scholarly journals Secondary bacterial infections and antimicrobial resistance in COVID-19: comparative evaluation of pre-pandemic and pandemic-era, a retrospective single center study

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Mustafa Karataş ◽  
Melike Yaşar-Duman ◽  
Alper Tünger ◽  
Feriha Çilli ◽  
Şöhret Aydemir ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Bacterial Infections ◽  
Respiratory Infections ◽  
Low Frequency ◽  
Positive Culture ◽  
Positive Sample ◽  
University Hospital ◽  
Control Groups ◽  
Extended Spectrum Beta Lactamase ◽  
Culture Positive

Abstract Purpose In this study, we aimed to evaluate the epidemiology and antimicrobial resistance (AMR) patterns of bacterial pathogens in COVID-19 patients and to compare the results with control groups from the pre-pandemic and pandemic era. Methods Microbiological database records of all the COVID-19 diagnosed patients in the Ege University Hospital between March 15, 2020, and June 15, 2020, evaluated retrospectively. Patients who acquired secondary bacterial infections (SBIs) and bacterial co-infections were analyzed. Etiology and AMR data of the bacterial infections were collected. Results were also compared to control groups from pre-pandemic and pandemic era data. Results In total, 4859 positive culture results from 3532 patients were analyzed. Fifty-two (3.59%) patients had 78 SBIs and 38 (2.62%) patients had 45 bacterial co-infections among 1447 COVID-19 patients. 22/85 (25.88%) patients died who had bacterial infections. The respiratory culture-positive sample rate was 39.02% among all culture-positive samples in the COVID-19 group. There was a significant decrease in extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales (8.94%) compared to samples from the pre-pandemic (20.76%) and pandemic era (20.74%) (p = 0.001 for both comparisons). Interestingly, Acinetobacter baumannii was the main pathogen in the respiratory infections of COVID-19 patients (9.76%) and the rate was significantly higher than pre-pandemic (3.49%, p < 0.002) and pandemic era control groups (3.11%, p < 0.001). Conclusion Due to the low frequency of SBIs reported during the ongoing pandemic, a more careful and targeted antimicrobial prescription should be taken. While patients with COVID-19 had lower levels of ESBL-producing Enterobacterales, the frequency of multidrug-resistant (MDR) A. baumannii is higher.

scholarly journals Secondary Bacterial Infections and Antimicrobial Resistance in COVID-19: Comparative Evaluation of Pre-Pandemic and Pandemic-Era, A Retrospective Single Center Study

2021 ◽  
Author(s):  
Mustafa Karataş ◽  
Melike Yaşar Duman ◽  
Alper Tünger ◽  
Feriha Çilli ◽  
Şöhret Aydemir ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Bacterial Infections ◽  
Respiratory Infections ◽  
Low Frequency ◽  
Positive Culture ◽  
Positive Sample ◽  
University Hospital ◽  
Control Groups ◽  
Extended Spectrum Beta Lactamase ◽  
Culture Positive

Abstract Purpose: In this study, we aimed to evaluate the epidemiology and antimicrobial resistance (AMR) patterns of bacterial pathogens in COVID-19 patients and to compare the results with control groups from the pre-pandemic and pandemic era.Methods: Microbiological database records of all the COVID-19 diagnosed patients in the Ege University Hospital between March 15, 2020, and June 15, 2020, evaluated retrospectively. Patients who acquired secondary bacterial infections (SBIs) and bacterial co-infections were analyzed. Etiology and AMR data of the bacterial infections were collected. Results were also compared to control groups from pre-pandemic and pandemic era data.Results: In total, 4,859 positive culture results from 3,532 patients were analyzed. Fifty-two (3.59%) patients had 78 SBIs and 38 (2.62%) patients had 45 bacterial co-infections among 1,447 COVID-19 patients. 22/85 (25.88%) patients died who had bacterial infections. The respiratory culture-positive sample rate was 39.02% among all culture-positive samples in the COVID-19 group. There was a significant decrease in extended-spectrum beta-lactamase-producing Enterobacterales (8.94%) compared to samples from the pre-pandemic (20.76%) and pandemic era (20.74%) (p=0.001 for both comparisons). Interestingly, Acinetobacter baumannii was the main pathogen in the respiratory infections of COVID-19 patients (%9.76) and the rate was significantly higher than pre-pandemic (3.49%, p<0.002) and pandemic era control groups (3.11%, p<0.001).Conclusion: Due to the low frequency of SBIs reported during the ongoing pandemic, a more careful and targeted antimicrobial prescription should be taken. While patients with COVID-19 had lower levels of ESBL producing Enterobacterales, the frequency of MDR A. baumannii is higher.

