Publications

antibiotic treatment and resistance in chronic wounds of vascular origin.	the problem of antibiotic resistance is worldwide and affects many types of pathogens. this phenomenon has been growing for decades and nowadays we are faced with a wide range of worrisome pathogens that are becoming resistant and many pathogens that may soon be untreatable. the aim of this study was to determine the resistance and antibiotic treatment in chronic wounds of vascular origin.	2016	27547055
structures of the activator of k. pneumonia biofilm formation, mrkh, indicates pilz domains involved in c-di-gmp and dna binding.	the pathogenesis of klebsiella pneumonia is linked to the bacteria's ability to form biofilms. mannose-resistant klebsiella-like (mrk) hemagglutinins are critical for k pneumonia biofilm development, and the expression of the genes encoding these proteins is activated by a 3',5'-cyclic diguanylic acid (c-di-gmp)-regulated transcription factor, mrkh. to gain insight into mrkh function, we performed structural and biochemical analyses. data revealed mrkh to be a monomer with a two-domain architect ...	2016	27551088
bacteremia due to citrobacter braakii: a case report and literature review.	among the citrobacter genus, the most commonly isolated bacteria from human specimens are citrobacter freundii and citrobacter koseri, and previous cases of infection due to citrobacter braakii have been rarely reported. we present a case of bacteremia due to c. braakii in a 38-year-old woman with cervical cancer. she was admitted to our hospital with complaints of a fever, chills, and nausea. blood culture results showed gram-negative bacilli identified as c. braakii via matrix-assisted laser d ...	2016	27553069
prevalence and antimicrobial resistance pattern of bacterial strains isolated from patients with urinary tract infection in messalata central hospital, libya.	to investigate the prevalence of urinary tract infection among patients at messalata central hospital, libya, to identify the causative bacteria, and to explore their resistance pattern to antimicrobials.	2016	27569886
prevalence and risk factors of gram-negative bacilli causing blood stream infection in patients with malignancy.	to evaluate the epidemiology, risk factors, and antibiotic resistance of gram negative bacteria (gnb) in patients with hematologic or solid organ malignancies.	2016	27570854
colistin- and carbapenem-resistant escherichia coli harboring mcr-1 and blandm-5, causing a complicated urinary tract infection in a patient from the united states.	colistin is increasingly used as an antibiotic of last resort for the treatment of carbapenem-resistant gram-negative infections. the plasmid-borne colistin resistance gene mcr-1 was initially identified in animal and clinical samples from china and subsequently reported worldwide, including in the united states. of particular concern is the spread of mcr-1 into carbapenem-resistant bacteria, thereby creating strains that approach pan-resistance. while several reports of mcr-1 have involved carb ...	2016	27578755
assessment of genetically engineered trabulsiella odontotermitis as a 'trojan horse' for paratransgenesis in termites.	the formosan subterranean termite, coptotermes formosanus is an invasive urban pest in the southeastern usa. paratransgenesis using a microbe expressed lytic peptide that targets the termite gut protozoa is currently being developed for the control of formosan subterranean termites. in this study, we evaluated trabulsiella odontotermitis, a termite-specific bacterium, for its potential to serve as a 'trojan horse' for expression of gene products in termite colonies.	2016	27595984
detection of a yersinia pestis gene homologue in rodent samples.	a homologue to a widely used genetic marker, pla, for yersinia pestis has been identified in tissue samples of two species of rat (rattus rattus and rattus norvegicus) and of mice (mus musculus and apodemus sylvaticus) using a microarray based platform to screen for zoonotic pathogens of interest. samples were from urban locations in the uk (liverpool) and canada (vancouver). the results indicate the presence of an unknown bacterium that shares a homologue for the pla gene of yersinia pestis, so ...	2016	27602258
bacteriophages in clinical samples can interfere with microbiological diagnostic tools.	bacteriophages are viruses that infect bacteria, and they are found everywhere their bacterial hosts are present, including the human body. to explore the presence of phages in clinical samples, we assessed 65 clinical samples (blood, ascitic fluid, urine, cerebrospinal fluid, and serum). infectious tailed phages were detected in >45% of ascitic fluid and urine samples. three examples of phage interference with bacterial isolation were observed. phages prevented the confluent bacterial growth re ...	2016	27609086
a review of shv extended-spectrum β-lactamases: neglected yet ubiquitous.	β-lactamases are the primary cause of resistance to β-lactams among members of the family enterobacteriaceae. shv enzymes have emerged in enterobacteriaceae causing infections in health care in the last decades of the twentieth century, and they are now observed in isolates in different epidemiological settings both in human, animal and the environment. likely originated from a chromosomal penicillinase of klebsiella pneumoniae, shv β-lactamases currently encompass a large number of allelic vari ...	2016	27656166
correction: clinical impact of maldi-tof ms identification and rapid susceptibility testing on adequate antimicrobial treatment in sepsis with positive blood cultures.	[this corrects the article doi: 10.1371/journal.pone.0156299.].	2016	27658295
