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Background: Staphylococcus aureus is one of the most important food-borne pathogens. The objective of this study was to determine the prevalence, molecular types and drug resistance pattern of S. aureus isolated from retail meat in Tabriz city. Materials & Methods: 60 raw meat samples (chicken and beef) were taken from different markets and were inoculated in selective Mueller Hinton broth media supplemented with 10% NaCl. Identification of S. aureus isolates was performed using conventional biochemical tests. Susceptibility to different antibiotics and genotypes of isolates were determined by disc diffusion and spa typing methods respectively. Results: Fifteen S. aureus strains were isolated from 60 different meat samples which belonged to spa types t14870, t3802, t1814, t491, t386, t3424 and spa type t14870 with the frequency of 33.3% was the most prevalent genotype among S. aureus isolates. spa types of three isolates were not found in Ridom Spa Server data base and were considered as novel types. About 46.6% of isolates were resistant to more than one antibiotic and 13.3% of isolates were identified as methicillin resistant S. aureus (MRSA). Tigecycline, imipenem and ceftaroline were found to be the most effective agents against S. aureus isolates. Conclusion: Oure results revealed a 25% contamination rate with S. aureus. Most of the molecular types of isolates were found to be linked to human infections. High rate of antibiotic resistance was observed among the isolates which poses a great threat to public health. [ABSTRACT FROM AUTHOR]

Purpose: Salmonellosis is one of several reportable diseases in Ontario (ON). Two or more cases of the same serotype that are linked to a common exposure or related to one another in time and/or space are considered a potential outbreak. While laboratory data can help to determine the molecular relatedness of cases, results may take up to several weeks. This study aimed to assess the utility of the retrospective spatial scan statistic in detecting clusters of Salmonella Heidelberg and Salmonella Typhimurium cases using data from ON in 2015. Identified clusters were validated by laboratory data (where available) to determine whether identified clusters were likely outbreaks. Methods: Data representing the location of each reported S. Heidelberg or S. Typhimurium case in 2015, responsible serotype and symptom onset date were exported to SaTScan for retrospective spatial, temporal, and space‐time analyses using the spatial scan statistic with Bernoulli models and a space‐time permutation model. Analyses were performed with and without those cases linked to known outbreaks. Laboratory subtyping data (i.e. pulsed field gel electrophoresis (PFGE) and/or phage type) and food and environmental exposure information (e.g. travel, animal contact, poultry and other food item consumption) were used to explore the relatedness of cases within identified clusters. Results: Spatial, temporal and space‐time analyses identified a known outbreak of S. Heidelberg in 2015 (n = 9 cases) and a previously unidentified cluster of S. Heidelberg cases. Most cases (94%) within a cluster detected via a space‐time permutation model of S. Heidelberg cases shared an identical PFGE pattern and appeared to represent a true outbreak. Conclusions: The spatial scan statistic, and particularly the space‐time permutation model, could assist in outbreak identification before laboratory data are available, allowing for faster cluster identification and implementation of control measures. [ABSTRACT FROM AUTHOR]

The viruses of bacteria – bacteriophages – were discovered 20 years after the discovery of viruses. However, this was mainly the bacteriophage research that, after the first 40 years, yielded the modern concept of the virus and to large extent formed the grounds of the emerging molecular genetics and molecular biology. Many specific aspects of the bacteriophage research history have been addressed in the existing publications. The integral outline of the events that led to the formation of the key concepts of modern virology is presented in this review. This includes the opposition of F. d'Herelle and J. Bordet viewpoints over the nature of the bacteriophage, the history of lysogeny discovery and of determination of the mechanisms of underlying this phenomenon, the work of the Phage group led by M. Delbruck in USA, the development of the genetic analysis of bacteriophages and other research that eventually led to emergence of the concept of the virus (bacteriophage) as a transmissive genetic program. The review also covers a brief history of early applications of the bacteriophages such as phage therapy and phage typing. [ABSTRACT FROM AUTHOR]

Group B Streptococcus (GBS) is a gram-positive pathogen mainly affecting humans, cattle, and fishes. Mobile genetic elements play an important role in the evolution of GBS, its adaptation to host species and niches, and its pathogenicity. In particular, lysogenic prophages have been associated with a high virulence of certain strains and with their ability to cause invasive infections in humans. It is therefore important to be able to accurately detect and classify prophages in GBS genomes. Several bioinformatic tools for the identification of prophages in bacterial genomes are available on-line. However, genome searches for most of these programs are affected by the composition of their reference database. Lack of databases specific to GBS results in failure to recognize all prophages in the species. Additionally, performance of these programs is affected by genome fragmentation in the case of draft genomes, leading to underestimation of the number of phages. They also prove impractical when dealing with large genome datasets and they do not offer a quick way of classifying bacteriophages. We developed a GBS-specific method to screen genome assemblies for the presence of prophages and to classify them based on a reproducible typing scheme. This was achieved through an extensive search of a vast number of high-quality GBS sequences (n = 572) originating from different host species and countries in order to build a database of phage integrase types, on which the scheme is based. The proposed typing scheme comprises 12 integration sites and sixteen prophage integrase types, including multiple subtypes per integration site and integrase genes that were not site-specific. Two putative phage-inducible chromosomal islands (PICI) and their insertion sites were also identified during the course of these analyses. Phages were common and diverse in all major clonal complexes associated with human disease and detected in isolates from every animal species and continent included in the study. This database will facilitate further work on the prevalence and role of prophages in GBS evolution, and identifies the roles of PICIs in GBS and of prophage in hypervirulent ST283 as areas for further research. [ABSTRACT FROM AUTHOR]

Acid adaptation enhances survival of foodborne pathogens under lethal acid conditions that prevail in several food-related ecosystems. In the present study, the role of undissociated acetic acid in inducing acid resistance of Salmonella Enteritidis Phage Type 4 both in laboratory media and in an acid food matrix was investigated. Several combinations of acetic acid (0, 15, 25, 35 and 45 mM) and pH values (4.0, 4.5, 5.0, 5.5, 6.0) were screened for their ability to activate acid resistance mechanisms of pathogen exposed to pH 2.5 (screening assay). Increased survival was observed when increasing undissociated acetic acid within a range of sublethal concentrations (1.9–5.4 mM), but only at pH 5.5 and 6.0. No effect was observed at lower pH values, regardless of the undissociated acetic acid levels. Three combinations (15mM/pH5.0, 35mM/pH5.5, 45mM/pH6.0) were selected and further used for adaptation prior to inoculation in commercial tarama (fish roe) salad, i.e., an acid spread (pH 4.35 ± 0.02), stored at 5°C. Surprisingly and contrary to the results of the screening assay, none of the acid adaptation treatments enhanced survival of Salmonella Enteritidis in the food matrix, as compared to non-adapted cells (control). Further examination of the food pH value, acidulant and storage (challenge) temperature on the responses of the pathogen adapted to 15mM/pH5.0, 35mM/pH5.5 and 45mM/pH6.0 was performed in culture media. Cells adapted to 35mM/pH5.5 were unable to induce acid resistance when exposed to pH 4.35 (tarama salad pH value) at 37°C and 5°C, whereas incubation under refrigeration (5°C) at pH 4.35 sensitized 45mM/pH6.0 adapted cells against the subsequent acid and cold stress. In conclusion, pre-exposure to undissociated acetic acid affected the adaptive responses of Salmonella Enteritidis Phage Type 4 in a concentration- and pH-dependent manner, with regard to conditions prevailing during acid challenge. [ABSTRACT FROM AUTHOR]

Background: Point-of-issue tests, such as the Verax Pan Genera Detection (PGD) test, can be used to mitigate the occurrence of septic reactions. Little is known about how widespread the adoption of the PGD test is across US hospitals.Study Design/methods: The Red Cross hemovigilance database was used to determine the numbers of PGD-positive test results between 2013 and 2018. An examination of the impact of a reactive PGD test on product availability was performed for 2018.Results: The number of reported cases doubled, rising from approximately 50 to 100 per year between 2013 and 2018. A total of 475 initially reactive PGD tests during the entire study period were reported, and 7 (1.5%) of these were determined to be true positives. Hospitals surveyed reported testing platelet units once, with no repeat testing if the unit was PGD reactive. Evaluation of the reported PGD reactive cases for apheresis platelets for 2018 (n = 93) resulted in an estimated cost to the blood center of $87,000, which included the labor and material costs of working up the cases and the estimated value of the lost 64 units and co-components. In addition, there was a loss of the opportunity to collect over 85 apheresis platelets during the time the implicated donor was temporarily deferred.Conclusions: The number of hospital reports of reactive PGD tests has shown modest growth in the past 5 years. The number of initially reactive PGD tests that were confirmed was minimal. Blood centers can incur cost and platelet inventory loss from initially false-positive test results. [ABSTRACT FROM AUTHOR]

