Biomedical subjects

Séamus Fanning

Publications and source records attributed to Séamus Fanning.

At least 19 recordsLinked to original sources

PubMed2007

Investigation of a global collection of nontyphoidal Salmonella of various serotypes cultured between 1953 and 2004 for the presence of class 1 integrons.

In this study, antibiotic resistance profiles, and the presence of class 1 integrons were determined for 108 Salmonella isolates comprising 37 serotypes cultured from a variety of sources between 1953 and 2004. Antibiogram analyses showed that all isolates were resistant to streptomycin/spectinomycin. Molecular analysis revealed that 50% of the collection contained an integrase-encoding gene (int1) and 25% contained class 1 integrons. A Salmonella Wien isolate possessing a complete class 1 integron with a dfrA5-ereA2 gene arrangement within the variable region was characterized.

Anti-Bacterial Agents↗

PubMed2006

Development and application of Multiple-Locus Variable number of tandem repeat Analysis (MLVA) to subtype a collection of Listeria monocytogenes.

In this study we report the development and application of a Multiple-Locus Variable number of tandem repeat Analysis (MLVA) strategy for subtyping Listeria monocytogenes. Genome profiles of a collection of forty-five food-borne L. monocytogenes isolates were compared using MLVA. These isolates were obtained as part of an active surveillance programme of foods in the south-east region of Ireland. MLVA successfully discriminated amongst the isolates. The method was easy to perform, relatively fast and could be deployed in any molecular laboratory with basic laboratory equipment. This approach is a valuable tool, which has the capability to provide comparable results when compared with other more established typing methods, including pulsed-field gel electrophoresis (PFGE).

Bacterial Typing Techniques↗

PubMed2006

Development and assessment of a rapid method to detect Escherichia coli O26, O111 and O157 in retail minced beef.

A molecular-based detection method was developed to detect Escherichia coli O26, O111 and O157 in minced (ground) beef samples. This method consists of an initial overnight enrichment in modified tryptone soya broth (mTSB) and novobiocin prior to DNA extraction and subsequent serogrouping using a triplex PCR. This method has a low limit of detection and results are available within 24 hours of receipt of samples. Once optimized, this rapid method was utilized to determine the prevalence of these E. coli serogroups in six hundred minced beef samples all of which were previously examined by immunomagnetic separation (IMS) and selective plating for E. coli O26 and O111. Using IMS, two E. coli O26 isolates were detected. No E. coli O111 were recovered. The multiplex PCR technique described here did not detect E. coli O111 nor O157 in any of the samples, however six minced beef samples were positive for E. coli O26 using our method, only two of these were previously detected by IMS and culture. Application of molecular methods are useful to support culture-based approaches thereby further contributing to risk reduction along the food chain.

Animals↗

PubMed2006

Antibiotic-resistant Campylobacter: could efflux pump inhibitors control infection?

Campylobacter is the most common cause of bacterial gastroenteritis in the world. Poultry is the main reservoir of human infections. The widespread use of antibiotics in agriculture and veterinary medicine has resulted in the emergence of an increasing number of antibiotic-resistant Campylobacter strains that can be transmitted to humans through the food chain. Of particular concern to public health is the prevalence of resistance to macrolides and fluoroquinolones that are used in the treatment of life-threatening campylobacteriosis. The CmeABC efflux system has been shown to contribute to the intrinsic and acquired resistance to these antibiotics. In addition, by mediating resistance to bile, it is essential for colonization of the chicken gut in vivo. Inhibition of CmeABC may provide an effective means of reversing antibiotic resistance and decreasing the transmission of Campylobacter via the food chain. This would positively impact on public health by decreasing the morbidity, mortality and increased healthcare costs associated with the treatment of antibiotic-resistant Campylobacter.

ATP Binding Cassette Transporter, Subfamily B↗

PubMed2006

High-level resistance to moxifloxacin and gatifloxacin associated with a novel mutation in gyrB in toxin-A-negative, toxin-B-positive Clostridium difficile.

