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1.
Infection ; 50(3): 767-770, 2022 Jun.
Article in English | MEDLINE | ID: covidwho-1872772

ABSTRACT

PURPOSE: The impact of SARS-CoV-2 pandemic on other pathogens is largely unknown. We aimed to compare the prevalence of vaccine-preventable invasive bacterial infections before and during the pandemic in Piedmont (Italy). METHODS: We defined the monthly incidence of S. pneumoniae, H. influenzae and N. meningitides-invasive diseases from January 2010 to June 2021. Then, we compared the mean monthly cases during the previous 5 years (2015-2019) and the monthly cases in 2020 or 2021. RESULTS: We found significant reductions for invasive pneumococcal diseases (IPDs) in adults and H. influenzae-invasive diseases in 2020 and 2021 in comparison to the previous years, but not for invasive meningococcal diseases and IPDs in children. CONCLUSIONS: Further data are needed to confirm these findings and define possible post-pandemic evolutions in the epidemiology of vaccine-preventable invasive bacterial diseases.


Subject(s)
Bacterial Infections , COVID-19 , Pneumococcal Infections , Vaccines , Adult , Bacteria , Bacterial Infections/epidemiology , COVID-19/epidemiology , COVID-19/prevention & control , Child , Haemophilus influenzae , Humans , Incidence , Infant , Pandemics/prevention & control , Pneumococcal Infections/epidemiology , Pneumococcal Infections/prevention & control , SARS-CoV-2 , Streptococcus pneumoniae
3.
Adv Sci (Weinh) ; 9(14): e2105955, 2022 05.
Article in English | MEDLINE | ID: covidwho-1843844

ABSTRACT

As a novel type of antibiotic alternative, peptide-based antibacterial drug shows potential application prospects attributable to their unique mechanism for lysing the membrane of pathogenic bacteria. However, peptide-based antibacterial drugs suffer from a series of problems, most notably their immature stability, which seriously hinders their application. In this study, self-assembling chimeric peptide nanoparticles (which offer excellent stability in the presence of proteases and salts) are constructed and applied to the treatment of bacterial infections. In vitro studies are used to demonstrate that peptide nanoparticles NPs1 and NPs2 offer broad-spectrum antibacterial activity and desirable biocompatibility, and they retain their antibacterial ability in physiological salt environments. Peptide nanoparticles NPs1 and NPs2 can resist degradation under high concentrations of proteases. In vivo studies illustrate that the toxicity caused by peptide nanoparticles NPs1 and NPs2 is negligible, and these nanoparticles can alleviate systemic bacterial infections in mice and piglets. The membrane permeation mechanism and interference with the cell cycle differ from that of antibiotics and mean that the nanoparticles are at a lower risk of inducing drug resistance. Collectively, these advances may accelerate the development of peptide-based antibacterial nanomaterials and can be applied to the construction of supramolecular nanomaterials.


Subject(s)
Bacterial Infections , Nanoparticles , Sepsis , Animals , Anti-Bacterial Agents/pharmacology , Bacteria , Bacterial Infections/drug therapy , Mice , Peptide Hydrolases , Peptides/pharmacology , Swine
4.
Int J Infect Dis ; 118: 197-202, 2022 May.
Article in English | MEDLINE | ID: covidwho-1838861

ABSTRACT

OBJECTIVES: We described the current incidence and risk factors of bacterial co-infection in hospitalized patients with COVID-19. METHODS: Observational cohort study was performed at the Hospital Clinic of Barcelona (February 2020-February 2021). All patients with COVID-19 who were admitted for >48 hours with microbiological sample collection and procalcitonin (PCT) determination within the first 48 hours were included. RESULTS: A total of 1125 consecutive adults met inclusion criteria. Co-infections were microbiologically documented in 102 (9.1%) patients. Most frequent microorganisms were Streptococcus pneumoniae (79%), Staphylococcus aureus (6.8%), and Haemophilus influenzae (6.8%). Test positivity was 1% (8/803) for blood cultures, 10.1% (79/780) for pneumococcal urinary antigen test, and 11.4% (15/132) for sputum culture. Patients with PCT higher than 0.2, 0.5, 1, and 2 ng/mL had significantly more co-infections than those with lower levels (p=0.017, p=0.031, p<0.001, and p<0.001, respectively). In multivariate analysis, oxygen saturation ≤94% (OR 2.47, CI 1.57-3.86), ferritin levels <338 ng/mL (OR 2.63, CI 1.69-4.07), and PCT higher than 0.2 ng/mL (OR 1.74, CI 1.11-2.72) were independent risk factors for co-infection at hospital admission owing to COVID-19. CONCLUSIONS: Bacterial co-infection in patients hospitalized for COVID-19 is relatively common. However, clinicians could spare antibiotics in patients with PCT values <0.2, especially with high ferritin values and oxygen saturation >94%.