Background: Recently, using antibacterial peptides has been considered as a strategy to manage the worldwide antibiotic-resistance crisis. Screening of Dasht-Desert Bacterial Culture Collection (DDBCC) for bacteriocin or bacteriocin-like producer was aimed in this study to introduce native antibacterial agent(s). Methods: In this study, 170 isolates were examined by the cross-streak method against G+ and G- indicators. Isolates with antimicrobial activity were compared using turbidity and well diffusion tests. The candidate isolate, DDBCC70, was molecularly and biochemically characterized. Then, the production of an antibacterial agent was physicochemically optimized. The supernatant was saturated ammonium sulfate. SDSPAGE and Thin-Layer Chromatography (TLC) analyses, cytotoxicity, and hemagglutination tests were performed. Results: First, 23 isolates were detected with antimicrobial activity against at least three of the indicator strains. DDBCC70 was distinguished with the broad-spectrum of antibacterial effects of the Cell-Free Supernatants (CFSs). The black pigments on BHI and a 98% similarity in 16S rDNA and similarity in biochemical tests confirmed the strain of DDBCC70 as Bacillus atrophaeus (B. atrophaeus). The highest amount of the antibacterial agent, Bac70, was obtained from the modified brain heart infusion medium. It was revealed that 70% ammonium sulfate-saturated Bac70 was 3.8 and 1.6 times more effective on Pseudomonas aeuroginosa (P. aeuroginosa) and Klebsiella pneumoniae (K. pneumoniae). Bac70, a >25 kDa protein and a safe compound for blood cells, neither agglutinated human erythrocyte nor lysed sheep blood. The purified bacteriocin-like molecule destroyed biofilms from P. aeruginosa and Staphylococcus aureus (S. aureus). Moreover, the fraction of Bac70 from the TLC plate showed higher inhibitory effects against K. pneumoniae. Conclusion: Based on the above-mentioned features, Bac70 is a potential alternative therapeutic agent in pharmaceutical, food preservative and biotech-related industries. [ABSTRACT FROM AUTHOR]

Purpose: Time-dependent surgical instrument contamination and the effect of covering during arthroplasty have not been investigated. This study aimed to evaluate time-dependent contamination of surgical instruments and the effect of covering on contamination as well as to perform bacterial typing of contaminated samples. The hypothesis was that covering the surgical instruments would decrease contamination rates.Methods: Sixty patients who underwent total knee arthroplasty were randomized and divided into two groups: surgical instruments covered with a sterile towel or surgical instruments left uncovered. K-wires were used to extract microbiological samples. The K-wires were placed in a liquid culture medium at 0, 15, 30, 60, 90, and 120 min. After 24-h incubation period, samples from liquid cultures were cultured on blood agar using swabs. Samples with growth after 48 h were considered contaminated. Microscopic, staining, and biochemical properties were used for bacterial typing.Results: Bacterial growth started after 30 and 60 min in the uncovered and covered groups, respectively. An increase in the number of K-wires contaminated with time was detected. At least 10,000 CFU/mL bacterial load was observed in the culture samples. Contamination was more significant in the uncovered group. A statistically significant difference in contamination was found between the uncovered and covered groups at 30-, 60-, 90-, and 120 min (p = 0.035, p = 0.012, p = 0.024, and p = 0.037, respectively). The most common bacteria on the contaminated instruments were coagulase-negative Staphylococci (60.4%), Staphylococcus aureus (22.9%), and Streptococcus agalactia (16.7%), respectively.Conclusion: The risk of contamination increases with time. However, it may decrease if surgical instruments are covered. In the clinical practice, empiric antibiotic regimens based on the type of identified microorganisms in this study may be developed for postoperative periprosthetic joint infection prophylaxis.Level Of Evidence: Prognostic, Level II. [ABSTRACT FROM AUTHOR]

Phages can fundamentally alter the physiology and metabolism of their hosts. Although these phages are ubiquitous in the bacterial world, they have seldom been described among endosymbiotic bacteria. One notable exception is the APSE phage that is found associated with the gammaproteobacterial Hamiltonella defensa , hosted by several insect species. This secondary facultative endosymbiont is not necessary for the survival of its hosts but can infect certain individuals or even whole populations. Its infection in aphids is often associated with protection against parasitoid wasps. This protective phenotype has actually been linked to the infection of the symbiont strain with an APSE, which carries a toxin cassette that varies among so-called "types." In the present work, we seek to expand our understanding of the diversity of APSE phages as well as the relations of their Hamiltonella hosts. For this, we assembled and annotated the full genomes of 16 APSE phages infecting Hamiltonella symbionts across ten insect species. Molecular and phylogenetic analyses suggest that recombination has occurred repeatedly among lineages. Comparative genomics of the phage genomes revealed two variable regions that are useful for phage typing. Additionally, we find that mobile elements could play a role in the acquisition of new genes in the toxin cassette. Altogether, we provide an unprecedented view of APSE diversity and their genome evolution across aphids. This genomic investigation will provide a valuable resource for the design and interpretation of experiments aiming at understanding the protective phenotype these phages confer to their insect hosts. [ABSTRACT FROM AUTHOR]

Background Clostridioides difficile infections are associated with morbidity and mortality in several countries. Their increasing incidence and frequent recurrence make them an urgent public health threat. The lack of adherence to international treatment guidelines for Clostridioides difficile infections is a proven mortality risk factor. Objective To evaluate long-term prescribers' adherence to recommendations on the management of Clostridioides difficile infections and its impact on clinical outcomes after an educational and Clostridioides difficile-prospective audit with intervention and feedback period. Setting All patients admitted to a 1500-bed university hospital with positive Clostridioides difficile tests identified were included. Methods Data were collected retrospectively over a baseline period (May-November 2014) and prospectively over a Clostridioides difficile-prospective audit with intervention and feedback period (November 2015-May 2016) and an observation period (November 2017-September 2018). All Clostridioides difficile cases were reviewed by a Clostridioides difficile-prospective audit with intervention and feedback team composed of pharmacists, an infectious diseases specialist and a microbiologist to obtain a complete overview of patient records in each area of expertise. Main outcome measures Percentage of conformity to the protocol, percentage of recovery at 10 days and percentage of relapse, as well as Clostridioides difficile incidence and percentage of Fidaxomicin use. Results A total of 183 patients were included over the three periods. A significant improvement in conformity to the local protocol was observed between the intervention period (23.9%) and the observation period (67.3%) (P < 10-3). Fidaxomicin prescriptions increased significantly (P = 0.006). Clinical outcomes improved significantly with an increase in the percentage of recovery at 10 days (P = 0.001) and a decrease in the percentage of relapse (P = 0.016). The Clostridioides difficile incidence rate improved significantly to 1.3 per 10,000 patient-days during the observation period. Conclusion This study shows the lasting effect of an educational and Clostridioides difficile-prospective audit with intervention and feedback period on prescribers' adherence to recommendations and a significant impact on clinical outcomes. [ABSTRACT FROM AUTHOR]

Purpose: Corynebacterium spp. (C. spp.) is commonly considered as a contaminant in respiratory specimens. No study has ever focused on its clinical relevance in the lower respiratory tract of patients admitted to the intensive care unit (ICU) and requiring mechanical ventilation. The aims were to describe the characteristics of ICU patients with a C. spp. positive deep respiratory specimen, to investigate the impact of C. spp. on the occurrence of pneumonia, and to evaluate the outcomes of these pneumonia. Methods: We retrospectively included all adult patients admitted to ICU in a 1000-bed University Hospital (2007–2017) who had a C. spp. positive lower respiratory tract specimen at a significant quantitative level. We used clinical, radiological, and microbiological criteria to classify the likelihood of such pneumonia. Results: Among the 31 patients included, acute respiratory failure and postoperative care after major surgery were the main reasons of admission. SAPS II was 47 [34–60]. C. spp. pneumonia was considered as probable, possible and unlikely in 10, 14, and 7 patients, respectively. Fifty-two and 94% of C. spp. strains were sensitive to amoxicillin, and vancomycin/linezolid, respectively. Seventeen patients had a complete course of antibiotic against C. spp. The overall ICU mortality was 58%. Conclusion: Corynebacterium spp seems to be responsible for authentic pneumonia in mechanically ventilated patients. It should be considered as clinically relevant when predominantly present in respiratory specimen from patients suspected with pneumonia in ICU, and empirically treated. [ABSTRACT FROM AUTHOR]

