Infectious Disease Reports

Ventilator-associated pneumonia (VAP) is associated with increased hospital stay and high morbidity and mortality in critically ill patients. The aims of this study were to (i) determine the incidence of multidrug-resistant (MDR) pathogens in the first episodes of VAP and to assess potential differences in bacterial profiles of subjects with early- versus late-onset VAP. This was a retrospective cohort study over a period of 18 months including all patients who had a first episode of VAP confirmed by positive bacterial culture. Subjects were distributed into two groups according to the number of intubation days: early-onset VAP (<5 days) or late-onset VAP (≥5 days). The primary endpoint was the nature of causative pathogens and their resistance profiles. Sixty patients were included, 29 men and 31 women, with an average age of 38 ± 16 years. The IGS 2 at admission was 40.5 [32–44] and APACHE was 19 [15–22]. Monomicrobial infections were diagnosed in 77% of patients (n = 46). The most frequently isolated bacteria were A. baumannii, 53% (n = 32); P. aeruginosa in 37% (n = 22); Enterobacterales in 28% (n = 17) and S. aureus in 5% (n = 3). Ninety-seven percent of the bacteria were MDR. The VAP group comprised 36 (60%) episodes of early-onset VAP and 24 (40%) episodes of late-onset VAP. There was no significant difference in the distribution of the bacterial isolates, nor in terms of antibacterial resistances between early- and late-onset VAPs. Our data support recent observations that there is no microbiological difference in the prevalence of potential MDR pathogens or in their resistance profiles associated with early- versus late-onset VAPs, especially in countries with high rates of MDR bacteria. Full article

Introduction: Enteric fever, a systemic infection caused by Salmonella enterica Typhi and S. enterica Paratyphi is one of the most common infections in developing countries such as Nepal. Aside from irrational practices of antibiotic use, mutations in chromosomal genes encoding DNA gyrase and Topoisomerase IV and by plasmid mediated quinolone resistant (PMQR) genes are suggested mechanisms for the development of resistance to nalidixic acid and reduced susceptibility to ciprofloxacin. Regardless of high endemicity of enteric fever in Nepal, there is paucity of studies on prevalence and drug-resistance of the pathogen. Therefore, this study aimed to assess the antibiotic susceptibility pattern of Salmonella isolates and determine the minimum inhibitory concentration of ciprofloxacin. Methods: A total of 1298 blood samples were obtained from patients with suspected enteric fever, attending Sukraraj Tropical and Infectious Disease Hospital (STIDH) during March–August, 2019. Blood samples were inoculated immediately into BACTEC culture bottles and further processed for isolation and identification of Salmonella Typhi and S. Paratyphi. Axenic cultures of the isolates were further subjected to antimicrobial susceptibility testing (AST) by using the modified Kirby–Bauer disc diffusion method based on the guidelines by CLSI. The minimum inhibitory concentration (MIC) of ciprofloxacin was determined by agar-dilution method. Results: Out of 1298 blood cultures, 40 (3.1%) were positive for Salmonella spp. among which 29 (72.5%) isolates were S. Typhi and 11 (27.5%) isolates were S. Paratyphi A. In AST, 12.5% (5/40), 15% (6/40) and 20% (8/40) of the Salmonella isolates were susceptible to nalidixic acid, ofloxacin and levofloxacin, respectively, whereas none of the isolates were susceptible to ciprofloxacin. The MIC value for ciprofloxacin ranged from 0.06-16 µg/mL in which, respectively, 5% (2/40) and 52.5% (21/40) of the isolates were susceptible and resistant to ciprofloxacin. None of the isolates showed multidrug-resistance (MDR) in this study. Conclusion: This study showed high prevalence of quinolone-resistant Salmonella spp., while there was marked re-emergence of susceptibilities to traditional first option drugs. Hence, conventional first-line-drugs and third-generation cephalosporins may find potential usage as the empirical drugs for enteric fever. Although our reporting was free of MDR strains, extensive surveillance, augmentation of diagnostic facilities and treatment protocol aided by AST report are recommended for addressing the escalating drug-resistance in the country. Full article

