Search

The aim of the study was to identify the isolation rate of thermotolerant campylobacters in a small-scale broiler-meat production farm over a one-year period. The second deliverable of the study was to determine the potential virulence markers. The laboratory investigation was performed on 283 samples (cloacal swabs, caeca, carcass swabs) collected on three sampling points (farm, slaughter line, and cold storage). The isolates obtained with the conventional microbiological method were confirmed with multiplex PCR for identification of campylobacters. The presence of 10 virulence genes was analyzed in the C. jejuni isolates (flaA, racR, virB11, dnaJ, wlaN, cadF, ciaB, cdtA, cdtB, cdtC). Out of 283 samples, 169 (59.7%) were confirmed as Campylobacter spp., 111 (39.2%) C. jejuni, and 43 (15.2%) C. coli. C. jejuni was the most prevalent in all sampling points. Campylobacter spp. showed a characteristically seasonal prevalence with the highest isolation rate during the warmer period of the year. We detected the cadF and ciaB genes in all C. jejuni isolates. The flaA gene was present in 50% of the examined strains. The cdt genes (cdtA, cdtB, and cdtC) were confirmed in 52.8%, 52.8%, and 47.2% of the C. jejuni strains, respectively. C. jejuni showed 15 profiles of virulence patterns with four predominant profiles.

Background and Objective: Dermatophyte infections require laboratory diagnosis before treatment is started. Although direct microscopy is routinely performed but culture of dermatophytes is the gold standard. However, it takes about 4 weeks for species identification on primary media. Our aim was to compare dermatophyte test medium (DTM) as a screening medium for the isolation of dermatophytes in comparison with sabouraud dextrose agar (SDA). Methods: It was a comparative study carried out at the Department of Microbiology of Post Graduate Medical Institute, Lahore over a period of nine months. Samples were collected from one hundred patients with clinically suspected dermatophytoses after taking informed written consent. The samples were examined microscopically and then inoculated on two types of culture media, one Sabouraud dextrose agar (SDA) with added chloramphenicol, gentacin and cycloheximide and other dermatophyte test medium (DTM) with added chlortetracycline, gentacin and cyclohexamide. Results: Fungal growth was observed in fifty-six samples on culture. Out of the fifty-six positive on cultures, nineteen were that of dermatophytes. Out of n = 100 patients, ten were positive on SDA while n = 14 dermatophyte species were able to grow on DTM. A significantly higher positivity (P ³ 0.05) for isolating dermatophytes was observed by DTM as compared to SDA. DTM was able to isolate (71%) of the dermatophytes in first 10 days. Isolation rate of dermatophyte species was higher (73.68%) on DTM as compared to SDA which was 52.6%. Conclusion: Authors recommend the use of dermatophyte test medium for the primary isolation and identification of dermatophyte species to be more effective and time saving. How to Cite This: Ahmad MR, Javed I, Mushtaq S, Hafeez R, Cheema KH. Evaluation of dermatophyte test medium and sabouraud dextrose agar for isolation of dermatophyte species. Biomedica. 2020; 36 (4): 362-6.Doi: https://doi.org/10.51441/BioMedica/5-80.

Background: Staphylococcus aureus (S. aureus) causes a difficult problem in the poultry industry because it causes diseases that are difficult to treat due to the resistance of these bacteria to antibiotics and their possession of a battery of virulence and resistance genes in addition to their ability to produce thick biofilms. Method: A cross-sectional study conducted to collect a total of 53 samples from different clinical cases in broilers during the period from August 2019 to February 2020 in Al-Najaf and Karbala cities, The clinical isolates were determined by using the conventional standard biochemical tests. All the specimens cultured on blood agar medium supplemented with 5% blood for primary isolation and selected by using selective media mannitol salt agar (MSA) for confirmation the mannitol fermentation, then subjected to gram’s staining, catalase, oxidase, and further slide coagulase test, then all S. aureus isolates tested by antibiotic susceptibility test, and screened for the presence of mecA and mecC genes using PCR for the detection of MRSA isolates, then subjected to the detection of virulence genes (pvl and eta), antibiotic resistance gene (cfr), identification of integron class 1, biofilm formation assay, the multi-druge resistance profiles (MDR) and multible antibiotics resistance (MAR) indexes were calculated. Results: the isolation rate of S. aureus from the broilers' clinical samples was 37.7%. The antibiotic susceptibility test revealed that 85% of S. aureus isolates were resistant to one or more of the antibiotic tested. All 53 isolates were assessed for the presence of mecA and mecC genes by using PCR. The mecA gene-specific PCR product was seen in 7 (35%) isolates and considered as MRSA. Among all S. aureus isolates, two isolates were positive for the eta gene, and 15 (75%) isolates harboring integron class 1, while the biofilm formation test revealed that 7 (35%) was positive biofilm producers and three of them were strong producers, consequentlly, 13 (65%) of the isolates were resisted to three or more antibiotics and considered as MDR strains. While pvl, cfr, and mecC gene were not detected among S. aureus isolates. Conclusion: the current study revealed that S. aureus possess a real threat in the poultry industry reflecting a public health problem due to the large acquisition of antibiotic resistance genes by these bacteria, the results indicated a high percentage of isolates having MDR characteristic, and two of them were resistant to all antibiotics tested. In addition to the presence of two MRSA isolates carrying the eta gene, this indicating that they are of human origin.

Highlights • A new a deterministic and stochastic epidemic model with varying total population size is proposed. • The thresholds of the deterministic and stochastic epidemic model are established respectively. • Our methods can improve some existing results. • We carry out numerical and find a critical isolation rate 0.0217. • The empirical probability density are presented., In this paper, a stochastic and a deterministic SIS epidemic model with isolation and varying total population size are proposed. For the deterministic model, we establish the threshold R0. When R0 is less than 1, the disease-free equilibrium is globally stable, which means the disease will die out. While R0 is greater than 1, the endemic equilibrium is globally stable, which implies that the disease will spread. Moreover, there is a critical isolation rate δ*, when the isolation rate is greater than it, the disease will be eliminated. For the stochastic model, we also present its threshold R0s. When R0s is less than 1, the disease will disappear with probability one. While R0s is greater than 1, the disease will persist. We find that stochastic perturbation of the transmission rate (or the valid contact coefficient) can help to reduce the spread of the disease. That is, compared with stochastic model, the deterministic epidemic model overestimates the spread capacity of disease. We further find that there exists a critical the stochastic perturbation intensity of the transmission rate σ*, when the stochastic perturbation intensity of the transmission rate is bigger than it, the disease will disappear. At last, we apply our theories to a realistic disease, pneumococcus amongst homosexuals, carry out numerical simulations and obtain the empirical probability density under different parameter values. The critical isolation rate δ* is presented. When the isolation rate δ is greater than δ*, the pneumococcus amongst will be eliminated.