OBJECTIVES: To determine the mechanism of high-level resistance to fluoroquinolone antimicrobials in toxin-A-negative, toxin-B-positive (A- B+) Clostridium difficile isolates. METHODS: Following culture 16-23S PCR ribotyping was used to determine genomic relationships between A- B+ C. difficile isolates. Antimicrobial susceptibilities were determined using Etests in the presence and absence of the efflux pump inhibitors reserpine (20 microg/mL), L-phenylalanine-L-arginine-beta-naphthylamide (PAbetaN; 20 microg/mL) and verapamil (100 microg/mL). Genomic regions including the quinolone-resistance-determining-region (QRDR) of gyrA and gyrB were amplified and characterized. RESULTS: PCR ribotyping profiles identified one major cluster of A- B+ C. difficile, universally resistant to the fluoroquinolones tested (ofloxacin, ciprofloxacin, levofloxacin, moxifloxacin and gatifloxacin; MICs > 32 mg/L). All isolates with high-level resistance had a transversion mutation (A-->T) resulting in the amino acid substitution Asp-426-->Val in gyrB. Non-clonal isolates were susceptible to moxifloxacin and gatifloxacin (MICs 0.3 and 0.4 mg/L, respectively) with reduced susceptibility to levofloxacin (MIC 3 mg/L) consistent with the wild-type genotype. The MICs for resistant isolates were not significantly affected by the addition of any of the efflux pump inhibitors. No amino acid substitutions were identified in the QRDR of gyrA. CONCLUSIONS: High-level resistance to fluoroquinolones in A- B+ C. difficile is associated with a novel transversion mutation in gyrB. The emergence of universal resistance in different C. difficile strain types may be a factor promoting outbreaks in hospitals.

Amino Acid Substitution↗

PubMed2006

Comparison of Listeria monocytogenes strain types in Irish smoked salmon and other foods.

An investigation of Listeria monocytogenes in Irish retail smoked salmon products and other unrelated food products was undertaken. Serotyping and genotyping methods were applied. Twenty-six L. monocytogenes isolates cultured from ready-to-eat smoked salmon and an additional 20 L. monocytogenes isolates from various commercially available food products (other than smoked salmon) were compared. Four serotypes, 12 ribotypes, 12 amplified fragment length polymorphism (AFLP) types and 17 pulsed-field gel electrophoresis (PFGE) types were identified among the 46 isolates studied. Genotyping identified a single dominant strain that accounted for 65% of those cultured from smoked salmon and this strain was present in product obtained from three out of five of the manufacturers surveyed. When compared to the food products obtained from a variety of sources, those from smoked salmon appeared to cluster as a single group. In Irish smoked salmon this strain may have adapted, and be capable of persisting in this food product. All isolates were grouped into genetic lineages based on their EcoR1 ribotypes. The attendant risk to public health following consumption of these foods is discussed.

Animals↗

PubMed2006

Toxin A-negative, toxin B-positive Clostridium difficile.

Clostridium difficile is a major cause of infectious diarrhea in hospitalized patients. Many pathogenic strains of Clostridium difficile produce two toxins TcdA and TcdB, both of which are pro-inflammatory and enterotoxic in human intestine. Clinically relevant toxin A-negative, toxin B-positive (A(-)B(+)) strains of Clostridium difficile that cause diarrhea and colitis in humans have been isolated with increasing frequency worldwide. This perspective describes these important toxin variant strains and highlights the need to use Clostridium difficile diagnostic methods that can detect both TcdA and TcdB.

Bacterial Proteins↗

PubMed2006

Characterization of a collection of Enterobacter sakazakii isolates from environmental and food sources.

