COVID-19, SARS and MERS: are they closely related?

BACKGROUND: The 2019 novel coronavirus (SARS-CoV-2) is a new human coronavirus which is spreading with epidemic features in China and other Asian countries; cases have also been reported worldwide. This novel coronavirus disease (COVID-19) is associated with a respiratory illness that may lead to severe pneumonia and acute respiratory distress syndrome (ARDS). Although related to the severe acute respiratory syndrome (SARS) and the Middle East respiratory syndrome (MERS), COVID-19 shows some peculiar pathogenetic, epidemiological and clinical features which to date are not completely understood. AIMS: To provide a review of the differences in pathogenesis, epidemiology and clinical features of COVID-19, SARS and MERS. SOURCES: The most recent literature in the English language regarding COVID-19 has been reviewed, and extracted data have been compared with the current scientific evidence about SARS and MERS epidemics. CONTENT: COVID-19 seems not to be very different from SARS regarding its clinical features. However, it has a fatality rate of 2.3%, lower than that of SARS (9.5%) and much lower than that of MERS (34.4%). The possibility cannot be excluded that because of the less severe clinical picture of COVID-19 it can spread in the community more easily than MERS and SARS. The actual basic reproductive number (R0) of COVID-19 (2.0-2.5) is still controversial. It is probably slightly higher than the R0 of SARS (1.7-1.9) and higher than that of MERS (<1). A gastrointestinal route of transmission for SARS-CoV-2, which has been assumed for SARS-CoV and MERS-CoV, cannot be ruled out and needs further investigation. IMPLICATIONS: There is still much more to know about COVID-19, especially as concerns mortality and its capacity to spread on a pandemic level. Nonetheless, all of the lessons we learned in the past from the SARS and MERS epidemics are the best cultural weapons with which to face this new global threat.

Profiling infectious diseases in Turkey after the influx of 3.5 million Syrian refugees.

BACKGROUND: Since 2011, the conflict in Syria has led to over five million refugees. Turkey hosts the highest number of Syrian refugees in the world. By February 2019 over 3.6 million people had fled to Turkey to seek safety. Only 6.1% of Syrian refugees live in temporary shelters. Owing to the disrupted healthcare services, many children coming from the conflict zones are less likely to have received vaccination. In temporary shelters immunization coverage is >95% and the refugee population is receptive to vaccination. AIMS: The objective of this study was to review the infectious diseases situation among Syrian refugees in Turkey. SOURCES: We have reviewed the reports and studies provided by the governmental and non-governmental organizations and obtained more detailed data from the Ministry of Health in Turkey. CONTENT: Between 2012 and 2016, 1 299 209 cases of respiratory tract infection and 158 058 episodes of diarrhoea with 59 bloody diarrhoeas were reported; 1354 hepatitis A cases and 108 active tuberculosis cases were detected and treated in the temporary shelters for Syrian refugees. Overall in Turkey, 7794 cutaneous leishmaniasis have been reported. IMPLICATIONS: Since the influx of Syrian refugees, there has been an increase in cases of leishmaniasis and measles. No significant increase was detected for tuberculosis, other vector-borne infections, and healthcare associated or sexually transmitted infections. The Syrian refugees can be considered as a vulnerable group in Turkey due to their living and working conditions. Based on available data and our detailed analysis, the numbers show a stable situation regarding infectious diseases.

A prospective prediction tool for understanding Crimean-Congo haemorrhagic fever dynamics in Turkey.

OBJECTIVES: We aimed to develop a prospective prediction tool on Crimean-Congo haemorrhagic fever (CCHF) to identify geographic regions at risk. The tool could support public health decision-makers in implementation of an effective control strategy in a timely manner. METHODS: We used monthly surveillance data between 2004 and 2015 to predict case counts between 2016 and 2017 prospectively. The Turkish nationwide surveillance data set collected by the Ministry of Health contained 10 411 confirmed CCHF cases. We collected potential explanatory covariates about climate, land use, and animal and human populations at risk to capture spatiotemporal transmission dynamics. We developed a structured Gaussian process algorithm and prospectively tested this tool predicting the future year's cases given past years' cases. RESULTS: We predicted the annual cases in 2016 and 2017 as 438 and 341, whereas the observed cases were 432 and 343, respectively. Pearson's correlation coefficient and normalized root mean squared error values for 2016 and 2017 predictions were (0.83; 0.58) and (0.87; 0.52), respectively. The most important covariates were found to be the number of settlements with fewer than 25 000 inhabitants, latitude, longitude and potential evapotranspiration (evaporation and transpiration). CONCLUSIONS: Main driving factors of CCHF dynamics were human population at risk in rural areas, geographical dependency and climate effect on ticks. Our model was able to prospectively predict the numbers of CCHF cases. Our proof-of-concept study also provided insight for understanding possible mechanisms of infectious diseases and found important directions for practice and policy to combat against emerging infectious diseases.

