isolated from blood cultures in 44 European Hospital Centres over a 4-y period (2020-2023). Diagnostic approach, epidemiology, and antimicrobial susceptibility according to EUCAST v. 15.0 were investigated.

RESULTS

Our study included 14,527 anaerobes, most of which were Gram-positive (45%) or Gram-negative (40%) bacilli. MALDI-TOF coupled to mass spectrometry was the most widely used tool for species identification (98%). Antimicrobial susceptibility testing was performed in the vast majority of centres, using mostly gradient diffusion strip (77%) and disk diffusion (45%) methods according to EUCAST guidelines. The most prevalent species were Cutibacterium acnes (18.7%), Bacteroides fragilis (16.3%), Clostridium perfringens (5.3%), Bacteroides thetaiotaomicron (4.2%), Fusobacterium nucleatum (3.5%), and Parvimonas micra (3.4%). C. acnes showed high resistance to benzylpenicillin (18%), clindamycin (39%), and imipenem (19% and 13% by MIC methods and disk diffusion, respectively). B. fragilis showed high resistance to amoxicillin/clavulanate (24%), piperacillin/tazobactam (22% and 14% by MIC methods and disk diffusion, respectively), clindamycin (22% by both MIC methods and disk diffusion), meropenem (13%), and metronidazole (10%, only by disk diffusion). A similar resistance pattern was observed in B. thetaiotaomicron, Bacteroides ovatus, and Parabacteroides distasonis. C. perfringens showed high resistance to clindamycin (69% and 45% by MIC methods and disk diffusion, respectively), while benzylpenicillin and metronidazole maintained over 90% activity. F. nucleatum showed high resistance to benzylpenicillin (11%), while Fusobacterium necrophorum showed alarming rates of resistance to clindamycin (12%), meropenem (16%) and metronidazole (11%).

CONCLUSIONS

This study presented an up-to-date analysis of the diagnostics and epidemiology of anaerobic bacteria in Europe, providing insights for future comparative analyses and the development of antimicrobial diagnostic and management strategies, as well as the optimization of current antibiotic treatments.

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.

Clostridium neonatale antimicrobial susceptibility, genetic resistance determinants, and genotyping: a multicentre spatiotemporal retrospective analysis

BACKGROUND

Clostridium neonatale was isolated during an outbreak of neonatal necrotizing enterocolitis (NEC) in 2002. C. neonatale was validated as a new species within the genus Clostridium sensu stricto in 2018. In the present study, we evaluated the antimicrobial susceptibility, genetic determinants of resistance, and phylogenetic relationships of a collection of clinical isolates of C. neonatale.

METHODS

C. neonatale strains (n = 68) were isolated from the stools of preterm neonates who either developed NEC or were asymptomatic carriers of C. neonatale in different periods and in different hospitals. Antimicrobial susceptibility was determined by the disc diffusion method. The MICs of clindamycin, cefotaxime and tetracycline were determined. Genetic determinants of resistance were screened by PCR (n = 68) and WGS (n = 35). Genotyping of the isolates was performed by MLST.

RESULTS

Antimicrobial resistance was found to clindamycin (n = 24; 35%), cefotaxime (n = 7; 10%) and tetracycline (n = 1; 1%). One clindamycin-resistant isolate carried erm(B) by PCR. In addition, one isolate carrying tet(M) was tetracycline resistant (MIC = 16 mg/L) and 44 isolates carrying either tet(O), tet(32) or tet(M) were tetracycline susceptible (MICs < 16 mg/L). MLST showed that ST2 and ST15 were significantly associated with tet(32) (P < 0.0001) and tet(O) (P < 0.0001), respectively. From WGS, we identified aph(3')-IIa and blaTEM-116 genes and a blaCBP-1-like gene.

CONCLUSIONS

C. neonatale is susceptible to anti-anaerobic molecules but resistant to clindamycin, cefotaxime and tetracycline. Genes encoding tetracycline ribosomal protection, macrolide-lincosamide-streptogramin B rRNA methyltransferase, aminoglycoside 3'-phosphotransferase and β-lactamases have been identified in genomic regions flanked by mobile genetic elements.

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.

Genomic analyses of Bacteroides fragilis: subdivisions I and II represent distinct species

Introduction. Bacteroides fragilis is a Gram-negative anaerobe that is a member of the human gastrointestinal microbiota and is frequently found as an extra-intestinal opportunistic pathogen. B. fragilis comprises two distinct groups - divisions I and II - characterized by the presence/absence of genes [cepA and ccrA (cfiA), respectively] that confer resistance to β-lactam antibiotics by either serine or metallo-β-lactamase production. No large-scale analyses of publicly available B. fragilis sequence data have been undertaken, and the resistome of the species remains poorly defined.Hypothesis/Gap Statement. Reclassification of divisions I and II B. fragilis as two distinct species has been proposed but additional evidence is required.Aims. To investigate the genomic diversity of GenBank B. fragilis genomes and establish the prevalence of division I and II strains among publicly available B. fragilis genomes, and to generate further evidence to demonstrate that B. fragilis division I and II strains represent distinct genomospecies.Methodology. High-quality (n=377) genomes listed as B. fragilis in GenBank were included in pangenome and functional analyses. Genome data were also subject to resistome profiling using The Comprehensive Antibiotic Resistance Database.Results. Average nucleotide identity and phylogenetic analyses showed B. fragilis divisions I and II represent distinct species: B. fragilis sensu stricto (n=275 genomes) and B. fragilis A (n=102 genomes; Genome Taxonomy Database designation), respectively. Exploration of the pangenome of B. fragilis sensu stricto and B. fragilis A revealed separation of the two species at the core and accessory gene levels.Conclusion. The findings indicate that B. fragilis A, previously referred to as division II B. fragilis, is an individual species and distinct from B. fragilis sensu stricto. The B. fragilis pangenome analysis supported previous genomic, phylogenetic and resistome screening analyses collectively reinforcing that divisions I and II are two separate species. In addition, it was confirmed that differences in the accessory genes of B. fragilis divisions I and II are primarily associated with carbohydrate metabolism and suggest that differences other than antimicrobial resistance could also be used to distinguish between these two species.