Subject(s)
Bacterial Infections , COVID-19 , Coinfection , Adult , Bacterial Infections/microbiology , COVID-19/epidemiology , Coinfection/epidemiology , Ferritins , Hospitals , Humans , Procalcitonin , Retrospective Studies , SARS-CoV-2
5.
Zhonghua Yu Fang Yi Xue Za Zhi ; 56(4): 401-404, 2022 Apr 06.
Article in Chinese | MEDLINE | ID: covidwho-1834948

ABSTRACT

Despite the fact that our cognition towards infectious disease prevention, the advanced technology and the economic status of the whole society has made a great progress in the last decade, the outbreak of COVID-19 pneumonia has again enabled the public to acquire more about super-challenges of infectious diseases, epidemics and the relevant preventive measurements. In order to identify the epidemic signals in early stage or even before the onset of epidemic, the data research and utilization of a series of factors related to the occurrence and transmission of infectious diseases have played a significant role in research of prevention and control during the whole period of surveillance and early warning. Laboratory-based monitoring for the etiology has always been an important part of infectious disease warning system due to pathogens as the direct cause of such diseases. China has initially established a laboratory-based monitoring and early warning system for bacterial infectious diseases based on the Chinese Pathogen Identification Network with an aim to identify pathogens, outbreaks and sources. This network has played an essential role in early detection, tracking and precise prevention and control of bacterial infectious diseases, such as plague, cholera, and epidemic cerebrospinal meningitis. This issue focuses on the function of laboratory-based monitoring during the period of early warning, prevention, and control of bacterial infectious diseases, and conducted a wide range of researches based on the analysis of the epidemic and outbreak isolates, together with field epidemiological studies and normal monitoring systems. All of these could illustrate the effect of laboratory surveillance in the infectious disease risk assessment and epidemic investigation. At the same time, we have put forward our review and expectation of scenarios about laboratory-based monitoring and early warning technologies to provide innovative thoughts for promoting a leapfrog development of infectious disease monitoring and early warning system in China.


Subject(s)
Bacterial Infections , COVID-19 , Communicable Diseases , Epidemics , Bacterial Infections/epidemiology , Communicable Diseases/epidemiology , Disease Outbreaks/prevention & control , Humans , Laboratories
6.
J Hosp Infect ; 124: 37-46, 2022 Jun.
Article in English | MEDLINE | ID: covidwho-1814717

ABSTRACT

BACKGROUND: The COVID-19 pandemic increased the use of broad-spectrum antibiotics due to diagnostic uncertainty, particularly in critical care. Multi-professional communication became more difficult, weakening stewardship activities. AIM: To determine changes in bacterial co-/secondary infections and antibiotics used in COVID-19 patients in critical care, and mortality rates, between the first and second waves. METHODS: Prospective audit comparing bacterial co-/secondary infections and their treatment during the first two waves of the pandemic in a single-centre teaching hospital intensive care unit. Data on demographics, daily antibiotic use, clinical outcomes, and culture results in patients diagnosed with COVID-19 infection were collected over 11 months. FINDINGS: From March 9th, 2020 to September 2nd, 2020 (Wave 1), there were 156 patients and between September 3rd, 2020 and February 1st, 2021 (Wave 2) there were 235 patients with COVID-19 infection admitted to intensive care. No significant difference was seen in mortality or positive blood culture rates between the two waves. The proportion of patients receiving antimicrobial therapy (93.0% vs 81.7%; P < 0.01) and the duration of meropenem use (median (interquartile range): 5 (2-7) vs 3 (2-5) days; P = 0.01) was lower in Wave 2. However, the number of patients with respiratory isolates of Pseudomonas aeruginosa (4/156 vs 21/235; P < 0.01) and bacteraemia from a respiratory source (3/156 vs 20/235; P < 0.01) increased in Wave 2, associated with an outbreak of infection. There was no significant difference between waves with respect to isolation of other pathogens. CONCLUSION: Reduced broad-spectrum antimicrobial use in the second wave of COVID-19 compared with the first wave was not associated with significant change in mortality.