Ninety random samples of fresh beef were collected from the cattle carcasses slaughtered at 3 different abattoirs in Menoufia governorate namely A, B and C (30 of each), represented by neck region (chuck) during summer and winter seasons in 2018 (45 samples of each season). The obtained results of serotyping of E. coli revealed that EHEC O26: H11 were the more prevalent than other serogroups 6.67%, 6.67% &13.33% and 6.67%, 13.33% & 6.67% .T The results of the total incidence were 46.67% , 40% & 26.67% and 26.67%, 26.67% & 20 for A, B&C abattoirs during the summer and the winter seasons , respectively. Serotyping of salmonella revealed S.Typhimurium was more prevalent during the summer 13.33%for each abattoir, the total isolation rate 33.33%, 26.67% & 20% for A, B and C abattoirs, respectively. The more prevalent serogoup during the winter was S. Enteritidis 13.33%, 6.67% and 6.67%,while the total isolation rate was 26.67% , 20% and 6.67% for A, B &C abattoirs, respectively .The contamination rate increased in abattoir A than B than C and the prevalence was increased during summer than in winter

Background: Extended spectrum β-lactamases have addressed the serious challenges worldwide as a threat to favorable outcomes of treatment of common infections in community and hospital settings since it is found to be increasing trends of multidrug resistance. The present study was aimed to determine the antibiotic profile of multidrug resistant E.coli and status of ESBLs producing E.coli. Methods: This was a cross-sectional study conducted over a period of 2 years (September 2017 to April 2019) at microbiology laboratory of Nepal Mediciti Hospital. A total of 16542 samples were processed. Various clinical samples were collected from both inpatients and outpatients aseptically and without contaminating skin commensals. Standard microbiological techniques were used for isolation and identification of pathogens. Extended spectrum beta-lactamases were phenotypically confirmed by combined disc method. Results: Out of 1449 E.coli isolates, 323(22.29%) were found to be MDR E.coli. Isolation rate of ESBL producing E.coli (66.56%) were found to be high among MDR E.coli isolates. Conclusion: There is increasing prevalence of ESBL producing E.coli. It is essential to monitor antibiotic susceptibility pattern and formulate antibiotic policy to prevent the spread of MDR and ESBL producers. Keywords: E.coli, Extended spectrum β-lactamase, Multidrug resistant

Aim: To determine the appropriateness of blood volume in automated blood culture bottles of the BACT/ALERT 3D system, its effect on isolation rate and time to positivity of pathogens. Materials and Methods: The study was carried out in a tertiary care hospital in South India from 1st March 2018 to 31st August 2018. Automated blood culture bottles sent to Microbiology laboratory for blood culture were included in the study. The bottles were weighted by electronic weighing balance. The filled blood culture bottles received at microbiology laboratory were re-weighed and was categorized into appropriately filled and inappropriately filled bottles. Frequency of appropriately filled bottles and inappropriately filled bottles was expressed in percentage. Result: A total of 8740 blood culture bottles were included in the study, out of which the blood volume was found to be suboptimum in 3978 bottles (45.5%), optimum in 3498 bottles (40%) and overfilled in 1264 bottles (14.5%). There was an increase in the number of blood culture bottles with optimum blood volume from 35.1% in March to 58.12% in August. The average TTP for true pathogens was found to be 16.72 hrs. with optimum blood volume, 17 hrs. with overfilled blood volume and 21.5 hrs. with sub-optimum blood volume. The isolation rate for true pathogens was found to be 88.62% with optimum blood volume, 86.43% with overfilled blood volume and 70.01% with sub-optimum. The false positive rate was found to be 4.1% with overfilled blood volume, 1.6%with sub-optimum and 1.4%with optimum blood volume. Conclusion: Through this study, the correlation between the blood volume with the isolation rate, time to positivity and false positivity of blood culture isolates was established. Keywords: Blood culture, Blood volume, BACT/ALERT 3D, Time to positivity, Isolation rate.

espanolIntroduccion: La sepsis neonatal causa una alta morbimortalidad en esta poblacion; en America del Sur su incidencia esta entre 3,5 a 8,9 por cada 1000 nacidos vivos. Esto podria obedecer a que pesar de que el “gold estandar” para la confirmacion diagnostica es el hemocultivo, carece de sensibilidad por su baja tasa de aislamiento. Por lo anterior, se hace indispensable identificar de manera acertada factores de riesgo asociados a su presentacion para con ello aumentar la probabilidad de realizar un diagnostico y manejo oportuno.Objetivo: Identificar los factores asociados al desarrollo de sepsis bacteriana en los recien nacidos que ingresaron al Hospital Infantil Napoleon Franco Pareja en Cartagena. Metodos: estudio de corte transversal con las historias clinicas de recien nacidos hospitalizados con sospecha de sepsis neonatal temprana o tardia. Se midieron variables sociodemograficas del recien nacido, de la madre, la presentacion clinica y el tratamiento. Se estimaron odds ratios crudos y ajustados mediante regresion logistica de las variables clinicas identificadas como causales de sepsis neonatal.Resultados: la sepsis estuvo presente en 19,1 % de los 230 recien nacidos con sospecha, de estos en el 63,6 % se identifico como etiologia a Sthapylococcus coagulasa-negativo spp. Se encontraron como factores de riesgo para sepsis neonatal el ser madre adolescente (OR = 3,21) y elevacion de la PCR (OR = 2,41).Conclusiones: La sepsis neonatal y su diagnostico continuan siendo un desafio clinico importante en paises en via de desarrollo. El presente estudio sugiere que los hijos de madre adolescente y la elevacion de la PCR se relacionan con un diagnostico positivo como metodos previos a los hemocultivos que continuan como estandar de oro a pesar de su bajo rendimiento. EnglishIntroduction: Neonatal sepsis (SN) causes high morbidity and mortality in this population; in South America its incidence is between 3.5 to 8.9 per 1,000 live births. This might be due to the fact that, although the “gold standard” for diagnostic confirmation is blood culture, it lacks sensitivity because of its low isolation rate. Therefore, it is essential to correctly identify risk factors associated with its presentation in order to increase the probability of making a diagnosis and timely treatment.Objective: To identify the factors associated with the development of bacterial sepsis in newborns admitted to the Napoleon Franco Pareja Children's Hospital in the city of Cartagena.Methods: Cross-sectional study of the medical records of hospitalized newborns with suspected early or late SN. Sociodemographic variables of newborn, mother, clinical presentation and treatment were measured. Raw and adjusted OR were estimated by logistic regression of clinical variables as causal of SN.Results: Sepsis was present in 19.1 % of the 230 suspected newborns, of these, 63.6 % were identified as Sthapylococcus coagulase negative spp. The adjusted association analysis showed as risk factors for SN, being a teenage mother with OR = 3.21 (95 % CI: 1.13 - 9.18) and high CRP with OR = 2.41 (95 % CI 1.17- 4.99).Conclusion: Neonatal sepsis and its diagnosis continue to be a major clinical challenge in developing countries. The present study suggests that the children of an adolescent mother and the elevated CRP are related to a positive diagnosis as methods prior to blood cultures, which continue to be the gold standard despite their low performance.