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.

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.

Antimicrobial Susceptibility Profile of Rare Anaerobic Bacteria

Anaerobes play an important role in clinically relevant infections and resistance is increasing worldwide. We tested 120 rare anaerobic isolates belonging to 16 genera for antimicrobial resistance using the agar dilution method and compared those results to the time-saving E-test method. The susceptibility data for 12 antimicrobial substances (benzylpenicillin, ampicillin/sulbactam, piperacillin/tazobactam, imipenem, meropenem, cefoxitin, metronidazole, moxifloxacin, clindamycin, doxycycline, tigecycline, eravacycline) were collected. Susceptibility testing showed low resistance to β-lactam/β-lactamase inhibitor combinations and no resistance to carbapenems and tigecycline. We observed moderate to high rates of resistance to moxifloxacin and clindamycin which differed depending on the methodology used. The essential and categorical agreement was over 90% for ampicillin/sulbactam, meropenem, moxifloxacin, and tigecycline. For metronidazole and clindamycin, the essential agreement was below 90% but the categorical agreement was near or above 90%. Penicillin presented with the lowest categorical agreement of 86.7% and a very high very major error rate of 13.3%. The resistance rates reported in this study are concerning and show the importance of routine susceptibility testing. Further investigations are necessary to determine the reason for high error rates and how to improve susceptibility testing of fastidious anaerobes.

Time to reconsider moxifloxacin anti-anaerobic activity?

Large data on moxifloxacin activity on anaerobes are old. Moxifloxacin is often used for empiric therapy therefore the knowledge of current epidemiologic data is fundamental. We analyzed 69 anaerobic strains, from a recent multicenter Italian study, for moxifloxacin susceptibility. Using EUCAST criteria 81% of Bacteroides spp. and 48% of anaerobes other than Bacteroides were resistant to moxifloxacin. Using CLSI criteria moxifloxacin resistance rates decrease to 35% for all anaerobes, and to 41% for Bacteroides spp. We reported an alarming increase in moxifloxacin resistance among anaerobes in Italy.

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 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.

Total Laboratory Automation for Rapid Detection and Identification of Microorganisms and Their Antimicrobial Resistance Profiles

At a time when diagnostic bacteriological testing procedures have become more complex and their associated costs are steadily increasing, the expected benefits of Total laboratory automation (TLA) cannot just be a simple transposition of the traditional manual procedures used to process clinical specimens. In contrast, automation should drive a fundamental change in the laboratory workflow and prompt users to reconsider all the approaches currently used in the diagnostic work-up including the accurate identification of pathogens and the antimicrobial susceptibility testing methods. This review describes the impact of TLA in the laboratory efficiency improvement, as well as a new fully automated solution for AST by disk diffusion testing, and summarizes the evidence that implementing these methods can impact clinical outcomes.

Antimicrobial susceptibility patterns of anaerobic bacteria at an Irish University Hospital over a ten-year period (2010-2020)

OBJECTIVES

In recent years various clinical studies have demonstrated poor outcomes in infections caused by anaerobic bacteria due to inappropriate therapy, directly due to emergence of resistant strains. This is a concern given that many anaerobic infections are treated empirically with metronidazole or a beta-lactam/beta-lactamase inhibitor combinations (e.g., co-amoxiclav, piperacillin-tazobactam). To date there is a paucity of available data on antimicrobial resistance trends of anaerobic bacteria in Ireland, and our study aims to determine such patterns among isolates processed at our institution over the last ten years.

METHODS

Significant anaerobic bacteria isolated from clinical specimens processed at our laboratory from January 2010 to January 2020 inclusive were reviewed. Bacteria were identified using MALDI-TOF, with E-tests used for antimicrobial susceptibility testing. Data was processed through WHONET.

RESULTS

A total of 2098 clinically significant anaerobic bacterial isolates from blood cultures (31%), theatre/intraoperative specimens (30%), aspirates and drain fluid (22%) and wound swabs (17%) were reviewed during the study period; with the majority of isolates being Bacteroides spp (32.79%, n = 688) and Clostridium spp (18.68%, n = 392). With isolates demonstrating well-recognised or inherent resistances excluded, overall resistance to tested antimicrobials was 6.40% to penicillin, 1.71% to metronidazole, 1.43% to co-amoxiclav, 13.63% to clindamycin, 0.43% to piperacillin-tazobactam and 0% to meropenem.

CONCLUSION

Metronidazole and beta-lactam/beta-lactamase inhibitor combinations remain highly efficacious against the majority of anaerobic isolates reviewed, and can safely be used as empiric therapy in suspected anaerobic infections. However, periodic surveillance of resistance trends remains important.

The facultative human oral pathogen Prevotella histicola in equine cheek tooth apical/ periapical infection: a case report

BACKGROUND

Prevotella histicola is a facultative oral pathogen that under certain conditions causes pathologies such as caries and periodontitis in humans. Prevotella spp. also colonize the oral cavity of horses and can cause disease, but P. histicola has not yet been identified.

CASE PRESENTATION

A 12-year-old Tinker mare was referred to the clinic for persistent, malodorous purulent nasal discharge and quidding. Conservative antibiotic (penicillin), antiphlogistic (meloxicam), and mucolytic (dembrexine-hydrochloride) treatment prior to referral was unsuccessful and symptoms worsened. Oral examination, radiography, sino-/ rhinoscopy, and standing computed tomography revealed severe apical/ periapical infection of the upper cheek tooth 209 with accompanying unilateral sinonasal inflammation and conchal necrosis. The tooth exhibited extensive subocclusal mesial infundibular cemental hypoplasia and caries, and an occlusal fissure fracture. After mechanical debridement and thermoplastic resin filling of the spacious subocclusal carious infundibular lesion, the tooth was extracted intraorally. The sinusitis and conchal necrosis were treated transendoscopically. Selective bacteriological swab cultures of affected tooth roots and subsequent matrix-assisted laser desorption ionization-time of flight mass spectrometry showed an infection with the obligate anaerobic, Gram-negative bacterium P. histicola. Surgical intervention and adapted antibiotic therapy led to normal healing without complications.