Enterobacter sakazakii has emerged as a rare cause of neonatal meningitis, septicemia and enterocolitis. Contaminated infant milk formula (IMF) has been identified as one infection route. A small number of clinical outbreaks have been epidemiologically linked to IMF contaminated post-pasteurization during manufacture and/or mishandled when reconstituted. Currently no agreed standardized typing protocol has been developed to trace E. sakazakii. The objectives of this study were to apply biochemical and genetic methods to characterize 51 environmental and food E. sakazakii isolates and 6 E. sakazakii type strains. Isolates were presumptively identified using biochemical profiles based on API 20E and ID32E methods and by culture on differential selective Druggan Forsythe Iversen (DFI) agar. Identification was subsequently confirmed by real time polymerase chain reaction (PCR). All but one of the isolates was identified as E. sakazakii by biochemical profiling. One isolate was identified as Escherichia vulneris by ID 32E and as Pantoea agglomerans by API 20E. All isolates produced green/blue colonies on DFI medium characteristic of this organism. Real time PCR could differentiate between E. sakazakii, Enterobacter spp. and other Enterobacteriacae. Analysis of RAPD banding patterns revealed 3 major clusters of E. sakazakii. There was a large degree of diversity noted amongst the remaining isolates. Our findings indicate that RAPD may be applied as a useful and reliable tool for direct comparison of E. sakazakii isolates providing traceability through the infant formula food chain.

Cluster Analysis↗

PubMed2006

The epidemiology of antibiotic resistance in Campylobacter.

Antibiotic resistance, particularly with the fluoroquinolones and macrolide antibiotics, has now emerged globally with thermophilic campylobacters, including Campylobacter jejuni and C. coli, giving rise to concerns about how these organisms have acquired such resistance characteristics, as well as consequences for human and animal treatment. This review examines (i) the clinical epidemiology of antibiotic resistance in human and animal thermophilic campylobacters, (ii) an update on resistance rates globally, (iii) surveillance of antimicrobial resistance in campylobacters originating from animals, particularly poultry, (iv) the role of the environment in the acquisition and transmission of antibiotic-resistant campylobacters, as well as (v) issues of biocide resistance in campylobacters.

Animals↗

PubMed2006

Antimicrobial resistance islands: resistance gene clusters in Salmonella chromosome and plasmids.

Genes conferring simultaneous resistance to different classes of antimicrobials, confer a selective advantage to the host, particularly when those corresponding antibiotics are administered. Multiple resistance genes clustered within the same genetic locus (resistance island) can be transferred en bloc to other organisms. In this chapter we review novel multidrug resistance islands recently described in Salmonella.

Anti-Bacterial Agents↗

PubMed2006

Mechanisms of fluoroquinolone and macrolide resistance in Campylobacter spp.

The incidence of human Campylobacter infections is increasing worldwide, as well as the proportion of isolates resistant to fluoroquinolones and/or macrolides, the drugs of choice to treat campylobacteriosis. In this review, we report recent developments in the understanding of the resistance mechanisms to fluoroquinolones and macrolides. In addition, we will discuss the recent findings on multidrug resistance in Campylobacter spp.

Anti-Bacterial Agents↗

PubMed2006

Antimicrobial resistance in nontyphoidal Salmonella from food sources in Colombia: evidence for an unusual plasmid-localized class 1 integron in serotypes Typhimurium and Anatum.

Seventy-two isolates representing 18 serotypes recovered from various food samples collected in Colombia were tested for antimicrobial susceptibilities. The collection was further characterized for extended-spectrum cephalosporin, aminoglycoside, and tetracycline resistance markers. Multidrug resistant (MDR) isolates were further investigated for class 1 integrons and were evaluated for the presence of conjugative plasmids along with a determination of the incompatibility group by polymerase chain reaction (PCR). Antibiogram analysis showed that the incidence rate of ceftiofur resistance was moderately high (15%). A similar level of resistance to neomycin and oxytetracycline (11% and 10%, respectively) was also observed. There was a high prevalence of gene cassettes as part of one or more class 1 integrons (61%), many of which contained determinants that contributed to the resistance profile. Class 1 integrons identified in MDR Salmonella enterica serotypes Typhimurium and Anatum isolates were characterized. Sequencing identified several incomplete open reading frames (ORFs) as part of a gene cassette (bla-( imp-13 ), dfr7, blr1088, and aac8) along with a complete gene cassette (bla-(oxa2)) in each case. A mosaic of gene cassettes was identical in the two Salmonella serotypes. These integrons were located to a conjugative replicon. Plasmid profiling and incompatibility typing identified three plasmids belonging to Inc groups A/C, P, and W. Our study highlights the role of integrons, contributing to a MDR phenotype that is capable of dissemination to other bacteria.

