Your browser doesn't support javascript.
Show: 20 | 50 | 100
Results 1 - 20 de 100
Filter
1.
Epidemiol Infect ; 150: e195, 2022 Nov 08.
Article in English | MEDLINE | ID: covidwho-2106270

ABSTRACT

Episodes of bacterial superinfections have been well identified for several respiratory viruses, notably influenza. In this retrospective study, we compared the frequency of superinfections in COVID-19 patients to those found in influenza-positive patients, and to controls without viral infection. We included 42 468 patients who had been diagnosed with COVID-19 and 266 261 subjects who had tested COVID-19 negative between 26 February 2020 and 1 May 2021. In addition, 4059 patients were included who had tested positive for the influenza virus between 1 January 2017 and 31 December 2019. Bacterial infections in COVID-19 patients were more frequently healthcare-associated, and acquired in ICUs, were associated with longer ICU stays, and occurred in older and male patients when compared to controls and to influenza patients (P < 0.0001 for all). The most common pathogens proved to be less frequent in COVID-19 patients, including fewer cases of bacteraemia involving E. coli (P < 0.0001) and Klebsiella pneumoniae (P = 0.027) when compared to controls. In respiratory specimens Haemophilus influenzae (P < 0.0001) was more frequent in controls, while Streptococcus pneumoniae (P < 0.0001) was more frequent in influenza patients. Likewise, species associated with nosocomial transmission, such as Pseudomonas aeruginosa and Staphylococcus epidermidis, were more frequent among COVID-19 patients. Finally, we observed a high frequency of Enterococcus faecalis bacteraemia among COVID-19 patients, which were mainly ICU-acquired and associated with a longer timescale to acquisition.


Subject(s)
Bacteremia , Bacterial Infections , COVID-19 , Influenza, Human , Superinfection , Humans , Male , Aged , COVID-19/epidemiology , Retrospective Studies , Escherichia coli , Bacterial Infections/epidemiology , Hospitals , Bacteremia/epidemiology
2.
Infect Control Hosp Epidemiol ; 42(1): 89-92, 2021 01.
Article in English | MEDLINE | ID: covidwho-2096391
3.
Genome Med ; 14(1): 18, 2022 02 21.
Article in English | MEDLINE | ID: covidwho-1688773

ABSTRACT

BACKGROUND: Measuring host gene expression is a promising diagnostic strategy to discriminate bacterial and viral infections. Multiple signatures of varying size, complexity, and target populations have been described. However, there is little information to indicate how the performance of various published signatures compare to one another. METHODS: This systematic comparison of host gene expression signatures evaluated the performance of 28 signatures, validating them in 4589 subjects from 51 publicly available datasets. Thirteen COVID-specific datasets with 1416 subjects were included in a separate analysis. Individual signature performance was evaluated using the area under the receiving operating characteristic curve (AUC) value. Overall signature performance was evaluated using median AUCs and accuracies. RESULTS: Signature performance varied widely, with median AUCs ranging from 0.55 to 0.96 for bacterial classification and 0.69-0.97 for viral classification. Signature size varied (1-398 genes), with smaller signatures generally performing more poorly (P < 0.04). Viral infection was easier to diagnose than bacterial infection (84% vs. 79% overall accuracy, respectively; P < .001). Host gene expression classifiers performed more poorly in some pediatric populations (3 months-1 year and 2-11 years) compared to the adult population for both bacterial infection (73% and 70% vs. 82%, respectively; P < .001) and viral infection (80% and 79% vs. 88%, respectively; P < .001). We did not observe classification differences based on illness severity as defined by ICU admission for bacterial or viral infections. The median AUC across all signatures for COVID-19 classification was 0.80 compared to 0.83 for viral classification in the same datasets. CONCLUSIONS: In this systematic comparison of 28 host gene expression signatures, we observed differences based on a signature's size and characteristics of the validation population, including age and infection type. However, populations used for signature discovery did not impact performance, underscoring the redundancy among many of these signatures. Furthermore, differential performance in specific populations may only be observable through this type of large-scale validation.


