Annals of Clinical Microbiology and Antimicrobials - Latest Articles

Impact of a multidimensional infection control approach on central line-associated bloodstream infections rates in adult intensive care units of 8 cities of Turkey: findings of the International Nosocomial Infection Control Consortium (INICC)

Hakan Leblebicioglu — 2013-05-04T00:00:00Z

Background: Central line-associated bloodstream infections (CLABs) have long been associated with excess lengths of stay, increased hospital costs and mortality attributable to them. Different studies from developed countries have shown that practice bundles reduce the incidence of CLAB in intensive care units. However, the impact of the bundle strategy has not been systematically analyzed in the adult intensive care unit (ICU) setting in developing countries, such as Turkey. The aim of this study is to analyze the impact of the International Nosocomial Infection Control Consortium (INICC) multidimensional infection control approach to reduce the rates of CLAB in 13 ICUs of 13 INICC member hospitals from 8 cities of Turkey. Methods: We conducted active, prospective surveillance before-after study to determine CLAB rates in a cohort of 4,017 adults hospitalized in ICUs. We applied the definitions of the CDC/NHSN and INICC surveillance methods. The study was divided into baseline and intervention periods. During baseline, active outcome surveillance of CLAB rates was performed. During intervention, the INICC multidimensional approach for CLAB reduction was implemented and included the following measures: 1- bundle of infection control interventions, 2- education, 3- outcome surveillance, 4- process surveillance, 5- feedback of CLAB rates, and 6- performance feedback on infection control practices. CLAB rates obtained in baseline were compared with CLAB rates obtained during intervention. Results: During baseline, 3,129 central line (CL) days were recorded, and during intervention, we recorded 23,463 CL-days. We used random effects Poisson regression to account for clustering of CLAB rates within hospital across time periods. The baseline CLAB rate was 22.7 per 1000 CL days, which was decreased during the intervention period to 12.0 CLABs per 1000 CL days (IRR 0.613; 95% CI 0.43 -- 0.87; P 0.007). This amounted to a 39% reduction in the incidence rate of CLAB. Conclusions: The implementation of multidimensional infection control approach was associated with a significant reduction in the CLAB rates in adult ICUs of Turkey, and thus should be widely implemented.

Genetic characterization of antimicrobial resistance of Shigella flexneri 1c isolates from patients in Egypt and Pakistan

Salwa Ahmed — 2013-05-02T00:00:00Z

Background: Shigella flexneri serotype 1c emerged as a critical isolate from children in Egypt and Pakistan. The pattern of antimicrobial susceptibility (AMS) and resistance genes of this serotype have yet to be characterized.FindingsSixty nine S. flexneri 1c isolates isolates were identified from both Egypt (n-46) and Pakistan (n = 23) and tested for AMS by disk diffusion method and minimal inhibitory concentrations were also determined. Isolates were genotyped by pulsed field gel electrophoresis (PFGE) and five relevant resistance genes (blaTEM, blaSHV, blaOXA, sulI and sulII) were detected by polymerase chain reaction (PCR) and confirmed by DNA sequencing. High resistance was observed in all isolates for ampicillin (AM >96%); trimethoprim-sulphamethoxazole and tetracycline (>88%). Most AM-resistant isolates from Egypt (70%) harbored blaTEM resistance, while 52% of isolates from Pakistan expressed bla OXA. All isolates were closely related by PFGE, irrespective of source or time of collection. The sulII gene was present in 100% of isolates from pediatric cases in Egypt, 65% of Pakistan isolates, and 53% of isolates from older Egyptian patients. Conclusions: While different Shigella serotypes gathered in specific genotypic groups, 1c serotype isolates formed multiple clusters. Although AMS was considerably high to most commonly used drugs, genetic determinants were variable between countries over time. The data stress the need for a more careful selection of antibiotics in the treatment of shigellosis.

Uropathogenic Escherichia coli in Iran: Serogroup distributions, virulence factors and antimicrobial resistance properties

