Stability of repetitive-sequence PCR patterns with respect to culture age and subculture frequency

The Rise of Non-typhoidal Salmonella Infections in India: Causes, Symptoms, and Prevention

Non-typhoidal Salmonella infections (NTS) are a growing concern in India, posing a significant health risk to the population. These infections are becoming more common at worrisome rates, primarily because of inadequate surveillance. Salmonella non-typhoidal causes severe gastroenteritis and can even cause invasive infections, such as bacteremia, and focal infections, such as meningitis and septic arthritis, and is acquired through contaminated food and water sources. From moderate to severe, the symptoms might vary. Certain serovars exhibit a stronger propensity for specific syndromes, with serious infections more commonly observed in vulnerable populations. Consuming contaminated food, using inadequate sanitation procedures while handling meat from animals slaughtered, and contaminated water supplies are some of the causes of these diseases. Proper food and water treatment, better sanitary facilities, public awareness campaigns, and adherence to food safety laws are all part of prevention measures. The issue of antimicrobial resistance further emphasizes the necessity for prudent antibiotic usage. The Indian government has put in place programs including public awareness campaigns, better sanitary facilities, and stricter food safety laws. In the future, efforts should, however, concentrate on improving laws, boosting hygienic practices, and funding the development of new medicines and vaccines. These actions will lessen the burden of NTS infections in India by assisting in their prevention and management. This review aims to understand the reasons for this growing tendency, which is essential for creating efficient control and prevention strategies.

Non-serogroup O1/O139 agglutinable Vibrio cholerae: a phylogenetically and genealogically neglected yet emerging potential pathogen of clinical relevance

Somatic antigen agglutinable type-1/139 Vibrio cholerae (SAAT-1/139-Vc) members or O1/O139 V. cholerae have been described by various investigators as pathogenic due to their increasing virulence potential and production of choleragen. Reported cholera outbreak cases around the world have been associated with these choleragenic V. cholerae with high case fatality affecting various human and animals. These virulent Vibrio members have shown genealogical and phylogenetic relationship with the avirulent somatic antigen non-agglutinable strains of 1/139 V. cholerae (SANAS-1/139- Vc) or O1/O139 non-agglutinating V. cholerae (O1/O139-NAG-Vc). Reports on implication of O1/O139-NAGVc members in most sporadic cholera/cholera-like cases of diarrhea, production of cholera toxin and transmission via consumption and/or contact with contaminated water/seafood are currently on the rise. Some reported sporadic cases of cholera outbreaks and observed change in nature has also been tracable to these non-agglutinable Vibrio members (O1/O139-NAGVc) yet there is a sustained paucity of research interest on the non-agglutinable V. cholerae members. The emergence of fulminating extraintestinal and systemic vibriosis is another aspect of SANAS-1/139- Vc implication which has received low attention in terms of research driven interest. This review addresses the need to appraise and continually expand research based studies on the somatic antigen non-serogroup agglutinable type-1/139 V.cholerae members which are currently prevalent in studies of water bodies, fruits/vegetables, foods and terrestrial environment. Our opinion is amassed from interest in integrated surveillance studies, management/control of cholera outbreaks as well as diarrhea and other disease-related cases both in the rural, suburban and urban metropolis.

(GTG)5-PCR fingerprinting of multi-drug resistant Escherichia coli bacteria isolates from hospital in Ouagadougou, Burkina Faso

BACKGROUND

Escherichia coli (E. coli) is the most common bacterial species implicated in various types of infections including septicemia, gastroenteritis, urinary tract infections, meningitis and others pathologies. These involve several bacterial clones with multidrug resistance making them difficult to treat. The aims of this study was to perform molecular typing of E. coli strains using universal primer (GTG)₅. In this study, 53 E. coli strains were collected from inpatients and outpatients. The test of antimicrobial sensibility was realized using CA-SFM /EUCAST method and strains were identified by conventional microbiological tests. The carbapenemase-producing strains were demonstrated by phenotypic method. Bacterial DNA was extracted by boiling method. (GTG)₅-PCR was used for strain subtyping. The DendroUPGMA software was used for grouping of strains from the genetic fingerprints obtained by (GTG)₅-PCR.