CONCLUSIONS

This study provides the first documented case of dental infection in a horse caused by P. histicola at once indicating necessity of more sufficient microbiological diagnostics and targeted antibiotic treatment in equine dental practice. This finding is also conducive to understand species-specific Prevotella diversity and cross-species distribution.

Complete genome analysis of Lactobacillus fermentum YLF016 and its probiotic characteristics

Lactobacillus fermentum (L. fermentum) YLF016 is a well-characterized probiotic with several favorable characteristics. This study aimed to analyze the probiotic characteristics of L. fermentum and uncover the genes implicated in its potential probiotic ability on the base of its genomics features. The complete genome of L. fermentum YLF016 was found to have a circular chromosome of 2,094,354 bp, and 51.46% G + C content without any plasmid. Its chromosome contained 2,130 predicted protein-encoding genes, 58 tRNA, and 15 rRNA-encoding genes. Also, it was found to have many other probiotic properties, such as a high survival rate in the gastrointestinal tract with strong adherence to intestinal cells, antibacterial activity against pathogens, and antioxidant activity. Moreover, the genome sequence analysis demonstrated specific genes coding for carbon metabolism pathway, genetic adaption, stress resistance, and adhesive ability. Further analysis revealed its non-hemolytic activity and its non-functional ability of virulence factors. In conclusion, L. fermentum YLF016 possesses many valuable probiotic properties that refer to its potential probiotic ability.

Anaerobic infections in patients admitted in various surgical units of a tertiary care hospital of north India: neglected but important

Background and Objectives:

Anaerobic infections are usually caused by the host’s endogenous flora due to a breach in the anatomical barriers and Bacteroides spp. are the most notorious organisms associated with anaerobic infections. The identification of anaerobes has been a challenge since times. MALDI-TOF-MS is a boon for aiding the rapid detection of anaerobic organisms and has helped us to enlist the distribution of various anaerobic pathogens.

Materials and Methods:

This retrospective analysis (January 2018 to December 2019) was carried out in a tertiary care hospital in North India, in which the anaerobic microbiological profile of all patients admitted to surgical wards, ICU, and OPD of various departments (Orthopedics, Surgery, Gynecology, and Obstetrics) was reviewed. Samples received were immediately processed aerobically (5% sheep blood agar and Mac Conkeyagar) as well as anaerobically (RCM and freshly prepared sheep blood agar) as per the laboratory protocols.

Results:

Bacteroides fragilis (19.12%) was the most common anaerobe whereas among aerobes Escherichia coli (30.2%) followed by Klebsiella pneumoniae (10.34%) were most commonly isolated. The majority of patients were males (56%) and the most common presentation was with abscesses (21.4%). Polymicrobial infections (69.51%) outnumbered monomicrobial ones (30.48%).

Conclusion:

There is a paucity of literature on anaerobe isolation from surgical infections from our country which motivated us to study anaerobic infections and the high sample size in our institute enabled us to study surgical infections from an anaerobic perspective. This will add to the knowledge of microbiologists and clinicians. MALDI-TOF MS helped in rapid and accurate identification and hence we could report a wider spectrum of organisms in our study.

Etiology and antimicrobial susceptibility profiles of anaerobic bacteria isolated from clinical samples in a university hospital in Madrid, Spain

BACKGROUND

The anaerobic infection management is usually based on empirical treatment because anaerobic culture techniques take a long time due to their fastidious nature. The aim of this study was to analyze the etiological profile of severe anaerobic infections and AST data from clinical anaerobic bacteria isolated in a tertiary hospital in Madrid (Spain).

MATERIAL AND METHODS

A consecutive study was carried out over 19 months in Ramón y Cajal Universitary Hospital, Madrid. Clinical samples were processed in appropriate anaerobic media and incubated using Anoxomat system. Identification was performed by MALDI-TOF. AST were determined with gradient diffusion method using EUCAST (penicillin, co-amoxiclav, imipenem, clindamycine and metronidazole) or CLSI (cefoxitin) breakpoints.

RESULTS

During the period of study, 503 anaerobic microorganisms isolated from 424 clinical samples were included. Twenty-six percent of the cultures were monomicrobial, while 70.0% also contained aerobic bacteria. The most common source of infection was abscesses (26%), while blood infections represented the 11%. Anaerobic gram-negative bacilli were predominant (41%), being Bacteroides fragilis (13%) the most prevalent overall; anaerobic gram-positive bacilli represented 35%, anaerobic gram-positive cocci 19% and anaerobic gram-negative cocci 5%. Metronidazole and imipenem were the most effective agents tested against anaerobic bacteria, while clindamycin presented higher resistance rates.

CONCLUSION

Antimicrobial susceptibility surveillance of anaerobic bacteria should be performed to monitor changes in resistance patterns and to be able to optimize empiric antimicrobial treatment. Reliable species identification and quick reporting of results would guide clinicians to select the optimal antimicrobial therapy.

Disruption of Metallostasis in the Anaerobic Human Pathogen Fusobacterium nucleatum by the Zinc Ionophore PBT2

