Antimicrobial phenotypes and molecular basis in clinical strains of Clostridium difficile

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.

Antibiotic Resistances of Clostridioides difficile

The rapid evolution of antibiotic resistance in Clostridioides difficile and the consequent effects on prevention and treatment of C. difficile infections (CDIs) are a matter of concern for public health. Antibiotic resistance plays an important role in driving C. difficile epidemiology. Emergence of new types is often associated with the emergence of new resistances, and most of the epidemic C. difficile clinical isolates is currently resistant to multiple antibiotics. In particular, it is to worth to note the recent identification of strains with reduced susceptibility to the first-line antibiotics for CDI treatment and/or for relapsing infections. Antibiotic resistance in C. difficile has a multifactorial nature. Acquisition of genetic elements and alterations of the antibiotic target sites, as well as other factors, such as variations in the metabolic pathways or biofilm production, contribute to the survival of this pathogen in the presence of antibiotics. Different transfer mechanisms facilitate the spread of mobile elements among C. difficile strains and between C. difficile and other species. Furthermore, data indicate that both genetic elements and alterations in the antibiotic targets can be maintained in C. difficile regardless of the burden imposed on fitness, and therefore resistances may persist in C. difficile population in absence of antibiotic selective pressure.

Clostridioides difficile MreE (PBP2) variants facilitate clinical disease during cephalosporin exposures

Cephalosporins are the most common triggers of healthcare-associated Clostridioides difficile infections (CDI). Here, we confirm gene-level drivers of cephalosporin resistance and their roles in promoting disease. Genomic-epidemiologic analyses of 306 C. difficile isolates from a hospital surveillance program monitoring asymptomatic carriers and CDI patients identified prevalent third-generation cephalosporin resistance to ceftriaxone at >256 ug/mL in 26% of isolates. Resistance was associated with patient cephalosporin exposures 8-10 days before C. difficile detection. Genomic analyses identified variants in the mreE penicillin binding protein 2 (PBP2) associated with resistance to multiple beta-lactam classes. Transfer of variants into susceptible strain CD630 elevated resistance to first and third-generation cephalosporins. Transfer into the mouse-infective strain ATCC 43255 enabled disease when mice were exposed to 500ug/mL cefoperazone, a dose that inhibited the isogenic susceptible strain. Our findings establish roles of cephalosporins and mreE-cephalosporin-resistant variants in CDI and provide testable genetic loci for detecting resistance in patient strains.

Development and Clinical Application of a Rapid and Visual Loop-Mediated Isothermal Amplification Test for tetM gene in Clostridioides difficile Strains Cultured from Feces

OBJECTIVES

To develop a rapid and visual loop-mediated isothermal amplification (LAMP) assay targeting the tetM gene in Clostridioides difficile (C. difficile) strains cultured from feces.

METHODS

Primers were designed to recognize the tetM gene in C. difficile by LAMP, using turbidity and visual detection. The sensitivity and specificity of LAMP primers was determined. Besides, We conducted both LAMP and polymerase chain reaction (PCR) for the tcdA, tcdB, cdtA, cdtB, ermB, tetM genes in 300 toxigenic C. difficile strains cultured from feces.

RESULTS

The target DNA was amplified and visualized within 60 minutes at a temperature of 62°C. A total of 26 bacterial strains were found negative for tetM, which manifested high specificity of the primers. The detection limit of LAMP was 36.1 pg/µl, which was 100-fold more sensitive than PCR. The positive rate of tetM in toxigenic C. difficile strains cultured from feces was 93.3% by both LAMP and PCR. The proportion of toxin types in those C. difficile strains was 95.7% for A+B+CDT-, 4% for A-B+CDT-, and 0.3% for A+B+CDT+, respectively.

CONCLUSIONS

This is the first study examining tetM gene in C. difficile strains cultured from feces by LAMP. Its high specificity and sensitivity, as well as visual detection, make the new assay a powerful diagnostic tool for rapid testing.

Dogs as carriers of virulent and resistant genotypes of Clostridioides difficile

While previous research on zoonotic transmission of community-acquired Clostridioides difficile infection (CA-CDI) focused on food-producing animals, the present study aimed to investigate whether dogs are carriers of resistant and/or virulent C. difficile strains. Rectal swabs were collected from 323 dogs and 38 C. difficile isolates (11.8%) were obtained. Isolates were characterized by antimicrobial susceptibility testing, whole-genome sequencing (WGS) and a DNA hybridization assay. Multilocus sequence typing (MLST), core genome MLST (cgMLST) and screening for virulence and antimicrobial resistance genes were performed based on WGS. Minimum inhibitory concentrations for erythromycin, clindamycin, tetracycline, vancomycin and metronidazole were determined by E-test. Out of 38 C. difficile isolates, 28 (73.7%) carried genes for toxins. The majority of isolates belonged to MLST sequence types (STs) of clade I and one to clade V. Several isolates belonged to STs previously associated with human CA-CDI. However, cgMLST showed low genetic relatedness between the isolates of this study and C. difficile strains isolated from humans in Austria for which genome sequences were publicly available. Four isolates (10.5%) displayed resistance to three of the tested antimicrobial agents. Isolates exhibited resistance to erythromycin, clindamycin, tetracycline and metronidazole. These phenotypic resistances were supported by the presence of the resistance genes erm(B), cfr(C) and tet(M). All isolates were susceptible to vancomycin. Our results indicate that dogs may carry virulent and antimicrobial-resistant C. difficile strains.

Effect of Doxycycline in Decreasing the Severity of Clostridioides difficile Infection in Mice

Background: Doxycycline possesses antibacterial activity against Clostridioides difficile and anti-inflammatory effects. Materials and Methods: The influence of doxycycline on the development of CDI was studied in an established animal model of CDI using C57BL/6 mice. Results: Mice intraperitoneally administered doxycycline had higher cecum weight (1.3 ± 0.1 vs. 0.5 ± 0.1 g; p < 0.001) and less body weight reduction (0.7 ± 0.5 g vs. −17.4 ± 0.2 g; p < 0.001) than untreated mice infected with C. difficile. Oral doxycycline, metronidazole, or vancomycin therapy resulted in less body weight reduction in mice with CDI than in untreated mice (1.1 ± 0.1 g, 1.3 ± 0.2 g, 1.2 ± 0.1 g, vs. 2.9 ± 0.3 g; p < 0.001). Doxycycline therapy led to lower expression levels of inflammatory cytokines, such as macrophage inflammatory protein-2 (0.4 ± 0.1 vs. 2.9 ± 1.3, p = 0.02), and higher levels of zonula occludens-1 (1.2 ± 0.1 vs. 0.8 ± 0.1, p = 0.02) in colonic tissues than in untreated mice. Conclusions: Concurrent intraperitoneal administration of doxycycline and oral C. difficile challenge does not aggravate the disease severity of CDI, and oral doxycycline may be a potential therapeutic option for CDI.