carbapenem-resistant enterobacteriaceae: prevalence and risk factors in a single community-based hospital in korea.	carbapenemase-producing enterobacteriaceae (cpe) are gram-negative bacteria with increasing prevalence of infection worldwide. in korea, 25 cases of cpe isolates were reported by the korea centers for disease control and prevention in 2011. most cpe cases were detected mainly at tertiary referral hospitals. we analyzed the prevalence and risk factors for carbapenem-resistant enterobacteriaceae (cre) in a mid-sized community-based hospital in korea.	2016	27659436
bacterial etiology and antibiotic resistance profile of community-acquired urinary tract infections in a cameroonian city.	introduction. community-acquired urinary tract infections (cautis) are usually treated empirically. geographical variations in etiologic agents and their antibiotic sensitivity patterns are common. knowledge of antibiotic resistance trends is important for improving evidence-based recommendations for empirical treatment of utis. our aim was to determine the major bacterial etiologies of cautis and their antibiotic resistance patterns in a cosmopolitan area of cameroon for comparison with prescri ...	2016	27667998
characterization and genome sequencing of a citrobacter freundii phage cfp1 harboring a lysin active against multidrug-resistant isolates.	citrobacter spp., although frequently ignored, is emerging as an important nosocomial bacterium able to cause various superficial and systemic life-threatening infections. considered to be hard-to-treat bacterium due to its pattern of high antibiotic resistance, it is important to develop effective measures for early and efficient therapy. in this study, the first myovirus (vb_cfrm_cfp1) lytic for citrobacter freundii was microbiologically and genomically characterized. its morphology, activity ...	2016	27683211
genome sequences of 12 bacterial isolates obtained from the urine of pregnant women.	the presence of bacteria in urine can pose significant risks during pregnancy. however, there are few reference genome strains for many common urinary bacteria. we isolated 12 urinary strains of streptococcus, staphylococcus, citrobacter, gardnerella, and lactobacillus these strains and their genomes are now available to the research community.	2016	27688327
genome sequences of nine gram-negative vaginal bacterial isolates.	the vagina is home to a wide variety of bacteria that have great potential to impact human health. here, we announce reference strains (now available through bei resources) and draft genome sequences for 9 gram-negative vaginal isolates from the taxa citrobacter, klebsiella, fusobacterium, proteus, and prevotella.	2016	27688330
citrobacter koseri pneumonia as initial presentation of underlying pulmonary adenocarcinoma.	citrobacter koseri is a motile, gram-negative rod traditionally known to cause infection in individuals with significant comorbidities and immunocompromised status. while most cases represent nosocomial infections, rarely community-acquired infections have been reported. we present a previously healthy man in his 60s with c. koseri pneumonia who was subsequently found to have underlying pulmonary adenocarcinoma, illustrating the need for further investigation for immunodeficiency and/or intrapul ...	2016	27746678
a review of global initiatives to fight antibiotic resistance and recent antibiotics׳ discovery.	data from across the world have shown an overall decline in the antibiotic pipeline and continually rising resistance to all first-line and last-resort antibiotics. the gaps in our knowledge of existing prevalence and mechanisms of antibiotic resistance (abr) are all too well known. several decades of antibiotic abuse in humans, animals, and agricultural practices have created health emergency situations and huge socio-economic impact. this paper discusses key findings of the studies conducted b ...	2016	27818921
microbiome analysis reveals the abundance of bacterial pathogens in rousettus leschenaultii guano.	bats are crucial for proper functioning of an ecosystem. they provide various important services to ecosystem and environment. while, bats are well-known carrier of pathogenic viruses, their possible role as a potential carrier of pathogenic bacteria is under-explored. here, using culture-based approach, employing multiple bacteriological media, over thousand bacteria were cultivated and identified from rousettus leschenaultii (a frugivorous bat species), the majority of which were from the fami ...	2016	27845426
positive and strongly relaxed purifying selection drive the evolution of repeats in proteins.	protein repeats are considered hotspots of protein evolution, associated with acquisition of new functions and novel phenotypic traits, including disease. paradoxically, however, repeats are often strongly conserved through long spans of evolution. to resolve this conundrum, it is necessary to directly compare paralogous (horizontal) evolution of repeats within proteins with their orthologous (vertical) evolution through speciation. here we develop a rigorous methodology to identify highly perio ...	2016	27857066
mechanisms of evolution in high-consequence drug resistance plasmids.	the dissemination of resistance among bacteria has been facilitated by the fact that resistance genes are usually located on a diverse and evolving set of transmissible plasmids. however, the mechanisms generating diversity and enabling adaptation within highly successful resistance plasmids have remained obscure, despite their profound clinical significance. to understand these mechanisms, we have performed a detailed analysis of the mobilome (the entire mobile genetic element content) of a set ...	2016	27923922
