Prevalence of antibiotic resistance in anaerobic bacteria: worrisome developments

Prevalence of in vitro susceptibility to carbapenems among clinical isolates of the Bacteroides fragilis group from a Colombian tertiary hospital

Clinical isolates of the Bacteroides fragilis group (n=29) were collected from patients attending a tertiary care hospital in Medellin, Colombia, during 2012 and were tested for susceptibility to four carbapenems using the Clinical and Laboratory Standards Institute (CLSI) Etest method. Overall rates of percent susceptibility were as follows: meropenem, 93.1%; imipenem, 100%; ertapenem, 96.6%; and doripenem, 93.1%. This is the first study to show rates of resistance of Bacteroides spp. to carbapenems in Colombia among a species formerly thought to be fully susceptible to this type of antimicrobial.

Antianaerobic antimicrobials: spectrum and susceptibility testing

Susceptibility testing of anaerobic bacteria recovered from selected cases can influence the choice of antimicrobial therapy. The Clinical and Laboratory Standards Institute (CLSI) has standardized many laboratory procedures, including anaerobic susceptibility testing (AST), and has published documents for AST. The standardization of testing methods by the CLSI allows comparisons of resistance trends among various laboratories. Susceptibility testing should be performed on organisms recovered from sterile body sites, those that are isolated in pure culture, or those that are clinically important and have variable or unique susceptibility patterns. Organisms that should be considered for individual isolate testing include highly virulent pathogens for which susceptibility cannot be predicted, such as Bacteroides, Prevotella, Fusobacterium, and Clostridium spp.; Bilophila wadsworthia; and Sutterella wadsworthensis. This review describes the current methods for AST in research and reference laboratories. These methods include the use of agar dilution, broth microdilution, Etest, and the spiral gradient endpoint system. The antimicrobials potentially effective against anaerobic bacteria include beta-lactams, combinations of beta-lactams and beta-lactamase inhibitors, metronidazole, chloramphenicol, clindamycin, macrolides, tetracyclines, and fluoroquinolones. The spectrum of efficacy, antimicrobial resistance mechanisms, and resistance patterns against these agents are described.

Tigecycline: a novel glycylcycline antibiotic

Tigecycline, the first-in-class glycylcycline, was developed to recapture the broad spectrum of activity of the tetracycline class and to treat patients with difficult-to-treat bacterial infections. Tigecycline's in vitro spectrum of activity encompasses aerobic, facultative and anaerobic Gram-positive and -negative bacteria, including antimicrobial-resistant bacteria such as methicillin-resistant Staphylococcus aureus, vancomycin-resistant Enterococcus faecalis and Enterococcus faecium, and extended-spectrum beta-lactamase-producing Enterobacteriaceae. Clinical trials involving patients with complicated skin and skin-structure infections and complicated intra-abdominal infections, including patients infected with methicillin-resistant S. aureus, demonstrated that tigecycline was bacteriologically and clinically effective with mild-to-moderate gastrointestinal adverse events (i.e., nausea, vomiting and diarrhea) the most commonly reported. Tigecycline is a promising new broad-spectrum parenteral monotherapy for the treatment of patients with Gram-positive and -negative bacterial infections.

Ceftaroline plus avibactam demonstrates bactericidal activity against pathogenic anaerobic bacteria in a one-compartment in vitro pharmacokinetic/pharmacodynamic model

Anaerobic pathogens are often associated with polymicrobial infections, such as diabetic foot infections. Patients with these infections are often treated with broad-spectrum, multidrug therapies targeting resistant Gram-positive bacteria, such as methicillin-resistant Staphylococcus aureus, as well as Gram-negative bacteria and anaerobes. The broad-spectrum, non-beta-lactam, beta-lactamase inhibitor avibactam has been combined with ceftaroline and may provide a single-product alternative for complicated polymicrobial infections. We compared the activity of ceftaroline-avibactam (CPA) to that of ertapenem (ERT) against common anaerobic pathogens in an in vitro pharmacokinetic/pharmacodynamic (PK/PD) model. Simulations of doses of ceftaroline-fosamil at 600 mg every 8 h (q8h) (maximum free drug concentration [fCmax], 17.04 mg/liter, and half-life [t1/2], 2.66 h) plus avibactam at 600 mg q8h (fCmax, 11.72 mg/liter, and t1/2, 1.8 h) and of ertapenem at 1 g q24h (fCmax, 13 mg/liter, and t1/2, 4 h) were evaluated against two strains of Bacteroides fragilis, one strain of Prevotella bivia, and one strain of Finegoldia magna in an anaerobic one-compartment in vitro PK/PD model over 72 h with a starting inoculum of ∼8 log10 CFU/ml. Bactericidal activity was defined as a reduction of ≥3 log10 CFU/ml from the starting inoculum. Both CPA and ERT were bactericidal against all four strains. CPA demonstrated improved activity against Bacteroides strains compared to that of ERT but had similar activity against Finegoldia magna and P. bivia, although modest regrowth was observed with CPA against P. bivia. No resistance emerged from any of the models. The pharmacokinetics achieved were 92 to 105% of the targets. CPA has potent in vitro activity against common anaerobic pathogens at clinically relevant drug exposures and may be a suitable single product for the management of complicated polymicrobial infections.

PCR-based detection of resistance genes in anaerobic bacteria isolated from intra-abdominal infections

Little information is available on the distribution of antimicrobial resistance genes in anaerobes in Japan. To understand the background of antimicrobial resistance in anaerobes involved in intra-abdominal infections, we investigated the distribution of eight antimicrobial resistance genes (cepA, cfiA, cfxA, ermF, ermB, mefA, tetQ, and nim) and a mutation in the gyrA gene in a total of 152 organisms (Bacteroides spp., Prevotella spp., Fusobacterium spp., Porphyromonas spp., Bilophila wadsworthia, Desulfovibrio desulfuricans, Veillonella spp., gram-positive cocci, and non-spore-forming gram-positive bacilli) isolated between 2003 and 2004 in Japan. The cepA gene was distributed primarily in Bacteroides fragilis. Gene cfxA was detected in about 9 % of the Bacteroides isolates and 75 % of the Prevotella spp. isolates and did not appear to contribute to cephamycin resistance. Two strains of B. fragilis contained the metallo-β-lactamase gene cfiA, but they did not produce the protein product. Gene tetQ was detected in about 81, 44, and 63 % of B. fragilis isolates, other Bacteroides spp., and Prevotella spp. isolates, respectively. The ermF gene was detected in 25, 13, 56, 64, and 16 % of Bacteroides spp., Prevotella spp., Fusobacterium spp., B. wadsworthia, and anaerobic cocci, respectively. Gene mefA was found in only 10 % of the B. fragilis strains and 3 % of the non-B. fragilis strains. Genes nim and ermB were not detected in any isolate. Substitution at position 82 (Ser to Phe) in gyrA was detected in B. fragilis isolates that were less susceptible or resistant to moxifloxacin. This study is the first report on the distribution of resistance genes in anaerobes isolated from intra-abdominal infections in Japan. We expect that the results might help in understanding the resistance mechanisms of specific anaerobes.