Subject(s)
Bacterial Infections/diagnosis , Datasets as Topic/statistics & numerical data , Host-Pathogen Interactions/genetics , Transcriptome , Virus Diseases/diagnosis , Adult , Bacterial Infections/epidemiology , Bacterial Infections/genetics , Biomarkers/analysis , COVID-19/diagnosis , COVID-19/genetics , Child , Cohort Studies , Diagnosis, Differential , Gene Expression Profiling/statistics & numerical data , Genetic Association Studies/statistics & numerical data , Humans , Publications/statistics & numerical data , SARS-CoV-2/pathogenicity , Validation Studies as Topic , Virus Diseases/epidemiology , Virus Diseases/genetics
4.
West J Emerg Med ; 23(5): 754-759, 2022 Aug 10.
Article in English | MEDLINE | ID: covidwho-2056168

ABSTRACT

INTRODUCTION: The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) led to the coronavirus disease 2019 (COVID-19) pandemic that drastically impacted the United States. The evidence was not clear on how SARS-CoV-2 infection impacted children, given the high prevalence of SAR-CoV-2 infection. Febrile infants less than 60 days old are an ongoing challenge to risk-stratify for serious bacterial infection (SBI), including urinary tract infection (UTI), bacteremia, and meningitis. We hypothesized there would be a lower rate of SBI in SARS-CoV-2 positive febrile infants compared to those SARS-CoV-2 negative. METHODS: This was a retrospective chart review with a nested, age-matched, case-control study performed from March 2020-June 2021. Infants less than 60 days old presenting with fever were assigned groups based on SARS-CoV-2 infection. Blood, urine, and cerebrospinal fluid cultures were used as the gold standard to diagnose SBI. We compared overall rate of SBI as well as individual rates of SBI between each group. We performed a subgroup analysis evaluating the age group 29-60 days old. RESULTS: A total of 164 subjects met criteria for analysis: 30 COVID-19 positive and 134 COVID-19 negative subjects. Rate of SBI was 17.9% (95% confidence interval [CI]: 11.8-25.5%) in the COVID-19 negative group compared to 0% (95% CI: 0.0%-11.1%) in the COVID-19 group, which demonstrated statistical significance (p = 0.008). In the age-matched data, we found statistical significance for any SBI (p = <0.001). For individual rates of SBI, we found statistical significance for UTI (p = <0.001) and bacteremia (p = <0.001). The 29-60 days-old subgroup analysis did not achieve statistical significance (p = 0.11). CONCLUSION: This study demonstrated the utility of including SARS-CoV-2 infection as part of the risk stratification of febrile infants less than 60 days old. While overall there is a low incidence of bacteremia and meningitis in this age group, these results can contribute to existing literature and potentially help decrease invasive testing and exposure to broad-spectrum antibiotics.


Subject(s)
Bacteremia , Bacterial Infections , COVID-19 , Meningitis , Urinary Tract Infections , Anti-Bacterial Agents , Bacteremia/epidemiology , Bacteremia/microbiology , Bacterial Infections/diagnosis , Bacterial Infections/epidemiology , Bacterial Infections/microbiology , Case-Control Studies , Child , Fever/diagnosis , Humans , Infant , Infant, Newborn , Meningitis/complications , Meningitis/microbiology , Retrospective Studies , SARS-CoV-2 , Urinary Tract Infections/diagnosis , Urinary Tract Infections/epidemiology
5.
PLoS One ; 17(7): e0270770, 2022.
Article in English | MEDLINE | ID: covidwho-2039352

ABSTRACT

BACKGROUND: The risk and characteristics of upper respiratory tract (URT) bacterial infections (URT-BI) among HIV (+) patients is understudied. We analyzed factors associated with its occurrence and the spectrum of culturable pathogens among patients routinely followed at the HIV Out-Patient Clinic in Warsaw. METHODS: All HIV (+) patients with available URT swab culture were included into analyses. Patients were followed from the day of registration in the clinic until first positive URT swab culture or last clinical visit from January 1, 2007 to July 31, 2016. Cox proportional hazard models were used to identify factors associated with positive URT swabs culture (those with p<0.1 in univariate included into multivariable). RESULTS: In total 474 patients were included into the analyses, 166 with culturable URT swab. In general, 416 (87.8%) patients were male, 342 (72.1%) were infected through MSM contact, 253 (53.4%) were on antiretroviral therapy. Median follow-up time was 3.4 (1.3-5.7) years, age 35.2 (30.6-42.6) years and CD4+ count 528 (400-685) cells/µl. The most common cultured bacteria were S. aureus (40.4%) and S. pyogenes (13.9%) (Table 1). Patients with culturable URT-BI were more likely to be MSM (68.5% vs 78.9%; p<0.016), have detectable viral load (20.9% vs 12.0%; p<0.0001) and CD4+ cell count <500 cells/µl (55.2% vs 39.0%; p = 0.003) (Table 2). In multivariate survival analyses detectable viral load (HR3.13; 95%Cl: 2.34-4.19) and MSM (1.63;1.09-2.42) were increasing, but older age (0.63;0.58-0.69, per 5 years older) and higher CD4+ count (0.90;0.85-0.95, per 100 cells/µl) decreasing the risk of culturable URT-BI (Table 2). CONCLUSIONS: Culturable URT-BI are common among HIV-positive patients with high CD4+ count. Similarly to general population most common cultured bacteria were S. aureus and S. pyogenes. Risk factors identified in multivariate survival analysis indicate that younger MSM patients with detectable HIV viral load are at highest risk. In clinical practice this group of patients requires special attention.