Objective: The burden of pulmonary fungal infection is increasing and often misdiagnosed as pulmonary tuberculosis in developing countries where the prevalence of pulmonary tuberculosis is high. |Therefore, the purpose of this study is to determine the spectrum of potential pulmonary fungal pathogens and the prevalence of the association between pulmonary tuberculosis and potential fungal pathogens. Materials and methods: A cross-sectional study was conducted between October 2018 and May 2019. Sputum was collected from 636 study participants. Part of the sputum was inoculated onto Brain Heart Infusion agar, and fungi were identified following standard microbiological procedures. The remaining part of the sample was used for the investigation of pulmonary tuberculosis. Results: Among 636 sputum samples, 75.9% (483) and 25.6% (163) were positive for potential fungal pathogens and pulmonary tuberculosis, respectively. The prevalence of the association between pulmonary tuberculosis and potential fungal pathogens was 20.0%. Of fungal isolates, 81.4% were yeasts. The remaining 128 (18.6%) isolates were molds. The isolation rate of fungi was higher in males (51.6%) than in females (48.4%). There was no statistically significant association between the prevalence of potential pulmonary fungal pathogens and sex ( p = 0.239). Patients in the age group of 35 to 44 and above were slightly more affected than younger age groups. The association between potential fungal pathogens and age was not statistically significant ( p = 0.50). Conclusion: High prevalence of potential pulmonary fungal pathogens and the association of tuberculosis and potential fungal pathogens recorded in this study will enforce health personnel to pay due attention to these conditions and arise the interest of researchers to conduct further work on the burden of the association between tuberculosis and potential fungal pathogens. Our study also revealed the need to employ conventional microbiology tests along with clinical and radiological evidence since clinical manifestations and radiological pictures of tuberculosis mimic that of pulmonary fungal infection.

Background: Meropenem resistance of Pseudomonas aeruginosa (P. aeruginosa) is considered an increasing problem. Efflux pump is one of multiple mechanisms that are responsible for this resistance. This study aimed to phenotypically and genotypically detect prevalence of efflux pump mediated meropenem resistance among P. aeruginosa isolates. Methods: Pseudomonas aeruginosa was isolated from different clinical specimens and identified by conventional methods and confirmed by Vietek MS Malditof Mass Spectroscopy. Antibiotic susceptibility test was done by disc diffusion method then minimum inhibitory concentrations (MIC) for meropenem was detected twice by agar dilution method without and after addition of carbonyl cyanide m-chlorophenylhydrazone (CCCP). Efflux pump genes were detected by polymerase chain reaction ( PCR). Results: Out of 265 specimens, 78 P. aeruginosa were isolated with an isolation rate (29.4%). By disc diffusion method and MIC by agar dilution methods, 35 (44.8%) isolates were meropenem resistant. There was a significant difference regarding distribution of efflux pump genes in meropenem resistant isolates as 23 isolates (65.7%) were positive for efflux pump genes and 12 (34.3%) were negative (p value= 0.13). The MICs of meropenem for P. aeruginosa isolates were significantly decreased after addition of CCCP where MIC of 21 (60%) meropenem resistant isolates had an efflux pump-overexpressing phenotype (p value =0.001). Conclusion: High prevalence of meropenem resistance in P. aeruginosa is mediated by efflux pump genes including, mex A, mex B and opr M.

We present an epidemiological model, which extend the classical SEIR model by accounting for the presence of asymptomatic individuals and the effect of isolation of infected individuals based on testing. Moreover, we introduce two types of home quarantine, namely gradual and abrupt one. We compute the equilibria of the new model and derive its reproduction number. Using numerical simulations we analyze the effect of quarantine and testing on the epidemic dynamic. Given a constraint that limits the maximal number of simultaneous active cases, we demonstrate that the isolation rate, which enforces this constraint, decreases with the increasing testing rate. Our simulations show that massive testing allows to control the infection spread using a much lower isolation rate than in the case of indiscriminate quarantining. Finally, based on the effective reproduction number we suggest a strategy to manage the epidemic. It consists in introducing abrupt quarantine as well as relaxing the quarantine in such a way that the epidemic remains under control and further waves do not occur. We analyze the sensitivity of the model dynamic to the quarantine size, timing and strength of the restrictions.