Global fluoroquinolone resistance epidemiology and implictions for clinical use

This paper on the fluoroquinolone resistance epidemiology stratifies the data according to the different prescription patterns by either primary or tertiary caregivers and by indication. Global surveillance studies demonstrate that fluoroquinolone resistance rates increased in the past years in almost all bacterial species except S. pneumoniae and H. influenzae, causing community-acquired respiratory tract infections. However, 10 to 30% of these isolates harbored first-step mutations conferring low level fluoroquinolone resistance. Fluoroquinolone resistance increased in Enterobacteriaceae causing community acquired or healthcare associated urinary tract infections and intraabdominal infections, exceeding 50% in some parts of the world, particularly in Asia. One to two-thirds of Enterobacteriaceae producing extended spectrum β-lactamases were fluoroquinolone resistant too. Furthermore, fluoroquinolones select for methicillin resistance in Staphylococci. Neisseria gonorrhoeae acquired fluoroquinolone resistance rapidly; actual resistance rates are highly variable and can be as high as almost 100%, particularly in Asia, whereas resistance rates in Europe and North America range from <10% in rural areas to >30% in established sexual networks. In general, the continued increase in fluoroquinolone resistance affects patient management and necessitates changes in some guidelines, for example, treatment of urinary tract, intra-abdominal, skin and skin structure infections, and traveller's diarrhea, or even precludes the use in indications like sexually transmitted diseases and enteric fever.

Essentials for selecting antimicrobial therapy for intra-abdominal infections

Intra-abdominal infection (IAI) is a complex disease entity in which different aspects must be balanced in order to select the proper antimicrobial regimen and determine duration of therapy. A current classification indicates different faces of peritonitis. Primary peritonitis implies an intact gastrointestinal tract without overt barrier disruption. Secondary peritonitis refers to localized or diffuse peritoneal inflammation and abscess formation due to disruption of the anatomical barrier. Tertiary peritonitis includes cases that cannot be solved by a single or even sequential surgical intervention, often in combination with sequential courses of antimicrobial therapy. The most frequently used classification distinguishes ‘uncomplicated’ and ‘complicated’ IAI. In uncomplicated IAI, the infectious process is contained within a single organ, without anatomical disruption. In complicated IAI, disease is extended, with either localized or generalized peritonitis. However, there exists more than a single dimension of complexity in IAI, including severity of disease expression through systemic inflammation. As the currently used classifications of IAI often incite confusion by mixing elements of anatomical barrier disruption, severity of disease expression and (the likelihood of) resistance involvement, we propose an alternative for the current widely accepted classification. We suggest abandoning the terms ‘uncomplicated’ and ‘complicated’ IAI, as they merely confuse the issue. Furthermore, the term ‘tertiary peritonitis’ should likewise be discarded, as this simply refers to treatment failure of secondary peritonitis resulting in a state of persistent infection and/or inflammation. Hence, anatomical disruption and disease severity should be separated into different phenotypes for the same disease in combination with either presence or absence of risk factors for involvement of pathogens that are not routinely covered in first-line antimicrobial regimens (Pseudomonas aeruginosa, enterococci, Candida species and resistant pathogens). Generally, these risk factors can be brought back to recent exposure to antimicrobial agents and substantial length of stay in healthcare settings (5–7 days). As such, we developed a grid based on the different components of the classification: (i) anatomical disruption; (ii) severity of disease expression; and (iii) either community-acquired/early-onset healthcare-associated origin or healthcare-associated origin and/or recent antimicrobial exposure. The grid allows physicians to define the index case of IAI in a more unequivocal way and to select the most convenient empirical antimicrobial regimens. The grid advises on the necessity of covering nosocomial Gram-negative bacteria (including P. aeruginosa), enterococci and yeasts. The basis of antimicrobial therapy for IAI is that both Gram-negative and anaerobic bacteria should always be covered.

In recent years, some newer agents such as doripenem, moxifloxacin and tigecycline have been added to the antimicrobial armamentarium for IAI. For patients in whom the source can be adequately controlled, antimicrobial therapy should be restricted to a short course (e.g. 3–7 days in peritonitis).

Meropenem in the treatment of complicated skin and soft tissue infections

Meropenem is a broad-spectrum carbapenem antibiotic with excellent activity against many pathogens associated with complicated skin and soft tissue infections (cSSTIs). At least three studies have shown meropenem to have good clinical efficacy and to be well tolerated in the treatment of cSSTIs. Two open-label studies compared meropenem 500 mg every 8 hours (total evaluable n=146) with imipenem/cilastatin 500mg every 6 hours (n=147). Clinical efficacy rates in evaluable patients 7–14 days after end of treatment were similar, 92% and 100% in meropenem-treated groups versus 89% and 100% in groups receiving imipenem/cilastatin. An additional prospective, randomized, double-blind study evaluated meropenem 500mg every 8 hours (261 evaluable patients) versus imipenem/cilastatin 500 mg every 8 hours (287 patients). Clinical efficacy rates of meropenem and imipenem/cilastatin 7–28 days after end of treatment were 86.2% and 82.9%, respectively. Meropenem was well tolerated in all studies. Carbapenems are currently recommended as appropriate for initial treatment of certain cSSTIs such as those likely to involve mixed and/or multidrug-resistant pathogens. Meropenem is an effective and safe alternative for monotherapy when used for appropriate types of cSSTIs. Higher doses (ie, 1 g every 8 hours) should be considered for treatment of cSSTIs in higher-risk patients where Pseudomonas aeruginosa is a suspected or documented pathogen.