Hassan Momtaz — 2013-04-29T00:00:00Z

Background: Urinary tract infections (UTIs) are one of the most common bacterial infections with global expansion. These infections are predominantly caused by uropathogenic Escherichia coli (UPEC). Methods: Totally, 123 strains of Escherichia coli isolated from UTIs patients, using bacterial culture method were subjected to polymerase chain reactions for detection of various O- serogroups, some urovirulence factors, antibiotic resistance genes and resistance to 13 different antibiotics. Results: According to data, the distribution of O1, O2, O6, O7 and O16 serogroups were 2.43%, besides O22, O75 and O83 serogroups were 1.62%. Furthermore, the distribution of O4, O8, O15, O21 and O25 serogroups were 5.69%, 3.25%, 21.13%, 4.06% and 26.01%, respectively. Overall, the fim virulence gene had the highest (86.17%) while the usp virulence gene had the lowest distributions of virulence genes in UPEC strains isolated from UTIs patients. The vat and sen virulence genes were not detected in any UPEC strains. Totally, aadA1 (52.84%), and qnr (46.34%) were the most prevalent antibiotic resistance genes while the distribution of cat1 (15.44%), cmlA (15.44%) and dfrA1 (21.95%) were the least. Resistance to penicillin (100%) and tetracycline (73.98%) had the highest while resistance to nitrofurantoin (5.69%) and trimethoprim (16.26%) had the lowest frequencies. Conclusions: This study indicated that the UPEC strains which harbored the high numbers of virulence and antibiotic resistance genes had the high ability to cause diseases that are resistant to most antibiotics. In the current situation, it seems that the administration of penicillin and tetracycline for the treatment of UTIs is vain.

Phenotypic and genotypic comparison of ESBL production by Vaginal Escherichia coli isolates from pregnant and non-pregnant women

Sareaa Al-Mayahie — 2013-04-25T00:00:00Z

Background: Vaginal Escherichia coli is a reservoir along the fecal-vaginal-urinary/neonatal course of transmission in extraintestinal E. coli infections. They also causes genital tract infections especially vaginitis, so that detection of their antibiotic resistance is an important approach to control these infections. One important mechanism of resistance is ESBL production by Enterobacteriaceae especially Klebsiella spp. and Escherichia coli, which is now a worldwide problem that limits therapeutic options. Methods: Sixty one vaginal E. coli isolates from pregnant and non-pregnant women, were detected phenotypically and genotypically for ESBL production. Results: Most of pregnant and non-pregnant women's isolates, were resistant to cefotaxime (100% vs. 81.5%, respectively) and more than half of them to ceftazidime (56.5% vs. 71.0%, respectively). One hundred percent each, 52.1% vs. 68.4%, and 73.9% vs. 60.5%%, were ESBL producers by screening, confirmatory, and PCR tests, respectively. Pregnant women's isolates had: CTX-M- (69.5%), SHV- and OXA-type (each 4.3%) ESBLs. Only one isolate (4.3%) had two types of ESBLs. All 16 CTX-M-positive (100%) isolates had CTX-M-1. Non-pregnant women's isolates were predominated by SHV and CTX-M -type (44.7% vs. 39.4%, respectively), followed by OXA- (15.7%), and TEM-type (2.6%). Of these isolates, 42.1% had two types of ESBL genes. All 15 CTX-M-positive (100%) isolates had CTX-M-1. Pregnant and non-pregnant women's isolates differed significantly (P≤ 0.05) regarding the expression of SHV- (4.3% vs. 44.7%, respectively) and CTX-M-type (69.5% vs. 39.4%, respectively) ESBLs. In both, CTX-M-1 was the predominant CTX-M group (each 100%). All of the isolates were susceptible to imipenem and meropenem, while the highest rate of resistance was against β-lactams. Multidrug resistance was noted in 56.2% of ESBL-producing isolates. Conclusions: Ggenital tracts of pregnant and non-pregnant women represent different environments for propagation of ESBL-producing E. coli. In Iraq, nationwide study is required to make a precise estimation of this widespread of ESBL-producing bacteria.

Reviewer acknowledgement 2012

Hakan Leblebicioglu — 2013-04-05T00:00:00Z

Contributing reviewersAnnals of Clinical Microbiology and Antimicrobials would like to thank the following colleagues for their assistance with peer review of manuscripts for the journal in 2012.

Microbiological characterization of Streptococcus pneumoniae and non-typeable Haemophilus influenzae isolates as primary causes of acute otitis media in Bulgarian children before the introduction of conjugate vaccines