Genetic Diversity of Leuconostoc mesenteroides Isolates from Traditional Montenegrin Brine Cheese

In many dairy products, Leuconostoc spp. is a natural part of non-starter lactic acid bacteria (NSLAB) accounting for flavor development. However, data on the genomic diversity of Leuconostoc spp. isolates obtained from cheese are still scarce. The focus of this study was the genomic characterization of Leuconostoc spp. obtained from different traditional Montenegrin brine cheeses with the aim to explore their diversity and provide genetic information as a basis for the selection of strains for future cheese production. In 2019, sixteen Leuconostoc spp. isolates were obtained from white brine cheeses from nine different producers located in three municipalities in the northern region of Montenegro. All isolates were identified as Ln. mesenteroides. Classical multilocus sequence tying (MLST) and core genome (cg) MLST revealed a high diversity of the Montenegrin Ln. mesenteroides cheese isolates. All isolates carried genes of the bacteriocin biosynthetic gene clusters, eight out of 16 strains carried the citCDEFG operon, 14 carried butA, and all 16 isolates carried alsS and ilv, genes involved in forming important aromas and flavor compounds. Safety evaluation indicated that isolates carried no pathogenic factors and no virulence factors. In conclusion, Ln. mesenteroides isolates from Montenegrin traditional cheeses displayed a high genetic diversity and were unrelated to strains deposited in GenBank.

Phylogenomic analysis of Clostridioides difficile ribotype 106 strains reveals novel genetic islands and emergent phenotypes

Clostridioides difficile infection (CDI) is a major healthcare-associated diarrheal disease. Consistent with trends across the United States, C. difficile RT106 was the second-most prevalent molecular type in our surveillance in Arizona from 2015 to 2018. A representative RT106 strain displayed robust virulence and 100% lethality in the hamster model of acute CDI. We identified a unique 46 KB genomic island (GI1) in all RT106 strains sequenced to date, including those in public databases. GI1 was not found in its entirety in any other C. difficile clade, or indeed, in any other microbial genome; however, smaller segments were detected in Enterococcus faecium strains. Molecular clock analyses suggested that GI1 was horizontally acquired and sequentially assembled over time. GI1 encodes homologs of VanZ and a SrtB-anchored collagen-binding adhesin, and correspondingly, all tested RT106 strains had increased teicoplanin resistance, and a majority displayed collagen-dependent biofilm formation. Two additional genomic islands (GI2 and GI3) were also present in a subset of RT106 strains. All three islands are predicted to encode mobile genetic elements as well as virulence factors. Emergent phenotypes associated with these genetic islands may have contributed to the relatively rapid expansion of RT106 in US healthcare and community settings.

Chromosome and Plasmid Features of Two ST37 Clostridioides difficile Strains Isolated in China Reveal Distinct Multidrug Resistance and Virulence Determinants

Clostridioides difficile ST37 is an emerging and prevalent multilocus sequence type and represents a lineage of clinical significance. This study aimed to characterize two epidemic C. difficile ST37 strains, CD161 and CDT4. CD161 acquires a chromosome and two distinct plasmids, pCD161-L, sharing high similarity with Clostridium phage, and pCD161-S, while CDT4 has a chromosome and a plasmid pCDT4 identical to pCD161-S. In the chromosome of both strains, three CdISt1-like elements and a skin^Cd element, which might influence sporulation, were identified. The multidrug resistance of the strains was due to the mutation in 23S rDNA, gyrA, and gyrB genes and the acquisition of ermB, ant6-Ia, aac6'-aph2'', and tetM genes. In addition, a distinct pathogenicity locus (PaLoc) with truncated tcdA gene represents the genetic feature of ST37 strains. To our knowledge, this is the first complete genome, both chromosomes and plasmids, of epidemic C. difficile ST37 strains in China.

Molecular characteristics of Clostridium difficile in children with acute gastroenteritis from Zhejiang

Background

Clostridium difficile infection (CDI) has an increasing pediatric prevalence worldwide. However, molecular characteristics of C. difficile in Chinese children with acute gastroenteritis have not been reported.

Methods

A five-year cross-sectional study was conducted in a tertiary children’s hospital in Zhejiang. Consecutive stool specimens from outpatient children with acute gastroenteritis were cultured for C. difficile, and isolates then were analyzed for toxin genes, multi-locus sequence type and antimicrobial resistance. Diarrhea-related viruses were detected, and demographic data were collected.

Results

A total of 115 CDI cases (14.3%), and 69 co-infected cases with both viruses and toxigenic C. difficile, were found in the 804 stool samples. The 186 C. difficile isolates included 6 of toxin A-positive/toxin B-positive/binary toxin-positive (A⁺B⁺CDT⁺), 139 of A⁺B⁺CDT⁻, 3 of A⁻B⁺CDT⁺, 36 of A⁻B⁺CDT⁻ and 2 of A⁻B⁻CDT⁻. Sequence types 26 (17.7%), 35 (11.3%), 39 (12.4%), 54 (16.7%), and 152 (11.3%) were major genotypes with significant differences among different antimicrobial resistances (Fisher's exact test, P < 0.001). The A⁻B⁺ isolates had significantly higher resistance, compared to erythromycin, rifampin, moxifloxacin, and gatifloxacin, than that of the A⁺B⁺ (χ² = 7.78 to 29.26, P < 0.01). The positive CDI rate in infants (16.2%) was significantly higher than that of children over 1 year old (10.8%) (χ² = 4.39, P = 0.036).

Conclusions

CDI has been revealed as a major cause of acute gastroenteritis in children with various genotypes. The role of toxigenic C. difficile and risk factors of CDI should be emphatically considered in subsequent diarrhea surveillance in children from China.

Characterization of Microbial Communities in a Dairy Farm Matrix in Ningxia, China, by 16S rDNA Analysis

A large amount of dairy manure is produced annually in the Ningxia Hui Autonomous Region of China due to the increase in food-producing animal agriculture in this region. The presence of bovine-originated zoonotic, especially human, pathogenic bacteria in untreated manure poses a significant threat to the environment and to public health. However, little is known about the composition, diversity, and abundance of bacterial communities in untreated dairy manure in the Ningxia region. In this study, the microbial community structure of the dairy farm matrix was characterized through 16S rDNA sequencing. The impact of manure treatment methods on bacterial communities was also analyzed. The results showed that the microbial community in dairy manure contained both beneficial bacteria and pathogens, with Firmicutes, Bacteroidetes, Proteobacteria, Spirochaetes, and Actinobacteria as dominant phyla. The results also showed the diversity and variety of abundance of zoonotic pathogens among different matrices. The number of pathogens was found to increase significantly in the accumulated but untreated manure, which appeared to be the main matrix of dairy farms that accumulated pathogens including zoonotic pathogens. Findings from this study suggested that farm management, particularly proper treatment of manure, is essential to achieve a shift in the bacterial community composition and a reduction in the environmental load of pathogens including zoonotic pathogens.