Subject(s)
Bacterial Infections , HIV Infections , Respiratory Tract Infections , Sexual and Gender Minorities , Adult , Antiretroviral Therapy, Highly Active , Bacteria , Bacterial Infections/complications , Bacterial Infections/drug therapy , Bacterial Infections/epidemiology , CD4 Lymphocyte Count , Female , HIV Infections/drug therapy , Homosexuality, Male , Humans , Male , Reinfection , Respiratory System , Respiratory Tract Infections/complications , Respiratory Tract Infections/drug therapy , Respiratory Tract Infections/epidemiology , Risk Factors , Staphylococcus aureus , Viral Load
6.
J Glob Health ; 12: 05023, 2022 Sep 03.
Article in English | MEDLINE | ID: covidwho-2025295

ABSTRACT

Background: Essential health and nutrition services for pregnant women, newborns, and children, particularly in low- and middle-income countries (LMICs), are disrupted by the COVID-19 pandemic. This formative research was conducted at five LMICs to understand the pandemic's impact on barriers to and mitigation for strategies of care-seeking and managing possible serious bacterial infection (PSBI) in young infants. Methods: We used a convergent parallel mixed-method design to explore the possible factors influencing PSBI management, barriers, and facilitators at three levels: 1) national and local policy, 2) the health systems, public and private facilities, and 3) community and caregivers. We ascertained trends in service provision and utilisation across pre-lockdown, lockdown, and post-lockdown periods by examining facility records and community health worker registers. Results: The pandemic aggravated pre-existing challenges in the identification of young infants with PSBI; care-seeking, referral, and treatment due to several factors at the policy level (limited staff and resource reallocation), health facility level (staff quarantine, sub-optimal treatment in facilities, limited duration of service availability, lack of clear guidelines on the management of sick young infants, and inadequate supplies of protective kits and essential medicines) and at the community level (travel restrictions, lack of transportation, and fear of contracting the infection in hospitals). Care-seeking shifted to faith healers, traditional and informal private sources, or home remedies. However, caregivers were willing to admit their sick young infants to the hospital if advised by doctors. A review of facility records showed low attendance (<50%) of sick young infants in the OPD/emergencies during lockdowns in Bangladesh, India (both sites) and Pakistan, but it gradually increased as lockdowns eased. Stakeholders suggested aspirational and pragmatic mitigation strategies. Conclusions: We obtained useful insights on health system preparedness during catastrophes and strategies to strengthen services and improve utilisation regarding PSBI management. The current pandemic provides an opportunity for implementing various mitigation strategies at the policy, health system, and community levels to improve preparedness.


Subject(s)
Bacterial Infections , COVID-19 , Bacterial Infections/epidemiology , Bacterial Infections/microbiology , Bacterial Infections/therapy , COVID-19/epidemiology , Child , Communicable Disease Control , Female , Humans , Infant , Infant, Newborn , Pandemics , Pregnancy , Referral and Consultation
7.
Medicina (Kaunas) ; 58(8)2022 Aug 01.
Article in English | MEDLINE | ID: covidwho-2023901