Lena Setchanova — 2013-03-25T00:00:00Z

Background: Pneumococcal and Haemophilus influenzae type b (Hib) vaccines were introduced in our national immunisation program in April 2010. The aims of this retrospective, laboratory-based study were to determine the serotypes and antibiotic resistance of Streptococcus pneumoniae and H. influenzae isolates from middle ear fluid (MEF) collected before the introduction of immunization. Methods: S. pneumoniae (n = 128) and H. influenzae (n = 40) strains isolated from MEF of children with AOM between 1994 and 2011 were studied. MICs were determined by a microdilution assay. Serotyping of S. pneumoniae was done by Quellung method and PCR capsular typing was used for H. influenzae. Macrolide resistance genes were detected by PCR for erythromycin resistant S. pneumoniae (ERSP). DNA sequencing of ftsI gene was performed for ampicillin nonsusceptible H. influenzae. Results: The most common serotypes found among children with pneumococcal AOM were 19 F (20.3%), 6B (15.6%), and 19A (10.9%). The potential coverage rates by the PCV7, PCV10 and PCV13 of children aged < 5 years were 63.6%, 66.4% and 85.5%, respectively. Reduced susceptibility to oral penicillin was seen in 68.1%; resistance to erythromycin was 46.9%. We found erm(B) gene in 56.7% of the ERSP, mef(E) gene in 25%; 15% harbored both genes erm(B) + mef(E) and 3.3% had mutations of L4 ribosomal protein. Of the 40 H. influenzae isolates 97.5% were nontypeable. Nonsusceptibility to ampicillin occurred in 25%. Ampicillin resistance groups were: β-lactamase-positive ampicillin resistant (BLPAR) strains (10%), β-lactamase-negative ampicillin resistant (BLNAR) strains (12.5%) and β-lactamase-positive amoxicillin-clavulanate resistant (BLPACR) strains (2.5%). Among BLNAR and BLPACR most of the isolates (5/6) belonged to group II, defined by the Asn526Lys substitution. Conclusions: The levels of antibiotic resistance among S. pneumoniae and H. influenzae causing severe AOM in children are high in our settings. The existence of multidrug-resistant S. pneumoniae serotype 19A is of particular concern. The rate of BLNAR and BLPACR strains among H. influenzae isolates was 15%.

Antibacterial effects of silver diamine fluoride on multi-species cariogenic biofilm on caries

May Mei — 2013-02-26T00:00:00Z

BackgroundsSilver diamine fluoride (SDF) has clinical success in arresting dentin caries, this study aimed to investigate its mechanism of action. Methods: Using a computer-controlled artificial mouth, we studied the effect of 38% SDF on cariogenic biofilms and dentin carious lesions. We used five common cariogenic bacteria (Streptococcus mutans, Streptococcus sobrinus, Lactobacillus acidophilus, Lactobacillus rhamnosus and Actinomyces naeslundii) to form a cariogenic biofilm that generated carious lesions with a depth of approximately 70 um on human dentin blocks. We applied 38% SDF to the lesions in the test group and water to those in the control group. The blocks were incubated in the artificial mouth for 21 days before evaluation. Microbial kinetics, architecture, viability and distribution were evaluated every 7 days using colony forming unit (CFU), scanning electron microscopy and confocal laser scanning microscopy. The physical properties of the carious lesions were evaluated with microhardness testing, energy dispersive spectroscopy (EDS) and Fourier transform infra-red spectroscopy (FTIR). Results: The CFU results revealed fewer colony forming units in the test group compared with the control group (p < 0.01). Scanning electron microscopy and confocal microscopy showed less bacterial growth in the test group, and confluent cariogenic biofilm in the control group (p < 0.01). The microhardness and weight percentages of calcium and phosphorus in the test group from the outermost 50mum were higher than in the control group (p < 0.05). EDS showed that calcium and phosphous were higher in outer 50 mum in test groups than in the control FTIR revealed less exposed collagen I in the test lesions compared with the control group (p < 0.01). Conclusions: 38% SDF inhibits multi-species cariogenic biofilm formation on dentin carious lesions and reduces the demineralization process.

Primary antibiotic resistance and associated mechanisms in Helicobacter pylori isolates from Senegalese patients

Abdoulaye Seck — 2013-01-08T00:00:00Z

Background: Antibiotic combination therapy for Helicobacter pylori eradication must be adapted to local resistance patterns, but the epidemiology of H. pylori resistance to antibiotics is poorly documented in Africa. The aim was to determine the antibiotic resistance rates, as well as the associated molecular mechanisms, of strains isolated in Dakar, Senegal. Methods: One hundred and eight H. pylori strains were isolated between 2007 and 2009 from 108 patients presenting with upper abdominal pain to the Gastroenterology Department of Le Dantec Hospital. Antimicrobial susceptibility testing was performed for amoxicillin, clarithromycin, metronidazole, levofloxacin and tetracyclin using the E-test method. Mutations in the 23S rRNA gene of clarithromycin-resistant strains and in gyrA and gyrB of levofloxacin-resistant strains were investigated. Results: Isolates were characterized by no resistance to amoxicillin (0%), tetracycline (0%), and very low rate of resistance to clarithromycin (1%), but a high rate of resistance to metronidazole (85%). The clarithromycin-resistant strain displayed the A2143G mutation. A worrying rate of levofloxacin resistance was detected (15%). N87I and D91N were the most common mutations in the quinolone-resistance-determining region of gyrA. Conclusions: The first-line empirical regimen for H. pylori eradication in Senegal should include clarithromycin. Increasing rates of fluoroquinolone resistance detected should discourage the use of levofloxacin-containing regimens without prior antimicrobial susceptibility testing.