Predictors of fatality in influenza A virus subtype infections among inpatients in the 2015-2016 season.

BACKGROUND: Infection with the influenza A virus can cause severe disease and mortality. The effect of the different subtypes of influenza on morbidity and mortality is not yet known in Turkey. The aim of this study was to describe the predictors of fatality related to influenza A infection among hospitalized patients in Istanbul during the 2015-2016 influenza season, and to detail the differences between infections caused by H3N2 and H1N1. METHODS: This was a multicenter study performed by the Istanbul Respiratory Infections Study Group of The Turkish Society of Clinical Microbiology and Infectious Diseases (KLIMIK), among patients hospitalized for influenza in Istanbul during the 2015-2016 influenza season. RESULTS: A total of 222 patients hospitalized with laboratory-confirmed influenza during the 2015-2016 season were included in the study, of whom 25 (11.2%) died. The fatality rate was significantly higher among patients older than 65 years of age and those with chronic heart and kidney diseases (p<0.001), chronic neurological diseases (p=0.009), and malignancies (p=0.021). Thrombocyte counts were lower in those who died than in those who survived (p<0.004). The median alanine aminotransferase, aspartate aminotransferase, lactate dehydrogenase, creatinine phosphokinase, and C-reactive protein levels were higher among fatal cases. In the multivariate analysis for the prediction of fatality, being >65years old (odds ratio (OR) 6.9, 95% confidence interval (CI) 2.07-23.08, p=0.002), being infected with influenza A(H3N2) (OR 4.2, 95% CI 1.27-14.38, p=0.019), and a 1-day delay in antiviral use (OR 1.28, 95% CI 1.01-1.63, p=0.036) were found to be associated with an increased likelihood of fatality. CONCLUSIONS: The case fatality rate of influenza A(H3N2) was significantly higher than that of influenza A(H1N1). Detection of the infection, allowing the opportunity for the early use of antiviral agents, was found to be important for the prevention of fatality. The vaccination should be prioritized for at-risk groups.

The Role of AcrAB-TolC Efflux Pumps on Quinolone Resistance of E. coli ST131.

Escherichia coli ST131 is a cause for global concern because of its high multidrug resistance and several virulence factors. In this study, the contribution of acrAB-TolC efflux system of E. coli ST131 to fluoroquinolone resistance was evaluated. A total of nonrepetitive 111 ciprofloxacin-resistant E. coli isolates were included in the study. Multilocus sequence typing was used for genotyping. Expressions of acrA, acrB, and TolC efflux pump genes were measured by RT-PCR. Mutations in marA, gyrA, parC, and aac(6')-lb-cr positivity were studied by Sanger sequencing. Sixty-four (57.7%) of the isolates were classified as ST131, and 52 (81.3%) of the ST131 isolates belonged to H30-Rx subclone. In ST131, CTX-M 15 positivity (73%) and aac(6')-lb-cr carriage (75%) were significantly higher than those in non-ST131 (12.8% and 51%, respectively) (P < 0.05). The ampicillin-sulbactam (83%) resistance was higher, and gentamicin resistance (20%) was lower in ST131 than that in non-ST131 (64% and 55%, respectively) (P = 0.001 and P = 0.0002). Numbers of the isolates with MDR or XDR profiles did not differ in both groups. Multiple in-dels (up to 16) were recorded in all quinolone-resistant isolates. However, marA gene was more overexpressed in ST131 compared to that in non-ST131 (median 5.98 vs. 3.99; P = 0.0007). Belonging to H30-Rx subclone, isolation site, ciprofloxacin MIC values did not correlate with efflux pump expressions. In conclusion, the marA regulatory gene of AcrAB-TolC efflux pump system has a significant impact on quinolone resistance and progression to MDR profile in ST131 clone. Efflux pump inhibitors might be alternative drugs for the treatment of infections caused by E. coli ST131 if used synergistically in combination with antibiotics.