Prevalence, characteristics and antimicrobial susceptibility patterns of Clostridioides difficile isolated from hospitals in Iran

OBJECTIVES

Clostridioides (previously Clostridium) difficile is a major growing cause of nosocomial diarrhoea known as C. difficile infection (CDI). This study investigated the prevalence and antimicrobial resistance patterns of C. difficile isolated from patients suffering from diarrhoea in Iran between 2016-2018.

METHODS

A total of 151 stool specimens were collected and were screened for the presence of C. difficile. Specimens were examined for toxins by culture, enzyme immunoassay (EIA) and PCR. Antimicrobial susceptibility testing was performed for 12 antibiotics (metronidazole, vancomycin, clindamycin, tetracycline, erythromycin, ciprofloxacin, levofloxacin, moxifloxacin, fusidic acid, piperacillin, piperacillin/tazobactam and rifampicin) by the disk diffusion method according to the guidelines of the CLSI, EUCAST and CA-SFM.

RESULTS

Of 151 stool specimens, 66 (43.7%) were positive for C. difficile by PCR, whereas 2 (1.3%) were only positive for C. difficile toxins based on EIA. A total of 292 clostridial isolates were obtained from specimens by culture, of which 133 (45.5%) were finally confirmed as C. difficile by PCR. Of 121 isolates resistant to at least one antibiotic, 107 (88.4%) were resistant to three or more antimicrobials and thus were defined as multidrug-resistant (MDR). Different and diverse resistance patterns to the antimicrobial drugs were seen among the isolates.

CONCLUSION

This is the first report of the isolation of C. difficile from different governmental hospitals of Iran and indicates that CDI might be an important nosocomial infection in different hospital wards. Moreover, this study provides a comprehensive picture of the MDR phenotype characteristics of C. difficile isolates in Iran.

The impact of antimicrobial resistance on induction, transmission and treatment of Clostridium difficile infection

Clostridium difficile infection (CDI) of the gastrointestinal (GI) tract is a potentially life-threatening disease that has surpassed multi-drug-resistant Staphylococcus aureus as the commonest antimicrobial-resistant organism associated with healthcare1. This obligate anaerobic spore-forming Gram-positive bacillus colonises the GI tract and its numbers increase after disruption of the commensal GI microbiota often induced by exposure to antimicrobial agents2. Paradoxically, the disease that may follow its outgrowth necessitates further antimicrobial treatment. Already a major challenge to infection prevention and control strategies, there are indications that C. difficile is developing further resistance to currently used antimicrobial agents.

Nationwide surveillance of ribotypes and antimicrobial susceptibilities of toxigenic Clostridium difficile isolates with an emphasis on reduced doxycycline and tigecycline susceptibilities among ribotype 078 lineage isolates in Taiwan

Objectives

The information of antimicrobial susceptibility, toxin gene, and ribotype distribution of toxigenic Clostridium difficile isolates in Taiwan remain limited.

Patients and methods

The study was conducted from January 2015 to December 2016 in 5 hospitals in Taiwan. Adults aged ≥20 years with a hospital stay for >5 days were included, and those with colectomy or intestinal infection due to other enteropathogens were excluded. Multiplex PCR was used to detect tcdA, tcdB, cdtA, cdtB, and tcdC deletions, and antimicrobial susceptibility for metronidazole, vancomycin, doxycycline, and tigecycline was investigated. Ribotypes of those isolates with tcdC deletion and tcdA+/tcdB+ were determined.

Results

Of 1112 C. difficile isolates collected from adults at 5 hospitals, 842 were toxigenic, including 749 (89.0%) tcdA+/tcdB+ isolates and 93 (11.0%) tcdA−/tcdB+. Of the toxigenic isolates, 76 (9.0%) had a tcdC deletion and were cdtA+/cdtB+, indicative of hypervirulence, and RT078 lineage, including RT126, RT127, and RT078, predominated (n=53, 76.3%). Similar to the susceptibility data in Asia countries, metronidazole or vancomycin resistance was rare, noted in 1.2% or 2.1%, respectively. Reduced doxycycline susceptibility (minimum inhibitory concentration [MIC] of ≥8 mg/L) was more common among RT078 lineage than non-RT078 lineage (75.9%, 44/58 vs 6.0%, 47/784; P<0.001). Also reduced tigecycline susceptibility (MIC ≥0.125 mg/L) was more common among RT078 lineage (20.7%, 12/58 vs 6.5%, 51/784; P<0.001).

Conclusion

In Taiwan, toxigenic C. difficile isolates remain susceptible to metronidazole and vancomycin. RT078 lineage predominated among toxigenic isolates with cdtA, cdtB, and tcdC deletion, and more often had reduced doxycycline and tigecycline susceptibility than the isolates other than RT078 lineage.

Isolation of Toxigenic Clostridium difficile from Animal Manure and Composts Being Used as Biological Soil Amendments

The well-known nosocomial pathogen Clostridium difficile has recently been recognized as a community-associated pathogen. As livestock animals carry and shed C. difficile in their feces, animal manure-based composts may play an important role in disseminating toxigenic C. difficile strains into the agricultural environment. The present study surveyed C. difficile contamination of commercially available composts and animal manure. Presumptive C. difficile isolates were confirmed by testing for the tpi housekeeping gene in addition to Gram staining. The confirmed C. difficile isolates were further tested for toxigenicity, PCR ribotype, and susceptibilities to selected antibiotics. C. difficile was found in 51 out of 142 samples (36%). A total of 58 C. difficile strains were isolated from those 51 positive compost/manure samples. The presence of C. difficile in compost did not significantly correlate (P > 0.05) with the physical and most microbiological parameters, including the presence of fecal coliforms. The majority of C. difficile isolates were toxigenic, with 63.8% positive for the toxin A gene (tcdA) and 67.2% positive for the toxin B gene (tcdB). Only 3 isolates (5.17%) were positive for the binary toxins. There were 38 different PCR ribotypes among the 58 C. difficile isolates, and ribotype 106 was the most prevalent, followed by ribotypes 020 and 412. All C. difficile isolates were susceptible to the selected antibiotics, but >50% of the isolates had reduced susceptibility to clindamycin by the agar dilution method. This study indicates that compost may be a reservoir of toxigenic C. difficile strains.IMPORTANCEClostridium difficile infection (CDI) is a leading cause of antibiotic-associated diarrhea in health care facilities in developed countries. Extended hospital stays and recurrences severely increase the cost of treatments and the high mortality rate that is observed among the elderly. Community-associated CDI cases that occur without any recent contact with the hospital environment are increasing. Studies have reported the isolation of virulent C. difficile strains from water, soil, meat, vegetables, pets, livestock animals, and animal manure. The objective of this study was to isolate and characterize C. difficile strains from animal manure and commercially available compost products. Our results demonstrate that not only unprocessed animal manure but also finished composts made of different feedstocks can serve as a reservoir for C. difficile as well. Most importantly, our study revealed that properly processed compost is a potential source of toxigenic and clindamycin-resistant C. difficile isolates.