Epidemiological characteristics of infections caused by Bacteroides, Prevotella and Fusobacterium species: a prospective observational study

In order to investigate differences among infections due to Gram-negative anaerobic bacteria (Bacteroides, Prevotella and Fusobacterium spp.), clinical, epidemiological, and microbiological data were collected and evaluated from 206 anaerobic infections. The most frequently isolated species was Bacteroides fragilis. The majority of the cases were intra-abdominal infections (49%) followed by skin and soft tissue infections (24.7%). Logistic regression analysis showed that Bacteroides spp. strains were more often isolated from intra-abdominal infections (p = 0.002), whereas Prevotella spp. were isolated more frequently from cases with shorter duration of hospitalization (p = 0.026), and less frequently from bloodstream infections (p = 0.049). In addition, Bacteroides spp. were associated with coinfection due to Enterobacteriaceae species (p = 0.007), whereas Prevotella spp. were associated with coinfection due to Staphylococcus spp. (p = 0.002). Patients with an infection due to B. fragilis, were more frequently admitted in a general surgical ward (p = 0.017), or have been treated with a 2nd generation cephalosporin before anaerobic infection onset (p = 0.05). Total mortality was 10.9% and was associated with bacteremia (p = 0.026), and hematological (p = 0.028), or solid organ malignancy (p = 0.007). Metronidazole resistance was detected only among Prevotella spp. (16.2%) and B. fragilis group (0.8%) isolates. In conclusion, this study indicated differences between infections due to the most frequently isolated Gram-negative anaerobic species, differences that may affect the design and implementation of empirical antimicrobial chemotherapy guidelines.

[A case of liver abscess caused by Fusobacterium nucleatum in a patient with recurrent periodontal diseases]

Fusobacteria are anaerobic gram-negative, non-spore forming bacilli found in normal flora of the oral cavity, urogenital tract, and gastrointestinal tract. Fusobacterium nucleatum has been seldom reported as a cause of liver abscess, particularly in immunocompetent hosts. A 55-year-old man with frequent periodontal disease visited our hospital with intermittent fever and headache for 2 months. Abdominal CT scan revealed an 8.2 × 6 cm mass in the right hepatic lobe with central low density. Abscess culture revealed F. nucleatum as the causative organism. Percutaneous abscess drainage and intravenous administration of antibiotics for 4 weeks improved symptoms and decreased the abscess size. We report a rare case of liver abscess due to F. nucleatum in an immunocompetent man with periodontal disease.

Antibiotic optimization in the difficult-to-treat patient with complicated intra-abdominal or complicated skin and skin structure infections: focus on tigecycline

Complicated intra-abdominal and skin and skin structure infections are widely varied in presentation. These infections very often lead to an increase in length of hospital stay, with a resulting increase in costs and mortality. In addition, these infections may be caused by a wide variety of bacteria and are often polymicrobial with the possibility of the presence of antimicrobial-resistant strains, such as methicillin-resistant Staphylococcus aureus, vancomycin-resistant enterococci, extended-spectrum β-lactamase strains (Escherichia coli, Klebsiella pneumoniae), and K. pneumoniae carbapenemase-producing strains. In combination with patients’ immunosuppression or comorbidities, the treatment and management options for initial therapy success are few. Tigecycline, a new glycylcyline antimicrobial from the tetracycline drug class, represents a viable option for the successful treatment of these infections. It has been shown to have activity against a wide variety of bacteria, including the antimicrobial-resistant strains. As with all tetracycline drugs, it is not recommended for pregnant or nursing women. The potential side effects are those typical of tetracycline drugs: nausea, vomiting, and headaches. Drug–drug interactions are not expected, and renal function monitoring is not necessary.

Anaerobic infections: update on treatment considerations

Anaerobic bacteria are the predominant indigenous flora of humans and, as a result, play an important role in infections, some of which are serious with a high mortality rate. These opportunistic pathogens are frequently missed in cultures of clinical samples because of shortcomings in collection and transport procedures as well as lack of isolation and susceptibility testing of anaerobes in many clinical microbiology laboratories. Correlation of clinical failures with known antibacterial resistance of anaerobic bacteria is seldom possible. Changes in resistance over time, and the discovery and characterization of resistance determinants in anaerobic bacteria, has increased recognition of problems in empirical treatment and has even resulted in changes in treatment guidelines. This review discusses the role of anaerobic bacteria in the normal flora of humans, their involvement in different mixed infections, developments in antibacterial resistance of the most frequent anaerobic pathogens and possible new treatment options.

In vitro activity of ceftaroline against 623 diverse strains of anaerobic bacteria

The in vitro activities of ceftaroline, a novel, parenteral, broad-spectrum cephalosporin, and four comparator antimicrobials were determined against anaerobic bacteria. Against Gram-positive strains, the activity of ceftaroline was similar to that of amoxicillin-clavulanate and four to eight times greater than that of ceftriaxone. Against Gram-negative organisms, ceftaroline showed good activity against beta-lactamase-negative strains but not against the members of the Bacteroides fragilis group. Ceftaroline showed potent activity against a broad spectrum of anaerobes encountered in respiratory, skin, and soft tissue infections.

Identification of clinically important anaerobic bacteria by an oligonucleotide array

Anaerobic bacteria can cause a wide variety of infections, and some of these infections can be serious. Conventional identification methods based on biochemical tests are often lengthy and can produce inconclusive results. An oligonucleotide array based on the 16S-23S rRNA intergenic spacer (ITS) sequences was developed to identify 28 species of anaerobic bacteria and Veillonella. The method consisted of PCR amplification of the ITS regions with universal primers, followed by hybridization of the digoxigenin-labeled PCR products to a panel of 35 oligonucleotide probes (17- to 30-mers) immobilized on a nylon membrane. The performance of the array was determined by testing 310 target strains (strains which we aimed to identify), including 122 reference strains and 188 clinical isolates. In addition, 98 nontarget strains were used for specificity testing. The sensitivity and the specificity of the array for the identification of pure cultures were 99.7 and 97.1%, respectively. The array was further assessed for its ability to detect anaerobic bacteria in 49 clinical specimens. Two species (Finegoldia magna and Bacteroides vulgatus) were detected in two specimens by the array, and the results were in accordance with those obtained by culture. The whole procedure of array hybridization took about 8 h, starting with the isolated colonies. The array can be used as an accurate alternative to conventional methods for the identification of clinically important anaerobes.