Emerging souvenirs-clinical presentation of the returning traveller with imported arbovirus infections in Europe.

BACKGROUND: Arboviruses are an emerging group of viruses that are causing increasing health concerns globally, including in Europe. Clinical presentation usually consists of a nonspecific febrile illness that may be accompanied by rash, arthralgia and arthritis, with or without neurological or haemorrhagic syndromes. The range of differential diagnoses of other infectious and noninfectious aetiologies is broad, presenting a challenge for physicians. While knowledge of the geographical distribution of pathogens and the current epidemiological situation, incubation periods, exposure risk factors and vaccination history can help guide the diagnostic approach, the nonspecific and variable clinical presentation can delay final diagnosis. AIMS AND SOURCES: This narrative review aims to summarize the main clinical and laboratory-based findings of the three most common imported arboviruses in Europe. Evidence is extracted from published literature and clinical expertise of European arbovirus experts. CONTENT: We present three cases that highlight similarities and differences between some of the most common travel-related arboviruses imported to Europe. These include a patient with chikungunya virus infection presenting in Greece, a case of dengue fever in Turkey and a travel-related case of Zika virus infection in Romania. IMPLICATIONS: Early diagnosis of travel-imported cases is important to reduce the risk of localized outbreaks of tropical arboviruses such as dengue and chikungunya and the risk of local transmission from body fluids or vertical transmission. Given the global relevance of arboviruses and the continuous risk of (re)emerging arbovirus events, clinicians should be aware of the clinical syndromes of arbovirus fevers and the potential pitfalls in diagnosis.

Rapid emergence of colistin resistance and its impact on fatality among healthcare-associated infections.

This article describes the emergence of resistance and predictors of fatality for 1556 cases of healthcare-associated Gram-negative bloodstream infection in 2014 and 2015. The colistin resistance rate in Klebsiella pneumoniae was 16.1%, compared with 6% in 2013. In total, 660 (42.4%) cases were fatal. The highest fatality rate was among patients with Acinetobacter baumannii bacteraemia (58%), followed by Pseudomonas aeruginosa (45%), Klebsiella pneumoniae (41%), Enterobacter cloacae (32%) and Escherichia coli (28%). On multi-variate analysis, the minimum inhibitory concentrations for carbapenems [odds ratio (OR) 1.02, 95% confidence interval (CI) 1.01-1.04; P = 0.002] and colistin (OR 1.1, 95% CI 1.03-1.17; P = 0.001) were found to be significantly associated with fatality.

Preparing clinicians for (re-)emerging arbovirus infectious diseases in Europe.

BACKGROUND: Arthropod-borne virus (Arbovirus) infections are considered an emerging threat for Europe, with an increase in cases in recent decades. The increase in global travel and trade has contributed to the introduction of vectors and viruses into new geographical areas. Tropical arboviruses such as dengue and chikungunya have re-emerged causing local, sporadic outbreaks ignited by travel-imported cases. The recent Zika virus outbreak in the Americas highlighted a need to strengthen preparedness for (re-)emerging arbovirus infections globally. AIMS: To strengthen preparedness for the early identification of (re-)emerging arbovirus outbreaks in Europe and highlight areas for research. SOURCES: An evidence review of published and grey literature together with consultations with European arbovirus experts. CONTENT: This paper presents an overview of endemic and travel-imported arboviruses of clinical significance in Europe. The overview includes syndromic presentation, risk factors for infection and risk of transmission as well as an update on treatments and vaccinations and surveillance notifications and reporting. The paper also presents predictive modelled risks of further geographical expansion of vectors and viruses. IMPLICATIONS: There are a range of arboviruses of clinical significance to Europe. There has been an increase in notifications of endemic and travel-imported arbovirus cases in recent years and an increased geographical range of vectors and viruses. The heterogeneity in surveillance reporting indicates a risk for the early identification of (re-)emerging outbreaks. The data presented show a need to strengthen preparedness for (re-)emerging arbovirus infections and a need for research into neglected arboviruses, risks of non-vector transmission and effective therapeutics and vaccinations.