Subject(s)
Anti-Infective Agents , Bacterial Infections , COVID-19 , Coinfection , Anti-Bacterial Agents/therapeutic use , Anti-Infective Agents/therapeutic use , Bacterial Infections/epidemiology , COVID-19/drug therapy , Coinfection/drug therapy , Humans , Intensive Care Units , Pandemics , SARS-CoV-2
7.
Int J Environ Res Public Health ; 19(9)2022 04 26.
Article in English | MEDLINE | ID: covidwho-1809915

ABSTRACT

Bacterial co-infections may aggravate COVID-19 disease, and therefore being cognizant of other pathogens is imperative. We studied the types, frequency, antibiogram, case fatality rates (CFR), and clinical profiles of co-infecting-pathogens in 301 COVID-19 patients. Co-infection was 36% (n = 109), while CFR was 31.2% compared to 9.9% in non-co-infected patients (z-value = 3.1). Four bacterial species dominated, namely, multidrug-resistant Klebsiella pneumoniae (37%, n = 48), extremely drug-resistant Acinetobacter baumannii (26%, n = 34), multidrug-resistant Eschericia. coli (18.6%, n = 24), and extremely drug-resistant Pseudomonas aeruginosa (8.5%, n = 11), in addition to other bacterial species (9.3%, n = 12). Increased co-infection of K. pneumoniae and A. baumannii was associated with increased death rates of 29% (n = 14) and 32% (n = 11), respectively. Klebsiella pneumoniae was equally frequent in respiratory and urinary tract infections (UTI), while E. coli mostly caused UTI (67%), and A. baumannii and P. aeruginosa dominated respiratory infections (38% and 45%, respectively). Co-infections correlated with advance in age: seniors ≥ 50 years (71%), young adults 21-49 years (25.6%), and children 0-20 years (3%). These findings have significant clinical implications in the successful COVID-19 therapies, particularly in geriatric management. Future studies would reveal insights into the potential selective mechanism(s) of Gram-negative bacterial co-infection in COVID-19 patients.


Subject(s)
Bacterial Infections , COVID-19 , Coinfection , Gram-Negative Bacterial Infections , Urinary Tract Infections , Aged , Anti-Bacterial Agents/therapeutic use , Bacteria , Bacterial Infections/microbiology , COVID-19/epidemiology , Child , Coinfection/drug therapy , Coinfection/epidemiology , Escherichia coli , Female , Gram-Negative Bacteria , Gram-Negative Bacterial Infections/drug therapy , Gram-Negative Bacterial Infections/epidemiology , Humans , Klebsiella pneumoniae , Male , Microbial Sensitivity Tests , Middle Aged , Pseudomonas aeruginosa , Urinary Tract Infections/drug therapy
8.
Vnitr Lek ; 67(8): 448-454, 2021.
Article in English | MEDLINE | ID: covidwho-1801476

ABSTRACT

The COVID-19 pandemic may increase the current threat of antimicrobial resistance and exacerbate another, rather silent, pandemic posed by the increasing frequency of multidrug-resistant bacterial pathogens and the associated potential for loss of effective antibiotics. Antibiotic treatment has often been used in patients hospitalized for COVID-19 due to concerns about possible bacterial co-infection, as confirmed by previous experience with viral respiratory infections such as H1N1 influenza, SARS and MERS. Concerns or unknowns related to the COVID-19 pandemic have also affected physicians behavior, including the use of antibiotics. However, the high rate of antibiotic use in patients, especially those with mild to moderate COVID-19 disease, is inconsistent with the actual incidence of bacterial co-infections and/or secondary respiratory infections. Thus, it is clear that a careful assessment of the role of antibiotic treatment in patients hospitalized for COVID-19 is required. According to the current WHO recommendation, the application of antibiotics is especially suitable for patients with severe/critical degree of respiratory insufficiency requiring intensive oxygen therapy, artificial lung ventilation or support by extracorporeal membrane oxygenation.