Susceptibility of strict and facultative anaerobes Isolated from endodontic infections to metronidazole and beta-lactams

Endodontic infections are mixed aerobic-anaerobic infections and several microbial groups associated to these pathologies are also involved in orofacial infections. The goal of this study was to evaluate the susceptibility of microorganisms isolated from endodontic infections to beta-lactams and metronidazole and verify the production of beta-lactamases. Clinical specimens were collected from 58 endodontic infections of 52 patients. The microorganisms were isolated in selective and non-selective culture media, under anaerobiosis and aerobiosis, and identified using biochemical methods. In the susceptibility tests, it was used an agar dilution method, and Wilkins-Chalgren agar enriched with blood, hemin and menadione for the anaerobes, while Mueller-Hinton agar was employed for the facultative anaerobes. The production of beta-lactamases was evaluated through the biological and chromogenic cephalosporin methods. All tested isolates were sensitive to imipenem and 99.3% to amoxicillin/clavulanate association, while 16.1% showed resistance to amoxicillin and penicillin G, and 4.89% to cefoxitin. Resistance to metronidazole was just found in facultative anaerobes. Production of beta-lactamases was detected in 18.2% of the isolates and presented a correlation with resistance to beta-lactams.

Accumulation of tetracycline resistance genes in aquatic biofilms due to periodic waste loadings from swine lagoons

Antibiotic resistance genes (ARGs) are emerging contaminants found in the water and sediments surrounding animal feedlots. In this study, the fate of five tetracycline-resistance and 16S-rRNA genes released in swine waste were monitored for 21 days in the water column and biofilms in 12 mesocosms mimicking different natural receiving water bodies. Four treatments were employed in triplicate: two light exposures (light/ dark) and two loading scenarios (single/periodic). As seen previously, light exposure had a significant effect on disappearance rates of tet genes in both the water column and biofilms, although absolute rates were significantly lower in the biofilms. Further, periodic versus single loading events resulted in >2 orders of magnitude higher tet gene levels in associated tanks. Regardless of treatment, ARGs migrated quickly to biofilms, with 3% and >85% of detected tet determinants found in biofilms on days 1 and 4, respectively. Overall, these are the first quantitative data on specific ARG disappearance rates in biofilms, and also the first evidence of progressively accumulating ARG levels in biofilms under loading conditions typical of natural receiving waters. In summary, ARGs migrate rapidly to biofilms where they persist longer than adjacent waters, which suggests biofilms likely act as reservoirs for ARGs in nature.

Metronidazole resistance in Prevotella spp. and description of a new nim gene in Prevotella baroniae

Nonduplicate clinical isolates of Prevotella spp. recovered from patients hospitalized between 2003 and 2006 in two French tertiary-care teaching hospitals were investigated for their susceptibility to metronidazole and the presence of nim genes. Of the 188 strains tested, 3 isolates displayed reduced susceptibility to metronidazole after 48 h of incubation, while 27 additional isolates exhibited heterogeneous resistance after prolonged incubation; all 30 of the isolates were nim negative. Among the remaining 158 isolates, 7 nim-positive isolates were detected. All of these strains were identified as Prevotella baroniae by 16S rRNA gene sequence analysis and contained a new nim gene, named nimI, as determined by DNA sequence analysis. Chromosomal localization of this single-copy gene was demonstrated in all clinical isolates as well as in type strain P. baroniae DSM 16972 by using Southern hybridization. No known associated insertion sequence elements were detected upstream of the nimI gene in any of the nim-positive strains by PCR mapping. After prolonged exposure to metronidazole, stable resistant subpopulations could be selected in nimI-positive Prevotella isolates (n = 6) as well as in nim-negative Prevotella isolates (n = 6), irrespective of their initial susceptibility to this antibiotic. This study is the first description of a new nitroimidazole resistance gene in P. baroniae which seems to be silent and which might be intrinsic in this species. Moreover, our findings highlight the fact that high-level resistance to metronidazole may be easily induced in both nim-positive and nim-negative Prevotella sp. strains.

Infection after elective colorectal surgery: bacteriological analysis of failures in a randomized trial of cefotetan vs. ertapenem prophylaxis

BACKGROUND

A randomized study comparing single-dose cefotetan and ertapenem prophylaxis for elective colorectal surgery in 1,002 patients found ertapenem to be significantly more effective (p < 0.001). Failures of prophylaxis were thought to involve organisms resistant to both antimicrobial agents, isolated most often from deep or superficial incision sites.

METHODS

Further testing and analysis of the microbial data was performed. Susceptibility results were correlated with the clinical outcomes reported previously.

RESULTS

Of the 216 aerobes tested, 62.6% were resistant to cefotetan and 44% to ertapenem. Enterococci and methicillin-resistant Staphylococcus epidermidis were the aerobes recovered most frequently, and Bacteroides thetaiotaomicron, Clostridium innocuum, and Eubacterium lentum were the most frequent anaerobes. Enterococcus faecalis usually was associated in mixed culture with Bacteroides fragilis group species. Approximately one-half of the 158 anaerobes (50.7%), including all the species above, were resistant to cefotetan; most of these (61.4%) came from superficial incision sites. Only one anaerobe (Desulfovibrio fairfieldensis), found in a superficial incisional infection, was resistant to ertapenem, and no ertapenem-resistant enteric bacteria were recovered. In vitro resistance was associated with therapeutic failure.

CONCLUSIONS

The in vitro activity of ertapenem was superior to that of cefotetan against all anaerobic and many aerobic bacteria isolated from postoperative cultures of patients who failed prophylaxis with these agents. Our findings help to elucidate the results of the clinical trial.

Efflux-mediated drug resistance in bacteria: an update

Drug efflux pumps play a key role in drug resistance and also serve other functions in bacteria. There has been a growing list of multidrug and drug-specific efflux pumps characterized from bacteria of human, animal, plant and environmental origins. These pumps are mostly encoded on the chromosome, although they can also be plasmid-encoded. A previous article in this journal provided a comprehensive review regarding efflux-mediated drug resistance in bacteria. In the past 5 years, significant progress has been achieved in further understanding of drug resistance-related efflux transporters and this review focuses on the latest studies in this field since 2003. This has been demonstrated in multiple aspects that include but are not limited to: further molecular and biochemical characterization of the known drug efflux pumps and identification of novel drug efflux pumps; structural elucidation of the transport mechanisms of drug transporters; regulatory mechanisms of drug efflux pumps; determining the role of the drug efflux pumps in other functions such as stress responses, virulence and cell communication; and development of efflux pump inhibitors. Overall, the multifaceted implications of drug efflux transporters warrant novel strategies to combat multidrug resistance in bacteria.