Healthcare-associated Gram-negative bloodstream infections: antibiotic resistance and predictors of mortality.

This article describes the prevalence of antibiotic resistance and predictors of mortality for healthcare-associated (HA) Gram-negative bloodstream infections (GN-BSI). In total, 831 cases of HA GN-BSI from 17 intensive care units in different centres in Turkey were included; the all-cause mortality rate was 44%. Carbapenem resistance in Klebsiella pneumoniae was 38%, and the colistin resistance rate was 6%. Multi-variate analysis showed that age >70 years [odds ratio (OR) 2, 95% confidence interval (CI) 1.22-3.51], central venous catheter use (OR 2.1, 95% CI 1.09-4.07), ventilator-associated pneumonia (OR 1.9, 95% CI 1.1-3.16), carbapenem resistance (OR 1.8, 95% CI 1.11-2.95) and APACHE II score (OR 1.1, 95% CI 1.07-1.13) were significantly associated with mortality.

Bayesian framework for parametric bivariate accelerated lifetime modeling and its application to hospital acquired infections.

Infectious diseases that can be spread directly or indirectly from one person to another are caused by pathogenic microorganisms such as bacteria, viruses, parasites, or fungi. Infectious diseases remain one of the greatest threats to human health and the analysis of infectious disease data is among the most important application of statistics. In this article, we develop Bayesian methodology using parametric bivariate accelerated lifetime model to study dependency between the colonization and infection times for Acinetobacter baumannii bacteria which is leading cause of infection among the hospital infection agents. We also study their associations with covariates such as age, gender, apache score, antibiotics use 3 months before admission and invasive mechanical ventilation use. To account for singularity, we use Singular Bivariate Extreme Value distribution to model residuals in Bivariate Accelerated lifetime model under the fully Bayesian framework. We analyze a censored data related to the colonization and infection collected in five major hospitals in Turkey using our methodology. The data analysis done in this article is for illustration of our proposed method and can be applied to any situation that our model can be used.

Seroprevalence of hepatitis B and C virus infections and risk factors in Turkey: a fieldwork TURHEP study.

The present study was designed to determine the seroprevalence of hepatitis B and C virus (HBV, HCV) infections and risk factors in the Turkish general population. Participants were enrolled from urban and rural areas of the predetermined 23 EUROSTAT NUTS 2 region. A two-stage stratified sampling method was used to select participants from these regions (n = 5460; 50.9% females; mean (SD) age: 40.8 (14.7) years). Sociodemographics, clinical characteristics and risk factors were recorded at home visits. The seropositivity rates for hepatitis B surface antigen (HBsAg), anti-HCV, anti-HBs and anti-HBc total were 4.0%, 1.0%, 31.9% and 30.6%, respectively. Among HBsAg-positive cases, 94.5% were anti-HBe-positive, 70.2% were HBV-DNA-positive and 2.8% were anti-HDV total positive; 99.1% of HBV infections were of genotype D. Close contact with a hepatitis patient (OR 3.24; 95% CI 2.25-4.66; p < 0.001), living in the southeastern region (OR 2.74; 95% CI 1.7-4.45; p < 0.001), male gender (OR 1.77; 95% CI 1.28-2.46; p < 0.001), being married (OR 1.62; 95% CI 1.02-2.57; p 0.038), educational level less than high school (OR 1.53; 95% CI 1.04-2.26; p 0.03), orodental interventions (OR 1.54; 95% CI 1.01-2.35; p 0.047) and a history of non-disposable syringe use (OR 1.4; 95% CI 1.01-1.96; p 0.045) were significant determinants of HBsAg positivity. Age ≥50 years (OR 2; 95% CI 1.09-4.3; p 0.026) was the only significant predictor of anti-HCV positivity. In conclusion, our findings revealed an HBsAg positivity in 4% and anti-HCV positivity in 1% of the adult population and at least one-third of the population has been exposed to HBV infection in Turkey.

Predictors for limb loss among patient with diabetic foot infections: an observational retrospective multicentric study in Turkey.