Subject(s)
Bacterial Infections , COVID-19 , Influenza A Virus, H1N1 Subtype , Anti-Bacterial Agents/therapeutic use , Bacterial Infections/drug therapy , Bacterial Infections/epidemiology , Humans , Pandemics , SARS-CoV-2
10.
JAMA Netw Open ; 5(4): e227299, 2022 04 01.
Article in English | MEDLINE | ID: covidwho-1787611

ABSTRACT

Importance: Bacterial and viral causes of acute respiratory illness (ARI) are difficult to clinically distinguish, resulting in the inappropriate use of antibacterial therapy. The use of a host gene expression-based test that is able to discriminate bacterial from viral infection in less than 1 hour may improve care and antimicrobial stewardship. Objective: To validate the host response bacterial/viral (HR-B/V) test and assess its ability to accurately differentiate bacterial from viral infection among patients with ARI. Design, Setting, and Participants: This prospective multicenter diagnostic study enrolled 755 children and adults with febrile ARI of 7 or fewer days' duration from 10 US emergency departments. Participants were enrolled from October 3, 2014, to September 1, 2019, followed by additional enrollment of patients with COVID-19 from March 20 to December 3, 2020. Clinical adjudication of enrolled participants identified 616 individuals as having bacterial or viral infection. The primary analysis cohort included 334 participants with high-confidence reference adjudications (based on adjudicator concordance and the presence of an identified pathogen confirmed by microbiological testing). A secondary analysis of the entire cohort of 616 participants included cases with low-confidence reference adjudications (based on adjudicator discordance or the absence of an identified pathogen in microbiological testing). Thirty-three participants with COVID-19 were included post hoc. Interventions: The HR-B/V test quantified the expression of 45 host messenger RNAs in approximately 45 minutes to derive a probability of bacterial infection. Main Outcomes and Measures: Performance characteristics for the HR-B/V test compared with clinical adjudication were reported as either bacterial or viral infection or categorized into 4 likelihood groups (viral very likely [probability score <0.19], viral likely [probability score of 0.19-0.40], bacterial likely [probability score of 0.41-0.73], and bacterial very likely [probability score >0.73]) and compared with procalcitonin measurement. Results: Among 755 enrolled participants, the median age was 26 years (IQR, 16-52 years); 360 participants (47.7%) were female, and 395 (52.3%) were male. A total of 13 participants (1.7%) were American Indian, 13 (1.7%) were Asian, 368 (48.7%) were Black, 131 (17.4%) were Hispanic, 3 (0.4%) were Native Hawaiian or Pacific Islander, 297 (39.3%) were White, and 60 (7.9%) were of unspecified race and/or ethnicity. In the primary analysis involving 334 participants, the HR-B/V test had sensitivity of 89.8% (95% CI, 77.8%-96.2%), specificity of 82.1% (95% CI, 77.4%-86.6%), and a negative predictive value (NPV) of 97.9% (95% CI, 95.3%-99.1%) for bacterial infection. In comparison, the sensitivity of procalcitonin measurement was 28.6% (95% CI, 16.2%-40.9%; P < .001), the specificity was 87.0% (95% CI, 82.7%-90.7%; P = .006), and the NPV was 87.6% (95% CI, 85.5%-89.5%; P < .001). When stratified into likelihood groups, the HR-B/V test had an NPV of 98.9% (95% CI, 96.1%-100%) for bacterial infection in the viral very likely group and a positive predictive value of 63.4% (95% CI, 47.2%-77.9%) for bacterial infection in the bacterial very likely group. The HR-B/V test correctly identified 30 of 33 participants (90.9%) with acute COVID-19 as having a viral infection. Conclusions and Relevance: In this study, the HR-B/V test accurately discriminated bacterial from viral infection among patients with febrile ARI and was superior to procalcitonin measurement. The findings suggest that an accurate point-of-need host response test with high NPV may offer an opportunity to improve antibiotic stewardship and patient outcomes.


Subject(s)
Bacterial Infections , COVID-19 , Virus Diseases , Adult , Bacteria , Bacterial Infections/drug therapy , COVID-19/diagnosis , Child , Female , Fever/diagnosis , Gene Expression , Humans , Male , Procalcitonin , Virus Diseases/diagnosis
11.
Crit Care ; 25(1): 281, 2021 08 05.
Article in English | MEDLINE | ID: covidwho-1770564