Background: A rapidly growing number of publications cite “cytokine storm” as a contributing factor in coronavirus disease 2019 (COVID-19) pathology. However, a few recent reports led to questioning of “cytokine storm” theory in COVID-19. This study’s primary goal is to determine if exaggerated cytokine response in the range of a “cytokine storm” develops during the initial weeks of hospitalization in COVID-19 patients. Methods: Five proinflammatory cytokines reported to be involved in “cytokine storm” and elevated in COVID-19 (IL-6, IL-8, TNF-α, MCP-1, and IP-10) were analyzed in COVID-19, influenza (with “cytokine storm”: CS), and burn injury patients. The effect of dexamethasone use on cytokine response in COVID-19 was also analyzed. Results: None of the five cytokines in COVID-19 patients reached the lower threshold (95% CI) of the influenza (CS) group at any point during the study period. Furthermore, mean concentrations of all five cytokines in the influenza (CS) group and IL-6, IL-8, TNF-α in the burn group were significantly greater than in COVID-19 patients (p < 0.01). Dexamethasone treatment did not significantly alter the concentrations of any of the cytokines analyzed. Conclusions: Exaggerated cytokine response similar to “cytokine storm” was not observed in COVID-19 patients during two weeks of hospitalization. Full article

Brucellosis is an endemic zoonotic disease in the Mediterranean basin and Middle East. The disease remains a diagnostic challenge due to an increasing trend of ambiguous and non-specific manifestations. We report a rare case of a 9-year-old boy who had a left frontotemporal arachnoid cyst with cystoperitoneal shunt who presented with fever for 2 weeks with gastrointestinal symptoms. He had no neurological manifestations. Diagnosis of Brucella shunt infection complicated with a peritoneal collection was established by isolation of the organism from cerebrospinal fluid (CSF) culture. Successful treatment was accomplished by shunt replacement and intravenous antibiotics followed by step-down oral therapy for an 18-month duration based on serological and radiological responses with no sequelae. We also reviewed the reported cases of CSF shunt infection in the literature for further guidance. Brucella shunt infection may be difficult to diagnose due to the diversity of signs and symptoms and the low yield on culture. Brucellosis should be always kept in mind in the differential diagnosis of patients living in endemic area with fever and non-specific symptoms. Diagnosis depends on a high index of suspicion. In addition to drug therapy, device replacement is advised to prevent treatment failure. Full article

Fungal skin infections and iatrogenic disease of companion animals continue to be an ongoing issue for veterinarians, where misdiagnosis or inapt medical treatment result in secondary conditions within animals. The widespread use of antifungals in both modern medicine and agriculture has resulted in concomitant resistance in species, where zoonotic transfer poses a risk to public health. Studies described herein assess the resistance of pathogenic species isolated from companion animals to a battery of conventional antimicrobial agents. Levels of resistance were detected using recognised in vitro methods, where additional novel therapeutic and biocide options were also extensively investigated. Results show high levels of resistance to the three main families of antifungal agents, namely caspofungin, Amp B and fluconazole. Resistance in Candida, Cryptococcal, Aspergillus and Trichophyton species is described herein, highlighting the need for defined species-specific antifungal breakpoints, and for Malassezia and Wickerhamomyces anomalus species which also have zoonotic potential. Novel compound phendione showed promising antimicrobial activity, with MICs determined for both fungal and bacterial species. The biocidal options investigated also showed potential to act as intermediate-level disinfectants, where peracetic acid proved most effective against fungal spore formers. Full article

The numbers of novel coronavirus cases continue to grow at an unprecedented rate across the world. Attempts to control the growth of the virus using masks and social-distancing, and, recently, double-masking as well, continue to be difficult to maintain, in part due to the extent of asymptomatic cases. Analyses of large datasets consisting of 219,075 individual cases in Ontario, indicated that asymptomatic and pre-symptomatic cases are substantial in number. Large numbers of cases in children aged 0–9 were asymptomatic or had only one symptom (35.0% and 31.4% of total cases, respectively) and resulted in fever as the most common symptom (30.6% of total cases). COVID-19 cases in children were more likely to be milder symptomatic with cough not seen as frequently as in adults aged over 40, and past research has shown children to be index cases in familial clusters. These findings highlight the importance of targeting asymptomatic and mild infections in the continuing effort to control the spread of COVID-19. The Pearson correlation coefficient between test positivity rates and asymptomatic rates of −0.729 indicates that estimates of the asymptomatic rates should be obtained when the test positivity rates are lowest as the best approach. Full article