The Gram-negative anaerobe Fusobacterium nucleatum is an opportunistic human pathogen, most frequently associated with periodontal disease through dental biofilm formation and, increasingly, with colorectal cancer development and progression. F. nucleatum infections are routinely treated by broad-spectrum β-lactam antibiotics and metronidazole. However, these antibiotics can negatively impact the normal microflora. Therefore, the development of novel narrow-spectrum antimicrobials active against anaerobic pathogens is of great interest. Here, we examined the antimicrobial Zn ionophore PBT2, an 8-hydroxyquinoline analogue with metal chelating properties, against a single type isolate F. nucleatum ATCC 25586. PBT2-Zn was a potent inhibitor of growth and exhibited synergistic bactericidal (>3-log₁₀ killing) activity at 5× MIC in planktonic cells, and at the MIC in biofilms grown in vitro. Physiological and transcriptional analyses uncovered a strong cellular response relating to Zn and Fe homeostasis in PBT2-Zn treated cells across subinhibitory and inhibitory concentrations. At 1× MIC, PBT2 alone induced a 3.75-fold increase in intracellular Zn, whereas PBT2-Zn challenge induced a 19-fold accumulation of intracellular Zn after 2 h. A corresponding 2.1-fold loss of Fe was observed at 1× MIC. Transcriptional analyses after subinhibitory PBT2-Zn challenge (0.125 μg/mL and 200 μM ZnSO₄) revealed significant differential expression of 15 genes at 0.5 h, and 12 genes at 1 h. Upregulated genes included those with roles in Zn homeostasis (e.g., a Zn-transporting ATPase and the Zn-sensing transcriptional regulator, smtB) and hemin transport (hmuTUV) to re-establish Fe homeostasis. A concentration-dependent protective effect was observed for cells pretreated with hemin (50 μg/mL) prior to PBT2-Zn challenge. The data presented here supports our proposal that targeting the disruption of metallostasis by Zn-translocating ionophores is a strategy worth investigating further for the treatment of Gram-negative anaerobic pathogens.

Broth Microdilution and Gradient Diffusion Strips vs. Reference Agar Dilution Method: First Evaluation for Clostridiales Species Antimicrobial Susceptibility Testing

Antimicrobial susceptibility testing of anaerobes is challenging. Because MIC determination is recommended by both CLSI and EUCAST, commercial broth microdilution and diffusion strip tests have been developed. The reliability of broth microdilution methods has not been assessed yet using the agar dilution reference method. In this work, we evaluated two broth microdilution kits (MICRONAUT-S Anaerobes^® MIC and Sensititre Anaerobe MIC^®) and one gradient diffusion strip method (Liofilchem^®) for antimicrobial susceptibility testing of 47 Clostridiales isolates (Clostridium, Clostridioides and Hungatella species) using the agar dilution method as a reference. The evaluation focused on comparing six antimicrobial molecules available in both microdilution kits. Analytical performances were evaluated according to the Food and Drug Administration (FDA) recommendations. Essential agreements (EA) and categorical agreements (CA) varied greatly according to the molecule and the evaluated method. Vancomycin had values of essential and categorical agreements above 90% for the three methods. The CA fulfilled the FDA criteria for three major molecules in the treatment of Gram-positive anaerobic infections (metronidazole, piperacillin/tazobactam and vancomycin). The highest rate of error was observed for clindamycin. Multicenter studies are needed to further validate these results.

Prevotella melaninogenica, a Sentinel Species of Antibiotic Resistance in Cystic Fibrosis Respiratory Niche?

The importance and abundance of strict anaerobic bacteria in the respiratory microbiota of people with cystic fibrosis (PWCF) is now established through studies based on high-throughput sequencing or extended-culture methods. In CF respiratory niche, one of the most prevalent anaerobic genera is Prevotella, and particularly the species Prevotella melaninogenica. The objective of this study was to evaluate the antibiotic susceptibility of this anaerobic species. Fifty isolates of P. melaninogenica cultured from sputum of 50 PWCF have been included. Antibiotic susceptibility testing was performed using the agar diffusion method. All isolates were susceptible to the following antibiotics: amoxicillin/clavulanic acid, piperacillin/tazobactam, imipenem and metronidazole. A total of 96% of the isolates (48/50) were resistant to amoxicillin (indicating beta-lactamase production), 34% to clindamycin (17/50) and 24% to moxifloxacin (12/50). Moreover, 10% (5/50) were multidrug-resistant. A significant and positive correlation was found between clindamycin resistance and chronic azithromycin administration. This preliminary study on a predominant species of the lung “anaerobiome” shows high percentages of resistance, potentially exacerbated by the initiation of long-term antibiotic therapy in PWCF. The anaerobic resistome characterization, focusing on species rather than genera, is needed in the future to better prevent the emergence of resistance within lung microbiota.

Antibiotic resistance pattern of Bacteroides fragilis isolated from clinical and colorectal specimens

BACKGROUND

Bacteroides fragilis is a part of the normal gastrointestinal flora, but it is also the most common anaerobic bacteria causing the infection. It is highly resistant to antibiotics and contains abundant antibiotic resistance mechanisms.

METHODS

The antibiotic resistance pattern of 78 isolates of B. fragilis (22 strains from clinical samples and 56 strains from the colorectal tissue) was investigated using agar dilution method. The gene encoding Bacteroides fargilis toxin bft, and antibiotic resistance genes were targeted by PCR assay.

RESULTS

The highest rate of resistance was observed for penicillin G (100%) followed by tetracycline (74.4%), clindamycin (41%) and cefoxitin (38.5%). Only a single isolate showed resistance to imipenem which contained cfiA and IS1186 genes. All isolates were susceptible to metronidazole. Accordingly, tetQ (87.2%), cepA (73.1%) and ermF (64.1%) were the most abundant antibiotic-resistant genes identified in this study. MIC values for penicillin, cefoxitin and clindamycin were significantly different among isolates with the cepA, cfxA and ermF in compare with those lacking such genes. In addition, 22.7 and 17.8% of clinical and GIT isolates had the bft gene, respectively.

CONCLUSIONS

The finding of this study shows that metronidazole is highly in vitro active agent against all of B. fragilis isolates and remain the first-line antimicrobial for empirical 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.

First case of abdominal infection caused by bacteroides fluxus

Bacteroides fluxus is a Gram-negative anaerobic bacillus isolated from human faeces in healthy individuals. Until now, this bacterium had not been involved in human diseases. We report the first case of abdominal infection due to this microorganism in an elderly patient. A 76-year-old man with a history of chronic pulmonary obstructive disease presented with dyspnea, orthopnea and cough. The clinical evolution worsened with both a colonic ischemia and further diffuse peritonitis of pancreatic origin. Peritoneal fluid was obtained and the culture yielded B. fluxus in pure culture. Resistance to penicillin, amoxicillin-clavulanate, clindamycin and moxifloxacin was documented. Treatment with meropenem + linezolid was started, but the patient finally died due to a multiorganic failure.