ABSTRACT

BACKGROUND: Procalcitonin (PCT) and C-reactive protein (CRP) were previously shown to have value for the detection of secondary infections in critically ill COVID-19 patients. However, since the introduction of immunomodulatory therapy, the value of these biomarkers is unclear. We investigated PCT and CRP kinetics in critically ill COVID-19 patients treated with dexamethasone with or without tocilizumab, and assessed the value of these biomarkers to detect secondary bacterial infections. METHODS: In this prospective study, 190 critically ill COVID-19 patients were divided into three treatment groups: no dexamethasone, no tocilizumab (D-T-), dexamethasone, no tocilizumab (D+T-), and dexamethasone and tocilizumab (D+T+). Serial data of PCT and CRP were aligned on the last day of dexamethasone treatment, and kinetics of these biomarkers were analyzed between 6 days prior to cessation of dexamethasone and 10 days afterwards. Furthermore, the D+T- and D+T+ groups were subdivided into secondary infection and no-secondary infection groups to analyze differences in PCT and CRP kinetics and calculate detection accuracy of these biomarkers for the occurrence of a secondary infection. RESULTS: Following cessation of dexamethasone, there was a rebound in PCT and CRP levels, most pronounced in the D+T- group. Upon occurrence of a secondary infection, no significant increase in PCT and CRP levels was observed in the D+T- group (p = 0.052 and p = 0.08, respectively). Although PCT levels increased significantly in patients of the D+T+ group who developed a secondary infection (p = 0.0003), this rise was only apparent from day 2 post-infection onwards. CRP levels remained suppressed in the D+T+ group. Receiver operating curve analysis of PCT and CRP levels yielded area under the curves of 0.52 and 0.55, respectively, which are both markedly lower than those found in the group of COVID-19 patients not treated with immunomodulatory drugs (0.80 and 0.76, respectively, with p values for differences between groups of 0.001 and 0.02, respectively). CONCLUSIONS: Cessation of dexamethasone in critically ill COVID-19 patients results in a rebound increase in PCT and CRP levels unrelated to the occurrence of secondary bacterial infections. Furthermore, immunomodulatory treatment with dexamethasone and tocilizumab considerably reduces the value of PCT and CRP for detection of secondary infections in COVID-19 patients.


Subject(s)
Antibodies, Monoclonal, Humanized/therapeutic use , Bacterial Infections/diagnosis , COVID-19/drug therapy , Coinfection/diagnosis , Dexamethasone/therapeutic use , Aged , C-Reactive Protein/analysis , COVID-19/complications , Critical Illness , Female , Humans , Male , Middle Aged , Netherlands , Procalcitonin/analysis , Prospective Studies
12.
Pediatr Emerg Care ; 38(1): e398-e403, 2022 Jan 01.
Article in English | MEDLINE | ID: covidwho-1767003

ABSTRACT

OBJECTIVES: Respiratory syncytial virus (RSV) in pediatric patients has been associated with low risk of concomitant bacterial infection. However, in children with severe disease, it occurs in 22% to 50% of patients. As viral testing becomes routine, bacterial codetections are increasingly identified in patients with non-RSV viruses. We hypothesized, among patients intubated for respiratory failure secondary to suspected infection, there are similar rates of codetection between RSV and non-RSV viral detections. METHODS: This retrospective chart review, conducted over a 5-year period, included all patients younger than 2 years who required intubation secondary to respiratory failure from an infectious etiology in a single pediatric emergency department. Patients intubated for noninfectious causes were excluded. RESULTS: We reviewed 274 patients, of which 181 had positive viral testing. Of these, 48% were RSV-positive and 52% were positive for viruses other than RSV. Codetection of bacteria was found in 76% (n = 65; 95% confidence interval [CI], 66%, 84%) of RSV-positive patients and 66% (n = 63, 95% CI: 57%, 76%) of patients positive with non-RSV viruses. Among patients with negative viral testing, 33% had bacterial growth on lower respiratory culture. Male sex was the only patient-related factor associated with increased odds of codetection (odds ratio [OR], 2.2; 95% CI, 1.08-4.38). The odds of codetection between RSV-positive patients and non-RSV viruses were not significantly different (OR, 1.3; 95% CI, 0.62-2.71). CONCLUSIONS: Bacterial codetection is common and not associated with anticipated patient-related factors or with a specific virus. These results suggest consideration of empiric antibiotics in infants with respiratory illness requiring intubation.