Tuberculosis caused by concurrent infection with multiple Mycobacterium tuberculosis strains (i.e., mixed infection) challenges clinical and epidemiologic paradigms. We explored possible transmission mechanisms of mixed infection in a population-based, molecular epidemiology study in Botswana during 2012-2016. We defined mixed infection as multiple repeats of alleles at >2 loci within a discrete mycobacterial interspersed repetitive unit-variable-number tandem-repeat (MIRU-VNTR) result. We compared mixed infection MIRU-VNTR results with all study MIRU-VNTR results by considering all permutations at each multiple allele locus; matched MIRU-VNTR results were considered evidence of recently acquired strains and nonmatched to any other results were considered evidence of remotely acquired strains. Among 2,051 patients, 34 (1.7%) had mixed infection, of which 23 (68%) had recently and remotely acquired strains. This finding might support the mixed infection mechanism of recent transmission and simultaneous remote reactivation. Further exploration is needed to determine proportions of transmission mechanisms in settings where mixed infections are prevalent. [ABSTRACT FROM AUTHOR]

Context.--Consolidation of clinical microbiology laboratory services has resulted in extended transit time for blood cultures from service points distant from the laboratory. Sepsis is critical; delays in identification of etiologic agents of diseases could adversely impact patient care. Objective.--To examine the effect of total preanalytic time and blood culture volume on the instrument time-to-detection for bacterial pathogens in blood cultures. A secondary objective was to obtain relevant blood culture information by questionnaire. Design.--Participants in this Q-Probes study recorded date, time, and volume information for the first 50 positive blood cultures collected during the 12-week study period. Additional information regarding blood culture collection practices was obtained through questionnaire. Results.--Prolonged overall time-to-detection was secondary to prolonged preanalytic time, particularly prolonged transit time, rather than slower organism growth once bottles were placed on the instrument. Among 1578 blood cultures, the overall time from collection to positive result was significantly less for blood cultures collected onsite than for off-site locations. Most institutions lack sufficient training programs and do not monitor preanalytic time metrics associated with blood cultures. Four hundred fifty-six of the 1580 blood cultures with blood volume adequacy reported (28.9%) were inadequately filled. Conclusions.--Overall process time (specimen collection to positive blood culture detection) is predicted to be higher for blood cultures collected off-site. Transit time is a variable that can be reduced to decrease overall time to detection. Thus, improved training and closer attention to preanalytic metrics associated with blood cultures could decrease hospital stays and mortality rates. [ABSTRACT FROM AUTHOR]

In this study, mycobacteria, which were previously identified as Mycobacterium tuberculosis complex (MTC), and mycobacteria other than tuberculosis (MOTT) with cord factor and the p‐nitro‐alpha‐acetyl‐amino‐beta‐hydroxypropiophenone (NAP) test were reanalysed using the polymerase chain reaction—restriction fragment length polymorphism (PCR‐RFLP) analysis method in order to confirm the identification, and at the same time, species accepted as MOTT were identified. Although the results of the NAP test were obtained within 3‐5 days, the PCR‐RFLP results were obtained in 1 day. Ten species identified as MTC with the NAP test and cord factor were confirmed with the PCR‐RFLP method. Fourteen species accepted as MOTT were identified as Mycobacterium species with the evaluation of the bands observed after the restriction of PCR product with the PCR‐RFLP method. These were as follows: three species Mycobacterium intracellulare type I, two species Mycobacterium phlei, two species Mycobacterium kansasii, one species Mycobacterium fortuitum type I, one species Mycobacterium gordonae type I, one species Mycobacterium abscessus type I, one species Mycobacterium scrofulaceum, one species Mycobacterium szulgai type I, one species Mycobacterium avium type II, and one species Mycobacterium terrae. Hence, the results of both the cord factor and the NAP test were confirmed with the molecular method, and at the same time, mycobacteria species identification was made by determining the fastest, easiest, and the most accurate result‐giving method. Because PCR‐RFLP is a very rapid method that provides exact identification of mycobacteria species, it can be performed in routine procedures. [ABSTRACT FROM AUTHOR]

Background: Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most pathogens associated with health care. Molecular typing methods are vital for outbreak investigations of MRSA. The aim of this study was characterization of SCCmec, spa types and multidrug resistant of methicillin-resistant Staphylococcus aureus isolates in Ahvaz, Iran. Methods: A total of 50 MRSA isolates were determined by using the phenotypic method and mecA gene. Antibiotic resistance profile and SCCmec types were screened using disc diffusion method and PCR, respectively. For spa typing of MRSA isolates, two molecular typing methods including the PCR-sequencing and high-resolution melting (HRM) analysis were used. Results: In the present study, the highest sensitivity of MRSA was to vancomycin and linezolid and the lowest to clindamycin. In the MRSA isolates, 22% were XDR and 78% were MDR. SCCmec type III was found commonly among MRSA. Based on PCR-sequencing and HRM results, 10 different spa types were identified. The spa types t037 and t030 were the most common in this study. Conclusion: This study emphasizes the spa variation among MRSA isolates, which may be considered as an important criterion when treating staphylococcal infections. Accurate and early detection of MDR, XDR, or even PDR MRSA isolates strains must be commenced by all clinical microbiology laboratories to reduce the menace of antimicrobial resistance. [ABSTRACT FROM AUTHOR]

The aim of this research was to identify the role of mycoplasma bacteria in eyes infections. A 100 samples were isolated from patients whom suffering from eye infections for 2nd Jan - 30th June 2018 . The clinical isolates were cultivated on mycoplasma media. Biochemical tests were then performed. Three types of mycoplasma were isolated (M. pneumoniaein 42 cases, M. salivariumin 30 cases & M.hominisin three cases). Six cases were recorded single infection. The highest incidence of mycoplasma in the age group (11-20 years). [ABSTRACT FROM AUTHOR]

The virus that infects bacteria known as phage, plays a crucial role in the biogeochemical cycling of nutrients. However, the community structure and potential functions of phages in silage fermentation remain largely unexplored. In this study, we utilized viral metagenomics (viromics) to investigate the types, lifestyles, functions, and nutrient utilization patterns of phages in silage. Our findings indicated a high prevalence of annotated phages belonging to Caudovirales and Geplafuvirales, as well as unclassified phages in silage. The predominant host types for these phages were Campylobacterales and Enterobacterales. Virulent phages dominated the silage environment due to their broader range of hosts and enhanced survival capabilities. All identified phages present in silage were found to be non-pathogenic. Although temperate and virulent phages carried distinct genes associated with nutrient cycling processes, the shared genes (prsA) involved in carbon metabolism underscore the potential significance of phages in regulating carbon metabolism in silage. Overall, our findings provide a valuable foundation for further exploring the complex interactions between phages and microorganisms in regulating silage fermentation quality. • The viruses present in silage are primally phages and non-pathogenic. • The primary bacterial host of phages belong to the Proteobacteria. • Virulent phages show higher abundance and broader host range than temperate phages. • The phages could express the genes associated with nitrogen and carbon metabolism. [ABSTRACT FROM AUTHOR]

Bacterial plant pathogens pose significant challenges to global food production, leading to antibiotics and copper being used for their control. Bacteriophages (or phages), which infect bacterial pathogens, have been proposed as an environmentally friendly alternatives for managing these pathogens in crops. However, whether the release of phages into the environment can be considered safe and environmentally friendly has not been well studied. Here, we examined whether the exogenous treatments of various phages with biocontrol potential against Erwinia amylovora, Pectobacterium odoriferum, and Pseudomonas syringae pv. actinidiae impact bacterial communities within soils. To achieve this, five different phages infecting three distinct host bacteria were individually introduced into in soils obtained from an apple orchard, kimchi cabbage field, and a kiwifruit orchard. After one week of phage treatment, soil microbiomes were analyzed using the 16S rRNA gene-based approach. The microbiome analysis results revealed that the phage treatments did not alter the alpha and beta diversities of the bacterial communities, irrespective of the phage types used. Moreover, the overall distribution of microbial taxa remained unaffected by the phage treatment, although slight changes were observed in the abundance of a few taxa. These results indicate that the adverse effects of exogenous phage treatment on soil bacterial communities are minimal, thus the phage treatment in soils can be considered an environmentally friendly strategy. • Five different phages infecting three different plant-pathogenic bacteria were used. • The adverse effects of phage treatment on soil bacterial communities are minimal. • The phage application can be considered an environmentally friendly strategy. [ABSTRACT FROM AUTHOR]