Species identification of clinical isolates of Bacteroides by matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry

Bacteroides fragilis and related species are important human pathogens involved in mixed infections of different origins. The B. fragilis group isolates are phenotypically very similar, grow more slowly than aerobic bacteria and, accordingly, are frequently misidentifed with classical or automated phenotypical identification methods. Recent taxonomic changes and new species accepted as members of the Bacteroides genus are not included in the different databases of commercially available identification kits. The use of matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was therefore evaluated for the species identification of 277 clinical isolates of the Bacteroides genus. Species identification was carried out with MALDI Bruker Daltonik Biotyper software (Bruker Daltonik GmbH, Bremen, Germany) by comparing the mass spectrum of each strain with the mass spectra of the 3260 reference strains currently available. The results of conventional phenotypical identification of the isolates were used as a reference. 16S rRNA gene sequencing was performed for a selection of the strains that gave discrepant results and for all those inconclusively identified by MALDI-TOF MS; 270 isolates (97.5%) were unequivocally identified [log(score) >/=2.0] by comparison with the reference strains present in the MALDI Biotyper database. Of the 23 isolates for which the MALDI-TOF MS species identification differed from the conventional phenotypical identification, 11 were sequenced. The sequencing data confirmed the MALDI-TOF MS result in ten cases and, for the remaining isolate, the sequencing data did not lead to the determination of the species, but only to that of the genus (Bacteroides sp.). The discriminating power and identification accuracy of MALDI-TOF MS proved to be superior to that of biochemical testing for Bacteroides thetaiotaomicron, Bacteroides ovatus and Bacteroides uniformis.

Clinical features and prognostic factors of anaerobic infections: a 7-year retrospective study

BACKGROUND/AIMS

Risk factors for mortality resulting from anaerobic infection are incompletely defined. The clinical significance of a broad range of pathogenic obligate anaerobic organisms was examined, and factors independently associated with mortality were identified in patients with clinically significant anaerobic infections.

METHODS

The medical records of 1,050 patients with anaerobic infections were retrospectively reviewed at Severance Hospital in Seoul, Korea.

RESULTS

The mean age of the patients was 54.1+/-16.8 years, and 57.7% were men. Overall, 320 (30.5%) patients with case-defined illness experienced pain at the affected site, and 230 (21.9%) experienced pus flow from lesions. Ten (1.4%) patients presented with shock, and 80.3% of the clinically significant cases were polymicrobial anaerobic infections. The mean number of pathogens, including aerobic and anaerobic bacteria, was 3.7+/-1.0 (minimum 1, maximum 5), and the number of anaerobic organisms was 1.0+/-0.3 in each specimen. The major pathogens by rank were the Bacteroides fragilis group, which accounted for 41.8% of anaerobic infections, followed by Clostridium spp. (11.8%), Prevotella spp. (9.4%), and Peptostreptococcus spp. (8.4%). Escherichia coli (17.5%), Staphylococcus aureus (7.5%), and Klebsiella pneumoniae (7.5%) were common concomitant aerobic organisms. The overall crude mortality rate resulting from anaerobic infection was 29.7%. Among the determining factors associated with mortality, liver disease (p=0.003) and old age (p=0.005) were significant in multivariate analysis.

CONCLUSIONS

Anaerobic infection is polymicrobial and has a significant role in morbidity and mortality. Underlying liver disease was associated with poor prognosis in anaerobic infection.

Activity of a novel carbapenem, doripenem, against anaerobic pathogens

Doripenem, a synthetic 1-beta-methyl carbapenem, has a broad-spectrum of activity against almost all species of anaerobic bacteria, including all Bacteroides fragilis group species, most with MIC(90) results at <or=1 microg/mL (with the exception of Sutterella wadsworthensis). Against Clostridium difficile strains, it has a narrow range of inhibitory concentrations (1-4 microg/mL) that "may be achievable in the colon", potentially resulting in lower disease rates. It has been shown to be active in vitro against strains isolated from a variety of clinical infections, including bacteremias, diabetic foot and other soft tissues infections and in intra-abdominal and pelvic sites. In addition, a study of a pyometrium animal model of mixed infections noted a better microbiologic response than with imipenem. Two phase 3 multinational clinical trials of complicated mixed aerobic/anaerobic intra-abdominal infections noted "noninferiority" of doripenem when compared with meropenem, but in vitro against the anaerobes, it was "more potent than meropenem, ertapenem, ... and similar to imipenem". Doripenem activity against anaerobes seems comparable with the other extant carbapenems. Although resistance among anaerobic bacteria to this agent is possible, it remains relatively rare.

Prognostic factors and impact of antibiotherapy in 117 cases of anaerobic bacteraemia

Bacteraemia due to anaerobic bacteria occurs infrequently, making the systematic use of an anaerobic blood sample bottle in patients with sepsis controversial. We retrospectively reviewed the clinical and microbiological data from all cases of anaerobic bacteraemia in a teaching hospital over 2 years and determined the prognostic factors and antibiotic management. With the goal of evaluating the morbidity and mortality of bacteraemia due to anaerobic bacteria, a case-control study was also performed. One hundred eighty-four blood cultures from 125 patients grew at least one anaerobic bacterium, representing 0.5% of all and 7.0% of the positive blood cultures. One hundred seventeen patients were studied. In 24 cases, anaerobic blood cultures were associated with concomitant aerobic bacteria isolation. The most frequently isolated anaerobic species were Bacteroides sp. (n = 62), Clostridium sp. (n = 25), and Fusobacterium sp. (n = 12). The most frequent site of origin was the digestive tract (n = 61). In 51 cases, patients did not receive adequate empirical antianaerobic therapy. The mortality rate was 27%. Age [odds ratio (OR) 1.059; 95% confidence interval (CI) 1.021-1.100], cancer history (OR 3.21, 95% CI 1.126-9.156), and ineffective definitive antibiotherapy (OR 19.292, 95% CI 5.330-69.832) were independently associated with increased hospital mortality. The 72 patients that could be matched with patients without anaerobic bacteria according to their primary diagnosis had a longer hospitalisation and a trend toward increased mortality (P = 0.08). Anaerobic bacteraemia contributed significantly to the morbidity of the patients, and adequate empirical antibiotherapy may play an important role in the clinical outcomes.