Subject(s)
Bacterial Infections , Respiratory Syncytial Virus Infections , Respiratory Syncytial Virus, Human , Respiratory Tract Infections , Bacteria , Child , Humans , Infant , Male , Respiratory Syncytial Virus Infections/complications , Respiratory Syncytial Virus Infections/diagnosis , Respiratory Syncytial Virus Infections/epidemiology , Respiratory Tract Infections/diagnosis , Respiratory Tract Infections/epidemiology , Retrospective Studies
15.
Antimicrob Resist Infect Control ; 11(1): 45, 2022 03 07.
Article in English | MEDLINE | ID: covidwho-1731546

ABSTRACT

BACKGROUND: Pneumonia from SARS-CoV-2 is difficult to distinguish from other viral and bacterial etiologies. Broad-spectrum antimicrobials are frequently prescribed to patients hospitalized with COVID-19 which potentially acts as a catalyst for the development of antimicrobial resistance (AMR). OBJECTIVES: We conducted a systematic review and meta-analysis during the first 18 months of the pandemic to quantify the prevalence and types of resistant co-infecting organisms in patients with COVID-19 and explore differences across hospital and geographic settings. METHODS: We searched MEDLINE, Embase, Web of Science (BioSIS), and Scopus from November 1, 2019 to May 28, 2021 to identify relevant articles pertaining to resistant co-infections in patients with laboratory confirmed SARS-CoV-2. Patient- and study-level analyses were conducted. We calculated pooled prevalence estimates of co-infection with resistant bacterial or fungal organisms using random effects models. Stratified meta-analysis by hospital and geographic setting was also performed to elucidate any differences. RESULTS: Of 1331 articles identified, 38 met inclusion criteria. A total of 1959 unique isolates were identified with 29% (569) resistant organisms identified. Co-infection with resistant bacterial or fungal organisms ranged from 0.2 to 100% among included studies. Pooled prevalence of co-infection with resistant bacterial and fungal organisms was 24% (95% CI 8-40%; n = 25 studies: I2 = 99%) and 0.3% (95% CI 0.1-0.6%; n = 8 studies: I2 = 78%), respectively. Among multi-drug resistant organisms, methicillin-resistant Staphylococcus aureus, carbapenem-resistant Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa and multi-drug resistant Candida auris were most commonly reported. Stratified analyses found higher proportions of AMR outside of Europe and in ICU settings, though these results were not statistically significant. Patient-level analysis demonstrated > 50% (n = 58) mortality, whereby all but 6 patients were infected with a resistant organism. CONCLUSIONS: During the first 18 months of the pandemic, AMR prevalence was high in COVID-19 patients and varied by hospital and geography although there was substantial heterogeneity. Given the variation in patient populations within these studies, clinical settings, practice patterns, and definitions of AMR, further research is warranted to quantify AMR in COVID-19 patients to improve surveillance programs, infection prevention and control practices and antimicrobial stewardship programs globally.


Subject(s)
Bacteria/drug effects , Bacterial Infections/drug therapy , COVID-19/complications , Drug Resistance, Bacterial , Drug Resistance, Fungal , Mycoses/drug therapy , Anti-Bacterial Agents/pharmacology , Antifungal Agents/pharmacology , Bacteria/classification , Bacteria/genetics , Bacteria/isolation & purification , Bacterial Infections/etiology , Bacterial Infections/microbiology , COVID-19/virology , Fungi/classification , Fungi/drug effects , Fungi/genetics , Fungi/isolation & purification , Humans , Mycoses/etiology , Mycoses/microbiology , SARS-CoV-2/physiology
16.
Rev Assoc Med Bras (1992) ; 68(2): 142-146, 2022 Feb.
Article in English | MEDLINE | ID: covidwho-1725074

ABSTRACT

OBJECTIVE: The vast majority of patients who hospitalized with coronavirus disease 2019 are given empirical antibiotic therapy. However, information on the frequency, microorganism species, and resistance rates of secondary bacterial infections in coronavirus disease 2019 patients are insufficient. We aimed to show the frequency of secondary infections and resistance conditions in patients with coronavirus disease 2019 hospitalized in the intensive care unit. METHODS: The results of tracheal aspirate culture, blood culture, and urine culture obtained from coronavirus disease 2019 patients - at least 2 days after their admission to the intensive care unit - were examined microbiologically. RESULTS: A total of 514 patients hospitalized in intensive care unit were included in our study. Tracheal aspirate, blood, or urine cultures were collected from 369 patients (71.8%). Bacterial reproduction was detected in at least one sample in 171 (33.3%) of all patients. The rate of respiratory tract infection and/or bloodstream infection was found to be 21%. Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa in tracheal aspirate culture; Coagulase-negative staphylococci, K. pneumoniae, and A. baumannii in blood culture; and Escherichia coli, K. pneumoniae, and Enterococcus faecalis in urine culture were the most common microorganisms. A. baumannii was resistant to most antibiotics except colistin and P. aeruginosa strains were resistant to most antibiotics except amikacin, colistin, cefepime, and imipenem. In K. pneumoniae, the highest meropenem sensitivity (73%) was observed; there was a strong resistance to most of the remaining antibiotics. CONCLUSIONS: We think that our study can be useful in choosing empirical antibiotic therapy in the coronavirus disease 2019 pandemic and reducing the mortality that may occur with secondary infection.