The novel coronavirus disease (COVID-19) is an ongoing pandemic with large global attention. However, spreading false news on social media sites like Twitter is creating unnecessary anxiety towards this disease. The motto behind this study is to analyses tweets by Indian netizens during the COVID-19 lockdown. The data included tweets collected on the dates between 23 March 2020 and 15 July 2020 and the text has been labelled as fear, sad, anger, and joy. Data analysis was conducted by Bidirectional Encoder Representations from Transformers (BERT) model, which is a new deep-learning model for text analysis and performance and was compared with three other models such as logistic regression (LR), support vector machines (SVM), and long-short term memory (LSTM). Accuracy for every sentiment was separately calculated. The BERT model produced 89% accuracy and the other three models produced 75%, 74.75%, and 65%, respectively. Each sentiment classification has accuracy ranging from 75.88–87.33% with a median accuracy of 79.34%, which is a relatively considerable value in text mining algorithms. Our findings present the high prevalence of keywords and associated terms among Indian tweets during COVID-19. Further, this work clarifies public opinion on pandemics and lead public health authorities for a better society. Full article

Containment strategies to combat epidemics such as SARS-CoV-2/COVID-19 require the availability of epidemiological parameters, e.g., the effective reproduction number. Parametric models such as the commonly used susceptible-infected-removed (SIR) compartment models fitted to observed incidence time series have limitations due to the time-dependency of the parameters. Furthermore, fatalities are delayed with respect to the counts of new cases, and the reproduction cycle leads to periodic patterns in incidence time series. Therefore, based on comprehensible nonparametric methods including time-delay correlation analyses, estimates of crucial parameters that characterise the COVID-19 pandemic with a focus on the German epidemic are presented using publicly available time-series data on prevalence and fatalities. The estimates for Germany are compared with the results for seven other countries (France, Italy, the United States of America, the United Kingdom, Spain, Switzerland, and Brazil). The duration from diagnosis to death resulting from delay-time correlations turns out to be 13 days with high accuracy for Germany and Switzerland. For the other countries, the time-to-death durations have wider confidence intervals. With respect to the German data, the two time series of new cases and fatalities exhibit a strong coherence. Based on the time lag between diagnoses and deaths, properly delayed asymptotic as well as instantaneous fatality–case ratios are calculated. The temporal median of the instantaneous fatality–case ratio with time lag of 13 days between cases and deaths for Germany turns out to be $0.02$. Time courses of asymptotic fatality–case ratios are presented for other countries, which substantially differ during the first half of the pandemic but converge to a narrow range with standard deviation $0.0057$ and mean $0.024$. Similar results are obtained from comparing time courses of instantaneous fatality–case ratios with optimal delay for the 8 exemplarily chosen countries. The basic reproduction number, $R_0$, for Germany is estimated to be between $2.4$ and $3.4$ depending on the generation time, which is estimated based on a delay autocorrelation analysis. Resonances at about 4 days and 7 days are observed, partially attributable to weekly periodicity of sampling. The instantaneous (time-dependent) reproduction number is estimated from the incident (counts of new) cases, thus allowing us to infer the temporal behaviour of the reproduction number during the epidemic course. The time course of the reproduction number turns out to be consistent with the time-dependent per capita growth. Full article

We analyze the data about casualties in Italy in the period 1 January 2015 to 30 September 2020 released by the Italian National Institute of Statistics (ISTAT). The aim of this article was the description of a statistically robust methodology to extract quantitative values for the seasonal excesses of deaths featured by the data, accompanying them with correct estimates of the relative uncertainties. We will describe the advantages of the method adopted with respect to others listed in literature. The data exhibit a clear sinusoidal behavior, whose fit allows for a robust subtraction of the baseline trend of casualties in Italy, with a surplus of mortality in correspondence to the flu epidemics in winter and to the hottest periods in summer. The overall quality of the fit to the data turns out to be very good, an indication of the validity of the chosen model. We discuss the trend of casualties in Italy by different classes of ages and for the different genders. We finally compare the data-subtracted casualties, as reported by ISTAT, with those reported by the Italian Department for Civil Protection (DPC) relative to the deaths directly attributed to the Coronavirus Disease 2019 caused by the SARS-CoV-2 virus (COVID-19), and we point out the differences in the two samples, collected under different assumptions. Full article