Beta-lactam Resistance Mechanisms in Pathogens Isolated from Patients Admitted to Intensive Care Unit

2017 ◽  
Vol 68 (6) ◽  
pp. 1225-1228
Author(s):  
Carmen Axente ◽  
Delia Muntean ◽  
Luminita Baditoiu ◽  
Roxana Moldovan ◽  
Elena Hogea ◽  
...  
Keyword(s):  
Intensive Care Unit ◽  
Intensive Care ◽  
Antimicrobial Resistance ◽  
Resistance Mechanisms ◽  
University Hospital ◽  
Beta Lactam ◽  
Extended Spectrum Beta Lactamase ◽  
Beta Lactam Antibiotics ◽  
Current Context ◽  
A Prospective Study

Intensive care units (ICUs) are often referred to as the epicentre of infection diseases in a hospital. Many studies highlighted the importance of using local antimicrobial resistance data, to guide empirical antibiotic therapy. As a consequence, the present study is particularly important, especially in the current context, when we are witnessing an ascending trend of antimicrobial resistance. Beta-lactams are the most frequently used class of antibiotics for treating patients infected with various germs. The aim of this study is to analyse the modalities by which microorganisms become resistant to antibiotics of this class, in an intensive care unit of a Romanian university hospital. During the period between January, the 1st 2012 and December the 31st 2013, a prospective study was conducted in the largest ICU from the Western part of Romania. Various resistance mechanisms to beta-lactam antibiotics were detected. Among these, there is great concern regarding the high number of extended-spectrum beta-lactamase producing microorganisms, as in most cases they determine the use of carbapenems, thus increasing the risk of occurrence and dissemination of carbapenemase-producing bacteria.

scholarly journals Impact of parental smoking on influenza and others respiratory infections in children

2020 ◽  
pp. 475-482
Keyword(s):  
General Population ◽  
Respiratory Tract ◽  
Bacterial Infections ◽  
Respiratory Tract Infections ◽  
Respiratory Infections ◽  
University Hospital ◽  
Side Stream ◽  
Quitting Smoking ◽  
Observational Cohort ◽  
Tract Infections

BACKGROUND. The predisposition of cigarette smokers for the development of respiratory infections, including influenza, have been well documented. As well, those exposed to side stream smoke are prone to viral and bacterial infections of the respiratory tract. AIM. The study aimed to evaluate whether the prevalence of smoking parents is higher among children with respiratory tract infections, including influenza, in comparison to the general population. MATERIAL AND METHODS. Observational, cohort study. The authors surveyed a cohort of patients and their families, hospitalized in the Paediatric University Hospital in Warsaw during 2018 influenza season. Patients were diagnosed with influenza (using PCR) or other respiratory tract infections. A questionnaire on smoking habits was performed. RESULTS. Overall, 72 patients were included in the study, median age 2 years and 9 months (IQR: 1.4 – 7.2), influenza was diagnosed in 43% (n= 31) of patients. The percentage of regularly smoking parents in the whole cohort amounted to 33.3% (44 of 132) and was statistically significantly higher (p < 0.05) than in the general population (22.7%), whereas in the subgroup with influenza and non-influenza infections it reached 32.2% and 34.2%, respectively. CONCLUSIONS. The prevalence of smoking parents of children with acute respiratory tract infections is higher than in the general population: exposing children to tobacco smoke is one of the risk factors for acquiring influenza and others respiratory tract infections. Quitting smoking can decrease the risk of infectious diseases.