Genotypic diversity of anaerobic isolates from bloodstream infections

Accurate species determination for anaerobes from blood culture bottles has become increasingly important with the reemergence of anaerobic bacteremia and prevalence of multiple-drug-resistant microorganisms. Our knowledge of the taxonomical diversity of anaerobes that cause bloodstream infections is extremely limited, because identification historically has relied on conventional methods. Over a 5-year period, we profiled anaerobic bacteremia at a large tertiary care hospital with 16S rRNA gene sequencing to gain a better understanding of the taxonomical diversity of the bacteria. Of 316 isolates, 16S rRNA gene sequencing and phylogenetic analysis identified 316 (100%) to the genus or taxonomical group level and 289 (91%) to the species level. Conventional methods identified 279 (88%) to the genus level and 208 (66%) to the species level; 75 (24%) were misidentified at the species level, and 33 (10%) results were inconclusive. High intragenus variability was observed for Bacteroides and Clostridium species, and high intraspecies variability was observed for Bacteroides thetaiotaomicron and Fusobacterium nucleatum. Sequence-based identification has potential benefits in comparison to conventional methods, because it more accurately characterizes anaerobes within taxonomically related clusters and thereby may enable better correlation with specific clinical syndromes and antibiotic resistance patterns.

Bacteroides: the good, the bad, and the nitty-gritty

SUMMARY

Bacteroides species are significant clinical pathogens and are found in most anaerobic infections, with an associated mortality of more than 19%. The bacteria maintain a complex and generally beneficial relationship with the host when retained in the gut, but when they escape this environment they can cause significant pathology, including bacteremia and abscess formation in multiple body sites. Genomic and proteomic analyses have vastly added to our understanding of the manner in which Bacteroides species adapt to, and thrive in, the human gut. A few examples are (i) complex systems to sense and adapt to nutrient availability, (ii) multiple pump systems to expel toxic substances, and (iii) the ability to influence the host immune system so that it controls other (competing) pathogens. B. fragilis, which accounts for only 0.5% of the human colonic flora, is the most commonly isolated anaerobic pathogen due, in part, to its potent virulence factors. Species of the genus Bacteroides have the most antibiotic resistance mechanisms and the highest resistance rates of all anaerobic pathogens. Clinically, Bacteroides species have exhibited increasing resistance to many antibiotics, including cefoxitin, clindamycin, metronidazole, carbapenems, and fluoroquinolones (e.g., gatifloxacin, levofloxacin, and moxifloxacin).

Antimicrobial profiles of Prevotella spp. and Fusobacterium nucleatum isolated from periodontal infections in a selected area of southern Italy

In view of the increasing antibiotic resistance of anaerobic Gram-negative bacteria, we determined the antimicrobial profile of 55 periodontal anaerobic Gram-negative bacteria correlated with human infections, comprising 16 strains of Fusobacterium nucleatum and 39 strains of Prevotella spp. isolated from periodontal pockets of 26 adults suffering from chronic periodontitis. All the strains of F. nucleatum were susceptible to amoxicillin/clavulanic acid, doxycycline, metronidazole, moxifloxacin and levofloxacin, whilst 2/16 strains were both resistant to amoxicillin and beta-lactamase-positive and 11/16 were resistant to clarithromycin. All of the Prevotella strains were susceptible to amoxicillin/clavulanic acid, doxycycline and metronidazole, whereas 7/39 strains were beta-lactamase-positive and resistant to amoxicillin, 5/39 were resistant to clarithromycin and 3/39 were resistant to both moxifloxacin and levofloxacin. Our findings confirm that there is an increasing need to encourage practitioners to use laboratory investigations to limit the risk of an incorrect therapeutic approach and to avoid the overuse of antimicrobial agents.

Interaction of Bacteroides fragilis pLV22a relaxase and transfer DNA with Escherichia coli RP4-TraG coupling protein

Many Bacteroides transfer factors are mobilizable in Escherichia coli when coresident with the IncP conjugative plasmid RP4, but not F. To begin characterization and potential interaction between Bacteroides mobilizable transfer factors and the RP4 mating channel, both mutants and deletions of the DNA processing (dtr), mating pair formation (mpf) and traG coupling genes of RP4 were tested for mobilization of Bacteroides plasmid pLV22a. All 10 mpf but none of the four dtr genes were required for mobilization of pLV22a. The RP4 TraG coupling protein (CP) was also required for mobilization of pLV22a, but could be substituted by a C-terminal deletion mutant of the F TraD CP. Potential interactions of the TraG CP with relaxase protein(s) and transfer DNA of both RP4 and pLV22a were assessed. Overlay assays identified productive interactions between TraG and the relaxase proteins of both MbpB and TraI from pLV22a and RP4 respectively. The Agrobacterium Transfer-ImmunoPrecipitation (TrIP) assay also identified an interaction between TraG and both RP4 and pLV22a transfer DNA. Thus, mobilization of the Bacteroides pLV22a in E. coli utilizes both RP4 Mpf and CP functions including an interaction between the relaxosome and the RP4 CP similar to that of cognate RP4 plasmid.

Antimicrobial resistance and the management of anaerobic infections

Management of anaerobic infections encompasses surgical procedures, antibacterial therapy and adjuncts. At present, metronidazole, penems, beta-lactam/beta-lactamase inhibitor combinations and chloramphenicol have the highest activity against obligate anaerobes. Tigecycline is a promising new agent. Other antibacterials (e.g., nitazoxanide, moxifloxacin, garenoxacin and ramoplanin) and nonantibiotic agents show potential but need further investigation. The patient's characteristics, mixed anaerobic/aerobic infections, infection sites, bacterial resistance patterns, bactericidal activity of agents and their pharmacokinetics, toxicity and influence on the normal flora should be considered. Susceptibility patterns of anaerobes have become less predictable owing to increasing antibacterial resistance. Emergence of highly virulent or multidrug-resistant strains is challenging the current therapy. To counteract these trends, regular resistance surveillance in anaerobes, rational antibiotic use and evaluation of new treatment alternatives are important.