SARS-CoV-2 (COVID-19) has been changing the world since December 2019. A comprehensive search into many COVID-19 treatment guidelines was conducted and reported in this article. This is a review paper to probe differences in COVID-19 managing strategies and explore the most common treatment plans among countries. Published guidelines from 23 countries and three references guidelines—until the end of 2020—were included in this article. The majority of COVID-19 treatment options were reported in this review and it includes antiviral drugs, antimalarial drugs, antibiotics, corticosteroids, immunotherapy, anticoagulants, and other pharmacological treatment. The presence of such information from different countries in a single comprehensive review article could help in understanding and speculation of variation in the recommended treatment in each country. This might be related to the cost of medications, the access to the medications, availability of medication that could potentially be useful in managing COVID-19 cases, and the availability/capacity of healthcare facilities. Finally, although there are various treatment groups listed in the published therapeutic guidelines worldwide, unfortunately, there is no evidence for effectiveness of most of these medications in reducing the COVID-19 mortality curve over more than one year of this global pandemic. Full article

The impact of the coronavirus disease (COVID-19), caused by the novel coronavirus SARS-CoV-2, continues to be widespread, with more than 100 million cases diagnosed in more than 220 countries since the virus was first identified in January 2020. Although patients with mild to moderate forms of COVID-19 could be efficiently managed at home, thus reducing the pressure on the healthcare system and minimizing socio-psychological impact on patients, no trial has been proposed, conducted, or even published on COVID-19 home therapy to date. These expert opinions provide indications on the therapeutical at home management of COVID-19 patients, based on the evidence from the literature and on current guidelines. Full article

As Coronavirus Disease 2019 (COVID-19) hospitalization rates remain high, there is an urgent need to identify prognostic factors to improve patient outcomes. Existing prognostic models mostly consider the impact of biomarkers at presentation on the risk of a single patient outcome at a single follow up time. We collected data for 553 Polymerase Chain Reaction (PCR)-positive COVID-19 patients admitted to hospital whose eventual outcomes were known. The data collected for the patients included demographics, comorbidities and laboratory values taken at admission and throughout the course of hospitalization. We trained multivariate Markov prognostic models to identify high-risk patients at admission along with a dynamic measure of risk incorporating time-dependent changes in patients’ laboratory values. From the set of factors available upon admission, the Markov model determined that age >80 years, history of coronary artery disease and chronic obstructive pulmonary disease increased mortality risk. The lab values upon admission most associated with mortality included neutrophil percentage, red blood cells (RBC), red cell distribution width (RDW), protein levels, platelets count, albumin levels and mean corpuscular hemoglobin concentration (MCHC). Incorporating dynamic changes in lab values throughout hospitalization lead to dramatic gains in the predictive accuracy of the model and indicated a catalogue of variables for determining high-risk patients including eosinophil percentage, white blood cells (WBC), platelets, pCO2, RDW, large unstained cells (LUC) count, alkaline phosphatase and albumin. Our prognostic model highlights the nuance of determining risk for COVID-19 patients and indicates that, rather than a single variable, a range of factors (at different points in hospitalization) are needed for effective risk stratification. Full article