We aimed to investigate the predictors for limb loss among patients with diabetes who have complicated skin/soft-tissue infections. In this observational study, consecutive patients with diabetic foot infection (DFI) from 17 centres in Turkey, between May 2011 and May 2013 were included. The Turkish DFI Working Group performed the study. Predictors of limb loss were investigated by multivariate analysis. In total, 455 patients with DFI were included. Median age was 61 years, 68% were male, 65% of the patients were hospitalized, 52% of the patients had used antibiotics within the last month, and 121 (27%) had osteomyelitis. Of the 208 microorganisms isolated, 92 (44.2%) were Gram-positive cocci and 114 (54.8%) were Gram-negative rods (GNR). The most common GNR was Pseudomonas; the second was Escherichia coli, with extended spectrum ß-lactamase positivity of 33%. Methicillin-resistant Staphylococcus species were found in 14% (29/208). Amputations were performed in 126/455 (28%) patients, 44/126 (34%) of these were major amputations. In multivariate analysis, significant predictors for limb loss were, male gender (OR 1.75, 95% CI 1.04-2.96, p 0.034), duration of diabetes >20 years (OR 1.9, 95% CI 1.18-3.11, p 0.008), infected ulcer versus cellulitis (OR 1.9, 95% CI 1.11-3.18, p 0.019), history of peripheral vascular disease (OR 2, 95% CI 1.26-3.27, p 0.004), retinopathy (OR 2.25, 95% CI 1.19-4.25, p 0.012), erythrocyte sedimentation rate >70 mm/hr (OR 1.6, 95% CI 1.01-2.68, p 0.05), and infection with GNR (OR 1.8, 95% CI 1.08-3.02, p 0.02). Multivariate analysis revealed that, besides the known risk factors such as male gender, duration of diabetes >20 years, infected ulcers, history of peripheral vascular disease and retinopathy, detection of GNR was a significant predictor of limb loss.

Vertebral osteomyelitis: clinical features and diagnosis.

We aimed to describe clinical and diagnostic features of vertebral osteomyelitis for differential diagnosis and treatment. This is a prospective observational study performed between 2002 and 2012 in Ankara Numune Education and Research Hospital in Ankara, Turkey. All the patients with vertebral osteomyelitis were followed for from 6 months to 3 years. In total, 214 patients were included in the study, 113 out of 214 (53%) were female. Out of 214 patients, 96 (45%) had brucellar vertebral osteomyelitis (BVO), 63 (29%) had tuberculous vertebral osteomyelitis (TVO), and 55 (26%) had pyogenic vertebral osteomyelitis (PVO). Mean number of days between onset of symptoms and establishment of diagnosis was greater with the patients with TVO (266 days) than BVO (115 days) or PVO (151 days, p <0.001). In blood cultures, Brucella spp. were isolated from 35 of 96 BVO patients (35%). Among 55 PVO patients, the aetiological agent was isolated in 11 (20%) patients. For tuberculin skin test >15 mm, sensitivity was 0.66, specificity was 0.97, positive predictive value was 0.89, negative predictive value was 0.88, and receiver operating characteristics area was 0.8. Tuberculous and brucellar vertebral osteomyelitis remained the leading causes of vertebral osteomyelitis with delayed diagnosis. In differential diagnosis of vertebral osteomyelitis, consumption of unpasteurized cheese, dealing with husbandry, sweating, arthralgia, hepatomegaly, elevated alanine transaminase, and lumbar involvement in magnetic resonance imaging were found to be predictors of BVO, thoracic involvement in magnetic resonance imaging and tuberculin skin test > 15 mm were found to be predictors of TVO, and history of spinal surgery and leucocytosis were found to be predictors of PVO.

Preferences of different tick species for human hosts in Turkey.

The ticks removed from the patients who applied to the hospitals in Istanbul and neighboring cities, Turkey, with the complaint of tick bite were examined in this study, on account of their species, biological stages, attachment sites on the body, and the age of the affected patients. A total of 16,969 ticks were identified. Encountered species were as follows: 33.6 % Ixodes spp. immature, 25.3 % Hyalomma spp. immature, 24.3 % I. ricinus, 9.5 % Rhipicephalus sanguineus gr., 3.2 % R. bursa, 2.2 % Hyalomma marginatum, 1.96 % Haemaphysalis adults, 1.66 % Hyalomma aegyptium, 0.52 % Dermacentor marginatus, 0.39 % Rhipicephalus spp. nymphs, 0.12 % Dermacentor spp. nymphs, 0.11 % Haemaphysalis spp. nymphs, 0.09 % Hyalomma scupense, and 0.03 % Hyalomma excavatum. The distribution of attachment sites of the species and instars showed significant differences. Furthermore, age data of the patients also revealed that certain tick species were more common within certain age groups.