Human viruses are ubiquitous contaminants in surface waters, where they can persist over extended periods of time. Among the factors governing their environmental persistence, the control (removal or inactivation) by microorganisms remains poorly understood. Here, we determined the contribution of indigenous bacteria and protists to the decay of human viruses in surface waters. Incubation of echovirus 11 (E11) in freshwater from Lake Geneva and seawater from the Mediterranean Sea led to a 2.5-log10 reduction in the infectious virus concentration within 48 h at 22°C, whereas E11 was stable in sterile controls. The observed virus reduction was attributed to the action of both bacteria and protists in the biologically active matrices. The effect of microorganisms on viruses was temperature dependent, with a complete inhibition of microbial virus control in lake water at temperatures of ≤16°C. Among three protist isolates tested (Paraphysomonas sp., Uronema marinum, and Caecitellus paraparvulus), Caecitellus paraparvulus was particularly efficient at controlling E11 (2.1-log10 reduction over 4 days with an initial protist concentration of 103 cells ml-1). In addition, other viruses (human adenovirus type 2 and bacteriophage H6) exhibited different grazing kinetics than E11, indicating that the efficacy of antiviral action also depended on the type of virus. In conclusion, indigenous bacteria and protists in lake water and seawater can modulate the persistence of E11. These results pave the way for further research to understand how microorganisms control human viral pathogens in aquatic ecosystems and to exploit this process as a treatment solution to enhance microbial water safety. [ABSTRACT FROM AUTHOR]

Intrinsic low display level of polypeptides on phage is a fundamental and limiting hurdle in successful isolation of target-specific binders by phage display technology. To circumvent this challenge, we optimized the copy number of peptides displayed on the phage surface using type 33 phage vector. We randomized the first 67 amino acids of the wild type PIII to identify mutants that would result in its reduced expression. Consequently, the display level was improved by 30-fold due to higher incorporation of the synthetic PIII–peptide fusion protein on the phage surface. Utilization of this novel phage vector should provide a solid basis for the discovery of therapeutic peptides. [ABSTRACT FROM AUTHOR]

Background The impact of healthcare personnel hand contamination in multidrug-resistant organism (MDRO) transmission is important and well studied; however, the role of patient hand contamination needs to be characterized further. Methods Patients from 2 hospitals in southeast Michigan were recruited within 24 hours of arrival to their room and followed prospectively using microbial surveillance of nares, dominant hand, and 6 high-touch environmental surfaces. Sampling was performed on admission, days 3 and 7, and weekly until discharge. Paired samples of methicillin-resistant Staphylococcus aureus (MRSA) isolated from the patients' hand and room surfaces were evaluated for relatedness using pulsed-field gel electrophoresis and staphylococcal cassette chromosome mec , and Panton-Valentine leukocidin typing. Results A total of 399 patients (mean age, 60.8 years; 49% male) were enrolled and followed for 710 visits. Fourteen percent (n = 56/399) of patients were colonized with an MDRO at baseline; 10% (40/399) had an MDRO on their hands. Twenty-nine percent of rooms harbored an MDRO. Six percent (14/225 patients with at least 2 visits) newly acquired an MDRO on their hands during their stay. New MDRO acquisition in patients occurred at a rate of 24.6/1000 patient-days, and in rooms at a rate of 58.6/1000 patient-days. Typing demonstrated a high correlation between MRSA on patient hands and room surfaces. Conclusions Our data suggest that patient hand contamination with MDROs is common and correlates with contamination on high-touch room surfaces. Patient hand hygiene protocols should be considered to reduce transmission of pathogens and healthcare-associated infections. [ABSTRACT FROM AUTHOR]

Background: Surgical site infection (SSIs) is one of the most common healthcare-associated infections. It comprises a great risk to hospitalized patients in terms of morbidity, mortality and economic cost. Objectives: To identify the causative organism(s) responsible for surgical site infection following Cesarean section and to trace the source of that infection. Patients & methods: A total of 623 clinical samples and swabs were collected from Obstetrics & Gynecology Department at Al-Zahraa University Hospital. The study included 300 patients with provisional diagnosis of SSI from whom, wound swabs were taken, in addition to 23 swabs from medical staff and 300 environmental samples. Samples were subjected to conventional bacteriological identification, biochemical reactions, antibiogram and genotyping by Random Amplified Polymorphic DNA (RAPD) assay of the dominated isolates. Results: Out of 300 wound swabs from patients with SSI following CS surgery, 62 (20.7%) yielded aerobic microbial growth. Eighty three out of 323 swabs (26%) collected from health care workers (HCWs) & environment were positive on culture. The most common organism isolated from both sources (clinical & environmental specimens) was Methicillin resistant Staphylococcus aureus (MRSA) isolates 35/623 (5.6%). Genotyping of MRSA isolates revealed 20 distinct Random Amplified Polymorphic DNA (RAPD) patterns, indicating high rate of genetic heterogeneity among MRSA isolates. Conclusion: There were clonally related MRSA isolates obtained from operating room and from patients, indicating that the operating room was accused as a source of infection. [ABSTRACT FROM AUTHOR]

Objectives: To demonstrate the utility of a natural language processing (NLP) algorithm for mining kidney stone composition in a large-scale electronic health records (EHR) repository.Methods: We developed StoneX, a pattern-matching method for extracting kidney stone composition information from clinical notes. We trained the extraction algorithm on manually annotated text mentions of calcium oxalate monohydrate, calcium oxalate dihydrate, hydroxyapatite, brushite, uric acid, and struvite stones. We employed StoneX to identify patients with kidney stone composition data and mine >125 million notes from our institutional EHR. Analyses performed on the extracted patients included stone type conversions over time, survival analysis from a second stone surgery, and disease associations by stone composition to validate the phenotyping method against known associations.Results: The NLP algorithm identified 45,235 text mentions corresponding to 11,585 patients. Overall, the system achieved positive predictive value >90% for calcium oxalate monohydrate, calcium oxalate dihydrate, hydroxyapatite, brushite, and struvite; except for uric acid (positive predictive value = 87.5%). Survival analysis from a second stone surgery showed statistically significant differences among stone types (P = .03). Several phenotype associations were found: uric acid-type 2 diabetes (odds ratio, OR = 2.69, 95% confidence intervals, CI = 1.91-3.79), struvite-neurogenic bladder (OR = 12.27, 95% CI = 4.33-34.79), struvite-urinary tract infection (OR = 7.36, 95% CI = 3.01-17.99), hydroxyapatite-pulmonary collapse (OR = 3.67, 95% CI = 2.10-6.42), hydroxyapatite-neurogenic bladder (OR = 5.23, 95% CI = 2.05-13.36), brushite-calcium metabolism disorder (OR = 4.59, 95% CI = 2.14-9.81), and brushite-hypercalcemia (OR = 4.09, 95% CI = 1.90-8.80).Conclusion: NLP extraction of kidney stone composition from large-scale EHRs is feasible with high precision, enabling high-throughput epidemiological studies of kidney stone disease. These tools will enable high fidelity kidney stone research from the EHR. [ABSTRACT FROM AUTHOR]