Rapid identification of bacteria and candida using pna-fish from blood and peritoneal fluid cultures: a retrospective clinical study

Dana Harris — 2013-01-07T00:00:00Z

Background: Peptide nucleic acid fluorescent in situ hybridization (PNA-FISH) is a rapid and established method for identification of Candida sp., Gram positive, and Gram negative bacteria from positive blood cultures. This study reports clinical experience in the evaluation of 103 positive blood cultures and 17 positive peritoneal fluid cultures from 120 patients using PNA-FISH. Our study provides evidence as to potential pharmaceutical cost savings based on rapid pathogen identification, in addition to the novel application of PNA-FISH to peritoneal fluid specimens. Methods: Identification accuracy and elapsed time to identification of Gram positives, Gram negatives, and Candida sp., isolated from blood and peritoneal fluid cultures were assessed using PNA-FISH (AdvanDx), as compared to standard culture methods. Patient charts were reviewed to extrapolate potential pharmaceutical cost savings due to adjustment of antimicrobial or antifungal therapy, based on identification by PNA-FISH. Results: In blood cultures, time to identification by standard culture methods for bacteria and Candida sp., averaged 83.6 hours (95% CI 56.7 to 110.5). Identification by PNA-FISH averaged 11.2 hours (95% CI 4.8 to 17.6). Overall PNA-FISH identification accuracy was 98.8% (83/84, 95% CI 93.5% to 99.9%) as compared to culture. In peritoneal fluid, identification of bacteria by culture averaged 87.4 hours (95% CI −92.4 to 267.1). Identification by PNA-FISH averaged 16.4 hours (95% CI −57.3 to 90.0). Overall PNA-FISH identification accuracy was 100% (13/13, 95% CI 75.3% to 100%). For Candida sp., pharmaceutical cost savings based on PNA-FISH identification could be $377.74/day. For coagulase-negative staphylococcus (CoNS), discontinuation of vancomycin could result in savings of $20.00/day. Conclusions: In this retrospective study, excellent accuracy of PNA-FISH in blood and peritoneal fluids with reduced time to identification was observed, as compared to conventional culture-based techniques. Species-level identification based on PNA-FISH could contribute to notable cost savings due to adjustments in empiric antimicrobial or antifungal therapy as appropriate to the pathogen identified.

30-yr course and favorable outcome of alveolar echinococcosis despite multiple metastatic organ involvement in a non-immune suppressed patient

Karine Bardonnet — 2013-01-02T00:00:00Z

We report the 30-yr history of a well-documented human case of alveolar echinococcosis, with a lung lesion at presentation followed by the discovery of a liver lesion, both removed by surgery. Subsequently, within the 13 years following diagnosis, metastases were disclosed in eye, brain and skull, as well as additional lung lesions. This patient had no immune suppression, and did not have the genetic background known to predispose to severe alveolar echinococcosis; it may thus be hypothesized that iterative multi-organ involvement was mostly due to the poor adherence to benzimidazole treatment for the first decade after diagnosis. Conversely, after a new alveolar echinococcosis recurrence was found in the right lung in 1994, the patient accepted to take albendazole continuously at the right dosage. After serology became negative and a fluoro-deoxy-glucose-Positron Emission Tomography performed in 2005 showed a total regression of the lesions in all organs, albendazole treatment could be definitively withdrawn. In 2011, the fluoro-deoxy-glucose-Positron Emission Tomography showed a total absence of parasitic metabolic activity and the patient had no clinical symptoms related to alveolar echinococcosis.The history of this patient suggests that multi-organ involvement and alveolar echinococcosis recurrence over time may occur in non-immune suppressed patients despite an apparently “radical” surgery. Metastatic dissemination might be favored by a poor adherence to chemotherapy. Combined surgery and continuous administration of albendazole at high dosage may allow alveolar echinococcosis patients to survive more than 30 years after diagnosis despite multi-organ involvement.