Subject(s)
Acinetobacter baumannii , Bacterial Infections , COVID-19 , Coinfection , Pneumonia , Anti-Bacterial Agents/therapeutic use , Bacterial Infections/complications , Bacterial Infections/drug therapy , COVID-19/complications , Humans , Microbial Sensitivity Tests , Pseudomonas aeruginosa , SARS-CoV-2
17.
Pediatr Infect Dis J ; 41(2): 91-96, 2022 02 01.
Article in English | MEDLINE | ID: covidwho-1722660

ABSTRACT

BACKGROUND: Invasive bacterial infection (IBI) remains a major burden of mortality and morbidity in children. As coronavirus disease 2019 (COVID-19) emerged, stringent nonpharmaceutical interventions (NPIs) were applied worldwide. This study aimed to evaluate the impact of NPIs on pediatric IBI in Korea. METHODS: From January 2018 to December 2020, surveillance for pediatric IBIs caused by 9 pathogens (S. pneumoniae, H. influenzae, N. meningitidis, S. agalactiae, S. pyogenes, S. aureus, Salmonella species, L. monocytogenes and E. coli) was performed at 22 hospitals throughout Korea. Annual incidence rates were compared before and after the COVID-19 pandemic. RESULTS: A total of 651 cases were identified and the annual incidence was 194.0 cases per 100,000 in-patients in 2018, 170.0 in 2019 and 172.4 in 2020. Most common pathogen by age group was S. agalactiae in infants < 3 months (n = 129, 46.7%), S. aureus in 3 to < 24 months (n = 35, 37.2%), Salmonella spp. in 24 to < 60 months (n = 24, 34.8%) and S. aureus in children ≥ 5 years (n = 128, 60.7%). Compared with 2018 to 2019, the incidence rate in 2020 decreased by 57% for invasive pneumococcal disease (26.6 vs. 11.5 per 100,000 in-patients, P = 0.014) and 59% for Salmonella spp. infection (22.8 vs. 9.4 per 100,000 in-patients, P = 0.018). In contrast, no significant changes were observed in invasive infections due to S. aureus, S. agalactiae and E. coli. CONCLUSIONS: The NPIs implemented during the COVID-19 pandemic reduced invasive diseases caused by S. pneumoniae and Salmonella spp. but not S. aureus, S. agalactiae and E. coli in children.


Subject(s)
Bacterial Infections/classification , Bacterial Infections/epidemiology , Communicable Disease Control/methods , COVID-19/prevention & control , Child , Child, Preschool , Epidemiological Monitoring , Hospitals , Humans , Incidence , Infant , Republic of Korea/epidemiology , Retrospective Studies , SARS-CoV-2
18.
Microb Drug Resist ; 28(3): 338-345, 2022 Mar.
Article in English | MEDLINE | ID: covidwho-1722178