Next-generation sequencing-based clinical metagenomics identifies Prevotella pleuritidis in a diabetic adolescent with large parapneumonic effusion and negative growth of pleural fluid culture: a case report

We report a 12-year-old diabetic boy with a right-sided parapneumonic effusion and pneumonia who failed initial empirical antibiotics. Prevotella pleuritidis was identified from the pleural fluid using next-generation sequencing-based clinical metagenomics with cultures of pleural fluid and blood resulting negative. The patient responded well to intravenous meropenem followed by oral metronidazole.

Antimicrobial Susceptibility Patterns and Wild-Type MIC Distributions of Anaerobic Bacteria at a German University Hospital: A Five-Year Retrospective Study (2015-2019)

Local antimicrobial susceptibility surveys are crucial for optimal empirical therapy guidelines and for aiding in antibiotic stewardship and treatment decisions. For many laboratories, a comprehensive overview of local antimicrobial susceptibility patterns of anaerobic bacteria is still lacking due to the long incubation time and effort involved. The present study investigates the antimicrobial susceptibility patterns and related clinical and demographic data of 2856 clinical isolates of anaerobic bacteria that were submitted for analysis to the Institute for Medical Microbiology and Hygiene of the Freiburg University Medical Center (a tertiary university medical center in Southern Germany) between 2015 and 2019. Antimicrobial susceptibility testing has been carried out according to the European Committee on Antimicrobial Susceptibility Testing (EUCAST) guideline. Minimum inhibitory concentration (MIC)₅₀ and MIC₉₀ for penicillin, metronidazole, moxifloxacin, and clindamycin were established for Gram-positive anaerobes and for ampicillin-sulbactam, meropenem, metronidazole, moxifloxacin, and clindamycin for Gram-negative anaerobes. The distribution of MIC-values for various antibiotics against anaerobic bacteria was also established, especially for those having no specific breakpoints according to EUCAST guidelines. Most clinically relevant anaerobic bacteria originated from general surgery, neurological, and orthopedic wards. A high proportion of isolates were resistant to moxifloxacin and clindamycin indicating the importance of their susceptibility testing before administration. Based on our study metronidazole and other β-lactam/β-lactamase inhibitor combinations such as ampicillin-sulbactam remain suitable for empirical treatment of infections with anaerobic bacteria.

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.

Antibiotic Resistance of Human Periodontal Pathogen Parvimonas micra Over 10 Years

Changes were evaluated over 10 years in the in vitro resistance of human periodontopathic strains of Parvimonas micra to four antibiotics. Subgingival biofilms culture positive for P. micra from 300 United States adults with severe periodontitis in 2006, and from a similar group of 300 patients in 2016, were plated onto anaerobically incubated enriched Brucella blood agar alone, or supplemented with either doxycycline (4 mg/L), clindamycin (4 mg/L), amoxicillin (8 mg/L), or metronidazole (16 mg/L). P. micra growth on antibiotic-supplemented media indicated in vitro resistance to the evaluated antibiotic concentration. P. micra resistance was significantly more frequent among patients in 2016, as compared to 2006, for doxycycline (11.3% vs. 0.3% patients; 37.7-fold increase), and clindamycin (47.3% vs. 2.0% patients; 23.7-fold increase) (both p < 0.001), whereas resistance to amoxicillin (2.3% vs. 1.0% patients) and metronidazole (0% vs. 0.3% patients) remained low and statistically unchanged between the two patient groups (p-values > 0.05). No P. micra isolates in 2006 or 2016 were jointly resistant in vitro to both amoxicillin and metronidazole. The alarming increases in subgingival P. micra resistance to doxycycline and clindamycin raise serious questions about the empiric use of these antibiotics, either locally or systemically, in the treatment of United States periodontitis patients harboring subgingival P. micra.

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.

Antimicrobial Susceptibility and Clonality of Vaginally Derived Multidrug-Resistant Mobiluncus Isolates in China

Here, the antimicrobial susceptibility, resistance mechanisms, and clonality of Mobiluncus sp. isolates recovered from gynecological outpatients in China were investigated. Compared to M. mulieris, M. curtisii exhibited higher antimicrobial resistance to metronidazole, clindamycin, and tetracycline. Whole-genome sequencing indicated that the clindamycin resistance gene erm(X) was located on a transposable element, Tn5432, which was composed of two IS1249 sequences. Phylogenetic analysis indicated that Mobiluncus spp. had high diversity, with isolates being grouped into several sporadic clades.

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.

Trends and Impact in Antimicrobial Resistance Among Bacteroides and Parabacteroides Species in 2007-2012 Compared to 2013-2017

Purpose: The aim of this study was to analyze the susceptibility of Bacteroides and Parabacteroides spp. strains, isolated from patients hospitalized in the clinical hospital in Poland to penicillin, amoxicillin with clavulanic acid, imipenem, clindamycin, and metronidazole. Methods: We analyzed susceptibility of 476 isolates to routinely use for the treatment of anaerobic bacterial infections antibiotics. E test method was used to determining the minimal inhibitory concentration values. To show the trend of drug resistance, we compared data from two periods within the years 2003-2017. Results: Research results indicate that the problem of resistance is mainly related to strains belonging to non-fragilis Bacteroides. In the analyzed periods, there was an increase in the percentage of clindamycin-resistant isolates (35.21% vs. 53.33%), amoxicillin/clavulanic acid (2.83% vs. 8.15%), and imipenem (1.41% vs. 3.7%). In isolates belonging to Parabacteroides distasonis, we observed a constant high (∼50%) percentage of clindamycin-resistant strains. The overwhelming majority of B. fragilis strains were resistant to penicillin (>95%) and about 20% of the isolates were not susceptible to clindamycin. Conclusions: Clindamycin, due to the high and increasing percentage of resistant strains, may not be a good choice in the empirical therapy of infections caused by Bacteroides and P. distasonis. Our study highlighted the importance of a routine or at least periodic monitoring of antimicrobial susceptibility of anaerobic Gram-negative bacilli, providing important information for appropriate therapy. The study shows that infection caused (or suspected of being caused) by Bacteroides and Parabacteroides spp. can be empirically treated with metronidazole or imipenem.