Molecular epidemiology and antimicrobial susceptibility of human Clostridium difficile isolates from a single institution in Northern China

Because the epidemiology of Clostridium difficile infection (CDI) is region-specific, the present study was undertaken to examine the epidemiology of C difficile outbreaks in Beijing, China.Eighty nonduplicate isolates were collected from March, 2016 to December, 2016. The molecular type and phylogenetic analysis were evaluated by multilocus sequence typing (MLST). The minimum inhibitory concentrations (MICs) for 11 antibiotics and the resistance mechanisms were investigated.Sixty-five toxigenic strains (81.25%), including 22 tcdABCDT strains (27.5%) and 43 tcdABCDT strains (53.75%), and also 15 nontoxigenic strains (tcdABCDT; 18.75%) were detected. MLST identified 21 different sequence types (STs), including 2 novel types (ST409 and ST416). All isolates were susceptible to metronidazole, vancomycin, fidaxomicin, piperacillin/tazobactam, and meropenem, and all were effectively inhibited by emodin (MICs 4-8 μg/mL). The resistance rates to rifaximin, ceftriaxone, clindamycin, erythromycin, and ciprofloxacin were 8.75%, 51.25%, 96.25%, 81.25%, and 96.25%, respectively; 81.25% (65/80) of isolates were multidrug-resistant. Amino acid mutations in GyrA and/or GyrB conferred quinolone resistance. One novel amino acid substitution, F86Y in GyrA, was found in 1 CIP-intermediate strain. The erm(B) gene played a key role in mediating macrolide-lincosamide-streptogramin B (MLSB) resistance. Erm(G) was also found in erm(B)-negative strains that were resistant to both erythromycin and clindamycin. RpoB mutations were associated with rifampin resistance, and 2 new amino mutations were identified in 1 intermediate strain (E573A and E603N).Regional diversity and gene heterogeneity exist in both the ST type and resistant patterns of clinical C difficile isolates in Northern China.

Clostridium difficile Infections: A Global Overview of Drug Sensitivity and Resistance Mechanisms

Clostridium difficile (C. difficile) is the most prevalent causative pathogen of healthcare-associated diarrhea. Notably, over the past 10 years, the number of Clostridium difficile outbreaks has increased with the rate of morbidity and mortality. The occurrence and spread of C. difficile strains that are resistant to multiple antimicrobial drugs complicate prevention as well as potential treatment options. Most C. difficile isolates are still susceptible to metronidazole and vancomycin. Incidences of C. difficile resistance to other antimicrobial drugs have also been reported. Most of the antibiotics correlated with C. difficile infection (CDI), such as ampicillin, amoxicillin, cephalosporins, clindamycin, and fluoroquinolones, continue to be associated with the highest risk for CDI. Still, the detailed mechanism of resistance to metronidazole or vancomycin is not clear. Alternation in the target sites of the antibiotics is the main mechanism of erythromycin, fluoroquinolone, and rifamycin resistance in C. difficile. In this review, different antimicrobial agents are discussed and C. difficile resistance patterns and their mechanism of survival are summarized.

Genomic and phenotypic diversity of Clostridium difficile during long-term sequential recurrences of infection

Infection with the emerging pathogen Clostridioides (Clostridium) difficile might lead to colonization of the gastrointestinal tract of humans and mammals eventually resulting in antibiotic-associated diarrhea, which can be mild to possibly life-threatening. Recurrences after antibiotic treatment have been described in 15-30% of the cases and are either caused by the original (relapse) or by new strains (reinfection). In this study, we describe a patient with ongoing recurrent C. difficile infections over 13 months. During this time, ten C. difficile strains of six different ribotypes could be isolated that were further characterized by phenotypic and genomic analyses including motility and sporulation assays, growth fitness and antibiotic susceptibility as well as whole-genome sequencing. PCR ribotyping of the isolates confirmed that the recurrences were a mixture of relapses and reinfections. One recurrence was due to a mixed infection with three different strains of two different ribotypes. Furthermore, genomes were sequenced and multi-locus sequence typing (MLST) was carried out, which identified the strains as members of sequence types (STs) 10, 11, 14 and 76. Comparison of the genomes of isolates of the same ST originating from recurrent CDI (relapses) indicated little within-patient microevolution and some concurrent within-patient diversity of closely related strains. Isolates of ribotype 126 that are binary toxin positive differed from other ribotypes in various phenotypic aspects including motility, sporulation behavior and cell morphology. Ribotype 126 is genetically related to ribotype 078 that has been associated with increased virulence. Isolates of the ribotype 126 exhibited elongated cells and a chaining phenotype, which was confirmed by membrane staining and scanning electron microscopy. Furthermore, this strain exhibits a sinking behavior in liquid medium in stationary growth phase. Taken together, our observation has proven multiple CDI recurrences that were based on a mixture of relapses and reinfections.

Antibiotic Resistances of Clostridium difficile

The rapid evolution of antibiotic resistance in Clostridium difficile and the consequent effects on prevention and treatment of C. difficile infections (CDIs) are matter of concern for public health. Antibiotic resistance plays an important role in driving C. difficile epidemiology. Emergence of new types is often associated with the emergence of new resistances and most of epidemic C. difficile clinical isolates is currently resistant to multiple antibiotics. In particular, it is to worth to note the recent identification of strains with reduced susceptibility to the first-line antibiotics for CDI treatment and/or for relapsing infections. Antibiotic resistance in C. difficile has a multifactorial nature. Acquisition of genetic elements and alterations of the antibiotic target sites, as well as other factors, such as variations in the metabolic pathways and biofilm production, contribute to the survival of this pathogen in the presence of antibiotics. Different transfer mechanisms facilitate the spread of mobile elements among C. difficile strains and between C. difficile and other species. Furthermore, recent data indicate that both genetic elements and alterations in the antibiotic targets can be maintained in C. difficile regardless of the burden imposed on fitness, and therefore resistances may persist in C. difficile population in absence of antibiotic selective pressure.