Introduction: The prevalence of nosocomial infection by Elizabethkingia meningoseptica (E. meningoseptica) has increased. It has been found to be associated with outbreaks of neonatal, adult and device related infections with mortality rates as high as 50%. Conventional empirical antibiotics against Gram-Negative Bacteria (GNB) are not effective against E. meningoseptica and interpretive Minimum Inhibitory Concentration (MIC) breakpoints are not available yet, making the treatment tricky. Hence, early detection is essential to prevent morbidity and mortality associated with E. meningoseptica. Aim: To know the incidence, clinical profile, associated risk factors and antibiotic susceptibility of E. meningoseptica isolates from suspected patients. Materials and Methods: This prospective study was done on patients admitted from January 2017-December 2018 to a tertiary care Hepatobilliary center in India. Clinical details, demographic details, associated risk factors and antibiotic sensitivity pattern of E. meningoseptica isolates obtained from various clinical samples during the study period were analysed. Analysis was done using SPSS software version 22. The categorical data was represented in frequency (%) and continuous data in mean. Results: A total of 32 isolates from 20 patients were included. Out of the 20 patients, 15 (75%) were males with a mean age of 43.05 years (range, 2-71 years). E. meningoseptica was most frequently isolated from respiratory samples (87.5%). Risk factors were chronic liver disease (75%), diabetes mellitus (50%), prolonged hospital admission (55%), prior ICU stay (100%), invasive procedures like insertion of Central Venous Catheter (CVC) (100%), need for life supports like prolonged ventilation (70%) and haemodialysis (55%). Minocycline was the most susceptible drug with 100% sensitivity followed by cotrimoxazole (65.6%). Conclusion: Patients with E. meningoseptica infection have significant morbidity and mortality. Hence awareness about the organism, active surveillance and investigation for the source of the organism will help in implementation of appropriate infection control measures and prevent outbreaks or recurrence. [ABSTRACT FROM AUTHOR]

• Implant-related infections are a devastating complication of orthopaedic surgery. • The emergence of multidrug-resistant bacteria increases concern for their treatment. • High specificity and effectiveness make phages candidates as an orthopaedic therapeutic. • Isolated phages were efficient in infecting and reducing multidrug-resistant bacteria. • Phage therapy could be suitable to treat pathogenic bacteria in orthopaedic infections. Orthopaedic implant-associated infections are a devastating complication of orthopaedic surgery with a significant impact on patients and healthcare systems. The aims of this work were to describe the patterns of antimicrobial resistance, pathogenicity and virulence of clinical bacterial isolates from orthopaedic implant-associated infections and to further isolate and characterise bacteriophages that are efficient in controlling these bacteria. Staphylococcus aureus, Enterococcus faecalis and Escherichia coli isolated from orthopaedic infections showed multiresistance patterns to the most frequently used antibiotics in clinical settings. The presence of mobile genetic elements (mecA , Tn 916 /Tn 1545 and intl1) and virulence determinants (icaB, cna, hlb, cylLs, cylM, agg, gelE, fsr and fimA) highlighted the pathogenicity of these isolates. Moreover, the isolates belonged to clonal complexes associated with the acquisition of pathogenicity islands and antimicrobial resistance genes by recombination and horizontal gene transfer. Bacteriophages vB_SauM_LM12, vB_EfaS_LM99 and vB_EcoM_JB75 were characterised and their ability to infect clinical isolates of S. aureus, E. faecalis and E. coli , respectively, was assessed. Morphological and genomic analyses revealed that vB_EfaS_LM99 and vB_EcoM_JB75 belong to the Siphoviridae and Myoviridae families, respectively, and no genes associated with lysogeny were found. The bacteriophages showed low latent periods, high burst sizes, broad host ranges and tolerance to several environmental conditions. Moreover, they showed high efficiency and specificity to infect and reduce clinical bacteria, including methicillin-resistant S. aureus and vancomycin-resistant enterococci. Therefore, the results obtained suggest that the bacteriophages used in this work are a promising approach to control these pathogens involved in orthopaedic implant-associated infections. [ABSTRACT FROM AUTHOR]

Background: In response to Clostridioides (Clostridium) difficile infections (CDI), infection prevention and control practices in hospital settings tend to focus on symptomatic patients, potentially neglecting other sources of C. difficile. The purpose of the study was to identify epidemiological connections between C. difficile positive patients to explore the possibility of transmission occurring. This would allow an assessment of IPAC practices to ensure resources were being optimized and targeted to the most appropriate strategies to prevent transmission. Methods: C. difficile was isolated and characterized from 125 patient stool specimens. Isolates were subjected to toxin profiling and ribotyping. Patient locations in the hospital were mapped and epidemiological connections between patients with the same C. difficile ribotype were assessed. Results: A total of 47 distinct ribotypes were identified, with the most common being ribotype 027/NAP1. Of the 41 cases identified as hospital-associated, only four (9.8%) of the cases could be epidemiologically linked to another patient with known CDI. Conclusions: A small minority of hospital-associated infections were found to have an epidemiological link to another known case of CDI suggesting transmission from known cases is rare. This suggested that current IPAC practices were effective in preventing transmission from symptomatic patients, but other sources of C. difficile are potentially unrecognized. [ABSTRACT FROM AUTHOR]

Melioidosis and leptospirosis, caused by two different bacteria, Burkholderia pseudomallei and Leptospira spp., are potentially fatal infections that share a very similar spectrum of clinical features and cause significant mortality and morbidity in humans and livestock. Early detection is important for better clinical consequences. To our knowledge, there is no diagnostic tool available to simultaneously detect and differentiate melioidosis and leptospirosis in humans and animals. In this study, we described a duplex TaqMan probe-based qPCR for the detection of B. pseudomallei and Leptospira spp. DNA. The performance of the assay was evaluated on 20 B. pseudomallei isolates, 23 Leptospira strains, and 39 other microorganisms, as well as two sets of serially diluted reference strains. The duplex qPCR assay was able to detect 0.02 pg (~ 4 copies) Leptospira spp. DNA and 0.2 pg (~ 25.6 copies) B. pseudomallei DNA. No undesired amplification was observed in other microorganisms. In conclusion, the duplex qPCR assay was sensitive and specific for the detection of B. pseudomallei & Leptospira spp. DNA and is suitable for further analytical and clinical evaluation. [ABSTRACT FROM AUTHOR]

Background: Invasive infections due to Haemophilus influenzae are infrequent following the implementation of vaccination against H. influenzae of serotype b. However, their changing epidemiology may not be clear due to a lack of appropriate genotyping methods combined with antibiotic susceptibility analyses which do not discriminate invasive and non-invasive isolates. We aimed to describe recent epidemiological trends of invasive H. influenzae infections in France and explore the microbiological characteristics of invasive versus non-invasive isolates.Methods: All culture- and PCR-confirmed cases due to H. influenzae isolated from a sterile site, that were received at the French national reference centre for H. influenzae during the year 2017 (n = 138) were characterized by whole genome sequencing (WGS), serotyping and antibiotic susceptibility testing. We also included 100 isolates that were received from non-invasive infections.Findings: Most of the non-invasive isolates were non-typeable (99%) and this proportion was significantly less among invasive isolates 75%, p < 0.0001). Serotype f was the most frequently observed but serotypes b and a were also present among invasive isolates. WGS analysis suggested a serotype b to a capsule switching event. Non-typeable isolates showed extensive heterogeneity. Antibiotic susceptibility testing indicated that 24% of the invasive isolates were resistant to ampicillin but this percentage was significantly higher (51%, p < 0.001) among the non-invasive isolates. Moreover, the proportion of beta-lactamase negative ampicillin resistant isolates (BLNAR) was significantly higher among non-invasive isolates compared to that of invasive isolates (24% versus 7%, p < 0.001). BLNAR isolates were linked to modification in the ftsI gene encoding the penicillin binding protein 3 (PBP3). In particular, ftsI alleles that harboured the mutations D350N, S357N, M377I and S385T were resistant to ampicillin and third generation cephalosporins. These isolates were more frequent among non-invasive isolates.Interpretation: Our data suggest that invasive H. influenzae isolates differed phenotypically and genotypically from non-invasive isolates. The high proportion of ampicillin resistance by mutation in ftsI among non-invasive isolates may suggest a biological cost of these mutations on the function of PBP3 that can lead to lower bacterial invasiveness. WGS should be used routinely for the characterization of H. influenzae isolates in order to reliably follow the emergence, spread and mechanism of antibiotic resistance. [ABSTRACT FROM AUTHOR]