[Will we still have antibiotics tomorrow?]

Since the discovery of antibiotics, it has been generally believed that these antimicrobials are capable of curing almost all bacterial infections. More recently, the appearance of increasing resistance to antibiotics and the emergence of multiresistant microorganisms have given rise to growing concern among physicians, and that concern has now started to filter through to society in general. The problem is further aggravated by a situation that not many people are currently aware of, that is, the limited prospects for future development of new antibiotics in the short to medium term. Appropriate use of available antibiotics based on a thorough understanding of their in vivo activity and the emergence of new forms of administration, such as inhalers, may help to alleviate the problem.

Genetic analysis of mechanisms of multidrug resistance in a clinical isolate of Bacteroides fragilis

This study investigated the mechanisms of multidrug resistance (MDR) in an isolate of Bacteroides fragilis (WI1) from a patient with anaerobic sepsis. The MDR of WI1 affected susceptibility to beta-lactams, clindamycin, fluoroquinolones, metronidazole and tetracycline. In addition to its 5.31-Mb chromosome, WI1 possessed two low-copy-number plasmids, pHagl (5.6 kb) and pHag2 (9.9 kb), that were absent from B. fragilis NCTC 9343. Restriction digestion with EcoRV, HindIII and SstI, combined with DNA sequencing, revealed that pHAG2 contained a tet(Q) gene at base position 3689 that resided on the conjugative transposon CTn341. Genes cfiA (encoding a metallo-beta-lactamase) and erm(F) (encoding a macrolide-lincosamide-streptogramin B resistance determinant) were also found in WI1, but were absent from B. fragilis NCTC 9343. Nitrocefin hydrolysis revealed that WI1 had high beta-lactamase activity. Sequencing of the gyrA quinolone resistance-determining region revealed a mutation causing a Ser82 --> Phe substitution, and comparative quantitative real-time RT-PCR revealed that the cfiA, erm(F) and tet(Q) genes were all expressed in WI1. In addition, the resistance-nodulation-division efflux pump genes bmeB9 and bmeB15 were significantly over-expressed (12.30 +/- 0.42-fold and 3541.1 +/- 95.4-fold, respectively), and the efflux pump inhibitors carbonyl cyanide m-chlorophenylhydrazone and reserpine significantly increased the susceptibility of the isolate to several unrelated antibiotics (p <0.005). These data suggested that WI1 was highly multidrug-resistant because of the additive effects of chromosome- and plasmid-encoded resistance determinants.

Clostridium aldenense sp. nov. and Clostridium citroniae sp. nov. isolated from human clinical infections

One hundred eight isolates were previously identified in our laboratory as Clostridium clostridioforme by colonial and cellular morphology, as well as biochemical tests. Recent studies have indicated that there are actually three different species in this C. clostridioforme group: C. hathewayi, C. bolteae, and C. clostridioforme. Our isolates were reexamined using biochemical and enzymatic tests and molecular methods. Forty-six isolates were reidentified as C. hathewayi, 34 as C. bolteae, five as C. clostridioforme, and one as C. symbiosum. Twenty-two strains were identified only to the genus level by 16S rRNA gene sequencing, and although they are microscopically and morphologically indistinguishable from the above-mentioned three species, they are phenotypically different and only 96 to 98% similar by gene sequencing. Twenty of these 22 strains were indole positive and formed two novel species. We propose Clostridium aldenense sp. nov. and Clostridium citroniae sp. nov. as names for these new species. They are differentiated from each other by results for raffinose, rhamnose, alpha-galactosidase, and beta-galactosidase: positive, negative, positive, and positive, respectively, for the former species and negative, positive, negative, and negative, respectively, for the latter species. The type strain of C. aldenense is RMA 9741 (ATCC BAA-1318; CCUG 52204), and the type strain of C. citroniae is RMA 16102 (ATCC BAA-1317; CCUG 52203).

Population pharmacokinetic modeling and Monte Carlo simulation of varying doses of intravenous metronidazole

Population pharmacokinetic modeling and Monte Carlo simulation (MCS) are approaches used to determine probability of target attainment (PTA) of antimicrobial therapy. The objectives of this study were 1) to determine a population pharmacokinetic model (PPM) using metronidazole and hydroxy-metronidazole concentrations from healthy subjects and critically ill patients, and 2) to determine the probability of attaining the pharmacodynamic target area under the plasma concentration (AUC)/MIC ratio >or=70 against 218 clinical isolates of Bacteroides fragilis using MCS. Eighteen healthy subjects were randomized to 3 dosages of intravenous metronidazole (500 mg every 8 h, 1000 mg day(-1), 1500 mg day(-1)) in an open-label 3-way crossover fashion. Serial blood samples were collected over 25.5 h on the 3rd day of each study period. An additional of 8 critically ill patients received intravenous metronidazole 500 mg every 8 h. Serial blood samples were collected over 8 h after the 2nd day of dosing. Plasma metronidazole and hydroxy-metronidazole concentrations were analyzed using a high-performance liquid chromatographic assay. The 834 plasma concentrations from 62 data sets were simultaneously modeled with Non-Parametric Adaptive Grid population modeling program. A 4-compartment model with a metabolite and zero-order infusion into the central compartment was used. The mean parameter vector and covariance matrix from PPM were inserted into the simulation module of ADAPT II. A 10,000-subject MCS was performed to determine the probability of PTA for a total drug AUC to MIC ratio >or=70 against 218 isolates of B. fragilis (MIC range, 0.125-2.0 mg L(-1)). Mean parameter values were CL(non-OH), 3.08 L h(-1); Vc, 35.4 L; K(OH), 0.04 h(-1); CL(OH), 2.78 L h(-1); and V(OH), 9.66 L. The regression values of the observed versus predicted concentrations (r2) of metronidazole and hydroxy-metronidazole were 0.972 and 0.980, respectively. The PTA for metronidazole 1500 mg day(-1) or 500 mg every 8 h (taken together) and 1000 mg day(-1) were 99.9% and 99.8%, respectively, over the reported MIC distribution range. For an MIC of 4 mg L(-1), the predicted PTA decreased to 80.0% and 28.5%, respectively. A PPM was determined by comodeling metronidazole and hydroxy-metronidazole concentrations from healthy subjects and critically ill patients. Based on this model, attainment of the target pharmacodynamic parameter (AUC/MIC ratio >or=70) against B. fragilis isolates is >99% when MICs are <2 mg L(-1), irrespective of the dosing interval of 24 h.