RESULTS

Antibiotic susceptibility test revealed that all strains were multi-drug resistant (MDR). Its strains showed resistance to at least three different families of antibiotics. Of this MDR strains, only one was a metallo-β-lactamase producer. The dendrogram obtained using genetic fingerprinting allowed the E. coli strains to be grouped into 22 clusters (G1 to G22).

CONCLUSION

The (GTG) 5-PCR assay enabled rapid molecular typing of E. coli strains. The strains of E. coli typed in this study would belong to different clones.

Non-typhoidal Salmonella infections across India: emergence of a neglected group of enteric pathogens

Objective

Non-typhoidal Salmonellae (NTS) are a neglected group of enteric pathogens whose prevalence is increasing at alarming rates across India. The disease burden is being underestimated because of a lack of effective surveillance of NTS infections in the Indian population. This study depicts the acquisition of NTS infection, and its persistence and spread through a diverse range of hosts, including humans and animals, and food and environmental sources.

Methods

During the study period from 2016 to 2018, a total of 999 suspected NTS isolates were received from across India and were phenotypically and serologically characterized for the presence of NTS.

Results

Of the 999 isolates, 539 (53.95%) were confirmed as NTS, consisting of 17 different NTS serovars. The majority were isolated from human samples (n = 319, 59.18%), followed by food products (n = 99, 18.37%), animals (n = 83, 15.4%) and the environment (n = 38, 7.05%). Some predominant serovars obtained included S. Typhimurium (n = 167, 30.98%), S. Lindenberg (n = 135, 25.05%), S. Enteritidis (n = 56, 10.39%), S. Weltevreden (n = 44, 8.16%), S. Choleraesuis (n = 41, 7.61%) and S. Mathura (n = 33, 6.12%).

Conclusion

This study depicts the NTS disease burden across India, on the basis of the isolation of NTS serovars across diverse geographic locations. The emergence of newer or less common NTS serovars implicated in human infection poses a potential challenge to the healthcare system in India. Therefore, national and regional level surveillance is needed to implement effective control strategies and safeguard community health in India.

Eradication of Methicillin-ResistantStaphylococcus AureusFrom a Neonatal Intensive Care Unit by Active Surveillance and Aggressive Infection Control Measures

Objectives:

To describe an outbreak of hospital-acquired MRSA in a NICU and to identify the risk factors for, outcomes of, and interventions that eliminated it.

Setting:

An 18-bed, level III-IV NICU in a community hospital.

Methods:

Interventions to control MRSA included active surveillance, aggressive contact isolation, and cohorting and decolonization of infants and HCWs with MRSA. A case–control study was performed to compare infants with and without MRSA.

Results:

A cluster of 6 cases of MRSA infection between September and October 2001 represented an increased attack rate of 21.2% compared with 5.3% in the previous months. Active surveillance identified unsuspected MRSA colonization in 6 (21.4%) of 28 patients and 6 (5.5%) of 110 HCWs screened. They were all successfully decolonized. There was an increased risk of MRSA colonization and infection among infants with low birth weight or younger gestational age. Multiple gestation was associated with an increased risk of colonization (OR, 37.5; CI95, 3.9–363.1) and infection (OR, 5.36; CI95, 1.37–20.96). Gavage feeding (OR, 10.33; CI95, 1.28–83.37) and intubation (OR, 5.97; CI95, 1.22–29.31) were associated with increased risk of infection. Infants with MRSA infection had a significantly longer hospital stay than infants without MRSA (51.83 vs 21.46 days;P= .003). Rep-PCR withmectyping and PVL analysis confirmed the presence of a single common strain of hospital-acquired MRSA.

Conclusion:

Active surveillance, aggressive implementation of contact isolation, cohorting, and decolonization effectively eradicated MRSA from the NICU for 2½ years following the outbreak. (Infect Control Hosp Epidemiol 2005;26:616-621)

Emergence of community-associated methicillin-resistant Staphylococcus aureus strains in the neonatal intensive care unit: an infection prevention and patient safety challenge