Background Clostridioides (formerly Clostridium) difficile infection (CDI) is associated with significant morbidity and mortality, including frequent hospitalizations. However, the impact of CDI after hospital discharge is poorly understood. The purpose of this study was to assess patient discharge disposition and understand CDI-related risk factors for nonhome discharge. Methods Using a nationally representative database of Veterans Health Administration (VHA) patients (2003–2014) and a validation database from hospitalized non-VHA patients in Houston, Texas, admission and discharge disposition was obtained for patients with CDI and matched controls. Incidence of and clinical/microbiologic risk factors for nonhome discharge were assessed using these databases. Results A total of 15173 VHA patients with CDI and 48599 non-CDI control patients originally admitted from the community were included. Significantly more patients with CDI were discharged to a nonhome location compared with controls (18% vs 8%; P <.0001), most commonly hospice/death (12%) or nursing home/long-term care facility (6%). Results were confirmed using a propensity-matched analysis and a validation cohort of 1941 hospitalized patients with CDI in Houston, Texas. Age, comorbidities, severe CDI, and ribotypes F027, F001, and F053-163 were associated with a nonhome discharge (P <.05 for all). Conclusions Hospitalized patients with CDI frequently required a higher level of medical care residence at discharge compared with non-CDI patients. Risk factors for discharge to a higher level of care included CDI disease severity and variables associated with recurrent CDI. [ABSTRACT FROM AUTHOR]

Background: The increased prevalence of syphilis in Cuba prompted us to map the circulating Treponema pallidum subsp. pallidum allelic profiles in this geographic region.Methods: Samples were collected from 2012 to 2017, from 83 male patients with ulcers or skin lesions, and were examined using multilocus sequence typing. Additionally, we analyzed the 23S rDNA and 16S rDNA regions for the presence of possible mutations leading to macrolide and tetracycline resistance.Results: Among 94% of fully typed strains, we found 7 different allelic profiles, of which 4 had not been previously described. More than 87% of patients were infected with the T. pallidum SS14-like group and only 8.2% with T. pallidum Nichols-like group. As in other countries, the 1.3.1 allelic profile (ie, SS14-like) was the most common. In addition, 1 of the newly described allelic profiles represents T. pallidum strains that arose by recombination events between members of different T. pallidum subgroups. More than 90% of patients were infected with treponemes harboring the A2058G mutation. However, we found no potential tetracycline-resistant T. pallidum mutations.Conclusions: Our results suggest that, in Cuba, tetracycline antibiotics could be used to treat syphilis in penicillin-allergic patients instead of macrolides. [ABSTRACT FROM AUTHOR]

Medicolegal entomology—a subfield of forensic entomology—is mainly used in medicolegal investigations to estimate the postmortem interval (PMI). The minimum PMI of a corpse invaded by necrophagous immature insects can be estimated because the PMI is near to or earlier than the oviposition time of the larvae that hatched and fed on the corpse. As the growth speeds of larvae differ depending on temperature and species, species-specific growth data are used to estimate the minimum PMI. While morphological identification of adult necrophagous flies can be done by a well-trained entomologist, identification of larvae is relatively difficult. Larvae can only be identified up to the family level and developmental stage by observing the posterior spiracles. For these reasons, the molecular biology method of DNA barcoding has been developed. DNA barcoding that targets the mitochondrial cytochrome c oxidase subunit I (COI) gene is commonly used. COI sequences are currently acquired using polymerase chain reaction (PCR) and Sanger sequencing, which are too time-consuming and complex for practical use in medicolegal investigations. To compensate for these limitations and facilitate the use of entomology for medicolegal investigation, we designed a multiplex real-time PCR system to identify nineteen forensically important species of Calliphoridae and Sarcophagidae flies collected in South Korea. In contrast to the Sanger nucleotide sequencing process, this technology only requires a one-step real-time PCR with melt curve analysis of amplicons generated by primers targeting species-specific single nucleotide polymorphisms (SNPs). Multiplex real-time PCR was performed for twelve species of Calliphoridae (four reactions) and for seven species of Sarcophagidae (three reactions). This assay is expected to make it easier and faster for investigating authorities to identify major species of necrophagous flies at beginning of investigation and to increase the utilization of entomological evidence in forensic investigations. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • MDR bacterial infections are a prevalent, growing and complex healthcare problem in decompensated cirrhosis and ACLF. • Prevalence increased from 29% to 38% in culture-positive infections from 2011 to 2017-2018. • Antibiotic resistance negatively impacts prognosis and is associated with higher mortality rates. • Nosocomial infection, ICU admission and recent hospitalization are independent risk factors of MDR infection. • Strategies aimed at preventing the spread of antibiotic resistance in cirrhosis should be urgently evaluated. Background & Aims Antibiotic resistance has been increasingly reported in patients with decompensated cirrhosis in single-center studies. Prospective investigations reporting broad epidemiological data are scarce. We aimed to analyze epidemiological changes in bacterial infections in patients with decompensated cirrhosis. Methods This was a prospective evaluation of 2 series of patients hospitalized with decompensated cirrhosis. The Canonic series included 1,146 patients from Northern, Southern and Western Europe in 2011. Data on epidemiology, clinical characteristics of bacterial infections, microbiology and empirical antibiotic schedules were assessed. A second series of 883 patients from Eastern, Southern and Western Europe was investigated between 2017–2018. Results A total of 455 patients developed 520 infections (39.7%) in the first series, with spontaneous bacterial peritonitis, urinary tract infections and pneumonia the most frequent infections. Nosocomial episodes predominated in this series. Nearly half of the infections were culture-positive, of which 29.2% were caused by multidrug-resistant organisms (MDROs). MDR strains were more frequently isolated in Northern and Western Europe. Extended-spectrum beta-lactamase-producing Enterobacteriaceae were the most frequent MDROs isolated in this series, although prevalence and type differed markedly among countries and centers. Antibiotic resistance was associated with poor prognosis and failure of antibiotic strategies, based on third-generation cephalosporins or quinolones. Nosocomial infection (odds ratio [OR] 2.74; p < 0.001), intensive care unit admission (OR 2.09; p = 0.02), and recent hospitalization (OR 1.93; p = 0.04) were identified as independent predictors of MDR infection. The prevalence of MDROs in the second series (392 infections/284 patients) was 23%; 38% in culture-positive infections. A mild increase in the rate of carbapenem-resistant Enterobacteriaceae was observed in this series. Conclusions MDR bacterial infections constitute a prevalent, growing and complex healthcare problem in patients with decompensated cirrhosis and acute-on-chronic liver failure across Europe, negatively impacting on prognosis. Strategies aimed at preventing the spread of antibiotic resistance in cirrhosis should be urgently evaluated. Lay summary Infections caused by bacteria resistant to the main antibiotic families are prevalent in patients with cirrhosis. This study demonstrates that this healthcare problem is increasing and extends through all European regions. Infections caused by these difficult to treat bacteria resolve less frequently and often cause the death of the patient. The type of resistant bacteria varies markedly among different hospitals. [ABSTRACT FROM AUTHOR]

Intraductal papillary mucinous neoplasms (IPMNs) are mucin-producing cystic lesions that involve the pancreatic ductal system. IPMNs that involve the main pancreatic duct have a higher risk of malignancy compared to IPMNs with exclusively branch duct engagement [[1]]. IPMN of the pancreas - does histological subtyping allow for improved stratification and follow-up? IPMNs engaging the main pancreatic duct are termed main duct type, those engaging branch ducts are termed branch duct type, and those communicating with both ducts are termed mixed type. [Extracted from the article]

Cholera is an acute diarrhoeal disease caused by Vibrio cholerae (V.cholerae). Based on antigenic differences of O antigen, O1 serogroup can be divided into three serotypes. In addition, by performing various biochemical reactions, O1 Serogroup can be differentiated into two biotypes. Outbreaks of Cholera occur seasonally. It is associated with monsoon season, warm temperature, heavy rainfall and increased plankton population. Aim: The aim was to determine the trends in resistance pattern and phenotypic Pattern of Vibrio cholerae. Materials and Methods: A retrospective study was conducted during the period from June 2019-December 2019. Culture of Stool specimens were done on different agar media. Biotyping was done by conventional methods. Serotyping and phage typing was also done along with the Antibiotic susceptibility testing. Descriptive analysis was used and presented in terms of percentage. Results: V.cholerae was isolated in 72 patients and they belonged to serogroup O1 and biotype El Tor. The most common serotype was Ogawa. The predominant phage type were T2 by old scheme and T27 by new scheme of phage typing. The maximum number of V. cholerae isolates was seen in the month of November, 2019 followed by October, 2019. Conclusion: The phenotypic pattern and fluctuating seasonal trend of V. cholerae and antimicrobial resistance encourage the continued epidemiological and microbiological surveillance of the disease. [ABSTRACT FROM AUTHOR]