Background and Objectives: Nontuberculous mycobacteria (NTM) infections are increasing worldwide. We evaluated the annual trends of NTM isolation on acid-fast bacillus (AFB) culture, compared to that of Mycobacterium tuberculosis, and the distribution of NTM species nationwide in South Korea. Materials and Methods: The study was conducted in a diagnostic center that is a major referral laboratory for the diagnosis of tuberculosis and NTM in South Korea. All laboratory results of AFB culture from January 2014 to December 2019 were collected. All NTM identified were definitively identified to the species level. Results: A total of 345,871 tests were performed for the diagnosis of mycobacteria. The isolation rate of NTM and M. tuberculosis was 3.7% (12,969 cases) and 4.4% (15,081 cases), respectively. The annual isolation rate of NTM increased gradually from 2.7% in 2014 to 4.8% in 2019, whereas that of M. tuberculosis decreased from 6.2% to 3.3%. There were 4988 cases of NTM identified to the species level. M. avium complex (MAC) was the most common species isolated from pulmonary sites (59.8%), followed by M. gordonae (9.2%), M. abscessus (7.0%), and M. fortuitum (5.5%). Extrapulmonary NTM were identified in 29 cases (0.6%). MAC was also the most common NTM species isolated from extrapulmonary sites (65.5%), followed by M. kansasii (10.3%), M. abscessus (6.9%), and M. fortuitum (6.9%). Conclusions: The annual isolation rate of NTM has increased gradually, whereas that of M. tuberculosis has decreased. Follow-up studies of the increases in NTM identification and NTM infections in South Korea are needed.

Background: Infections of the sterile body sites, when occurs typically have greater clinical urgency and these infections could be life threatening. For the appropriate management of patient, early detection and identification of organism is crucial. Hence, the present study was designed to evaluate the prevalence, organism profile and antimicrobial susceptibility pattern of isolates obtained from infection of body fluids.Methods: Laboratory and clinical records of all the sterile body fluid except blood and cerebrospinal fluid submitted to the Department of Microbiology, B. P. Koirala Institute of Health Sciences during the period of 5 years (January 2012 to December 2016) were analyzed.Results: Among 1835 samples, 196 fluids samples showed growth of organisms with an isolation rate of 10.68%. Escherichia coli (E. coli) was the most common organism followed by Staphylococcus aureus (S. aureus) and Acinetobacter calcoaceticus-baumannii complex. Antimicrobial susceptibility testing showed variable degree of resistance. Thirty percentage of organisms were multi-drug resistant, 10% were extensively-drug resistant, none was pan-drug resistant, 35% of E. coli and K. pneumoniae were extended spectrum ?-lactamase producer and 30% of S. aureus were methicillin-resistant S. aureus. The study showed increasing trends of multi-drug resistant, extensively-drug resistant, methicillin-resistant S. aureus and extended spectrum ?-lactamase over the years. Conclusions: The study showed infection rate of 10% among normally sterile body fluids. E.coli, S. aureus and Acinetobacter calcoaceticus-baumannii complex are the common organisms. The infections are associated with multi drug resistant organisms. Routine surveillance of multi-drug resistant in infection of body fluids is necessary to guide treatment. Keywords: Extensively-drug resistant; methicillin-resistant S. aureus; multi-drug resistant; sterile body fluid.

Introduction: Campylobacter-mediated diarrhoea is one of the major causes of gastroenteritis globally. A majority of the Campylobacter spp. that cause disease in humans have been isolated from animals. Faecal contamination of food and water is the identified frequent cause of human campylobacteriosis. Methodology: In the present study, faecal samples from patients with symptoms of acute diarrhoea (n = 310) and domestic animals including cows (n = 60), sheep (n = 45) and goats (n = 45) were collected from the same localities in the peri-urban Bhubaneswar city. Genomic DNA isolation followed by polymerase chain reaction and sequencing was employed to analyse Campylobacter spp.-positive samples. Results: Of the 460 faecal samples, 16.77% of human samples and 25.33% of animal samples were found to be positive for Campylobacter spp. Among animals, the isolation rate was highest in sheep followed by cows and goats with 9.33%, 8.66% and 7.33%, respectively. The highest number of Campylobacter-positive cases was diagnosed in infants of 2–5 years age. Concurrent infection of other pathogens in addition to Campylobacter spp. was frequently detected in the samples. Conclusion: The present study showed the incidence of Campylobacter infections in human and different animal species in and around Bhubaneswar, Odisha. The analysis suggested that domestic animals can be the potential sources for human campylobacteriosis in the region.

The endophytic fungi in different tissues of Artemisia annua was isolated and purified to explore their ecological distribution and tissue preference, and the extracellular enzyme activities of dominant endophytic fungi were determined to characterize the metabolic function of endophytic fungi. The results showed that a total of 67 endophytic fungi were obtained from Artemisia annua tissues. The number and species of endophytic fungi in different tissues were significantly different. The number, colonization rate (CR) and isolation rate (IR) of endophytic fungi in root were significantly higher than those of stem and leaf. The dominant endophytic fungi, diversity and similarity coefficient of endophytic fungi also showed significant difference among tissues. The extracellular enzyme activities of endophytic fungi in different tissues are significantly different. The enzyme activities of endophytic fungi isolated from root are significantly higher than those isolated from stem and leaf. The research results showed that the endophytic fungi in Artemisia annua had significant tissue preference, and the metabolic function of endophytic fungi showed significant difference among tissues. This will lay a foundation for further research, development and utilization of endophytic fungi, and also provide a theoretical basis for screening functional endophytic fungi in Artemisia annua.

본 연구에서는 일개 대학병원에서 2년간 분리된 혈액배양 양성배지에서 MALDI-TOF MS system을 이용하여 Gram-positive bacilli를 동정한 결과를 균종별, 분기별로 분석하였다. Corynebacterium striatum은 총 89균주 중 66균주 (74.2%), Bacillus cereus는 60균주 중 44 균주 (73.3%), Listeria monocytogenes는 25균주 중 25균주 (100%)로 2.0 이상의 높은 스코어에서 동정되었다. 미 동정 된 균주는 303균주 중 293균주는 혈액배양에서 1회 분리 균주로 감염균으로서의 의의가 없는 오염 균주로 간주되었다. 감염균으로서 의의가 있는 동일 환자 2회 이상 분리 균주 대상 16S-rRNA sequencing 비교결과 총 50균주 중 43균주가 일치해 86.0% 동정이 가능하였다. 일치하지 않은 7균주 중 5균주는 MALDI-TOF MS로도 동정이 되지 않았다. 결론적으로 혈액배양에서 Gram-positive bacilli가 동정되는 경우, 일차적으로 MALDI-TOF MS를 이용하여 동정해보고 이를 활용한다면 어렵고 비용이 많이 들던 Gram-positive bacilli 동정이 저비용으로 더욱 간편하고 정확해지며, Gram-positive bacilli에 의한 감염 진단에도 도움이 될 것으로 판단된다.