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.

Antimicrobial susceptibility profiles of anaerobic bacteria, isolated from human clinical specimens, within different European and surrounding countries. A joint ESGAI study

OBJECTIVES

Studies on the antimicrobial susceptibility profile of anaerobic bacteria are underrepresented in the literature. Within this study we aim to give an extensive overview of the differences in antimicrobial susceptibility profiles between different European and surrounding countries.

METHODS

Minimal inhibitory concentration (MIC) data of different antibiotics were collected from 10 participating laboratories, representing an equal number of countries. All MIC's were determined using Etest, according to the protocol used by the participating laboratory. Anaerobic genera represented by at least 10 clinical isolates were included in the study.

RESULTS

Each country tested different antibiotics, sometimes depending on the kind of infection and/or the anaerobic species isolated. All countries tested clindamycin and metronidazole. Resistance rates differed remarkably between the different countries. Especially in Kuwait, resistance was high for all tested antibiotics. Unexpected metronidazole resistance was observed for Finegoldia magna isolates, Peptoniphilus isolates and Eggerthella lenta isolates.

CONCLUSIONS

Due to the extensive differences in antimicrobial susceptibility profile of anaerobic bacteria isolated within different countries, we strongly recommend to perform this kind of study on a regular basis.

Zerumbone Suppresses Enterotoxigenic Bacteroides fragilis Infection-Induced Colonic Inflammation through Inhibition of NF-κΒ

Enterotoxigenic Bacteroides fragilis (ETBF) is human intestinal commensal bacterium and a potent initiator of colitis through secretion of the metalloprotease Bacteroides fragilis toxin (BFT). BFT induces cleavage of E-cadherin in colon cells, which subsequently leads to NF-κB activation. Zerumbone is a key component of the Zingiber zerumbet (L.) Smith plant and can exhibit anti-bacterial and anti-inflammatory effects. However, whether zerumbone has anti-inflammatory effects in ETBF-induced colitis remains unknown. The aim of this study was to determine the anti-inflammatory effect of orally administered zerumbone in a murine model of ETBF infection. Wild-type C57BL/6 mice were infected with ETBF and orally administered zerumbone (30 or 60 mg/kg) once a day for 7 days. Treatment of ETBF-infected mice with zerumbone prevented weight loss and splenomegaly and reduced colonic inflammation with decreased macrophage infiltration. Zerumbone treatment significantly decreased expression of IL-17A, TNF-α, KC, and inducible nitric oxide synthase (iNOS) in colonic tissues of ETBF-infected mice. In addition, serum levels of KC and nitrite was also diminished. Zerumbone-treated ETBF-infected mice also showed decreased NF-κB signaling in the colon. HT29/C1 colonic epithelial cells treated with zerumbone suppressed BFT-induced NF-κB signaling and IL-8 secretion. However, BFT-mediated E-cadherin cleavage was unaffected. Furthermore, zerumbone did not affect ETBF colonization in mice. In conclusion, zerumbone decreased ETBF-induced colitis through inhibition of NF-κB signaling.

Redundant combinations of antianaerobic antimicrobials: impact of pharmacist-based prospective audit and feedback and prescription characteristics

This study aimed to evaluate the impact of the intervention targeting the redundant combination of antianaerobic antimicrobials on its incidence and associated antimicrobial consumption. To reveal the characteristics of the combination and the change in the related workload over time was an additional aim of the study. The combinations of metronidazole or clindamycin with antianaerobic antimicrobials were classified into redundant or acceptable, according to the target indications. A pharmacist-based prospective audit and feedback targeting the redundant antianaerobic combination was conducted. Segmented regression analysis was performed to evaluate the impact of the intervention. As a quantitative index of the interventional activity, the change in the number of signed consultation notes was evaluated. After the initiation of the intervention, the median monthly cumulative incidence of the redundant combination decreased from 5.29 (Interquartile range [IQR] 4.94-5.70) to 3.33 (IQR 2.87-3.71) (p < 0.001) per 1000 admissions per month. The consumption of concurrently administered metronidazole and clindamycin decreased from 3.34 (IQR 2.97-4.10) to 1.74 (IQR 1.19-1.93) (p < 0.001) per 1000 patient-days per month. Segmented regression analysis revealed that the monthly cumulative incidence decreased by 28.5% after the initiation of the intervention (change in level - 1.640, p = 0.019) and the monthly consumption decreased by 33.9% (change in level - 1.409, p = 0.009). The number of consultation notes per 1000 admissions per month decreased over time (regression coefficient - 0.004, p < 0.001). The pharmacist-based intervention significantly reduced the incidence and associated antimicrobial consumption of the redundant antianaerobic combination. The overall related workload reduced steadily over time.

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.

Empirical metronidazole for patients with severe bacterial infection: A systematic review with meta-analysis and trial sequential analysis

BACKGROUND

Metronidazole is the preferred empirical anti-anaerobic agent for patients with suspected anaerobic infection. The balance between benefits and harms of empirical metronidazole is unclear. We aimed to assess patient-important benefits and harms of empirical metronidazole vs placebo/no treatment in adult patients with severe bacterial infection of any origin.

METHODS

We conducted a systematic review with meta-analysis and trial sequential analysis of randomized clinical trials assessing empirical metronidazole vs placebo/no treatment in adult hospitalized patients with severe bacterial infection. The review was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) statement, the Cochrane Handbook and the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) methodology. A protocol and statistical analysis plan was published prior to conducting the review.

RESULTS

We included a total of nine trials (n = 1753 patients), all of which were adjudicated as having high risk of bias. We found no difference in the primary outcome mortality within 90 days (relative risk 1.56, 95% confidence interval 0.39-6.25). Fewer patients receiving metronidazole had secondary infections (relative risk 0.43, 95% CI: 0.27-0.68). Trial sequential analysis indicated high risk of random errors due to lack of data, and the quality of evidence was very low for all outcomes.

CONCLUSIONS

There is low quantity and quality of evidence supporting the use of empirical metronidazole in adult patients with severe bacterial infections of any origin, and no firm evidence for benefit or harm.