A multiplayer game: species of Clostridium, Acinetobacter, and Pseudomonas are responsible for the persistence of antibiotic resistance genes in manure-treated soils

Antibiotics are routinely used in modern livestock farming. The manure from medicated animals is used for the fertilization of arable crops, which in turn leads to the accumulation of antibiotic resistance genes (ARGs) in the environment. This is a potentially serious public health issue, yet the identities of the bacterial taxa involved in ARG persistence are as yet undetermined. Using soil-manure microcosm experiments, we investigated the relationship between (i) the persistence of diverse ARGs and (ii) the dynamics of bacterial community members. We were able to identify, for the first time, the bacterial taxa involved in ARG enrichment in manured soils. They were gut-associated Clostridium species, and environmental species of Acinetobacter and Pseudomonas genera, all of them closely related to important nosocomial pathogens. Our data provide new clues on the routes by which ARGs may spread from farms to medical clinics.

Recent advances in the understanding of antibiotic resistance in Clostridium difficile infection

Clostridium difficile epidemiology has changed in recent years, with the emergence of highly virulent types associated with severe infections, high rates of recurrences and mortality. Antibiotic resistance plays an important role in driving these epidemiological changes and the emergence of new types. While clindamycin resistance was driving historical endemic types, new types are associated with resistance to fluoroquinolones. Furthermore, resistance to multiple antibiotics is a common feature of the newly emergent strains and, in general, of many epidemic isolates. A reduced susceptibility to antibiotics used for C. difficile infection (CDI) treatment, in particular to metronidazole, has recently been described in several studies. Furthermore, an increased number of strains show resistance to rifamycins, used for the treatment of relapsing CDI. Several mechanisms of resistance have been identified in C. difficile, including acquisition of genetic elements and alterations of the antibiotic target sites. The C. difficile genome contains a plethora of mobile genetic elements, many of them involved in antibiotic resistance. Transfer of genetic elements among C. difficile strains or between C. difficile and other bacterial species can occur through different mechanisms that facilitate their spread. Investigations of the fitness cost in C. difficile indicate that both genetic elements and mutations in the molecular targets of antibiotics can be maintained regardless of the burden imposed on fitness, suggesting that resistances may persist in the C. difficile population also in absence of antibiotic selective pressure. The rapid evolution of antibiotic resistance and its composite nature complicate strategies in the treatment and prevention of CDI. The rapid identification of new phenotypic and genotypic traits, the implementation of effective antimicrobial stewardship and infection control programs, and the development of alternative therapies are needed to prevent and contain the spread of resistance and to ensure an efficacious therapy for CDI.

Rapid detection of ermB gene in Clostridium difficile by loop-mediated isothermal amplification

Macrolide-lincosamide-streptogramin B resistance in Clostridium difficile is mostly due to the ermB resistance determinant. Here, we describe a sensitive and rapid molecular method to detect ermB in C. difficile to contribute to the wider epidemiological study. Five sets of loop-mediated isothermal amplification (LAMP) primers were designed and optimized for rapid detection of ermB. The specificity and sensitivity of the primers for ermB were detected, and the ermB LAMP assay was compared to conventional PCR with 80 clinical isolates of C. difficile. Real-time monitoring of turbidity and chromogenic reaction were used to determine negative and positive results. A total of 26 pathogenic bacterial strains of different species were found to be negative for ermB, which indicated the high specificity of the primers. ermB was detected in 78.8 % (63/80) of the clinical isolates by both LAMP and conventional PCR. The detection limit of LAMP was 36.1  pg DNA μl- 1 and its sensitivity was 10-fold greater than that of conventional PCR. This study is the first report regarding the development and application of the LAMP assay for detection of the ermB gene in C. difficile strains. The developed LAMP method is sensitive, specific and provides a user-friendly visual approach for the rapid detection of ermB-bearing C. difficile.

Antimicrobial Resistance and Reduced Susceptibility in Clostridium difficile: Potential Consequences for Induction, Treatment, and Recurrence of C. difficile Infection

Clostridium difficile infection (CDI) remains a substantial burden on healthcare systems and is likely to remain so given our reliance on antimicrobial therapies to treat bacterial infections, especially in an aging population in whom multiple co-morbidities are common. Antimicrobial agents are a key component in the aetiology of CDI, both in the establishment of the infection and also in its treatment. The purpose of this review is to summarise the role of antimicrobial agents in primary and recurrent CDI; assessing why certain antimicrobial classes may predispose to the induction of CDI according to a balance between antimicrobial activity against the gut microflora and C. difficile. Considering these aspects of CDI is important in both the prevention of the infection and in the development of new antimicrobial treatments.

Doxycycline and Tigecycline: Two Friendly Drugs with a Low Association with Clostridium Difficile Infection

Clostridium difficile infection (CDI) is known to be associated with prior exposure to many classes of antibiotics. Standard therapy for CDI (i.e., metronidazole and vancomycin) is associated with high recurrence rates. Although tetracycline derivatives such as tetracycline, doxycycline or tigecycline are not the standard therapeutic choices for CDI, they may serve as an alternative or a component of combination therapy. Previous tetracycline or doxycycline usage had been shown to have less association with CDI development. Tigecycline, a broad-spectrum glycylcycline with potency against many gram-positive or gram-negative pathogens, had been successfully used to treat severe or refractory CDI. The in vitro susceptibility of C. difficile clinical isolates to tigecycline in many studies showed low minimal inhibitory concentrations. Tigecycline can suppress in vitro toxin production in both historical and hypervirulent C. difficile strains and reduce spore production in a dose-dependent manner. Tetracycline compounds such as doxycycline, minocycline, and tigecycline possess anti-inflammatory properties that are independent of their antibiotic activity and may contribute to their therapeutic effect for CDI. Although clinical data are limited, doxycycline is less likely to induce CDI, and tigecycline can be considered one of the therapeutic choices for severe or refractory CDI.

Clostridium difficile PCR Ribotype 018, a Successful Epidemic Genotype

Clostridium difficile infection (CDI) became a public health problem for the global spreading of the so-called hypervirulent PCR ribotypes (RTs) 027 and 078, associated with increases in the transmission and severity of the disease. However, especially in Europe, several RTs are prevalent, and the concept of hypervirulence is currently debated. We investigated the toxin and resistance profiles and the genetic relatedness of 312 C. difficile strains isolated in a large Italian teaching hospital during a 5-year period. We evaluated the role of CDI-related antibiotic consumption and infection control practices on the RT predominance in association with their molecular features and transmission capacity. Excluding secondary cases due to nosocomial transmission, RT018 was the predominant genotype (42.4%) followed by RT078 (13.6%), while RT027 accounted for 0.8% of the strains. RT078 was most frequently isolated from patients in intensive care units. Its prevalence significantly increased over time, but its transmission capacity was very low. In contrast, RT018 was highly transmissible and accounted for 95.7% of the secondary cases. Patients with the RT018 genotype were significantly older than those with RT078 and other RTs, indicating an association between epidemic RT and age. We provide here the first epidemiological evidence to consider RT018 as a successful epidemic genotype that deserves more attention in clinical practice.