Background: Burn injuries are common and major health problem throughout the world. The burn wound represents as a favorable area for opportunistic colonization of microorganisms with exogenous and endogenous origin. In burns patients infections arise from multiple sources. Burn wounds become initially colonized and infected with Gram positive bacteria, mainly Staphylococci, that are superseded during the second week by Gram Negative bacteria. Objectives: it is a microbial surveillance retrospective study; that aimed to evaluate the significance of Rule of nine in diagnosis of aerobic bacterial burn wound infection and carried out in between June 2007 to September 2011 in the Department of Pharmaceutics, University of Karachi. Study Design: Descriptive retrospective study. Materials: A total of 118 patient irrespective of age, sex, date and time of burn, date and time of hospital admission, interval between time of burn and hospital admission, degree and percentage (%) of burn and duration of hospital stay (when specimen collected) were registered for this study. All patients were divided into two groups (A and B). Results: Out of 58 patients of group A isolation rate per patient was 1.1 while in group B it becomes 3.0. According to TBSA the isolation rate in group B rises with rise in TBSA. Most prevalent organism in these patients was found S. aureus(23%) P.aeruginosa(21%). Conclusions: Burn patients are incubator for variety of aerobic bacteria and rate of isolation of these organisms increase with rise in TBSA. The wounds of these patient must required continuous microbial surveillance that may reduce the rate of mortality

We compared candidemia due to Candida auris and other non-C.auris cases in hospitalized COVID-19 patients over a period of 9 months at our institution. Candidemia cases in all admitted patients (with or without COVID-19) from April to December 2020 were identified. Electronic records were accessed to record clinical data of COVID-19 patients with candidemia. For statistical analysis, independent samples Mann-Whitney U test was used for continuous and Fisher's exact test was used for categorical variables. A total of 26 candidemia cases (four C.auris, 22 non-C.auris) in 2438 admitted COVID-19 (10.7 per 1000 admissions) and 59 candidemia cases (six C.auris, 53 non-C.auris) in admitted non-COVID patients (8.2 per 1000 admission) were identified. The proportion of C.auris candidemia in COVID-19 and non-COVID-19 patients was 15.4 and 10%, respectively. 4/26 of COVID-19 candidemia patients were aged ≤ 15 years (10 months--15 years). Comparison of C.auris and non-C. auris candidemia cases reveal significant difference in prior antifungal exposure, present in 100% C. auris candidemia versus 27% non-C. auris candidemia patients (P-value 0.014). Although not statistically significant, C. auris candidemia patients had a longer stay in hospital before candidemia (20 vs. 9 days), higher isolation rate of multidrug resistant bacteria (100 vs. 50%), increased rate of prior colonization of Candida species (50 vs. 14%) and lower mean beta-d-glucan levels (48.73 pg/ml vs. 138.146 pg/ml). Both C. auris and non-C. auris COVID-19 patients had similar mortality rate (67 vs. 65%). A significant number of critically ill COVID-19 patients developed candidemia in our study highlighting the need for prompt diagnosis and management. Lay summary 26 candidemia cases (4 Candida auris;22 non-C. auris) in COVID-19 patients (April-December 2020) are reported from Pakistan. Compared to non-C. auris, C. auris candidemia patients had higher prior antifungal exposure, longer hospital stay, higher rates of MDR bacteria and Candida colonization.

A molecular epidemiology study was conducted between 2016 and 2017 by a network of collaborators from 12 provinces in the Islamic Republic of Iran. A total of 1484 soil samples from different habitats were screened for the presence of dermatophytes by using the hair baiting technique. The primary identification of isolates was carried out by amplification and MvaI restriction fragment length polymorphism (RFLP) of the internal transcribed spacers regions of ribosomal DNA (ITS-rDNA). The identifications, especially in the cases of isolates with unknown RFLP patterns, were confirmed by sequencing of the ITS-rDNA region. As a result, 256 isolates were recovered. The isolation rate was higher in soils with pH range 7.1–8.0, collected from animal habitats (n = 78; 34%) and parks and gardens (n = 75; 32%), geographically from Mazandaran Province (n = 115; 49.5%) and seasonally in the spring (n = 129; 50.4%), all of which were statistically significant (p < 0.05). The dermatophytes comprising five species of the two genera, viz., Nannizzia fulva (n = 214), N. gypsea (n = 34), Arthroderma quadrifidum (n = 5), A. gertleri (n = 2) and A. tuberculatum (n = 1), were isolated. The geophilic dermatophytes occurred in various soils from different parts of Iran; however, surprisingly, N. fulva emerged as the dominant species, outnumbering the common geophilic species of N. gypsea. For the definitive identification of soil inhabitant dermatophytes, DNA-based identification is strongly recommended.

Candida glabrata is a yeast genus fungus that can be found in the normal flora of healthy individuals and can lead to various infections in humans. Candida species cause local infections as well as fatal systemic infections. Recent years have seen an increase in the isolation rate of non-Candida albicans species, especially Candida glabrata. The most important reason for this increase is the change in factor distribution with prophylactic and empirical use of fluconazole. There are articles in the world and in our country reporting that the second isolation frequency after C. albicans is Candida glabrata. Unlike other Candida species, C. glabrata are not dimorphic; C. glabrata are found both commensally and pathogenically as blastoconidia. C. glabrata infections are difficult to treat and are often resistant to many azole antifungal agents, especially fluconazole. As a result, C. glabrata infections are among infections with a high mortality rate.