Background: Kytococcus schroeteri is a member of normal skin microflora, which can cause lethal infections in immunosuppressed hosts. In this review we attempted to draw patterns of its pathogenicity, which seem to vary regarding host immune status and the presence of implantable devices. Evidence suggests this pathogen houses many resistance-forming proteins, which serve to exacerbate the challenge in curing it. Available information on K. schroeteri antibacterial susceptibility is scarce. In this situation, a novel, genome-based antibiotic resistance analysis model, previously suggested by Su et al., could aid clinicians dealing with unknown infections. In this study we merged data from observed antibiotic resistance patterns with resistance data demonstrated by DNA sequences. Methods: We reviewed all available articles and reports on K. schroeteri, from peer-reviewed online databases (ClinicalKey, PMC, Scopus and WebOfScience). Information on patients was then subdivided into patient profiles and tabulated independently. We later performed K. schroeteri genome sequence analysis for resistance proteins to understand the trends K. schroeteri exhibits. Results: K. schroeteri is resistant to beta-lactams, macrolides and clindamycin. It is susceptible to aminoglycosides, tetracyclines and rifampicin. We combined data from the literature review and sequence analysis and found evidence for the existence of PBP, PBP-2A and efflux pumps as likely determinants of K. schroeteri. Conclusions: Reviewing the data permits the speculation that baseline immune status plays a role in the outcome of a Kytococcal infection. Nonetheless, our case report demonstrates that the outcome of a lower baseline immunity could still be favorable, possibly using rifampicin in first-line treatment of infection caused by K. schroeteri. Full article

Infections represent an important problem in neonates because of the high mortality. An increase in neonatal infections has been found in Cuban hospitals in recent years. The aim of this study was to provide evidence on the clinical and microbiological behavior of Gram-negative bacilli that cause neonatal infections in hospitals of Havana, Cuba. It was carried out as a descriptive cross-sectional investigation from September 2017 to July 2018 in The Tropical Medicine Institute “Pedro Kouri” (IPK). Sixty-one Gram-negative bacilli isolated from neonates with infections in six Gyneco-Obstetric and Pediatric Hospitals of Havana were analyzed for their species and antimicrobial susceptibility. Late-onset infections were more common than early-onset ones and included urinary tract infection in the community (87%) and sepsis in hospitals (63.3%). Catheter use (47%) and prolonged stay (38%) were the most frequent risk factors. Species of major pathogens were Escherichia coli (47%) and Klebsiella spp. (26%). The isolated Gram-negative bacilli showed high resistance rates to third-generation cephalosporins, ciprofloxacin and gentamicin, while being more susceptible to carbapenems, fosfomycin, colistin and amikacin. The present study revealed the clinical impact of Gram-negative bacilli in neonatology units in hospitals of Havana. Evaluation of antimicrobial susceptibilities to the isolates from neonates is necessary for selection of appropriate empirical therapy and promotion of the rational antibiotic use. Full article

We describe a case of cutaneous Larva Migrans in an 8-year-old Caucasian girl. The lesion appeared ten days after a bath in the river in a valley in the north-east of Piedmont. The patient was successfully treated with Albendazole 400 mg daily for 5 days. Autochthonous cases are rare, particularly in northern Italy. Probably the high temperatures and the high degree of humidity favored by the climate changes to which Europe is subjected are favorable to the development of larvae. The diagnosis of cutaneous Larva Migrans should, therefore, be considered also in individuals who have not traveled in geographic areas at risk for the climate. Full article

To date, there is only one published report of an outbreak of urinary tract infections by Salmonella species after cystoscopy. Disinfection procedures for cystoscope have come into question. The current study aimed to determine the odds of developing Salmonella bacteriuria after cystoscopy. A retrospective case-control study was conducted on all patients with Salmonella species in urine (case) and blood (control) from 2017 to 2019 in 16 hospitals in Eastern Ontario, Canada. Eight of the 11 patients had cystoscopy prior to Salmonella bacteriuria; three of the 74 patients had urological procedures prior to Salmonella bacteremia, but none of their procedures were cystoscopy. The odds ratio of urological procedures with Salmonella bacteriuria was 63.1 (95% CI 10.9 to 366.6; p < 0.0001). In the bacteriuria group, the most frequently identified isolates were Salmonella enteritidis (n = 8), followed by Salmonella oranienburg, and Salmonella heidelberg. Seven of the S. enteritidis isolates had identical susceptibilities (ampicillin-sensitive; sulfamethoxazole/trimethoprim-sensitive; ciprofloxacin intermediate). In the bacteremia group, the most frequently identified isolates were S. enteritidis (n = 22), followed by Salmonella typhi, S. heidelberg, S. oranienburg, and Salmonella typhimurium. The result suggested cystoscopy is a risk factor for Salmonella bacteriuria. Identification of Salmonella bacteriuria should prompt public health investigations of linkage between cystoscopy and Salmonella bacteriuria. Full article