Anti-Bacterial Agents↗

PubMed2006

Multi-drug resistance in Salmonella enterica: efflux mechanisms and their relationships with the development of chromosomal resistance gene clusters.

Bacterial drug resistance represents one of the most crucial problems in present day antibacterial chemotherapy. Of particular concern to public health is the continuing worldwide epidemic spread of Salmonella enterica serovar Typhimurium phage type DT104 harbouring a genomic island called Salmonella genomic island I (SGI-1). This island contains an antibiotic gene cluster conferring resistance to ampicillin, chloramphenicol, florfenicol, streptomycin, sulfonamides and tetracyclines. These resistance genes are assembled in a mosaic pattern, indicative of several independent recombinational events. The mobility of SGI-1 coupled with the ability of various antibiotic resistance genes to be integrated and lost from the chromosomal resistance locus allows for the transfer of stable antibiotic resistance to most of the commonly used antibiotics and adaptation to new antibiotic challenges. This, coupled with the incidence of increasing fluoroquinolone resistance in these strains increases the risk of therapeutic failure in cases of life-threatening salmonellosis. Fluoroquinolone resistance has largely been attributed to mutations occurring in the genes coding for intracellular targets of these drugs. However, efflux by the AcrAB-TolC multi-drug efflux pump has recently been shown to directly contribute to fluoroquinolone resistance. Furthermore, the resistance to chloramphenicol-florfenicol and tetracyclines in DT104 isolates, is due to interaction between specific transporters for these antibiotics encoded by genes mapping to the SGI-1 and the AcrAB-TolC tripartite efflux pump. The potential for the use of efflux pump inhibitors to restore therapeutic efficacy to fluoroquinolones and other antibiotics offers an exciting developmental area for drug discovery.

ATP Binding Cassette Transporter, Subfamily B↗

PubMed2005

An investigation of the molecular mechanisms contributing to high-level erythromycin resistance in Campylobacter.

The molecular mechanisms contributing to high-level erythromycin resistance in Campylobacter jejuni and Campylobacter coli isolates were investigated. The A2075G mutation in the 23S rRNA target genes was identified in all high-level erythromycin-resistant isolates. A number of amino acid substitutions together with insertions and deletions were identified in the corresponding genes encoding L4 and L22 ribosomal proteins both of resistant and susceptible isolates. Amino acid substitutions identified in the resistant strains were located outside regions known to be altered in these proteins. The efflux pump inhibitor L-phenylalanine-L-arginine-beta-naphthylamide (PAbetaN) increased the susceptibility to erythromycin in one of four isolates displaying high-level erythromycin resistance, and reduced the minimal inhibitory concentration displayed by an erythromycin-susceptible C. coli isolate. The A2075G mutation in the 23S rRNA appeared to be the main contributor to high-level erythromycin resistance in Campylobacter. Other mutations/amino acid substitutions found in the 50S ribosomal subunit encoding proteins L4 and L22 do not appear to be linked to the high-level erythromycin-resistant phenotype. Active efflux contributes to the intrinsic resistance to erythromycin in Campylobacter and may contribute to high-level resistance in some isolates.

Amino Acid Sequence↗

PubMed2005

Relative contribution of target gene mutation and efflux to varying quinolone resistance in Irish Campylobacter isolates.