Since 2008, veterinary authorities in Greece have implemented national control programmes (NSCPs) targeting S. Enteritidis (SE) and S. Typhimurium (ST) in poultry. We assessed the effect of the programs on the reported number of human isolates. Using monthly data for 2006&ndash, 2017, we defined two groups (SE, ST) and one control group with serotypes unrelated to poultry or eggs. For SE we also analysed data for 2006&ndash, 2015 due to a multi-county SE outbreak in 2016. We performed an interrupted time series analysis and used a negative binominal regression model. For both SE and ST, there was no significant trend of the isolation rate before or after NSCPs&rsquo, introduction. After the NSCPs&rsquo, introduction there was an increasing rate (IRR: 1.005, 95% CI: 1.001&ndash, 1.008) for control serotypes and a decreasing one for SE (IRR: 0.990, 95% CI: 0.986&ndash, 0.995) (for 2009 to 2015 analysis). From 2006 to 2017, NSCPs had a statistically significant impact on the number of SE isolates that decreased by 49% (IRR:0.511, 95% CI: 0.353&ndash, 0.739). No impact was shown on the number of ST (p-value = 0.741) and control isolates (p = 0.069). As a conclusion, NSCP&rsquo, s implementation was associated with decreased SE isolates and overall burden of salmonellosis, however further measures aiming at human salmonellosis due to ST, should be considered.

Background: The coronavirus disease 2019 (COVID-19) pandemic has brought about major changes in the medical field; the impact of the pandemic on antimicrobial resistance (AMR) is a major concern. Methods: We utilized comprehensive surveillance data, collected in a national AMR surveillance program, which included a total of 16·7 million samples of 5·9 million tested patients from >1,300 hospitals. We compared the number of patients and isolation rate of five types of pathogens , including antimicrobial susceptible and resistant bacteria of S. aureus, S. pneumoniae, E. coli, K. pneumoniae, and P. aeruginosa between 2019 and 2020. Findings: The number of patients and the isolation rate of S. aureus and methicillin-resistant S. aureus decreased slightly, those of S. pneumoniae and penicillin-resistant S. pneumoniae decreased by 60%, and third-generation cephalosporin-resistant K. pneumoniae increased compared to the previous year. Further, the isolation rate of the remaining pathogens apparently increased, although the number of patients decreased. The phenomenon was due to substantial decrease in the total number of tested patients (i.e., the denominator of the isolation rate), which was larger than that of the number of patients. Consistent results were obtained when the same data were re-aggregated according to the procedure defined by the World Health Organization Global Antimicrobial Resistance Surveillance System, demonstrating the general importance of this problem. Interpretation: Surveillance data during the COVID-19 pandemic must be carefully interpreted based on examination of both the numerator and denominator; the background factors that influence the denominator should be considered. Funding: This study was supported by the Research Program on Emerging and Re-emerging Infectious Diseases from the Japan Agency for Medical Research and Development (AMED) under grant number JP19fk0108061. Declaration of Interest: None to declare. Ethical Approval: This study was approved by the Ministry of Health, Labour and Welfare (approval number 0219–7) according to Article 32 of the Statistics Act.

Objectives A novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is responsible for the current coronavirus disease 2019 global pandemic. Only a few laboratories routinely isolate the virus, which is because the current co-culture strategy is highly time-consuming and requires a biosafety level 3 laboratory. This work aimed to develop a new high-throughput isolation strategy using novel technologies for rapid and automated isolation of SARS-CoV-2. Methods We used an automated microscope based on high-content screening (HCS), and we applied specific image analysis algorithms targeting cytopathic effects of SARS-CoV-2 on Vero E6 cells. A randomized panel of 104 samples, including 72 that tested positive by RT-PCR and 32 that tested negative, were processed with our HCS strategy and were compared with the classical isolation procedure. Results The isolation rate was 43% (31/72) with both strategies on RT-PCR-positive samples and was correlated with the initial RNA viral load in the samples, in which we obtained a positivity threshold of 27 Ct. Co-culture delays were shorter with the HCS strategy, where 80% (25/31) of the positive samples were recovered by the third day of co-culture, compared with only 26% (8/30) with the classic strategy. Moreover, only the HCS strategy allowed us to recover all the positive samples (31 with HCS versus 27 with classic strategy) after 1 week of co-culture. Conclusions This system allows the rapid and automated screening of clinical samples with minimal operator workload, which reduces the risk of contamination and paves the way for future applications in clinical microbiology, such as large-scale drug susceptibility testing.

Newly proposed SIQR model defines exponent λ of exponential function expressing daily number of isolated persons as linear equation of isolation rate q and social distancing ratio x. In order to dynamically analyze the process of COVID-19 epidemic in seven countries by means of regression analyses of λ, increasing rate of cumulative isolated persons(cases), IRCC, is proposed as practical index for the isolation rate q. IRCC is correlated with q in the form of q=C · IRCC, where C is a normalizing coefficient. At first, C is formulated in two modes, one is simple and the other complex, under the constraint conditions by definition 0≤x, q≤1, which give allowable narrow path of C between upper and lower boundaries. Then, the dynamic locus of q-x relation is analyzed for each of seven countries including Japan and the United States using formulated isolation rate q, and characteristic q-x behavior for each country is derived. At the same time, it is shown that specific path selection of C gives almost same linear loci of q-x relation derived by mathematical sequential method imitating a bipedal walk. In addition, increasing rates of cumulative PCR tests, IRCT, for six countries are discussed in relation with IRCC, and are shown that IRCT contributes to the promotion of the isolation rate via IRCC.

The Japanese Nosocomial Infections Surveillance (JANIS) is one of the largest national antimicrobial resistance (AMR) surveillance systems in the world. In particular, the JANIS Clinical Laboratory (CL) division collects comprehensive specimen-based data from diagnostic microbiology laboratories of participating hospitals to monitor the isolation rate of 11 major bacteria and specific AMR bacteria, and creating antibiograms of approximately 20 bacterial species. Data in the JANIS web-database system are also annually tabulated and provided to the WHO Global Antimicrobial Resistance Surveillance System (GLASS). To create a network of international AMR surveillance systems among Asian countries, Japan is developing an international web-database system named ASIan Antimicrobial Resistance Surveillance Network (ASIARS-Net) based on the JANIS system, but is open-source and available confidentially at almost no cost. JANIS further continues to evolve in multiple directions, some of which are selected and discussed in end of this review.