Targeting surface-layer proteins with single-domain antibodies: a potential therapeutic approach against Clostridium difficile-associated disease

Clostridium difficile is a leading cause of death from gastrointestinal infections in North America. Antibiotic therapy is effective, but the high incidence of relapse and the rise in hypervirulent strains warrant the search for novel treatments. Surface layer proteins (SLPs) cover the entire C. difficile bacterial surface, are composed of high-molecular-weight (HMW) and low-molecular-weight (LMW) subunits, and mediate adherence to host cells. Passive and active immunization against SLPs has enhanced hamster survival, suggesting that antibody-mediated neutralization may be an effective therapeutic strategy. Here, we isolated a panel of SLP-specific single-domain antibodies (V_HHs) using an immune llama phage display library and SLPs isolated from C. difficile hypervirulent strain QCD-32g58 (027 ribotype) as a target antigen. Binding studies revealed a number of V_HHs that bound QCD-32g58 SLPs with high affinity (K_D = 3–6 nM) and targeted epitopes located on the LMW subunit of the SLP. The V_HHs demonstrated melting temperatures as high as 75 °C, and a few were resistant to the gastrointestinal protease pepsin at physiologically relevant concentrations. In addition, we demonstrated the binding specificity of the V_HHs to the major C. difficile ribotypes by whole cell ELISA, where all V_HHs were found to bind 001 and 027 ribotypes, and a subset of antibodies were found to be broadly cross-reactive in binding cells representative of 012, 017, 023, and 078 ribotypes. Finally, we showed that several of the V_HHs inhibited C. difficile QCD-32g58 motility in vitro. Targeting SLPs with V_HHs may be a viable therapeutic approach against C. difficile-associated disease.

Potential for reduction of streptogramin A resistance revealed by structural analysis of acetyltransferase VatA

Combinations of group A and B streptogramins (i.e., dalfopristin and quinupristin) are "last-resort" antibiotics for the treatment of infections caused by Gram-positive pathogens, including methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus faecium. Resistance to streptogramins has arisen via multiple mechanisms, including the deactivation of the group A component by the large family of virginiamycin O-acetyltransferase (Vat) enzymes. Despite the structural elucidation performed for the VatD acetyltransferase, which provided a general molecular framework for activity, a detailed characterization of the essential catalytic and antibiotic substrate-binding determinants in Vat enzymes is still lacking. We have determined the crystal structure of S. aureus VatA in apo, virginiamycin M1- and acetyl-coenzyme A (CoA)-bound forms and provide an extensive mutagenesis and functional analysis of the structural determinants required for catalysis and streptogramin A recognition. Based on an updated genomic survey across the Vat enzyme family, we identified key conserved residues critical for VatA activity that are not part of the O-acetylation catalytic apparatus. Exploiting such constraints of the Vat active site may lead to the development of streptogramin A compounds that evade inactivation by Vat enzymes while retaining binding to their ribosomal target.

Clostridium perfringens and Clostridium difficile in cooked beef sold in Côte d'Ivoire and their antimicrobial susceptibility

The aim of this study was to evaluate the prevalence of Clostridium difficile and Clostridium perfringens in cooked beef sold in the streets in Côte d'Ivoire and their antimicrobial susceptibility. A total of 395 kidney and flesh samples of cooked beef were collected from vendors at Abidjan and subjected to C. difficile and C. perfringens isolation and identification by using biochemical tests, API 20A system and PCR detection. Subsequently, the antimicrobial susceptibility test was performed for confirmed isolates. Our results showed the prevalence of 12.4% for C. difficile (11.04% in kidney and 13.45% in flesh) and 5.06% for C. perfringens (2.32% in kidney and 7.17% in flesh). Metronidazole and vancomycin remained the most potent antimicrobial agents against C. difficile while metronidazole and penicillin G were the most potent agents against C. perfringens. The resistance rates to tetracycline, doxycycline, chloramphenicol and erythromycin against C. difficile and C. perfringens isolates ranged from 2.05% to 8.16% and from 20% to 50%, respectively. Among all antimicrobial agents tested against C. difficile, percentages of resistance to quinolones ciprofloxacin, norfloxacin and nalidixic acid as well as to gentamicin and cefotaxime were the highest. Eight resistant phenotypes were defined for C. difficile isolates and eleven resistant phenotypes for C. perfringens isolates. Clindamycin/gentamicin/cefotaxime/ciprofloxacin/norfloxacin/nalidixic acid resistance was the most common phenotype for C. difficile (55.10% of isolates) while norfloxacin/nalidixic acid resistance was the most common phenotype for C. perfringens (20% of isolates).

Clostridium difficile erm(B)-containing elements and the burden on the in vitro fitness

In Clostridium difficile, resistance to the macrolide-lincosamide-streptogramin B group of antibiotics generally relies on erm(B) genes. In this study, we investigated elements with a genetic organization different from Tn5398, the mobilizable non-conjugative element identified in C. difficile strain 630. Our results suggested that the elements most frequently found in strains isolated during the European surveillance study in 2005 were related to Tn6194, the conjugative transposon recently detected in different C. difficile types, including PCR-ribotype 027. We characterized a Tn6194-like and a novel element rarely found in clinical isolates. A burden on the in vitro fitness of C. difficile was observed after the acquisition of these elements as well as of Tn5398.

Antimicrobial-resistant strains of Clostridium difficile from North America

A total of 316 toxigenic Clostridium difficile clinical isolates of known PCR ribotypes from patients in North America were screened for resistance to clindamycin, metronidazole, moxifloxacin, and rifampin. Clindamycin resistance was observed among 16 different ribotypes, with ribotypes 017, 053, and 078 showing the highest proportions of resistance. All isolates were susceptible to metronidazole. Moxifloxacin resistance was present in >90% of PCR-ribotype 027 and 053 isolates but was less common among other ribotypes. Only 7.9% of the C. difficile isolates were resistant to rifampin. Multidrug resistance (clindamycin, moxifloxacin, and rifampin) was present in 27.5% of PCR-ribotype 027 strains but was rare in other ribotypes. These results suggest that antimicrobial resistance in North American isolates of C. difficile varies by strain type and parallels rates of resistance reported from Europe and the Far East.

Multidrug resistance in European Clostridium difficile clinical isolates

OBJECTIVES

Multidrug resistance and antibiotic resistance mechanisms were investigated in 316 Clostridium difficile clinical isolates collected during the first European surveillance on C. difficile in 2005.