Methicillin-resistant Staphylococcus aureus (MRSA) infections cause significant morbidity and mortality in neonatal intensive care units (NICUs). We characterized the clinical and molecular epidemiology of MRSA strains colonizing NICU patients. Nasal MRSA isolates (n = 250, from 96 NICU patients) recovered through active surveillance from 2009 to 2014 were characterized with staphylococcal cassette chromosome mec (SCCmec) typing and detection of mupA (marker of high-level mupirocin resistance) and qacA/B (marker associated with chlorhexidine resistance). Factors associated with community-associated (CA-) or healthcare-associated (HA-) MRSA were evaluated. The overall prevalence of MRSA nasal colonization was 3.9%. Of 96 neonates in our retrospective cohort, 60 (63%) were colonized with CA-MRSA strains and 35 (36%) were colonized with HA-MRSA strains. Patients colonized with HA-MRSA were more likely to develop MRSA infections than patients colonized with CA-MRSA (13/35, 37% versus 8/60, 13%; p 0.007), although the interval from colonization to infection was shorter in CA-MRSA-colonized infants (median 0 days, range -1 to 4 versus HA-MRSA-colonized infants, 7 days, -1 to 43; p 0.005). Maternal peripartum antibiotics were associated with CA-MRSA colonization (adjusted odds ratio (aOR) 8.7; 95% CI 1.7-45.0); intubation and surgical procedures were associated with HA-MRSA colonization (aOR 7.8; 95% CI 1.3-47.6 and aOR 6.0; 95% CI 1.4-24.4, respectively). Mupirocin- and chlorhexidine-resistant MRSA was isolated from four and eight patients, respectively; carriage of a mupirocin-resistant strain precluded decolonization. CA-MRSA strains are prominent in the NICU and associated with distinct risk factors. Given community reservoirs for MRSA acquisition and transmission, novel infection prevention strategies are needed.

Impact of neonatal intensive care bed configuration on rates of late-onset bacterial sepsis and methicillin-resistant Staphylococcus aureus colonization

BACKGROUND

Infections cause morbidity and mortality in neonatal intensive care units (NICUs). The association between nursery design and nosocomial infections is unclear.

OBJECTIVE

To determine whether rates of colonization by methicillin-resistant Staphylococcus aureus (MRSA), late-onset sepsis, and mortality are reduced in single-patient rooms. DESIGN Retrospective cohort study.

SETTING

NICU in a tertiary referral center.

METHODS

Our NICU is organized into single-patient and open-unit rooms. Clinical data sets including bed location and microbiology results were examined over 29 months. Differences in outcomes between bed configurations were determined by χ2 and Cox regression.

PATIENTS

All NICU patients.

RESULTS

Among 1,823 patients representing 55,166 patient-days, single-patient and open-unit models had similar incidences of MRSA colonization and MRSA colonization-free survival times. Average daily census was associated with MRSA colonization rates only in single-patient rooms (hazard ratio, 1.31; P=.039), whereas hand hygiene compliance on room entry and exit was associated with lower colonization rates independent of bed configuration (hazard ratios, 0.834 and 0.719 per 1% higher compliance, respectively). Late-onset sepsis rates were similar in single-patient and open-unit models as were sepsis-free survival and the combined outcome of sepsis or death. After controlling for demographic, clinical, and unit-based variables, multivariate Cox regression demonstrated that bed configuration had no effect on MRSA colonization, late-onset sepsis, or mortality.

CONCLUSIONS

MRSA colonization rate was impacted by hand hygiene compliance, regardless of room configuration, whereas average daily census affected only infants in single-patient rooms. Single-patient rooms did not reduce the rates of MRSA colonization, late-onset sepsis, or death.

Contamination of environmental surfaces with Staphylococcus aureus in households with children infected with methicillin-resistant S aureus

IMPORTANCE

Household environmental surfaces may serve as vectors for the acquisition and spread of methicillin-resistant Staphylococcus aureus (MRSA) among household members, although few studies have evaluated which objects are important reservoirs of MRSA.

OBJECTIVES

To determine the prevalence of environmental MRSA contamination in households of children with MRSA infection; define the molecular epidemiology of environmental, pet, and human MRSA strains within households; and identify factors associated with household MRSA contamination.

DESIGN, SETTING, AND PARTICIPANTS

Fifty children with active or recent culture-positive community-associated MRSA infection were enrolled from 2012 to 2013 at St Louis Children's Hospital and at community pediatric practices affiliated with the Washington University Pediatric and Adolescent Ambulatory Research Consortium in St Louis, Missouri.