Objective: Study the isolation rate and antibiotic susceptibility of H. influenza detected from nasopharynx of under 5 years old children with Acute Lower Respiratory Tract Infection in Thanh Hoa Pediatric Hospital from 01/01/2018 to 4/30/2018. Summary: The subjects were 2970 specimens collected from the children under 5 years old who were diagnosed with acute lower respiratory tract infection. Culture, isolation and antibiotic susceptibility testing by disk diffusion (Kirby - Bauer) following the guidelines of the Ministry of Health. Selection of antibiotic disks and interpretations of sensitive, intermediate and resistant results according to the guidelines of the Institute of Clinical and Laboratory Standards (CLSI) 2017. Result: The isolation rate of H. influenzae was 28.7%, male (28.6%), female children (28.8%), aged 2 - 6 months (27.6%), 7 - 24 months (28.9%) and 25 - 60 months (30.2%). The isolation rate of H. influenzae from bronchitis is 30.9%, followed by bronchiolitis (28.4%) and pneumonia (30.6%). H. influenzae is susceptible to cefotaxime (5.7%), ceftriaxone (11.9%), ceftazidime (1.2%), meropenem (82,6%), imipenem (81,7%), ciprofloxacin (89.4%). Conclusion: The isolation rate of H. influenzae from nasopharynxis 28.7%. There is no difference in the prevalence of H. influenzae by sex, by age and by disease.H. influenzae is less susceptible to cephalosporin antibiotics, highly susceptible with meropenem, imipenem and ciprofloxacin.

Streptococcus agalactiae (GBS) remains the leading cause of meningitis and neonatal sepsis in the world, and causes disease in pregnant and puerperal women. This is a retrospective study of GBS infections on women of childbearing age living in Comunitat Valenciana, Spain (years 2009-2014) and GBS colonization rate on pregnant women attending Hospital La Fe (years 2013-2015) according to their origin. An aggregated total of 6,641,960 women exposed during the study period had an average GBS isolation rate of 5.19 parts per thousand (5.14-5.25 parts per thousand), geographical group rates being: Western Europe (2.2 parts per thousand), North America (2.1 parts per thousand), Australia (3.7 parts per thousand), Spain (4.6 parts per thousand), Latin America II (4.5 parts per thousand), Eastern Europe (5.3 parts per thousand), Asia (6.7 parts per thousand), Latin America I (7.7 parts per thousand), Middle East (7.9 parts per thousand), Indian Subcontinent (17.2 parts per thousand), North Africa (17.8 parts per thousand), Sub-Saharan Africa (22.7 parts per thousand). The 4532 pregnant women studied had an average GBS colonization rate of 12.47% (11.51-13.43) and geographical group rates varied similar to geographical isolation rates. Low GDP and high temperatures of the birth country were associated with higher colonization rates. Thus, differences in GBS colonization depend on the country of origin; Africa and the Indian subcontinent presented the highest, while Western Europe and North America had the lowest. This variability portrays a geographical pattern influenced by temperature and GDP.

Salad vegetables are a source of fresh nutrition and can also serve a vehicle for foodborne pathogens. This was a cross sectional study conducted in February and March 2018 aimed at isolating some enteropathogens from some salad vegetables.Ten samples of each salad vegetable (carrots, cabbage, cucumbers and tomatoes) were collected from two supermarkets and two open-markets. A total of 160 samples were collected and analysed microbiologically for presence of Shigella spp, Vibrio spp and Salmonella spp. The isolated bacteria were identified by conventional biochemical tests.Vibrio spp were isolated from all the vegetables that were collected from both the two open markets (62.5% and 72.5%) and two supermarkets (67.5% and 77.5%), with the highest isolation rate recorded in cabbages. The frequency of occurrence of Shigella spp and Salmonella spp was higher in supermarkets (50% and 65%; 50% and 15%) than in the open markets (10% and 7.5%; 10% and 35%), respectively.The present study revealed the presence of potential bacterial hazards in salad vegetables sold in both open markets and supermarkets in Lusaka district. The isolated bacterial pathogens are aetiological agents of diarrheal disease that even at low dose could be infectious for sensitive populations.

Background Ningxia Hui Autonomous Region is an important cattle breeding area in China, and cattle breeding bases are located in this area. In Ningxia, dermatophytes have not been paid attention to, so dermatophytosis is becoming more and more serious. For effective control measures, it is important to determine the disease prevalence and isolate and identify the pathogenic microorganism. Results The study showed the prevalence of dermatophytes was 15.35% (74/482). The prevalence in calf was higher than adult cattle (p p p p p p Trichophyton was highest (61.1%). The phylogenetic tree constructed showed that the 11 pathogenic fungi were on the same branch as Trichophyton verrucosum. Conclusions This study reports, for the first time, the presence of Trichophyton verrucosum in cattle in Ningxia and showed that the incidence of dermatophytosis is related to different regions, ages and seasons. A better knowledge of the prevalence of dermatophytosis of cattle may allow the adoption of more efficient control measures and prophylaxis.

Varicella is an acute respiratory infectious diseases, with high transmissibility and quick dissemination. In this study, an SEIR (susceptible-exposed-infected-recovered) dynamic model was established to explore the optimal prevention and control measures according to the epidemiological characteristics about varicella outbreak in a school in a central city of China. Berkeley Madonna 8.3.18 and Microsoft Office Excel 2010 software were employed for the model simulation and data management, respectively. The result showed that the simulated result of SEIR model agreed well with the reported data when β (infected rate) equal to 0.067. Models showed that the cumulative number of cases was only 13 when isolation adopted when the infected individuals were identified (assuming isolation rate was up to 100%); the cumulative number of cases was only two and the TAR (total attack rate) was 0.56% when the vaccination coefficient reached 50%. The cumulative number of cases did not change significantly with the change of efficiency of ventilation and disinfection, but the peak time was delayed; when δ (vaccination coefficient) = 0.1, m (ventilation efficiency) = 0.7 or δ = 0.2, m = 0.5 or δ = 0.3, m = 0.1 or δ = 0.4 and above, the cumulative number of cases would reduce to one case and TAR would reduce to 0.28% with combined interventions. Varicella outbreak in school could be controlled through strict isolation or vaccination singly; combined interventions have been adopted when the vaccination coefficient was low.