ABSTRACT

Aim: This study aims to assess the changes in antimicrobial resistance among some critical and high-priority microorganisms collected previously and during the coronavirus disease 2019 (COVID-19) pandemic in Mexico. Methods: We collected antimicrobial susceptibility data for critical and high-priority microorganisms from blood, urine, respiratory samples, and from all specimens, in which the pathogen may be considered a causative agent. Data were stratified and compared for two periods: 2019 versus 2020 and second semester 2019 (prepandemic) versus the second semester 2020 (pandemic). Results: In the analysis of second semester 2019 versus the second semester 2020, in blood samples, increased resistance to oxacillin (15.2% vs. 36.9%), erythromycin (25.7% vs. 42.8%), and clindamycin (24.8% vs. 43.3%) (p ≤ 0.01) was detected for Staphylococcus aureus, to imipenem (13% vs. 23.4%) and meropenem (11.2% vs. 21.4) (p ≤ 0.01), for Klebsiella pneumoniae. In all specimens, increased ampicillin and tetracycline resistance was detected for Enterococcus faecium (p ≤ 0.01). In cefepime, meropenem, levofloxacin, and gentamicin (p ≤ 0.01), resistance was detected for Escherichia coli; and in piperacillin-tazobactam, cefepime, imipenem, meropenem, ciprofloxacin, levofloxacin, and gentamicin (p ≤ 0.01), resistance was detected for Pseudomonas aeruginosa. Conclusion: Antimicrobial resistance increased in Mexico during the COVID-19 pandemic. The increase in oxacillin resistance for S. aureus and carbapenem resistance for K. pneumoniae recovered from blood specimens deserves special attention. In addition, an increase in erythromycin resistance in S. aureus was detected, which may be associated with high azithromycin use. In general, for Acinetobacter baumannii and P. aeruginosa, increasing resistance rates were detected.


Subject(s)
Bacterial Infections/epidemiology , Bacterial Infections/microbiology , COVID-19/epidemiology , Drug Resistance, Multiple, Bacterial , Humans , Mexico/epidemiology , Microbial Sensitivity Tests , Pandemics , SARS-CoV-2
19.
J Med Virol ; 94(4): 1670-1688, 2022 04.
Article in English | MEDLINE | ID: covidwho-1718413

ABSTRACT

Bangladesh is experiencing a second wave of COVID-19 since March 2021, despite the nationwide vaccination drive with ChAdOx1 (Oxford-AstraZeneca) vaccine from early February 2021. Here, we characterized 19 nasopharyngeal swab (NPS) samples from COVID-19 suspect patients using genomic and metagenomic approaches. Screening for SARS-CoV-2 by reverse transcriptase polymerase chain reaction and metagenomic sequencing revealed 17 samples of COVID-19 positive (vaccinated = 10, nonvaccinated = 7) and 2 samples of COVID-19 negative. We did not find any significant correlation between associated factors including vaccination status, age or sex of the patients, diversity or abundance of the coinfected organisms/pathogens, and the abundance of SARS-CoV-2. Though the first wave of the pandemic was dominated by clade 20B, Beta, V2 (South African variant) dominated the second wave (January 2021 to May 2021), while the third wave (May 2021 to September 2021) was responsible for Delta variants of the epidemic in Bangladesh including both vaccinated and unvaccinated infections. Noteworthily, the receptor binding domain (RBD) region of S protein of all the isolates harbored similar substitutions including K417N, E484K, and N501Y that signify the Beta, while D614G, D215G, D80A, A67V, L18F, and A701V substitutions were commonly found in the non-RBD region of Spike proteins. ORF7b and ORF3a genes underwent a positive selection (dN/dS ratio 1.77 and 1.24, respectively), while the overall S protein of the Bangladeshi SARS-CoV-2 isolates underwent negative selection pressure (dN/dS = 0.621). Furthermore, we found different bacterial coinfections like Streptococcus agalactiae, Neisseria meningitidis, Elizabethkingia anophelis, Stenotrophomonas maltophilia, Klebsiella pneumoniae, and Pseudomonas plecoglossicida, expressing a number of antibiotic resistance genes such as tetA and tetM. Overall, this approach provides valuable insights on the SARS-CoV-2 genomes and microbiome composition from both vaccinated and nonvaccinated patients in Bangladesh.


Subject(s)
COVID-19/virology , Metagenomics , SARS-CoV-2/genetics , Adolescent , Adult , Aged , Bacteria/classification , Bacteria/genetics , Bacterial Infections/epidemiology , Bacterial Infections/microbiology , Bacterial Infections/virology , Bangladesh/epidemiology , COVID-19/epidemiology , COVID-19/microbiology , COVID-19/prevention & control , Coinfection/epidemiology , Coinfection/microbiology , Coinfection/virology , Drug Resistance, Bacterial/genetics , Female , Genome, Bacterial/genetics , Genome, Viral/genetics , Humans , Male , Microbiota/genetics , Middle Aged , Mutation , Phylogeny , SARS-CoV-2/classification , SARS-CoV-2/isolation & purification , Selection, Genetic , Vaccination , Viral Proteins/genetics , Young Adult
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