MAIN OUTCOMES AND MEASURES

Samples of participants' nares, axillae, and inguinal folds were cultured to detect S aureus colonization. Samples of 21 household environmental surfaces, as well as samples obtained from pet dogs and cats, were cultured. Molecular typing of S aureus strains was performed by repetitive-sequence polymerase chain reaction to determine strain relatedness within households.

RESULTS

Methicillin-resistant S aureus was recovered from samples of environmental surfaces in 23 of the 50 households (46%), most frequently from the participant's bed linens (18%), television remote control (16%), and bathroom hand towel (15%). It colonized 12% of dogs and 7% of cats. At least 1 surface was contaminated with a strain type matching the participant's isolate in 20 households (40%). Participants colonized with S aureus had a higher mean (SD) proportion of MRSA-contaminated surfaces (0.15 [0.17]) than noncolonized participants (0.03 [0.06]; mean difference, 0.12 [95% CI, 0.05-0.20]). A greater number of individuals per 1000 ft 2 (93 m2) were also associated with a higher proportion of MRSA-contaminated surfaces (β = 0.34, P = .03). The frequency of cleaning household surfaces was not associated with S aureus environmental contamination.

CONCLUSIONS AND RELEVANCE

Methicillin-resistant S aureus strains concordant with infecting and colonizing strains are present on commonly handled household surfaces, a factor that likely perpetuates MRSA transmission and recurrent disease. Future studies are needed to determine methods to eradicate environmental contamination and prevent MRSA transmission in households.

Adhesin genes and serum resistance in Haemophilus influenzae type f isolates

The incidence of invasive infections due to Haemophilus influenzae has decreased significantly in developed countries with high rates of vaccination against H. influenzae serotype b (Hib). This vaccine provides no protection against H. influenzae serotype f (Hif), typically associated with invasive infections in adults with chronic disease and/or immunodeficiency, and rarely in otherwise healthy adults and children. The specific properties of Hif associated with virulence remain largely uncharacterized. A panel of 26 Hif strains consisting of both invasive disease-associated and mucosal surface non-invasive disease-associated isolates was surveyed by DNA fingerprinting, biotyping and PCR detection of hmw1, hmw2, hsf, the hif fimbrial locus and the lipo-oligosaccharide (LOS) biosynthetic island, and assessment of β-lactamase expression and determination of resistance to the bactericidal activity of normal adult human serum. Repetitive sequence-based PCR fingerprinting differentiated the 26 strains into three clusters, with the majority of isolates (22/26, 84.6 %) clustered into a single indistinguishable group. Most isolates (24/26, 92.3 %) were of biotype I and two isolates produced β-lactamase with detection of a conjugative plasmid, and the isolates displayed a range of resistances to the bactericidal activity of human serum. All 26 isolates carried the adhesin hsf, 21 carried a partial hif fimbrial operon and 4 had the adhesin genes hmw1/2. A LOS biosynthetic island was detected in 20 isolates consisting of the genes lic2BC. It was concluded that Hif has many recognized virulence properties and comprises a relatively homogeneous group independent of the anatomical source from which it was isolated.

Development and evaluation of a novel, semiautomated Clostridium difficile typing platform

We describe a novel, semiautomated Clostridium difficile typing platform that is based on PCR-ribotyping in conjunction with a semiautomated molecular typing system. The platform is reproducible with minimal intra- or interassay variability. This method exhibited a discriminatory index of 0.954 and is therefore comparable to more arduous typing systems, such as pulsed-field gel electrophoresis.

Mupirocin and chlorhexidine resistance in Staphylococcus aureus in patients with community-onset skin and soft tissue infections