Since the outbreak of the novel coronavirus disease (COVID-19) at the beginning of December 2019, there have been more than 28.69 million cumulative confirmed cases worldwide as of 12th September 2020, affecting over 200 countries and regions with more than 920,463 deaths. The COVID-19 pandemic has been sweeping worldwide with unexpected rapidity. In this paper, a hybrid modelling strategy based on tessellation structure- (TS-) configured SEIR model is adopted to estimate the scale of the pandemic spread. Building on the data pertaining to the global pandemic transmission over the last six months around the world, key impact factors in the transmission and control procedure have been analysed, including isolation rate, number of the infected cases before taking prevention measures, degree of contact scope, and medical level, so as to capture the fundamental factor influencing the pandemic. The quantitative evaluation allowed us to illustrate the magnitude of risks of pandemic and to recommend appropriate national health policy of prevention measures for effectively controlling both intra- and interregional pandemic spread. Our modelling results clearly indicate that the early-stage preventive measures are the most effective action to be taken to contain the pandemic spread of the highly contagious nature of the COVID-19.

The outbreak of the novel coronavirus has resulted in significant morbidity and mortality in the affected 210 countries with 2.4 million people infected and over 163 thousand deaths. The COVID-19 spike protein is effective at binding to human cells, but this COVID-19 backbone differed substantially from other, already known coronaviruses and mostly resembled viruses found in bats and pangolins. To help predict possible dynamics of COVID-19 as well as ways to contain it, this paper develops a mathematical model for the disease, which includes two different infectious routes. The model’s predictions are fitted to data from the outbreak in New York State from the first reported case from March 01, 2020 to April 19, 2020. The containment time and the severity of the outbreaks depend crucially on the contact coefficients and the isolation rate constant. When randomness is added to the model coefficients, the simulations show that the model is sensitive to the scaled contact rate among people and to the isolation rate. The model is analyzed using stability theory for ordinary differential equations and indicates that when using only isolation for control and advising self-recovery, the endemic steady state is locally stable and attractive. After reaching the peak of COVID-19 on April 14, 2020, new infections by the virus would slow down, particularly from the beginning of May at New York State if people keep the isolation. Numerical simulations with parameters estimated from New York State illustrate the analytical results and the model behavior, which may have important implications for the disease containment in other cities. Indeed, the model highlights the importance of isolation of infected individuals and advising self-recovery may be used to assess other control measures. The model is general and may be used to analyze outbreaks in other states of the United States and other countries.

The race to discover and isolate giant viruses began 15 years ago. Metagenomics is counterbalancing coculture, with the detection of giant virus genomes becoming faster as sequencing technologies develop. Since the discovery of giant viruses, many efforts have been made to improve methods for coculturing amebas and giant viruses, which remains the key engine of isolation of these microorganisms. However, these techniques still lack the proper tools for high-speed detection. In this paper, we present advances in the isolation of giant viruses. A new strategy was developed using a high-throughput microscope for real-time monitoring of cocultures using optimized algorithms targeting infected amebas. After validating the strategy, we adapted a new tabletop scanning electron microscope for high-speed identification of giant viruses directly from culture. The speed and isolation rate of this strategy has raised the coculture to almost the same level as sequencing techniques in terms of detection speed and sensitivity., Rania Francis et al. develop a new strategy for the identification and isolation of giant viruses in real time by using optimized algorithms targeting infected amebas in co-cultures. This new approach, which does not require sequencing techniques, is highly sensitive and 100-fold faster than other high throughput procedures.

In order to clarify the main pathogens of tomato Fusarium wilt in Shanxi Province, China, morphological identification, elongation factor 1 alpha (EF-1α) sequence analysis, specific primer amplification and pathogenicity tests were applied to study the isolates which were recovered from diseased plants collected from 17 different districts of Shanxi Province. The results were as follows: 1) Through morphological and molecular identification, the following 7 species of Fusarium were identified: F. oxysporum, F. solani, F. verticillioides, F. subglutinans, F. chlamydosporum, F. sporotrichioides, and F. semitectum; 2) 56 isolates of F. oxysporum were identified using specific primer amplification, among which, 29, 5 and 6 isolates were respectively identified as F. oxysporum f. sp. lycopersici physiological race 1, race 2, and race 3; 3) pathogenicity test indicated the significant pathogenicity of F. oxysporum, F. solani, F. verticillioides, and F. subglutinans to tomato plant. Therefore, among these 4 species confirmed as pathogenic to tomato in Shanxi, the highest isolation rate (53.3%) corresponded to F. oxysporum. Three physiological species, race 1, race 2, and race 3 of F. oxysporum f. sp. lycopersici are detected in Shanxi, among which race 1 is the most widespread pathogen and is also considered as the predominant race.

The purpose of this study was to compare bacterial isolation rate using a corneal impression membrane (CIM) and a sharp instrument for obtaining corneal samples from patients with suspected microbial keratitis (MK). Data was retrospectively collected for all patients that had corneal samples taken for presumed MK between May 2014 and May 2020. Prior to May 2017 samples were collected by scraping the edges of the ulcer with a blade. From May 2017, samples were collected by placing a CIM (Millicell cell culture insert) against the ulcer. All corneal samples were processed using the same conventional diagnostic culture method. A total of 3099 corneal samples were included, of which 1214 (39.2%) were corneal scrapes and 1885 (60.9%) CIMs. Microorganisms were isolated from 235 (19.4%) and 1229 (65.2%) cases using a corneal scrape and CIM, respectively (p < 0.001). Of routinely described pathogenic microorganisms, there were significant increases in the isolations of S. aureus (2.4% to 11.3%) and Serratia (0.5% to 1.7%) using the CIM and no significant changes in the isolations of S. pneumoniae and P. aeruginosa. No significant differences were seen between the isolation rates of fungi or Acanthamoeba species. There was a significant increase in the isolation rates of other Streptococcal species (0.7% to 6.9%) and CNS species, specifically, S. epidermidis (2.1% to 26.2%), S. capitis (0.4% to 2.6%) and S. warneri (0.3% to 1.6%) using the CIM. The simplified CIM sampling method is an effective method for collecting corneal samples from patients with presumed MK in clinical practice.