The aim of this cross-sectional study was to investigate Staphylococcus aureus nasopharyngeal carriage epidemiology in relation to other nasopharyngeal bacterial colonizers among sickle cell disease (SCD) children about five years into pneumococcal conjugate vaccine 13 (PCV-13) introduction in Ghana. The study involved bacteriological culture of nasopharyngeal swabs obtained from 202 SCD children recruited from the Princess Marie Louise Children’s Hospital. S. aureus isolates were identified using standard methods and subjected to antimicrobial susceptibility testing using the Kirby-Bauer disc diffusion method. Cefoxitin-resistant S. aureus isolates were screened for carriage of the mecA, pvl, and tsst-1 genes using multiplex polymerase chain reaction. The carriage prevalence of S. aureus was 57.9% (n = 117), and that of methicillin-resistant S. aureus (MRSA) was 3.5% (n = 7). Carriage of the mecA, pvl, and tsst-1 genes were respectively demonstrated in 20.0% (n = 7), 85.7% (n = 30), and 11.4% (n = 4) of the cefoxitin-resistant S. aureus isolates. PCV-13 vaccination (OR = 0.356, p = 0.004) and colonization with coagulase-negative staphylococci (CoNS) (OR = 0.044, p < 0.0001) each protected against S. aureus carriage. However, none of these and other features of the participants emerged as a determinant of MRSA carriage. The following antimicrobial resistance rates were observed in MRSA compared to methicillin-sensitive S. aureus: clindamycin (28.6% vs. 4.3%), erythromycin (42.9% vs. 19.1%), tetracycline (100% vs. 42.6%), teicoplanin (14.3% vs. 2.6%), penicillin (100% vs. 99.1%), amoxiclav (28.6% vs. 3.5%), linezolid (14.3% vs. 0.0%), ciprofloxacin (42.9% vs. 13.9%), and gentamicin (42.9% vs. 13.0%). The proportion of S. aureus isolates that were multidrug resistant was 37.7% (n = 46). We conclude that S. aureus was the predominant colonizer of the nasopharynx of the SCD children, warranting the continuous monitoring of this risk group for invasive S. aureus infections. Full article

Cefazolin is a widely used first-generation cephalosporin. While generally well tolerated, several case reports have described severe coagulopathy induced by intravenous (IV) cefazolin. This was seen particularly in patients with impaired renal function, where antibiotic choice is limited and may require specific dose adjustments. Altered renal handling of antibiotics and their metabolites may potentiate toxicity and side effects. We report a case of a 72-year-old Chinese man who had been treated for methicillin-sensitive staphylococcus aureus (MSSA, coagulase-positive) infective endocarditis with cefazolin and, consequently, developed significantly elevated international normalised ratio (INR) while on therapy. This resolved within 48 h after cessation of cefazolin and administration of oral vitamin K. Malnourished patients with pre-existing or acute kidney injury may be at an increased risk of cefazolin-related coagulopathy. Full article

Central nervous system (CNS) tuberculosis is a rare manifestation of all tuberculosis presentations. The incidence of brain tuberculoma is increasing in developed countries due to HIV infection and immigration from tuberculosis-endemic countries. Symptoms and radiologic findings of CNS tuberculosis can be non-specific and lead to misdiagnosis or mistreatment. Intracranial tuberculoma can present with a seizure, intracranial hypertension, or focal neurologic symptoms. In our case, the diagnosis was challenging between neurosarcoidosis and intracranial tuberculoma due to inconclusive results of stereotactic brain biopsy and clinical presentation. The pathology result of the open brain biopsy revealed non-caseating granuloma. Finally, we were able to diagnose intracranial tuberculoma following acid-fast bacilli culture results of open brain biopsy. This report highlights the importance of including intracranial tuberculoma in the differential diagnosis of cerebral space-occupying lesions, even in patients with negative laboratory findings of tuberculosis. Full article