Antimicrobial susceptibility against metronidazole and carbapenem in clinical anaerobic isolates from Pakistan

Background

Globally metronidazole and carbapenem resistance in anaerobic organisms is increasing necessitating continuous surveillance to guide selection of empirical treatment. In this study we have determined metronidazole resistance in anaerobes using MIC Evaluator strips (M.I.C.E strips). Carbapenem resistance was evaluated only in metronidazole resistant isolates.

Material and methods

The study was conducted at the Aga Khan University (AKU) Hospital laboratory, Karachi, Pakistan (2014–2017). Metronidazole and imipenem resistance was evaluated using M.I.C.E strips and minimum inhibitory concentrations (MICs) were interpreted using Clinical Laboratory Standards Institute (CLSI) criteria. Clinical details including demographics, prolonged hospital stay, malignancy, transplant, dialysis, diabetes, site of infection and outcome were analyzed for association with metronidazole resistance.

Results

Of the 223 clinically significant isolates, 39 (17.5%) were metronidazole resistant (excluding the inherently resistant organisms; for example Cutibacterium species). Imipenem resistance was determined in 29 metronidazole resistant isolates and of these 7 (24.1%) were found to be resistant. Proportion of metronidazole resistant strains was highest amongst Bacteroides species. A significant increase in metronidazole resistance from 12.3% in 2010–2011 to 17.5% in the current study was found. Carbapenem resistance also emerged in the period 2014–2017.

Isolates from malignancy and transplant patients showed lower odds of developing metronidazole resistance (0.003(95% CI: 1.7–17.9)). Prolonged hospital stay was not associated with metronidazole resistance (1.1((95% CI: 0.5–2.5)).

Conclusion

The rising trend of metronidazole resistance and emergence of carbapenem resistance in anaerobic bacteria is alarming. Continued surveillance with strengthening of laboratory capacity regarding anaerobic susceptibility testing is urgently needed in Pakistan.

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 presence of antibiotic resistance genes and bft genes as well as antibiotic susceptibility testing of Bacteroides fragilis strains isolated from inpatients of the Infant Jesus Teaching Hospital, Warsaw during 2007-2012

The purpose of this study was to assess drug susceptibility of clinical B. fragilis strains and to determine any correlation between drug resistance and the presence of specific genes. Antimicrobial susceptibility was assessed using E-tests. All isolates were analyzed with the PCR technique for the presence of antibiotic resistance genes (cepA, cfxA, cfiA, ermF, ermB, ermG, nim), insertion sequences elements (IS1186, IS1187, IS1188, IS942), and enterotoxin-encoding genes (bft). Susceptibility tests yielded the following rates of resistance to the evaluated antibiotics: penicillin G (100%), clindamycin (22.5%), cefoxitin (6.3%), amoxicillin/clavulanic acid (1.8%). All strain were susceptible to imipenem, and metronidazole. The following antibiotic resistance genes were detected in the evaluated isolates: cepA (in 96.4% of isolates), cfxA (in 12.6%), cfiA (in 1.8%), and ermF (in 25.2%). Genes ermB, ermG, and nim were not found. The presence of the cepA gene showed no correlation with the penicillin G MIC. However, we observed a high correlation between cefoxitin MIC values and the presence of gene cfxA as well as a nearly complete correlation between clindamycin MIC values and the presence of gene ermF. The presence of a bft gene was detected in 14.4% of the analyzed B. fragilis isolates; with the bft-1 allele found in 75%, bft-2 in 25%, and bft-3 in none of the isolates. Antibiotic susceptibility profiles of enterotoxin gene-positive isolates in our study did not differ from those of enterotoxin gene-negative isolates.

The emergence of antimicrobial resistance in environmental strains of the Bacteroides fragilis group

Anaerobic bacteria of the genus Bacteroides are a large group of commensal microorganisms that colonize the human and animal digestive tract. The genus Bacteroides and the closely related genus Parabacteroides include the Bacteroides fragilis group (BFG) of potentially pathogenic bacteria which are frequently isolated from patients with anaerobic infections. The aim of this study was to assess the antimicrobial resistance of environmental strains of the Bacteroides fragilis group. Strains were isolated from human feces, hospital wastewater, influent (UWW) and effluent (TWW) wastewater from a wastewater treatment plant (WWTP), and from the feces of lab rats as a negative control to monitor the entire route of transmission of BFG strains from humans to the environment. The resistance of 123 environmental BFG strains to six antibiotic groups was analyzed with the use of culture-dependent methods. Additionally, the presence of 25 genes encoding antibiotic resistance was determined by PCR. The analyzed environmental BFG strains were highly resistant to the tested antibiotics. The percentage of resistant strains differed between the analyzed antibiotics and was determined at 97.56% for ciprofloxacin, 49.59% for erythromycin, 44.71% for ampicillin, 35.77% for tetracycline, 32.52% for amoxicillin/clavulanic acid, 26.83% for chloramphenicol, 26.01% for clindamycin, 11.38% for moxifloxacin, and 8.94% for metronidazole. The highest drug-resistance levels were observed in the strains isolated from UWW and TWW samples. The mechanisms of antibiotic-resistance were determined in phenotypically resistant strains of BFG. Research has demonstrated the widespread presence of genes encoding resistance to chloramphenicol (100% of all chloramphenicol-resistant strains), tetracyclines (97.78% of all tetracycline-resistant strains), macrolides, lincosamides and streptogramins (81.97% of all erythromycin-resistant strains). Genes encoding resistance to β-lactams and fluoroquinolones were less prevalent. None of the metronidazole-resistant strains harbored the gene encoding resistance to nitroimidazoles. BFG strains isolated from UWW and TWW samples were characterized by the highest diversity of antibiotic-resistance genes and were most often drug-resistant and multidrug-resistant. The present study examines the potential negative consequences of drug-resistant and multidrug-resistant BFG strains that are evacuated with treated wastewater into the environment. The transmission of these bacteria to surface water bodies can pose potential health threats for humans and animals; therefore, the quality of treated wastewater should be strictly monitored.