Decolonization measures, including mupirocin and chlorhexidine, are often prescribed to prevent Staphylococcus aureus skin and soft tissue infections (SSTI). The objective of this study was to determine the prevalence of high-level mupirocin and chlorhexidine resistance in S. aureus strains recovered from patients with SSTI before and after mupirocin and chlorhexidine administration and to determine whether carriage of a mupirocin- or chlorhexidine-resistant strain at baseline precluded S. aureus eradication. We recruited 1,089 patients with community-onset SSTI with or without S. aureus colonization. In addition to routine care, 483 patients were enrolled in a decolonization trial: 408 received intranasal mupirocin (with or without antimicrobial baths), and 258 performed chlorhexidine body washes. Patients were followed for up to 12 months with repeat colonization cultures. All S. aureus isolates were tested for high-level mupirocin and chlorhexidine resistance. At baseline, 23/1,089 (2.1%) patients carried a mupirocin-resistant S. aureus strain and 10/1,089 (0.9%) patients carried chlorhexidine-resistant S. aureus. Of 4 patients prescribed mupirocin, who carried a mupirocin-resistant S. aureus strain at baseline, 100% remained colonized at 1 month compared to 44% of the 324 patients without mupirocin resistance at baseline (P = 0.041). Of 2 patients prescribed chlorhexidine, who carried a chlorhexidine-resistant S. aureus strain at baseline, 50% remained colonized at 1 month compared to 48% of the 209 patients without chlorhexidine resistance at baseline (P = 1.0). The overall prevalence of mupirocin and chlorhexidine resistance is low in S. aureus isolates recovered from outpatients, but eradication efforts were less successful in patients carrying a mupirocin-resistant S. aureus strain at baseline.

Presence of the bla(Z) beta-lactamase gene in isolates of Staphylococcus aureus that appear penicillin susceptible by conventional phenotypic methods

Beta-lactamase production may not be reliably detected by commonly used susceptibility testing methods such as Kirby-Bauer penicillin disk diffusion and nitrocefin beta-lactamase detection. We assayed 105 apparently penicillin-susceptible Staphylococcus aureus isolates using multiple methods to detect beta-lactamase production. The bla(Z) beta-lactamase gene was detected by polymerase chain reaction in 10 (9.5%) of the 105 isolates. The average disk diffusion zone diameter was 34 and 38 mm for the bla(Z)-positive and -negative isolates, respectively (P < 0.001). Qualitative description of the zone edge was observer-dependent. The "cloverleaf assay" was positive in 6 of the 10 phenotypically susceptible isolates possessing bla(Z). The results of this study suggest that conventional methods for S. aureus penicillin susceptibility testing may not reliably detect penicillin resistance in all isolates; however, increasing the disk diffusion zone size interpretive criteria to 35 mm for this antimicrobial/organism combination from the current 29-mm breakpoint may improve the sensitivity of phenotypic penicillin susceptibility testing.

Comparison of a commercially available repetitive-element PCR system (DiversiLab) with PCR ribotyping for typing of clostridium difficile strains

This study compared a repetitive-element PCR (rep-PCR) method (DiversiLab system) to PCR ribotyping. The discriminatory power of rep-PCR was 0.997. Among the PCR ribotype 027 isolates tested, different rep types could be distinguished. rep-PCR showed a higher discriminatory power than PCR ribotyping. Nevertheless, this method requires technical skill, and visual interpretation of rep-PCR fingerprint patterns may be difficult.

Evaluation of MALDI-TOF MS as a tool for high-throughput dereplication

The present study examined the suitability of matrix assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) for the rapid grouping of bacterial isolates, i.e. dereplication. Dereplication is important in large-scale isolation campaigns and screening programs since it can significantly reduce labor intensity, time and costs in further downstream analyses. Still, current dereplication techniques are time consuming and costly. MALDI-TOF MS is an attractive tool since it performs fast and cheap analyses with the potential of automation. However, its taxonomic resolution for a broad diversity of bacteria remains largely unknown. To verify the suitability of MALDI-TOF MS for dereplication, a total of 249 unidentified bacterial isolates retrieved from the rhizosphere of potato plants, were analyzed with both MALDI-TOF MS and repetitive element sequence based polymerase chain reaction (rep-PCR). The latter technique was used as a benchmark. Cluster analysis and inspection of the profiles showed that for 204 isolates (82%) the taxonomic resolution of both techniques was comparable, while for 45 isolates (18%) one of both techniques had a higher taxonomic resolution. Additionally, 16S rRNA gene sequence analysis was performed on all members of each delineated cluster to gain insight in the identity and sequence similarity between members in each cluster. MALDI-TOF MS proved to have higher reproducibility than rep-PCR and seemed to be more promising with respect to high-throughput analyses, automation, and time and cost efficiency. Its taxonomic resolution was situated at the species to strain level. The present study demonstrated that MALDI-TOF MS is a powerful tool for dereplication.