METHODS

MICs of eight different antibiotics were determined using Etest. Reserpine- and carbonyl cyanide m-chlorophenylhydrazone-sensitive efflux was tested using the agar dilution method. Molecular analysis of the resistance mechanisms was performed using PCR assays, PCR mapping and sequencing.

RESULTS

One hundred and forty-eight C. difficile strains were resistant to at least one antibiotic and 82 (55%) were multidrug resistant. In particular, 48% of these isolates were resistant to erythromycin, clindamycin, moxifloxacin and rifampicin. New genetic elements or determinants conferring resistance to erythromycin/clindamycin or tetracycline were identified. Even if most multiresistant strains carried an erm(B) gene, quite a few were erm(B) negative. In-depth analysis of the underlying mechanism in these isolates was carried out, including analysis of 23S rDNA and the ribosomal proteins L4 and L22. Interestingly, resistance to rifampicin was observed in multidrug-resistant strains in association with resistance to fluoroquinolones. Mutations in the rpo(B) and gyrA genes were identified as the cause of resistance to these antibiotics, respectively.

CONCLUSIONS

Characterization of multidrug-resistant C. difficile clinical isolates shows that antibiotic resistance is changing, involving new determinants and mechanisms and providing this pathogen with potential advantages over the co-resident gut flora. The present paper provides, for the first time, a comprehensive picture of the different characteristics of multidrug-resistant C. difficile strains in Europe in 2005 and represents an important source of data for future comparative European studies.

Prevalence of antimicrobial resistance and association with toxin genes in Clostridium difficile in commercial swine

OBJECTIVE

To estimate prevalence and determine association between antimicrobia resistance and toxin gene profile of Clostridium difficile in commercial pigs at the preharvest food-safety level.

ANIMALS

68 sows and 251 young pigs from 5 farms in North Carolina and 3 in Ohio.

PROCEDURES

Fecal samples were collected from sows (8/farm) and matched young pigs (32/farm) at farrowing and again at the nursery and finishing stages. Clostridium difficile isolates were tested for susceptibility to 6 antimicrobials. A PCR assay was used to detect genes coding for enterotoxin A (tcdA), cytotoxin B (tcdB), and binary toxin (cdtB).

RESULTS

C difficile prevalence in young pigs at farrowing was 73% (n=183) with significantly higher prevalence in Ohio (875%) than in North Carolina (64%). Clostridium difficile was isolated from 32 (47%) sows with no significant difference between the 2 regions. A single pig had a positive test result at the nursery, and no isolate was recovered at the finishing farms. Resistance to ciprofloxacin was predominant in young pigs (91.3% of isolates) and sows (94%). The antimicrobial resistance profile ciprofloxacin-erythromycin-tetracycline was detected in 21.4% and 11.7% of isolates from young pigs and sows, respectively. Most isolates had positive results for tcdA (65%), tcdB (84%), and the binary toxin cdtB (77%) genes. Erythromycin resistance and tetracycline resistance were significantly associated with toxin gene profiles.

CONCLUSIONS AND CLINICAL RELEVANCE

The common occurrence of antimicrobial-resistant C difficile and the significant association of toxigenic strains with antimicrobial resistance could contribute to high morbidity in farms with farrowing pigs.

Array comparative hybridisation reveals a high degree of similarity between UK and European clinical isolates of hypervirulent Clostridium difficile

Background

Clostridium difficile is a Gram-positive, anaerobic, spore-forming bacterium that is responsible for C. difficile associated disease in humans and is currently the most common cause of nosocomial diarrhoea in the western world. This current status has been linked to the emergence of a highly virulent PCR-ribotype 027 strain. The aim of this work was to identify regions of sequence divergence that may be used as genetic markers of hypervirulent PCR-ribotype 027 strains and markers of the sequenced strain, CD630 by array comparative hybridisation.

Results

In this study, we examined 94 clinical strains of the most common PCR-ribotypes isolated in mainland Europe and the UK by array comparative genomic hybridisation. Our array was comprehensive with 40,097 oligonucleotides covering the C. difficile 630 genome and revealed a core genome for all the strains of 32%. The array also covered genes unique to two PCR-ribotype 027 strains, relative to C. difficile 630 which were represented by 681 probes. All of these genes were also found in the commonly occuring PCR-ribotypes 001 and 106, and the emerging hypervirulent PCR-ribotype 078 strains, indicating that these are markers for all highly virulent strains.

Conclusions

We have fulfilled the aims of this study by identifying markers for CD630 and markers associated with hypervirulence, albeit genes that are not just indicative of PCR-ribotype 027 strains. We have also extended this study and have defined a more stringent core gene set compared to those previously published due to the comprehensive array coverage. Further to this we have defined a list of genes absent from non-toxinogenic strains and defined the nature of the specific toxin deletion in the strain CD37.

Changes in antibiotic susceptibility and ribotypes in Clostridium difficile isolates from southern Scotland, 1979–2004

An increase in the incidence of clinical cases of Clostridium difficile infection has been reported in recent years, but few studies have examined changes in molecular epidemiology and antibiotic resistance over a long period of time. A collection of 179 isolates of C. difficile obtained from symptomatic adult patients in southern Scotland between 1979 and 2004 was used to determine changes in the prevalence of epidemiological types and antibiotic susceptibilities to common antibiotics. PCR ribotyping and MIC determination were performed on all isolates. A total of 56 different ribotypes were identified, among which ribotype 002 was the commonest type overall (14 .0%), followed by ribotypes 014 (7.3 %), 012 (5 .0%), 015 (5.0 %), 020 (5 .0%) and 001 (4.5 %). Ribotype 078 was also identified. The 10 commonest ribotypes comprised 55 % of the total isolates. Ribotype 001 increased in prevalence from 1.5 to 12.2 % over the study years, whereas the prevalence of ribotype 012 decreased from 8.7 to 2 .0%. Resistance to clindamycin, erythromycin and ceftriaxone was found in 95.5, 14.0 and 13.4 % of isolates, respectively. Resistance to vancomycin or metronidazole was not detected. Thirty-two (17.9 %) and 14 (7.8 %) isolates were resistant to two and three or more antibiotics, respectively. Ribotype 001 displayed maximum resistance, with 50 % of isolates resistant to erythromycin, moxifloxacin and ceftriaxone, and 100 % resistant to clindamycin. Over the 26 years of the study, antibiotic resistance and ribotype prevalence have changed, and antibiotic pressures may have been the major driver of this change.