Background: Many different etiologies have been proposed to be responsible for the pathogenesis of chronic rhinosinusitis, including dysbiosis of the sinus microbiome. Attempts have recently been made to identify a pathogenic organism via advanced culture mechanisms. The purpose of this study is to use culture-dependent and culture-independent means of microtyping to determine whether any association exists between the quantity and quality of bacteria identified in patients with recalcitrant chronic rhinosinusitis. Methods: Medical records were retrospectively reviewed for patients with a history of revision sinus surgery and persistent symptoms who underwent endoscopically directed culture and underwent quantitative polymerase chain reaction analysis of the 16S ribosomal RNA of bacteria and fungi from February 1, 2014, to January 1, 2017. A total of 21 patients met the inclusion criteria. Medical records were reviewed to determine the number of bacterial isolates and relative abundance of bacteria and fungi on culture and polymerase chain reaction. Results: Using culture-independent techniques of examining purulent secretions in patients with recalcitrant chronic rhinosinusitis, an average of 3.61 isolates were identified per specimen, compared with culture-dependent methods that revealed 2.10 isolates per specimen (P < .05). The dominant species identified on each culture was rarely the most abundant species identified using polymerase chain reaction techniques. Conclusions: Traditional culture methodologies may fail to identify potential pathogens or the dominant pathogen in patients with recalcitrant chronic rhinosinusitis with acute exacerbations. [ABSTRACT FROM AUTHOR]

Objectives: Acinetobacter baumannii (Ab) is an important cause of healthcare-associated infections. Multilocus sequence typing (MLST) provides a highly discriminative typing method. We aimed to determine the clinical impact of Ab sequence types (ST) in patients with bloodstream infection (BSI).Methods: Patients with Ab-BSI were followed prospectively from 2009 to 2014. We randomly selected one-third of non-duplicate bacteremic isolates for MLST and correlated the Ab ST with the clinical course. The primary outcome was all-cause in-hospital mortality.Results: We enrolled 148 patients. Seventy-seven (52.0%) of the isolates were ST2. Patients with ST2-BSI were less likely to be treated with appropriate empirical antimicrobial agents (31.1% vs. 60.6%; P < 0.001). They had greater mortality (66.2% vs. 40.8%; P = 0.003) than patients with non-ST2-BSI. In the multivariable analysis, ST2 independently predicted greater severity of infection (Pitt bacteremia score) (adjusted odds ratio (aOR), 3.38; 95% confidence interval (CI), 1.75-6.54; P < 0.001). Mediated by a higher Pitt bacteremia score (Sobel test P < 0.001), ST2 is an independent prognostic factor that predict mortality (aOR, 2.34; 95% CI, 1.07-5.11; P = 0.03).Conclusions: ST2 was associated with high rates of inappropriate antimicrobial therapy, severe infection and mortality. Further studies are needed to confirm our findings and explore the potential of role of the virulence. [ABSTRACT FROM AUTHOR]

Azithromycin is one of the drugs used in the combined therapy for syndromic treatment of gonorrhoea in many countries, including Brazil. Our research group, which receives isolates from clinical laboratories since 2006, has detected, after 2016, a tendency of rising rates of azithromycin resistance, with isolates showing higher minimal inhibitory concentrations (MICs) than those previously reported in this country. In this study, we report the susceptibility to azithromycin of 93 N. gonorrhoeae isolates obtained between 2014 and 2017. Strains with MIC ≥2 μg/mL were characterized according to azithromycin resistance mechanisms and strain typing. Results indicate that azithromycin resistance has emerged in all these years in unrelated MLST-STs, but after 2016 a clonal complex connected with ST1901 has been more frequently detected, grouping isolates with MIC varying from 2 to 64 μg/mL, with DelA mutations at the mtrR promoter region associated or not with mutations at rrl alleles. High rates of azithromycin resistance may compromise the use of this drug in the combined therapy with ceftriaxone. Inclusion of Rio de Janeiro in the Brazilian gonococcal surveillance program is important to evaluate if this data indicates an epidemiological phenomenon in the country. [ABSTRACT FROM AUTHOR]

Introduction: Microbes such as Salmonella, Campylobacter and S. aureus have been implicated in Foodborne disease outbreaks (FBDOs) worldwide, yet information on their occurrence in Barbados is scanty. The purpose of this study was to determine the aetiological agents, food vehicles, locations and peak seasons of FBDOs in Barbados; assess the quality of epidemiological investigations; and identify deficiencies in food production practices and laboratory detection. Methodology: A search of FBDOs occurring in Barbados between 1998-2009 was conducted among published and unpublished literature sources and reports. The search terms included the keywords “foodborne disease,” “outbreaks” and “Barbados”. Results: During the period 1998 to 2009, there were 24 foodborne outbreaks, 215 cases of illness, one hospitalisation and no deaths. Overall, 37.5% of outbreaks were associated with hotels/resorts. Salmonella Enteritidis phage type 8 was most commonly implicated with eggs and poultry being the primary vehicles. Three outbreak reports were available for assessment and revealed that there were deficiencies in the outbreak investigations. These reports also recorded high levels of food contamination with indicator organisms, suggesting that improvements in food hygiene and production practices were required. Conclusions: The number of FBDOs is low in comparison to developed countries. However, the data was likely affected by under-reporting and inadequacies in the outbreak investigations and laboratory detection. Improvements in these areas would lead to not only better detection and characterisation of FBDOs in Barbados but improved food safety control measures. [ABSTRACT FROM AUTHOR]

Objectives: To determine the molecular characteristics of ESBL-producing Escherichia coli (ESBL-E) collected during a longitudinal study on an organic broiler farm in order to investigate clonal expansion and horizontal gene transfer.Methods: Isolates were obtained from a longitudinal study performed previously on an organic broiler fattening farm. Samples from individually followed-up broilers, the broiler house, the transport van and persons that took the samples, taken at several timepoints (days 1, 3, 4, 7, 10, 42 and 70) within a production round and during the consecutive one (days 1, 2, 3 and 70), had been investigated for the occurrence of ESBL-E. In the current study, ESBL genes and MLST STs of these ESBL-E were determined. Plasmids were characterized and subtyped.Results: On arrival in round_1, ESBL-E of ST88 predominated, while on days 3, 4, 7 and 10 ST10 was most often found and at slaughter age ST155 and ST1551 prevailed. A shift in STs was also observed in round_2. None of the 35 individually selected broilers followed up in round_1 was positive for the same ESBL-E ST at all sampling times. All isolates carried CTX-M-1 group genes, confirmed as blaCTX-M-1 in 158 isolates. Further analysis of 36 isolates of different STs showed blaCTX-M-1 on IncI1/ST3 plasmids.Conclusions: The rapid dissemination of ESBL-E on this broiler farm was not due to the spread of one specific E. coli clone, but most likely the result of horizontal transfer of an IncI1/ST3 plasmid carrying blaCTX-M-1 resulting in a shift in the predominant ESBL-E population in broilers. [ABSTRACT FROM AUTHOR]

The aim of this study was to characterize virulence factors and antibiotic resistance patterns in E. faecalis strains obtained from community-acquired urinary tract infections. A total of 70 E. faecalis isolates from Labbafinejad Hospital in Tehran were collected. Antibiotic resistance and virulence determinants were examined by phenotypic and molecular methods. Among 70 E. faecalis isolates, efba (97.1%), ace (95.7%), and gelE (94.3%) were the most prevalent virulence genes. The most common antibiotic resistance pattern was tetracycline (88.6%) and minocycline (87.1%). Multi-drug resistant phenotype was detected among 10% of them. Our results showed capability of E. faecalis strains for infection of the urinary tract in community. Involvement of virulence determinants in the pathogenesis of community acquired E. faecalis strains was proposed due to their high prevalence rates. Food producing animals were proposed as their environmental reservoirs, due to dominance of tetracycline resistance phenotype among them. [ABSTRACT FROM AUTHOR]