scholarly journals Evaluation of the relationship between quantitative PCR results and cell culturing of SARS2-CoV with respect to symptoms onset and Viral load – a systematic review

2021 ◽  
Author(s):  
gilad rozenberg ◽  
Oran Erster ◽  
Itai Ghersin ◽  
Michal Mandelboim ◽  
Ami neuberger ◽  
...  
Keyword(s):  
Viral Load ◽  
Viral Genome ◽  
Positive Culture ◽  
Accurate Method ◽  
Positive Sample ◽  
Immunocompromised Patients ◽  
Ct Value ◽  
Asymptomatic Patients ◽  
Pcr Assays ◽  
Culture Positive

Background: Viral culture is currently the most accurate method to demonstrate viability and infectivity of Severe acute respiratory syndrome Coronavirus (SARS–2 CoV). Routine clinical diagnosis, however, is mostly performed by PCR – based assays that do not discriminate between infectious and non–virus. Herein, we aimed to determine the correlation between positive viral cultures and either PCR positivity, the Cycle Threshold (Ct) or the number of viral copies. Methods: A systematic electronic literature search was performed and studies that reported both viral SARS–CoV–2 culture and PCR–based assays were included. A separate search for samples from blood, urine, stool, breast milk and tears were performed. To convert Ct values reported in the reviewed studies were to viral genomic copies, calibration experiments with four different reaction performed, using quantified RNA molecules. Results: A total 540 articles were reviewed, and 38 studies were included in this review. Out of 276 positive–culture of non-severe patients, 272 (98.55%) were negative ten days after symptoms onset, while PCR assays remained positive for up to 67 days. In severely ill or immunocompromised patients positive-culture was obtained up to 32 days and out of 168 cultures, 31 (18.45%) stayed positive after day 10. In non-severe patients, in Ct value greater than 30 only 10.8% were still culture–positive while in Ct >35 it was nearly universally negative. The minimal calculated number of viral genome copies in culture- positive sample was 2.5 X 103 copies / mL. These findings were similar in immunocompromised patients. Recovering positive culture from non–respiratory samples was sporadically obtained in stool or urine samples. Conversion of Ct values to viral genome copies showed variability between different PCR assays and highlighted the need to standardize reports to correctly compare results obtained in different laboratories. Conclusion: During the pandemic phase, non-severe COVID-19 patients who are recovering and are not immuno-suppressed, can be regarded as non–infectious, within 10 days from symptom onset, or with Ct value greater than 35 (or a calculated viral load lower than 1.2X103 copies / mL). These findings have important implications for recovering patients and asymptomatic patients, with respect to isolation criteria. The conversion of Cq values to viral genome copies described herein may be useful in future work, enabling a more standardized comparison between results reported in different studies from different laboratories.

Nontuberculous Mycobacteria under Scrutiny in the Geneva Area (2015–2020)

Respiration ◽  
2021 ◽  
pp. 1-9
Author(s):  
Rechana Vongthilath-Moeung ◽  
Jérôme Plojoux ◽  
Antoine Poncet ◽  
Gesuele Renzi ◽  
Nicolas Veziris ◽  
...  
Keyword(s):  
Nontuberculous Mycobacteria ◽  
Specific Treatment ◽  
Positive Culture ◽  
University Hospital ◽  
Mycobacterium Chelonae ◽  
Mycobacterium Xenopi ◽  
Episodes Of Care ◽  
Low Bmi ◽  
Relative Prevalence ◽  
Culture Positive