risk factors for bacteremia in patients with urinary catheter-associated bacteriuria.	catheter-associated bacteriuria is complicated by secondary bacteremia in 0.4% to 4.0% of cases. the directly attributable mortality rate is 12.7%.	2016	27965229
cutaneous complications of molecular targeted therapy used in oncology.	the new molecular targeted therapy has been developed over the past decades by using the molecular targeted molecular changes discovered in specific types of cancer. unfortunately, most of these agents (epidermal growth factor receptors, multi-targeted small molecule tyrosine kinase inhibitors, monoclonal antibodies) have severe cutaneous adverse reactions, that not only interfere with the patient's quality of life, but also are dose-limiting and may require treatment interruptions. these cutane ...	2016	27974909
intestinal enterobacteriaceae that protect nematodes from the effects of benzimidazoles.	the objective of this study was to investigate an interaction between nematodes and gut enterobacteriaceae that use benzimidazoles as a carbon source. by addressing this objective, we identified an anthelmintic resistance-like mechanism for gastrointestinal nematodes. we isolated 30 gut bacteria (family enterobacteriaceae) that subsist on and putatively catabolize benzimidazole-class anthelmintics. c. elegans was protected from the effects of benzimidazoles when co-incubated with these enterobac ...	2016	28066686
outcomes of infectious versus sterile perforated corneal ulcers after therapeutic penetrating keratoplasty in the united states.	purpose. to compare the long-term outcomes of infectious versus sterile perforated corneal ulcers after therapeutic penetrating keratoplasty in the united states. methods. the charts of 45 consecutive eyes that underwent primary therapeutic penetrating keratoplasty for a perforated corneal ulcer at a single center were retrospectively reviewed. the perforated ulcers were classified as infectious or sterile and the underlying demographics, clinical features, and 36-month outcomes were compared am ...	2016	28070416
identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates.	the initial microbiome impacts the health and future development of premature infants. methodological limitations have led to gaps in our understanding of the habitat range and subpopulation complexity of founding strains, as well as how different body sites support microbial growth. here, we used metagenomics to reconstruct genomes of strains that colonized the skin, mouth, and gut of two hospitalized premature infants during the first month of life. seven bacterial populations, considered to b ...	2017	28073918
detection of ampc β-lactamase producing bacteria isolated in neonatal sepsis.	the objective of this study was to determine the occurrence and antimicrobial profile of ampc β-lactamase producing bacteria.	2016	28083055
urinary tract infection caused by citrobacter koseri in a patient with spina bifida, an ileal conduit and renal caluli progressing to peri-nephric abscess and empyema.	urological problems are common in spina bifida and are often treated with urinary diversions. spina bifida and ileal conduits put patients at increased risk for ascending urinary tract infections. here we present a novel case of a citrobacter koseri urinary tract infection complicated by a perinephric abscess with pleural extension. to our knowledge, no case of an ascending c. koseri uti progressing to peri-nephric abscess and empyema by direct extension exists in the literature.	2017	28083480
intestinal bacterial colonization in the first 2 weeks of life of nigerian neonates using standard culture methods.	the pattern and timing of development of intestinal microflora in nigerian infants have been scarcely researched. this study was carried out to investigate the bacteria flora in the rectum of healthy neonates in ibadan, nigeria.	2016	28083526
whole genome sequencing reveals high-resolution epidemiological links between clinical and environmental klebsiella pneumoniae.	klebsiella pneumoniae is a gram-negative bacterial species capable of occupying a broad range of environmental and clinical habitats. known as an opportunistic pathogen, it has recently become a major causative agent of clinical infections worldwide. despite growing knowledge about the highly diverse population of k. pneumoniae, the evolution and clinical significance of environmental k. pneumoniae, as well as the relationship between clinical and environmental k. pneumoniae, are poorly defined.	2017	28118859
outcomes, cost comparison, and patient satisfaction during long-term central venous access in cancer patients: experience from a tertiary care cancer institute in south india.	prolonged treatment, frequent administration of chemotherapy, antibiotics and blood products in cancer patients requires long term venous access. central venous catheters (cvc) inserted into the subclavian vein or internal jugular vein, peripherally inserted central venous catheters (picc) and chemoport (cp) are the commonly used central venous access devices (cvad).	2016	28144088
igm-mediated autoimmune responses to oxidative specific epitopes, but not nitrosylated adducts, are significantly decreased in pregnancy: association with bacterial translocation, perinatal and lifetime major depression and the tryptophan catabolite (trycat) pathway.	immunoglubulin (ig)m responses directed to oxidative specific epitopes (oses) and nitric oxide (no)-adducts are significantly associated with major depression and physio-somatic symptoms. end of term serum igm responses to oses and no-adducts were assayed in pregnant women with (n = 24) and without prenatal depression (n = 25) as well as in 24 non-pregnant women. associations of igm/iga responses to gram-negative gut commensal bacteria (leaky gut index) and iga/igm responses to tryptophan catabo ...	2017	28600633