The search for new antimicrobials: why we need new options

The increasing identification of antibiotic-resistant pathogens that cause serious infections cannot be ignored. Although the future cannot be predicted with certainty, it is surely possible that an extensive epidemic of resistant bacterial infections could potentially harm millions of people. Given that it takes more than 10 years to establish the efficacy and safety of new compounds, there is an urgent need to restock the antibiotic pipeline. Only a few new antibacterial agents have received approval by the US Food and Drug Administration in the last 5 years, including linezolid in 2001, cefditoren, pivoxil and ertapenem in 2002, gemifloxacin and daptomycin in 2003, and telithromycin in 2004. Many of these agents are improved derivatives from established classes of antibiotics, and several are directed primarily at resistant Gram-positive bacteria (e.g., linezolid and daptomycin). One promising new addition is the recent approval of tigecycline (Tigacyl, Wyeth) in June 2005.

Fluoroquinolones and Anaerobes

The usefulness of fluoroquinolones for the treatment of mixed aerobic and anaerobic infections has been investigated since these agents started being used in clinical practice. Newer compounds have increased in vitro activity against anaerobes, but clinically relevant susceptibility breakpoints for these bacteria have not been established. Pharmacodynamic analyses and corroboration by new data from clinical trials have enhanced our knowledge concerning the use of fluoroquinolones to treat selective anaerobic pathogens. These studies suggest that newer agents could be useful in the treatment of several types of mixed aerobic and anaerobic infections, including skin and soft-tissue, intra-abdominal, and respiratory infections. The major concerns with expanding the use of fluoroquinolones to treat anaerobic infections have been reports of increasing resistance in Bacteroides group isolates and the impact of these antibiotics on the incidence of Clostridium difficile-associated disease.

Bacteroides fragilis mobilizable transposon Tn5520 requires a 71 base pair origin of transfer sequence and a single mobilization protein for relaxosome formation during conjugation

Tn5520 is the smallest known bacterial mobilizable transposon and was isolated from an antibiotic resistant Bacteroides fragilis clinical isolate. When a conjugation apparatus is provided in trans, Tn5520 is mobilized (transferred) efficiently within, and from, both Bacteroides spp. and Escherichia coli. Only two genes are present on Tn5520; one encodes an integrase, and the other a multifunctional mobilization (Mob) protein BmpH. BmpH is essential for Tn5520 mobility. The focus of this study was to identify the Tn5520 origin of conjugative transfer (oriT) and to study BmpH-oriT binding. We delimited the functional Tn5520 oriT to a 71 bp sequence upstream of the bmpH gene. A plasmid vector harbouring this minimal 71 bp oriT was mobilized at the same frequency as that of intact Tn5520. The minimal oriT contains one 17 bp inverted repeat (IR) sequence. We constructed and tested multiple IR mutants and showed that the IR was essential in its entirety for mobilization. A nick site sequence (5'-GCTAC-3') was also identified within the minimal oriT; this sequence resembled nick sites found in plasmids of Gram positive origin. We further showed that mutation of a highly conserved GC dinucleotide in the nick site sequence completely abolished mobilization. We also purified BmpH and showed that it specifically bound a Tn5520 oriT fragment in electrophoretic mobility shift assays. We also identified non-nick site sequences within the minimal oriT that were essential for mobilization. We hypothesize that transposon-based single Mob protein systems may contribute to efficient gene dissemination from Bacteroides spp., because fewer DNA processing proteins are required for relaxosome formation.

In vitro activity of 11 antibiotics against 74 anaerobes isolated from pediatric intra-abdominal infections

The in vitro activity of 11 antimicrobials was tested against 74 recent anaerobic isolates obtained from pretreatment cultures in pediatric patients with complicated intra-abdominal infections using the CLSI M11-A-6 agar dilution method. Carbapenems, beta-lactamase inhibitor combinations and metronidazole retained good activity, while all Bacteroides fragilis group species produced beta-lactamase and were penicillin resistant and 43% were either intermediately susceptible or resistant to clindamycin. Cefoxitin had moderate activity against B. fragilis but poor activity against Bacteroides thetaiotaomicron and other B. fragilis group isolates.

In vitro activity of moxifloxacin against 923 anaerobes isolated from human intra-abdominal infections

The in vitro activity of moxifloxacin against 923 recent anaerobic isolates obtained from pretreatment cultures in patients with complicated intra-abdominal infections was studied using the CLSI M11-A-6 agar dilution method. Moxifloxacin was active against 87% (96 of 110) Bacteroides fragilis strains at < or = 1 microg/ml and 87% (79 of 90) B. thetaiotaomicron strains at < or = 2 microg/ml. Species variation was seen, with B. uniformis, B. vulgatus, Clostridium clostridioforme, and C. symbiosum being least susceptible and accounting for most of the resistant isolates; excluding the aforementioned four resistant species, 86% (303 of 363) of Bacteroides species isolates and 94% (417 of 450) of all other genera and species were susceptible to < or = 2 microg/ml of moxifloxacin. Overall, moxifloxacin was active against 763 of 923 (83%) of strains at < or = 2 microg/ml, supporting its use as a monotherapy for some community-acquired intra-abdominal infections.

Bacteroides fragilis Group: Trends in Resistance

Representing the major part of the human colon microflora, members of the Bacteroides fragilis group are frequently involved in mixed aerobic and anaerobic infections. Recent studies show an increased resistance of the B. fragilis group against several antimicrobial agents. The aim of the present study was to determine the susceptibility of 87 B. fragilis group strains isolated in 2003/2004 in Western Austria against eight antimicrobial agents by Etest. Furthermore, the resistance patterns were compared with those of 45 B. fragilis group strains isolated in 1992 and referred to the world wide trend towards increased resistance. In 1992 as well as in 2003/2004, all strains were susceptible against metronidazole and imipenem. However, comparing the MIC-values of the B. fragilis group strains collected 1992 with data from 2003/2004, a significant increase in resistance was found for clindamycin (p<0.01). Regarding cefoxitin, a similar trend could be observed. However, this difference was not yet significant (p=0.144). Our findings underline the emerging resistance of the B. fragilis group against antimicrobial agents and underscore the importance of susceptibility testing of anaerobes even in routine laboratories.