<b><i>Background:</i></b> Nontuberculous mycobacteria (NTM) are increasingly identified in industrialized countries, and their role as pathogens is more frequently recognized. The relative prevalence of NTM strains shows an important geographical variability. Thus, establishing the local relative prevalence of NTM strains is relevant and useful for clinicians. <b><i>Methods:</i></b> Retrospective analysis (2015–2020) of a comprehensive database was conducted including all results of cultures for mycobacteria in a University Hospital (Geneva, Switzerland), covering a population of approximately 500,000 inhabitants. All NTM culture-positive patients were included in the analyses. Patients’ characteristics, NTM strains, and time to culture positivity were reported. <b><i>Results:</i></b> Among 38,065 samples analyzed during the study period, 411 were culture-positive for NTM, representing 236 strains, and 231 episodes of care which occurred in 222 patients. Patients in whom NTM were identified were predominantly female (55%), with a median age of 62 years, and a low BMI (median: 22.6 kg/m<sup>2</sup>). The <i>Mycobacterium avium</i> complex (MAC) was the most frequently identified group (37% of strains) followed by <i>Mycobacterium gordonae</i> (25%) and <i>Mycobacterium xenopi</i> (12%) among the slowly growing mycobacteria (SGM), while the <i>Mycobacterium chelonae/abscessus</i> group (11%) were the most frequently identified rapidly growing mycobacteria (RGM). Only 19% of all patients were treated, mostly for pulmonary infections: the MAC was the most frequently treated NTM (<i>n</i> = 19, 43% of cases in patients treated) followed by RGM (<i>n</i> = 15, 34%) and <i>M. xenopi</i> (<i>n</i> = 6, 14%). Among those treated, 23% were immunosuppressed, 12% had pulmonary comorbidities, and 5% systemic comorbidities. Cultures became positive after a median of 41 days (IQR: 23; 68) for SGM and 28 days (14; 35) for RGM. <b><i>Conclusions:</i></b> In Western Switzerland, <i>M. avium</i> and <i>M. gordonae</i> were the most prevalent NTM identified. Positive cultures for NTM led to a specific treatment in 19% of subjects. Patients with a positive culture for NTM were mostly female, with a median age of 62 years, a low BMI, and a low prevalence of immunosuppression or associated severe comorbidities.

scholarly journals Etiological Trends and Patterns of Antimicrobial Resistance in Respiratory Infections

2018 ◽  
Vol 12 (1) ◽  
pp. 34-40 ◽  
Author(s):  
Salma M. Al-Zain Ahmed ◽  
Sara S. Abdelrahman ◽  
Doua M. Saad ◽  
Isra S. Osman ◽  
Modasir G. Osman ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Respiratory Infection ◽  
Antimicrobial Agents ◽  
Susceptibility Testing ◽  
Respiratory Infections ◽  
Resistance Rate ◽  
High Rate ◽  
Culture Positive ◽  
Global Health Problem ◽  
Respiratory Specimens

Background:Respiratory infections are one of the commonest causes of morbidity and mortality related to infectious diseases worldwide. The emergence of antimicrobial resistance is a major global health problem which is well established in developing countries. Good clinical suspicion and correct laboratory identification of respiratory infection causing organisms followed by the appropriate management are needed to compact both community-acquired and nosocomial infection respiratory infections.Objectives:A retrospective study was carried out to elucidate the etiology of respiratory infections in Sudan, as well as to guide the physician to the best antimicrobial alternatives used in the treatment of respiratory infection.Method:Respiratory isolates that have been morphologically identified and biologically characterized were subjected to antibiotic susceptibility testing.Results:A total of 1481 respiratory specimens were examined, recovering 377 organisms from 350 culture positive samples [225(59.7%) sputum, 94(24.9%) broncho-alveolar lavage (BAL), 58(15.4%) Pleural fluid], the commonest organisms wereKlebsiella ssp. (25.20%) andmycobacterium tuberculosis(25.20%), followed byStaphylococcus aureus(19.89%) andPseudomonas aeruginosa(8.49%). High rate of resistance of bacterial isolates was observed to Co-trimoxazole (BA), Ampicillin sulbactam (AS), Cefotaxime (CF) and Tetracycline (TE), being 80%, 72.3%, 68.8% and 66.9% respectively; on the other hand, very low resistance rate was found to Amikacin (AK) and Levofloxacin (LE), being 4.6% and 8.5%, respectively.Conclusion:Guided prescription of antimicrobial agents must be implemented and controlled to limit further spread of antimicrobial resistance.