Clostridium difficile and the disease it causes

Clostridium difficile is a spore-forming, toxin-producing, anaerobic bacterium abundant in soils and water. Frequent and early colonization of the human intestinal flora is common and often asymptomatic. Antimicrobials given commonly disrupt the intestinal microflora and through proliferation in colon and production of toxin A and B it precipitates C. difficile infection (CDI). The enterocytic detachment and bowel inflammation provoke C. difficile-associated diarrhoea (CDAD) sometimes developing into severe pseudomembranous colitis (PMC) and paralytic ileus. Infection is acquired from an endogenous source or from spores in the environment, most easily facilitated during hospital stay. In the elderly, comorbidity, hospitalization and antimicrobial treatment present as major risk factors and the slow recolonization of the normal flora likely responsible for single or multiple recurrences of CDI (25-50%) post therapy. The key procedure for diagnosis is toxin detection from stool specimens and sometimes in combination with culture to increase sensitivity. In mild cases stopping the offending antimicrobial will lead to resolution (25%) but standard therapy still consist of either oral metronidazole or vancomycin. Alternative agents are presently being developed and fidaxomicin, as well as nitrothiazolide are promising. Furthermore, host factors like low antitoxin A levels in serum relates to increased risk of recurrence and small numbers of patients have received immunoglobulin with good results. An immunogenic toxoid vaccine has been developed and human colostrum rich in specific secretory Ig A also support the future use of immunotherapy. Today we experience a tenfold increase of CDI incidence in the western world and both epidemics and therapeutic failure of metronidazole is contributing to morbidity and mortality. The current epidemic of the C. difficile strain NAP1/027 emerging in 2002 in Canada and the USA has now spread to most parts of Europe and virulence factors like high toxin production and sporulation challenge the therapeutic situation and cause great concern among infection control workers. Excessive use of modern fluoroquinolones is thought to play an important role in facilitating this epidemic since NAP1/027 was shown to have acquired moxifloxacin resistance compared to historical strains of the same genotype. Both the current epidemic like this and other local outbreaks from resistant or virulent strains warrant culture to be routinely performed enabling susceptibility testing and typing of the pathogen. Genotyping is most commonly done today by pulse-field gel electrophoresis (PFGE) or PCR ribotyping but multilocus variable-number tandem-repeat analysis (MLVA) seems promising. Epidemiological surveillance using all these tools will help us to better understand the global spread of C. difficile.

The ClosTron: Mutagenesis in Clostridium refined and streamlined

The recent development of the ClosTron Group II intron directed mutagenesis tool for Clostridium has advanced genetics in this genus, and here we present several significant improvements. We have shown how marker re-cycling can be used to construct strains with multiple mutations, demonstrated using FLP/FRT in Clostridium acetobutylicum; tested the capacity of the system for the delivery of transgenes to the chromosome of Clostridium sporogenes, which proved feasible for 1.0kbp transgenes in addition to a marker; and extended the host range of the system, constructing mutants in Clostridium beijerinckii and, for the first time, in a B1/NAP1/027 'epidemic' strain of Clostridium difficile. Automated intron design bioinformatics are now available free-of-charge at our website http://clostron.com; the out-sourced construction of re-targeted intron plasmids has become cost-effective as well as rapid; and the combination of constitutive intron expression with direct selection for intron insertions has made mutant isolation trivial. These developments mean mutants can now be constructed with very little time and effort for the researcher. Those who prefer to construct plasmids in-house are no longer reliant on a commercial kit, as a mixture of two new plasmids provides unlimited template for intron re-targeting by Splicing by Overlap Extension (SOE) PCR. The new ClosTron plasmids also offer blue-white screening and other options for identification of recombinant plasmids. The improved ClosTron system supersedes the prototype plasmid pMTL007 and the original method, and exploits the potential of Group II introns more fully.

Antimicrobial resistance in Clostridium difficile

Clostridium difficile is the leading cause of hospital-acquired diarrhoea and the number of outbreaks has risen markedly since 2003. The emergence and spread of resistance in C. difficile is complicating treatment and prevention. Most isolates are still susceptible to vancomycin and metronidazole (MTZ), however transient and heteroresistance to MTZ have been reported. The prevalence of resistance to other antimicrobial agents is highly variable in different populations and in different countries, ranging from 0% to 100%. Isolates of common polymerase chain reaction (PCR) ribotypes are more resistant than uncommon ribotypes. Most of the resistance mechanisms that have been identified in C. difficile are similar to those in other Gram-positive bacteria, including mutation, selection and acquisition of the genetic information that encodes resistance. Better antibiotic stewardship and infection control are needed to prevent further spread of resistance in C. difficile.

Distinct ribotypes and rates of antimicrobial drug resistance in Clostridium difficile from Shanghai and Stockholm

Seventy-five clinical isolates of Clostridium difficile from Shanghai and 80 from Stockholm were investigated. The prevalence of toxin A-negative, toxin B-positive isolates of C. difficile among isolates from Shanghai (33.3%) was significantly higher than among isolates from Stockholm (0%). Both sets of isolates were fully susceptible to metronidazole and vancomycin. However, the MICs of fluoroquinolones, erythromycin-clindamycin, tetracycline, rifampin and fusidic acid were significantly higher for the Shanghai isolates than for the Stockholm isolates. Thirty-three PCR ribotypes were identified; a dominant clone, 017, accounted for 18.7% of Shanghai isolates, whereas clone 005 dominated among Stockholm isolates, accounting for 11.3%. Strains 027 and 078 were not detected. No outbreak occurred during the study period.

[Antimicrobial susceptibility of Clostridium difficile clinical isolates collected from 2001 to 2007 in a French university hospital]

AIM

The aim of this study was to determine the antimicrobial susceptibilities of Clostridium difficile clinical isolates obtained from symptomatic patients suffering from diarrhoea.

METHODS

In vitro activities of 22 antimicrobial agents were evaluated against 401 clinical isolates of C. difficile collected from patients hospitalized in a French university hospital (Henri Mondor hospital) between 2001 and 2007. The in vitro antibiotic susceptibility testing was performed using the disc diffusion method according to recommendations of the antibiogram committee of the French society for microbiology.

RESULTS

All strains were found to be susceptible to metronidazole and vancomycin but resistant to clindamycin, gentamicin, and colistin. Most of them were susceptible to pristinamycin (97.8%), rifampin (94.8%), and chloramphenicol (97.3%), and variable degrees of resistance were found for erythromycin and spiramycin (72.8%), as well as for tetracycline (85.6%). Note that none of the strain was susceptible to ofloxacin, and that 80.5% of them showed a high-level resistance. For beta-lactams, all strains were resistant to tested cephalosporins, and nine isolates (2.2%) were also resistant to penicillins combined or not to a beta-lactamase inhibitor. Finally, 28 (7%) and 38 (9.5%) of tested strains were categorized intermediate and resistant to imipenem (with a heterogeneous aspect), respectively.

CONCLUSION

All tested strains were found to be susceptible to metronidazole and vancomycin which remain antimicrobial agents for the treatment of infections caused by C. difficile.