Identification of Staphylococcus spp. using (GTG)₅-PCR fingerprinting

A group of 212 type and reference strains deposited in the Czech Collection of Microorganisms (Brno, Czech Republic) and covering 41 Staphylococcus species comprising 21 subspecies was characterised using rep-PCR fingerprinting with the (GTG)₅ primer in order to evaluate this method for identification of staphylococci. All strains were typeable using the (GTG)₅ primer and generated PCR products ranging from 200 to 4500 bp. Numerical analysis of the obtained fingerprints revealed (sub)species-specific clustering corresponding with the taxonomic position of analysed strains. Taxonomic position of selected strains representing the (sub)species that were distributed over multiple rep-PCR clusters was verified and confirmed by the partial rpoB gene sequencing. Staphylococcus caprae, Staphylococcus equorum, Staphylococcus sciuri, Staphylococcus piscifermentans, Staphylococcus xylosus, and Staphylococcus saprophyticus revealed heterogeneous fingerprints and each (sub)species was distributed over several clusters. However, representatives of the remaining Staphylococcus spp. were clearly separated in single (sub)species-specific clusters. These results showed rep-PCR with the (GTG)₅ primer as a fast and reliable method applicable for differentiation and straightforward identification of majority of Staphylococcus spp.

Distribution and diversity of Escherichia coli populations in the South Nation River drainage basin, eastern Ontario, Canada

We investigated the prevalence and diversity of Escherichia coli strains isolated from surface waters from multiple watersheds within the South Nation River basin in eastern Ontario, Canada. The basin is composed of mixed but primarily agricultural land uses. From March 2004 to November 2007, a total of 2,004 surface water samples were collected from 24 sampling sites. E. coli densities ranged from undetectable to 1.64 x 10(5) CFU 100 ml(-1) and were correlated with stream order and proximity to livestock production systems. The diversity of 21,307 E. coli isolates was characterized using repetitive extragenic palindromic PCR (rep-PCR), allowing for the identification of as many as 7,325 distinct genotypes, without capturing all of the diversity. The community was temporally and spatially dominated by a few dominant genotypes (clusters of more than 500 isolates) and several genotypes of intermediary abundance (clustering between 10 and 499 isolates). Simpson diversity indices, assessed on a normalized number of isolates per sample, ranged from 0.050 to 0.668. Simpson indices could be statistically discriminated on the basis of year and stream order, but land use, discharge, weather, and water physical-chemical properties were not statistically important discriminators. The detection of Campylobacter species was associated with statistically lower Simpson indices (greater diversity; P < 0.05). Waterborne E. coli isolates from genotypes of dominant and intermediary abundance were clustered with isolates obtained from fecal samples collected in the study area over the same period, and 90% of the isolates tested proved to share genotypes with fecal isolates. Overall, our data indicated that the densities and distribution of E. coli in these mixed-use watersheds were linked to stream order and livestock-based land uses. Waterborne E. coli populations that were distinct from fecal isolates were detected and, on this basis, were possibly naturalized E. coli strains.

Applications of the rep-PCR DNA fingerprinting technique to study microbial diversity, ecology and evolution

A large number of repetitive DNA sequences are found in multiple sites in the genomes of numerous bacteria, archaea and eukarya. While the functions of many of these repetitive sequence elements are unknown, they have proven to be useful as the basis of several powerful tools for use in molecular diagnostics, medical microbiology, epidemiological analyses and environmental microbiology. The repetitive sequence-based PCR or rep-PCR DNA fingerprint technique uses primers targeting several of these repetitive elements and PCR to generate unique DNA profiles or 'fingerprints' of individual microbial strains. Although this technique has been extensively used to examine diversity among variety of prokaryotic microorganisms, rep-PCR DNA fingerprinting can also be applied to microbial ecology and microbial evolution studies since it has the power to distinguish microbes at the strain or isolate level. Recent advancement in rep-PCR methodology has resulted in increased accuracy, reproducibility and throughput. In this minireview, we summarize recent improvements in rep-PCR DNA fingerprinting methodology, and discuss its applications to address fundamentally important questions in microbial ecology and evolution.