The contribution of target gene mutations and active efflux to varying levels of quinolone resistance in Irish Campylobacter isolates was studied. The Thr-86-Ile modification of GyrA did not correlate with the level of quinolone resistance. The efflux pump inhibitor Phe-Arg-beta-Naphthylamide (PAbetaN) had no effect on the MICs to ciprofloxacin. In contrast, a PAbetaN sensitive efflux system contributed to the low-level nalixidic acid resistance phenotype. The lack of effect of PAbetaN in high-level resistant nalidixic isolates may be attributable to mutations identified in the CmeB efflux pump of these isolates. PAbetaN may have limited diagnostic value in the assessment of the contribution of efflux pump activity to ciprofloxacin resistance in Campylobacter.

Amino Acid Sequence↗

PubMed2005

Characterization of a 2.6 kbp variable region within a class 1 integron found in an Acinetobacter baumannii strain isolated from a horse.

OBJECTIVES: A complete gene cassette contained in a class 1 integron from a multidrug-resistant (MDR) isolate of Acinetobacter baumannii cultured from a horse was characterized by molecular methods. METHODS: Template genomic DNA purified from the A. baumannii isolate was investigated by PCR. A gene cassette-associated amplicon was detected and completely characterized. RESULTS: A 2.6 kbp DNA fragment containing four gene cassettes was amplified from the MDR A. baumannii isolate. Sequence analysis showed it was similar to sequences recently reported in Klebsiella pneumoniae, Serratia marcescens and an Escherichia coli plasmid p1658/97 which conferred aminoglycoside resistance. Aminoglycoside resistance-encoding genes aacC1 and aadA1 were located within the 2.6 kbp amplicon, separated by two open reading frames (ORFs) coding for unknown products. This cassette structure (and some variants) was identified in unrelated Acinetobacter spp. from human sources, based on sequence comparisons of the current databases. CONCLUSIONS: Identification of a complete class 1 integron in an equine isolate of A. baumannii suggests that the screening of isolates from animals for these elements should be considered, as this information could influence the selection of chemotherapeutic agents.

Acinetobacter baumannii↗

PubMed2005

In-line milk filter analysis: Escherichia coli O157 surveillance of milk production holdings.

Escherichia coli O157 is a major etiological agent of food-borne illness. Bovine animals are recognized reservoirs for this organism and represent a significant source from where these pathogens can enter the food chain. Food products derived from these animals are convenient vehicles, and are often the focal point(s) of infection. As a useful strategy to provide herd-level surveillance and to investigate for the presence of this pathogen in a population of Irish dairy cattle, milk filters from 97 farms were analysed by conventional culture and other methods. Five hundred and thirty-six milk filters were evaluated over a 2-year period. Filters from 12 of the 97 farms (12%) were found to contain E. coli O157, based on culture methods. Sixteen verocytotoxigenic E. coli O157 organisms were recovered and characterized in detail. The farm families in each case were consuming raw milk from their respective herds. The potential risk to public health associated with the detection of E. coli O157 and the local consumption of raw milk are discussed.

Animals↗

PubMed2005

Antimicrobial resistance in isolates of Salmonella spp. from pigs and the characterization of an S. Infantis gene cassette.

One hundred and seven Salmonella isolates of various serotypes were investigated for resistance to a panel of nine antimicrobial agents by standardized methods. Thirty four isolates were susceptible to the selected antimicrobial agents. Thirty-six (of 107) were resistant to three or more antimicrobial agents and defined as multidrug resistant (MDR). Salmonella Typhimurium was the most resistant serotype. All resistant isolates were examined for the presence of class 1 integrons. Thirty-two integron-associated gene cassettes (of varying sizes) were identified. A 1,000-bp amplicon similar to that flanking the distal region of the Salmonella Genomic Island (SGI)-1 in Salmonella Typhimurium was detected in a majority of the S. Typhimurium isolates in this study. In contrast, a 1,800-bp amplicon was identified in all Salmonella Infantis isolates. This amplicon was completely characterized in one isolate. The presence of class 1 integrons in Salmonella spp. in pigs may be important if these zoonotic pathogens were to enter the food chain.

Abattoirs↗