scholarly journals Antimicrobial resistance in patients with decompensated liver cirrhosis and bacterial infections in a tertiary center in Northern Germany

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Annika Hillert ◽  
Marie Schultalbers ◽  
Tammo L. Tergast ◽  
Ralf-Peter Vonberg ◽  
Jessica Rademacher ◽  
...  
Keyword(s):  
Liver Cirrhosis ◽  
Antimicrobial Resistance ◽  
Nosocomial Infections ◽  
Bacterial Infections ◽  
Empiric Therapy ◽  
Multidrug Resistant ◽  
Gram Positive ◽  
Decompensated Liver Cirrhosis ◽  
Tertiary Center ◽  
Culture Positive

Abstract Background and aims Bacterial infections are common in patients with decompensated liver cirrhosis and a leading cause of death. Reliable data on antibiotic resistance are required to initiate effective empiric therapy. We here aim to assess the antimicrobial resistance profile of bacteria among patients with liver cirrhosis and infection. Methods Overall, 666 cirrhotic patients admitted to Hannover Medical School between January 2012 and April 2018 with ascites were assessed for bacterial infection. In case of infection, bacteria cultured from microbiological specimens of ascites, blood or urine were identified and analyzed for resistances against common antibiotic agents. Furthermore, analyses compared two periods of time and community-acquired vs. nosocomial infections. Results In 281 patients with infection, microbiological sampling was performed and culture-positive results were obtained in 56.9%. Multidrug-resistant (MDR)-bacteria were found in 54 patients (19.2%). Gram-positive organisms were more common (n = 141/261, 54.0%) and detected in 116/192 culture-positive infections (60.4%). Comparing infections before and after 2015, a numerical decline for MDR-bacteria (23.8% vs. 15.6%, p = 0.08) was observed with a significant decline in meropenem resistance (34.9% vs. 19.5%, p = 0.03). MDR-bacteria were more frequent in the case of nosocomial infections. Of note, in ascites the majority of the tested bacteria were resistant against ceftriaxone (73.8%) whereas significantly less were resistant against meropenem (27.0%) and vancomycin (25.9%). Conclusions In our tertiary center, distinct ratios of gram-positive infection with overall low ratios of MDR-bacteria were found. Adequate gram-positive coverage in the empiric therapy should be considered. Carbapenem treatment may be omitted even in nosocomial infection. In contrast, 3rd generation cephalosporins cannot be recommended even in community-acquired infection in our cirrhotic population.

scholarly journals Antimicrobial resistance patterns of phenotype Extended Spectrum Beta-Lactamase producing bacterial isolates in a referral hospital in northern Tanzania

2015 ◽  
Vol 17 (3) ◽  
Author(s):  
Debora C. Kajeguka ◽  
Petro P. Nambunga ◽  
Frank Kabissi ◽  
Benjamin Kamugisha ◽  
Nancy Kassam ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Bacterial Infections ◽  
Clinical Laboratory ◽  
Treatment Protocol ◽  
Resistance Pattern ◽  
Beta Lactamase ◽  
Blood Samples ◽  
Extended Spectrum Beta Lactamase ◽  
Extended Spectrum ◽  
Esbl Producers