Fluorescent-BOX-PCR for resolving bacterial genetic diversity, endemism and biogeography

Background

BOX-A1R-based repetitive extragenic palindromic-PCR (BOX-PCR) is one of the most used techniques in biogeography studies of microbial isolates. However the traditional separation of BOX-PCR patterns by agarose gel electrophoresis suffers many limitations. The aim of this research was to set up a fluorescent BOX-PCR (F-BOX-PCR) assay in which separation of PCR products is automated in a capillary electrophoresis system. F-BOX-PCR was compared with the traditional BOX-PCR using bacterial strains with different G+C content (Bacillus cereus; Escherichia coli; isolates of the family Geodermatophilaceae). Resolution, discriminatory power and reproducibility were evaluated by assaying different electrophoretic runs, PCR reactions and independent DNA extractions. BOX-PCR and F-BOX-PCR were compared for the analysis of 29 strains of Modestobacter multiseptatus isolated from three different microsites in an altered carbonatic wall from Cagliari, Italy, and 45 strains of Streptococcus thermophilus isolated from 34 samples of the hand-made, yogurt-like product Matsoni, collected in different locations in Georgia.

Results

Fluorophore 6-FAM proved more informative than HEX and BOX-PCR both in agarose gel electrophoresis (p < 0.004 and p < 0.00003) and in capillary electrophoresis (compared only with HEX, p < 2 × 10^-7). 6-FAM- and HEX-based F-BOX-PCR respectively detected up to 12.0 and 11.3 times more fragments than BOX-PCR. Replicate separations of F-BOX-PCR showed an accuracy of the size calling of ± 0.5 bp until 500 bp, constantly decreasing to ± 10 bp at 2000 bp. Cluster analysis of F-BOX-PCR profiles grouped M. multiseptatus strains according to the microsite of isolation and S. thermophilus strains according to the geographical origin of Matsoni, but resulted intermixed when a BOX-PCR dataset was used.

Conclusion

F-BOX-PCR represents an improved method for addressing bacterial biogeography studies both in term of sensitivity, reproducibility and data analysis.

Hot tub folliculitis or hot hand–foot syndrome caused by Pseudomonas aeruginosa

Pseudomonas aeruginosa is a ubiquitous gram-negative rod that can cause a well-recognized, acquired skin infection from bacterial colonization of contaminated water called "hot tub folliculitis." We report an outbreak of pseudomonas skin infection associated with the use of a hot tub at a pool party in 33 children. In particular, 2 of the children were admitted to our hospital; both presented with high leukocyte counts, intermittent low grade fevers, and painful, erythematous nodules and papules on their palms and soles. One of the 2 children also presented with small erythematous pustular lesions on the face and trunk, which led to the diagnosis. Cultures from these pustules grew P aeruginosa. Thirty two other children at this pool/hot tub party developed similar lesions of varying severity 6 to 48 hours after the party. These findings were most consistent with the diagnosis of pseudomonas folliculitis/hot hand.

Panton-Valentine Leukocidin-Positive Methicillin-Resistant Staphylococcus aureus Lung Infection in Patients With Cystic Fibrosis

BACKGROUND

Panton-Valentine Leukocidin-expressing (PVL+) methicillin-resistant Staphylococcus aureus (MRSA) is an emerging pathogen worldwide causing fatal necrotizing pneumonias in otherwise healthy individuals but has not been described in patients with cystic fibrosis (CF). Following two cases of patients with CF admitted with lung abscesses in association with PVL+ MRSA, we examined the incidence and the clinical characteristics of MRSA acquisition in our CF patient population.

METHODS

Newly acquired MRSA isolates from patients with CF followed up at St. Louis Children's Hospital were analyzed for the presence of Panton-Valentine leukocidin coding region, clindamycin susceptibility, staphylococcal cassette chromosome (SCC) mec type, and multilocus sequence type. Medical records and pulmonary function studies at the time of MRSA isolation were reviewed.

RESULTS

MRSA isolates from 40 CF patients were available for analysis. Six children (15%) had PVL+ MRSA infection. All PVL+ organisms were clindamycin susceptible. Patients who acquired a PVL+ organism were more likely to have a focal pulmonary infiltrate on chest radiograph, including cavitary lung lesions in two patients (p = 0.04), a markedly greater decline in FEV1 at the time of MRSA detection (p = 0.01), and a significantly higher WBC count (p = 0.04) and absolute neutrophil count (p = 0.04). These patients were more likely to be admitted for IV antibiotic therapy for respiratory illnesses (p < 0.01).