Metronidazole: an update on metabolism, structure-cytotoxicity and resistance mechanisms

Metronidazole, a nitroimidazole, remains a front-line choice for treatment of infections related to inflammatory disorders of the gastrointestinal tract including colitis linked to Clostridium difficile. Despite >60 years of research, the metabolism of metronidazole and associated cytotoxicity is not definitively characterized. Nitroimidazoles are prodrugs that are reductively activated (the nitro group is reduced) under low oxygen tension, leading to imidazole fragmentation and cytotoxicity. It remains unclear if nitroimidazole reduction (activation) contributes to the cytotoxicity profile, or whether subsequent fragmentation of the imidazole ring and formed metabolites alone mediate cytotoxicity. A molecular mechanism underpinning high level (>256 mg/L) bacterial resistance to metronidazole also remains elusive. Considering the widespread use of metronidazole and other nitroimidazoles, this review was undertaken to emphasize the structure-cytotoxicity profile of the numerous metabolites of metronidazole in human and murine models and to examine conflicting reports regarding metabolite-DNA interactions. An alternative hypothesis, that DNA synthesis and repair of existing DNA is indirectly inhibited by metronidazole is proposed. Prokaryotic metabolism of metronidazole is detailed to discuss new resistance mechanisms. Additionally, the review contextualizes the history and current use of metronidazole, rates of metronidazole resistance including metronidazole MDR as well as the biosynthesis of azomycin, the natural precursor of metronidazole. Changes in the gastrointestinal microbiome and the host after metronidazole administration are also reviewed. Finally, novel nitroimidazoles and new antibiotic strategies are discussed.

Photodynamic therapy versus systemic antibiotic for the treatment of periodontitis in a rat model

BACKGROUND

To compare the therapeutic effect of photodynamic therapy (PDT) with Toluidine blue O hydrogel versus systemic antibiotic (SA) in treating periodontitis on rats.

METHODS

Thirty-two Wistar rats were divided into four groups and treated differently: Negative control (NC) group, normal rats; positive control (PC) group, rats with periodontitis; SA group, rats with periodontitis treated with systemic antibiotic; PDT group, rats with periodontitis treated with PDT. After treatment, gingival sulcus bacterial load was measured by counting the colony forming units per milliliter (CFU mL^-1 ). The tooth and periodontal tissues were histologically processed to analyze histological and immunohistochemical profile. Gingival samples were obtained to quantify interleukin-1 beta (IL-1β) and tumor necrosis factor-alpha (TNF-α) levels.

RESULTS

Gingival sulcus bacteria load is significantly lower in PDT group compared with the SA group. The histological analysis showed that some extremely effective repair signs of periodontal tissue were presented in PDT group, such as no periodontal pocket, no bone resorption, few inflammatory cells, massive fibroblasts and collagen fibers. Several effective repair signs of periodontal tissue were also observed in SA group, such as shallow periodontal pocket, small amount of inflammatory cells, substantial fibroblasts and collagen fibers. There were lower cyclooxygenase-2, matrix metalloproteinase -8 (MMP-8) and RANK immunolabeling, higher osteoprotegerin immunolabeling in PDT group compared with SA group. The IL-1β and TNF-α levels in PDT group were lower than those in NC group, but higher than those in SA group.

CONCLUSION

PDT was effective to treat experimental periodontitis and was superior to systemic metronidazole as a treatment for periodontitis.

A comparison of Sensititre™ Anaerobe MIC plate with ATB ANA® test for the routine susceptibility testing of common anaerobe pathogens

The accuracy of the Thermo Scientific™ Sensititre™ Anaerobe MIC plate was assessed against the ATB ANA® test (bioMérieux) on 56 clinically relevant anaerobic strains collected at Geneva University Hospitals. The overall categorical agreement between both methods reached 95%. The Sensititre™ Anaerobe MIC plate had excellent accuracy for most antibiotics tested. When the Sensititre™ Anaerobe MIC plate disagreed with ATB ANA® test, the gradient strip method resolved the antimicrobial susceptibility categories of all the antibiotics tested, except for piperacillin, piperacillin-tazobactam, and penicillin, in favor of the Sensititre™ Anaerobe MIC plate (58% [21 out of 36]). Several very major errors were observed for piperacillin (12.5% [7 out of 56]), piperacillin-tazobactam (12.5% [7 out of 56]), and penicillin (2% [1 out of 56]). The gradient strip method revealed that the categorical differences for piperacillin, piperacillin-tazobactam, and penicillin were at least partly explained by heterogeneity in resistance expression. The Sensititre™ Anaerobe MIC plate offers therefore a useful alternative to the ATB ANA® test for the routine antimicrobial susceptibility testing of anaerobes in clinical microbiology laboratories.

Performance of mass spectrometric identification of clinical Prevotella species using the VITEK MS system: A prospective multi-center study

Prevotella species, members of the human microbiota, can cause opportunistic infections. Rapid and accurate identification of Prevotella isolates plays a critical role in successful treatment, especially since the antibiotic susceptibility profile differs between species. Studies, mostly carried out using the Matrix Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) Biotyper system, showed that MALDI-TOF MS is an accurate, rapid and satisfactory method for the identification of clinically important anaerobes. In this multi-center study, we assessed the performance of the MALDI-TOF MS VITEK MS system for the identification of clinical Prevotella isolates. A total of 508 Prevotella isolates, representing 19 different species, collected from 11 European countries, Kuwait and Turkey between January 2014 and April 2016, were identified using VITEK MS (v3.0). The reliability of the identification was assessed by 16S rRNA gene sequencing. Using VITEK MS, 422 (83.1%) of the 508 isolates were identified on the species level, 459 (90.4%) on the genus level. A total of 49 (9.6%) isolates were not identified correctly. 16S rRNA gene sequencing results showed that this was partly due to the fact that several species were not represented in the database. However, some species that were represented in the database were also not identified. Five Prevotella strains were misidentified at the genus level, 2 of these strains belonged to a species not represented in the database. In general, the VITEK MS offers a reliable and rapid identification of Prevotella species, however the databases needs to be expanded.