Background: Production of Extended Spectrum Beta-Lactamase (ESBL) by bacteria is a chronic problem in a health care set up. In order to have adequate information for treatment of bacterial infections especially ESBL producing isolates, it is crucial to understand the trends in the antibiotic-resistance pattern, occurrence and their geographical spread.  The objective of this study was to determine the antimicrobial resistance pattern among phenotype ESBL producing isolates in northern Tanzania.Methods: From July 2013 to January 2014, urine, pus and blood samples were collected from patients suspected to have bacterial infections at Kilimanjaro Christian Medical Centre in Moshi, Tanzania. The isolates were identified based on standard laboratory procedures. Antimicrobial susceptibility tests were carried out using various antimicrobial discs as per the recommendations of Clinical Laboratory Standard Institute.Results: A total of 330 specimens were collected. They consisted of 46 urine, 264 pus (from wound) and 20 blood samples. Among isolated bacteria, ESBL producers were 29.7% (98) and non-producers were 70.5% (232).  Escherichia coli and Klebsiella pneumoniae were the most isolated bacteria and dominant ESBL producers.  ESBL production was highly associated with moderate condition at discharge and longer periods of admission. More than 60% of the ESBL producing E. coli were resistant to ceftazidime, cefpodoxime, cefotaxime, amoxycilin, ciprofloxacin, and gentamycin. More than 80% of ESBL producing K. pneumonia and Proteus mirabilis were resistant to ceftazidime and cefotaxime. Fifty four percent of ESBL producing K. pneumonia were resistant to gentamycin.Conclusion: This study shows that ESLB phenotypes among Gram-negative bacteria are common among patients attending a tertiary hospital in northern in Tanzania. The findings suggest that clinical microbiology laboratories should take into account the diagnosis of ESBL producers in order to define the degree of the problem so as to establish a proper treatment protocol.

scholarly journals Urban Migrant Labourers as Potential Source for Transfer of Antimicrobial Resistance to Rural Community

2020 ◽  
Vol 14 (4) ◽  
pp. 2371-2381
Author(s):  
Debasish Chattopadhya ◽  
Leimapokpam Sumitra Devi ◽  
Shyam Sunder Grover ◽  
Shobha Broor
Keyword(s):  
Antimicrobial Resistance ◽  
Rural Community ◽  
Bacterial Infections ◽  
Beta Lactamase ◽  
Low Literacy ◽  
Local Resident ◽  
Carriage Rate ◽  
Extended Spectrum Beta Lactamase ◽  
History Of ◽  
Urban Migrant

The aim of the study was to investigate potential evidence for spread of antimicrobial resistance (AMR) from urban migrant labourers to labourers from local resident rural community due to sharing of common residential premises and other civic amenities. Two groups of unskilled labourers, enrolled for civil construction in a peri-urban area viz. (i) labourers having migrated from urban zone and (ii) labourers from local resident village community were compared in terms of demographic profile, history of various risk factors towards acquisition of AMR and prevalence of extended-spectrum beta-lactamase (ESBL), carbapenemase and New Delhi metallo-beta-lactamase type 1 (NDM-1) categories of AMR at enrolment and after one year of sharing of common residential premises with associated sanitation facilities using Escherichia coli as indicator organism. Higher percentage of urban migrant labourers were characterised by low literacy level, history of inhabitation in makeshift shelters without dedicated access to drinking water or cooking space, practice of defecation in open, episodes of illness suggestive of bacterial infections, faulty treatment seeking behaviour and intestinal carriage rate of E. coli with various categories of AMR compared to the non-migrant labourers from rural community. The later group showed an increase in the prevalence of carbapenem resistance with NDM-1 production during the duration of co-inhabitation with urban migrant labourers. The present study provided potential evidence for transfer of AMR by urban migrant labourers to non-migrant labourers from rural community that may serve as vehicle for further transmission of AMR to the rural community hitherto unexposed or less exposed to the problem.

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