CONCLUSIONS

We describe the emergence of PVL+ MRSA in our CF population in association with development of invasive lung infections including lung abscesses. Early identification and treatment of CF patients with newly acquired PVL+ MRSA may be crucial.

Molecular subtyping of poultry-associated type A Clostridium perfringens isolates by repetitive-element PCR

Clostridium perfringens strains (type A) isolated from an integrated poultry operation were subtyped using repetitive-element PCR with Dt primers. Isolates were obtained from fecal, egg shell, fluff, and carcass rinse samples as part of a previously reported temporally linked epidemiological survey. A total of 48 isolates of C. perfringens were obtained from different stages of the broiler chicken production chain from two separate breeder farms that supplied a single hatchery that in turn provided chicks to a single grow-out farm whose flocks were processed at a single plant. All 48 isolates were typeable (100% typeability) by repetitive-element PCR with Dt primers. This subtyping method was highly reproducible and discriminatory. By repetitive-element PCR with Dt primers, isolates were classified into four major branches with 12 subgroups or clades. The Simpson's index of discrimination was calculated to be 0.96 for groupings of >95% correlation. Toxin gene profiles of the isolates indicated that all of the isolates were C. perfringens alpha-toxin gene positive and 46 of 48 isolates were beta2-toxin gene positive. All strains were negative for beta- and epsilon-toxin genes. Repetitive sequence-based PCR was found to be a technically practical and reproducible means of subtyping C. perfringens libraries from specific epidemiological or production environment settings.

Evaluation of (GTG)5-PCR for identification of Enterococcus spp

A set of reference strains and a group of previously unidentified enterococci were analysed by rep-PCR with the (GTG)(5) primer to evaluate the discriminatory power and suitability of this method for typing and identification of enterococcal species. A total of 49 strains representing all validly described species were obtained from bacterial collections. For more extensive evaluation of this identification approach 112 well-defined and identified enterococci isolated from bryndza cheese were tested. The (GTG)(5)-PCR fingerprinting assigned all strains into well-differentiated clusters representing individual species. Subsequently, a group including 44 unidentified enterococci isolated from surface waters was analysed to evaluate this method for identification of unknown isolates. Obtained band patterns allowed us to identify all the strains clearly to the species level. This study proved that rep-PCR with (GTG)(5) primer is a reliable and fast method for species identification of enterococci.

Microbial DNA typing by automated repetitive-sequence-based PCR

Repetitive sequence-based PCR (rep-PCR) has been recognized as an effective method for bacterial strain typing. Recently, rep-PCR has been commercially adapted to an automated format known as the DiversiLab system to provide a reliable PCR-based typing system for clinical laboratories. We describe the adaptations made to automate rep-PCR and explore the performance and reproducibility of the system as a molecular genotyping tool for bacterial strain typing. The modifications for automation included changes in rep-PCR chemistry and thermal cycling parameters, incorporation of microfluidics-based DNA amplicon fractionation and detection, and Internet-based computer-assisted analysis, reporting, and data storage. The performance and reproducibility of the automated rep-PCR were examined by performing DNA typing and replicate testing with multiple laboratories, personnel, instruments, DNA template concentrations, and culture conditions prior to DNA isolation. Finally, we demonstrated the use of automated rep-PCR for clinical laboratory applications by using isolates from an outbreak of Neisseria meningitidis infections. N. meningitidis outbreak-related strains were distinguished from other isolates. The DiversiLab system is a highly integrated, convenient, and rapid testing platform that may allow clinical laboratories to realize the potential of microbial DNA typing.

Enterococcus faecalisResistant to Linezolid: Case Series and Review of the Literature

Reports of linezolid resistance among Enterococcus faecalis have been relatively rare. We describe three patients with linezolid-resistant strains of E. faecalis, discovered after the patients had received long courses (> 30 days) of linezolid therapy. All strains contained the G2576U mutation in 23S rRNA. A literature review revealed one other case in the United States and three cases in Europe; all involved patients who had received long courses of therapy. It appears that recent or extended linezolid therapy may be a risk factor for development of resistant E. faecalis. In patients who have recently been treated with linezolid and have an identified new systemic enterococcal isolate, linezolid sensitivity should be verified as soon as possible to guide therapy. This strategy also should be considered for patients with a breakthrough enterococcal isolate during linezolid therapy.