Nosocomial outbreak of disseminated orf infection in a burn unit, Gaziantep, Turkey, October to December 2012.

We report the first outbreak of nosocomial orf infection in a hospital burn unit in Gaziantep, Turkey. The outbreak lasted from October to December 2012 and involved a total of thirteen cases. It demonstrates the risk of introduction of orf virus to a burn unit, and the potential for extensive transmission among patients with compromised skin integrity. The importance of hygiene measures and infection control are highlighted and possible transmission routes of the virus discussed.

Laboratory-acquired brucellosis in Turkey.

BACKGROUND: Laboratory healthcare workers (HCWs) are at risk of laboratory-acquired brucellosis (LAB). AIM: To describe the risk factors of LAB among HCWs. METHODS: A multicentre survey study was conducted by face-to-face interview in 38 hospitals from 17 provinces of Turkey. A structured survey was administered to the HCWs, working in infectious diseases clinics and microbiology departments, who were at risk of brucella infection. FINDINGS: The survey response rate was 100%. Of the 667 laboratory workers, 38 (5.8%) had a history of LAB. In multivariate analysis, factors independently associated with an increased risk of LAB included working with the brucella bacteria (odds ratio: 5.12; 95% confidence interval: 2.28-11.52; P < 0.001) and male gender (2.14; 1.02-4.45; P = 0.042). Using a biosafety cabinet level 2 (0.13; 0.03-0.60; P = 0.009), full adherence to glove use (0.27; 0.11-0.65; P = 0.004) and longer duration of professional life (0.86; 0.80-0.92; P < 0.001) were found to be protective. CONCLUSIONS: Working with the brucella bacteria, being male, a lack of compliance with personal protective equipment and biosafety cabinets were the independent risk factors for the development of LAB in our series. Increased adherence to personal protective equipment and use of biosafety cabinets should be priority targets to prevent LAB.

Evaluation of the therapeutic use of antibiotics in Aegean Region hospitals of Turkey: a multicentric study.

PURPOSE: The antibiotic restriction policy has been validated nationwide since February 2003 by the Ministry of Health because the excessive consumption of antimicrobials causes a high cost. The aim of this study was to evaluate the therapeutic use of antibiotics in Aegean Region hospitals and to assess the impact of this nationwide antibiotic restriction policy. This new policy is based on justification that the infectious disease (ID) physicians should be primarily responsible for the prescription of antimicrobials. MATERIALS AND METHODS: Eight university and government hospitals were included in the study. The criteria of the Council for Appropriate and Rational Antibiotic Therapy (CARAT) were considered. Both patient-based and antibiotic-based analyses were performed. For the analysis of inappropriate use, logistic regression was modeled. RESULTS: Therapeutic use was determined in 540 patients by a total of 29 ID physicians.In the study, 30.2% of the patients were given antimicrobials and empirically started antibiotics accounted for 79% cases of therapeutic antibiotic use, and 60% of those were inappropriate (P = 0.001). The appropriate use of ID level antibiotics (P = 0.000) were very compatible with other antimicrobial groups. CONCLUSION: The study shows that the Turkish government's new intervention policy on antimicrobial prescribing has been effective.

Crimean-Congo hemorrhagic fever in Europe: current situation calls for preparedness.

During the last decade Crimean-Congo hemorrhagic fever (CCHF) emerged and/or re-emerged in several Balkan countries, Turkey, southwestern regions of the Russian Federation, and the Ukraine, with considerable high fatality rates. Reasons for re-emergence of CCHF include climate and anthropogenic factors such as changes in land use, agricultural practices or hunting activities, movement of livestock that may influence host-tick-virus dynamics. In order to be able to design prevention and control measures targeted at the disease, mapping of endemic areas and risk assessment for CCHF in Europe should be completed. Furthermore, areas at risk for further CCHF expansion should be identified and human, vector and animal surveillance be strengthened.