Background Bacteremia caused by extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae (ESBL-E) is associated with inadequate empirical therapy and substantial mortality in neutropenic patients. Strategies are needed to identify neutropenic patients at high risk of these infections. Methods From April 2014 to September 2016, we collected perianal swabs, both at admission and weekly thereafter, from patients undergoing hematopoietic stem cell transplantation (HSCT). Patients received prophylactic levofloxacin while neutropenic. Swabs were plated onto selective agar, colonies were identified and underwent antimicrobial susceptibility testing, and phenotypic ESBL testing and polymerase chain reaction for β-lactamase genes were performed on ceftriaxone-resistant Enterobacteriaceae. We then determined the prevalence of pre-transplant ESBL-E colonization and risk of ESBL-E bacteremia. Colonizing and bloodstream isolates from patients with ESBL-E bacteremia underwent multilocus sequence typing and pulsed-field gel electrophoresis. Results We analyzed 312 patients, including 212 allogeneic and 100 autologous HSCT recipients. Ten percent (31/312) of patients had pre-transplant ESBL-E colonization. Susceptibility rates of colonizing ESBL-E were: levofloxacin, 25%; cefepime, 9%; piperacillin-tazobactam, 84%; and meropenem, 97%. Of 31 patients colonized with ESBL-E pre-transplant, 10 (32%) developed ESBL-E bacteremia during their transplant admission, compared to 1 (0.4%) of 281 patients not colonized with ESBL-E (P <.001). All bloodstream ESBL-E were levofloxacin-resistant and colonizing and bloodstream isolates from individual patients had identical genotypic profiles. Conclusions HSCT recipients who are colonized with levofloxacin-resistant ESBL-E pre-transplant and receive levofloxacin prophylaxis have high rates of bacteremia from their colonizing strain during neutropenia. Assessing for ESBL-E colonization in neutropenic patients could lead to optimization of empirical antibacterial therapy. [ABSTRACT FROM AUTHOR]

Objective: Type 1 diabetes is associated with compositional differences in gut microbiota. To date, no microbiome studies have been performed in maturity-onset diabetes of the young 2 (MODY2), a monogenic cause of diabetes. Gut microbiota of type 1 diabetes, MODY2, and healthy control subjects was compared.Research Design and Methods: This was a case-control study in 15 children with type 1 diabetes, 15 children with MODY2, and 13 healthy children. Metabolic control and potential factors modifying gut microbiota were controlled. Microbiome composition was determined by 16S rRNA pyrosequencing.Results: Compared with healthy control subjects, type 1 diabetes was associated with a significantly lower microbiota diversity, a significantly higher relative abundance of Bacteroides, Ruminococcus, Veillonella, Blautia, and Streptococcus genera, and a lower relative abundance of Bifidobacterium, Roseburia, Faecalibacterium, and Lachnospira. Children with MODY2 showed a significantly higher Prevotella abundance and a lower Ruminococcus and Bacteroides abundance. Proinflammatory cytokines and lipopolysaccharides were increased in type 1 diabetes, and gut permeability (determined by zonulin levels) was significantly increased in type 1 diabetes and MODY2. The PICRUSt analysis found an increment of genes related to lipid and amino acid metabolism, ABC transport, lipopolysaccharide biosynthesis, arachidonic acid metabolism, antigen processing and presentation, and chemokine signaling pathways in type 1 diabetes.Conclusions: Gut microbiota in type 1 diabetes differs at taxonomic and functional levels not only in comparison with healthy subjects but fundamentally with regard to a model of nonautoimmune diabetes. Future longitudinal studies should be aimed at evaluating if the modulation of gut microbiota in patients with a high risk of type 1 diabetes could modify the natural history of this autoimmune disease. [ABSTRACT FROM AUTHOR]

Background No study has used whole-genome sequencing (WGS) to investigate risk factors for Clostridium difficile (CD) transmission between cases, or assessed the impact of recent acquisition on patient outcome. Methods This 20 month retrospective cohort study included consecutive cytotoxin-positive diarrheal samples, which underwent culture, ribotyping, and WGS (Illumina). Sequenced isolates were compared using single nucleotide variants (SNVs). Independent predictors of acquisition from another case, onward transmission, 120-day recurrence, and 30-day mortality were identified using logistic regression with backwards elimination. Results Of 660 CD cases, 640 (97%) were sequenced, of which 567 (89%) shared a ribotype with a prior case, but only 227 (35%) were ≤2 SNVs from a prior case, supporting recent acquisition. Plausible (<2 SNVs) recent ward-based acquisition from a symptomatic case was more frequent in certain ribotypes; 64% (67/105) for ribotype-027 cases, compared with 11% (6/57) for ribotype-078. Independent risk factors (adjusted P <.05) for CD acquisition included older age, longer inpatient duration, and ribotype; these factors, and male sex, increased onward transmission. Patients with a plausible donor had a greater risk of recurrence (adjusted P =.001) and trended towards greater 30-day mortality (adjusted P =.06). Ribotype had no additional mortality or recurrence impact after adjusting for acquisition (P >.1). Conclusions Greater transmission of certain lineages suggests CD may have different reservoirs and modes of transmission. Acquiring CD from a recent case is associated with poorer clinical outcomes. Clinical characteristics associated with increased healthcare-associated CD transmission could be used to target preventative interventions. [ABSTRACT FROM AUTHOR]

The bacterium Burkholderia thailandensis, a member of the Burkholderia pseudomallei complex, is generally considered nonpathogenic; however, on rare occasions, B. thailandensis infections have been reported. We describe a clinical isolate of B. thailandensis, BtAR2017, recovered from a patient with an infected wound in Arkansas, USA, in 2017. [ABSTRACT FROM AUTHOR]

To clarify year-to-year changes in capsular serotypes, resistance genotypes, and multilocus sequence types of Streptococcus pneumoniae, we compared isolates collected from patients with invasive pneumococcal disease before and after introductions of 7- and 13-valent pneumococcal conjugate vaccines (PCV7 and PVC13, respectively). From April 2010 through March 2017, we collected 2,856 isolates from children and adults throughout Japan. Proportions of PCV13 serotypes among children decreased from 89.0% in fiscal year 2010 to 12.1% in fiscal year 2016 and among adults from 74.1% to 36.2%. Although nonvaccine serotypes increased after introduction of PCV13, genotypic penicillin resistance decreased from 54.3% in 2010 to 11.2% in 2016 among children and from 32.4% to 15.5% among adults. However, genotypic penicillin resistance emerged in 9 nonvaccine serotypes, but not 15A and 35B. Multilocus sequence typing suggested that resistant strains among nonvaccine serotypes may have evolved from clonal complexes 156 and 81. A more broadly effective vaccine is needed. [ABSTRACT FROM AUTHOR]

Objectives: To analyse VIM/IMP-type MBL-producing Enterobacteriaceae isolates identified in Poland during 2006-12.Methods: Isolates were typed by PFGE, followed by MLST. blaVIM/IMP genes were amplified and sequenced within class 1 integrons. Their plasmidic versus chromosomal location was assessed by nuclease S1 and I-CeuI plus hybridization experiments. Plasmids were characterized by transfer assays and PCR-based replicon typing.Results: One hundred and nineteen VIM/IMP-positive Enterobacteriaceae cases were reported in Poland from the first case in 2006 until 2012. The patients were in 54 hospitals and were infected or colonized by 121 organisms, including Enterobacter cloacae complex (n = 64), Klebsiella oxytoca (n = 23), Serratia marcescens (n = 20) and Klebsiella pneumoniae (n = 11). The isolates represented numerous pulsotypes and mainly original STs, and carried eight integrons with blaVIM-1-like genes (blaVIM-1/-4/-28/-37/-40; n = 101), three with blaVIM-2 variants (blaVIM-2/-20; n = 17) and one with blaIMP-19 (n = 3). Six integrons were new, and five and two formed prevalent families of In238-like (n = 96) and In1008-like (n = 16) elements, respectively. In238 (aacA4-blaVIM-4rpt) and In1008 (blaVIM-2-aacA4) had been originally observed in Polish Pseudomonas aeruginosa, suggestive of their transfer to enterobacteria, followed by spread and diversification. Four organisms have disseminated inter-regionally, i.e. Enterobacter hormaechei ST90 with plasmidic In238/In238a integrons (n = 36), K. oxytoca ST145 with a chromosomal In237-like element (n = 18) and two subclones of E. hormaechei ST89 with In1008- or In238-type variants (n = 8 and n = 7, respectively).Conclusions: The epidemiology of VIM/IMP-producing Enterobacteriaceae in Poland has revealed a remarkable number of specific or novel characteristics of the organisms, with some possible links to other mid-southern European countries. [ABSTRACT FROM AUTHOR]