ABSTRACT

Background and Objectives: Burning mouth syndrome (BMS) is a state in which a patient experiences intraoral burning or a dysesthetic sensation without clinically evident causative lesions in the oropharyngeal area. The disorder is linked to a variety of conditions, including dry mouth, Candida, and bacterial infections. The aim of this study was to determine the incidence of oral Candida and/or bacterial infections among patients with BMS and whether they have an effect on pain/burning and salivary flow levels. Objectives: (1) Gather patient data regarding the presence of oral infections, dry mouth, and pain levels in the morning, afternoon, and evening periods; (2) data analysis and assessment to determine medians, means, frequencies, correlations, and statistically significant differences between patient groups. Materials and Methods: Overall, 173 patients (23 males and 150 females) with BMS and 13 controls (five males and eight females) took part in the study. We measured pain/burning levels, unstimulated and stimulated salivary flow, the percentage of patients infected with Candida species and/or bacterial species, and the said species growth in Petri dishes. Results: Candida albicans was the most commonly found infection among patients with BMS (n = 28, 16.2%). Overall, 21.4% patients with BMS were diagnosed with either C. albicans or another Candida species. Enterobacter had the richest growth among patients with BMS (7.5% out of the infected 10.4% BMS patients). No statistical significance could be noted between the existence of either Candida species or bacterial species infections and changes in pain/burning and salivary flow levels. Negative correlations were noted between age and unstimulated and stimulated salivary flow, and positive correlations were noted between age and Candida andspecific bacteria species' growth levels. Conclusions: Although patients with present bacterial or Candida infections showed a marginal increase in pain/burning levels, no direct statistically significant associations could be made between the presence of Candida species or other bacteria and the symptoms among patients with BMS.


Subject(s)
Bacterial Infections , Burning Mouth Syndrome , Candidiasis , Xerostomia , Bacterial Infections/complications , Bacterial Infections/epidemiology , Burning Mouth Syndrome/complications , Burning Mouth Syndrome/epidemiology , Burning Mouth Syndrome/microbiology , Candidiasis/complications , Candidiasis/epidemiology , Female , Humans , Male , Pain
8.
Curr Opin Crit Care ; 28(5): 463-469, 2022 10 01.
Article in English | MEDLINE | ID: covidwho-2008657

ABSTRACT

PURPOSE OF REVIEW: Since the beginning of the severe acute respiratory syndrome coronavirus 2 pandemic, there has been a large increase in the consumption of antimicrobials, both as a form of treatment for viral pneumonia, which has been shown to be ineffective, and in the treatment of secondary infections that arise over the course of the severe presentation of coronavirus disease 2019 (COVID-19). This increase in consumption, often empirical, ends up causing an increase in the incidence of colonization and secondary infections by multi and pan-resistant germs. RECENT FINDINGS: The presence of a hyperinflammatory condition induced by the primary infection, associated with the structural damage caused by viral pneumonia and by the greater colonization by bacteria, generally multiresistant, are important risk factors for the acquisition of secondary infections in COVID-19. Consequently, there is an increased prevalence of secondary infections, associated with a higher consumption of antimicrobials and a significant increase in the incidence of infections by multi and pan-resistant bacteria. SUMMARY: Antimicrobial stewardship and improvement in diagnostic techniques, improving the accuracy of bacterial infection diagnosis, may impact the antibiotic consumption and the incidence of infections by resistant pathogens.


Subject(s)
Anti-Infective Agents , Bacterial Infections , COVID-19 , Coinfection , Pneumonia, Viral , Anti-Bacterial Agents/therapeutic use , Bacterial Infections/drug therapy , Bacterial Infections/epidemiology , COVID-19/epidemiology , Coinfection/drug therapy , Coinfection/epidemiology , Humans , Pneumonia, Viral/complications , Pneumonia, Viral/drug therapy , Pneumonia, Viral/epidemiology
9.
PLoS One ; 17(8): e0272375, 2022.
Article in English | MEDLINE | ID: covidwho-1987157

ABSTRACT

BACKGROUND: Evidence around prevalence of bacterial coinfection and pattern of antibiotic use in COVID-19 is controversial although high prevalence rates of bacterial coinfection have been reported in previous similar global viral respiratory pandemics. Early data on the prevalence of antibiotic prescribing in COVID-19 indicates conflicting low and high prevalence of antibiotic prescribing which challenges antimicrobial stewardship programmes and increases risk of antimicrobial resistance (AMR). AIM: To determine current prevalence of bacterial coinfection and antibiotic prescribing in COVID-19 patients. DATA SOURCE: OVID MEDLINE, OVID EMBASE, Cochrane and MedRxiv between January 2020 and June 2021. STUDY ELIGIBILITY: English language studies of laboratory-confirmed COVID-19 patients which reported (a) prevalence of bacterial coinfection and/or (b) prevalence of antibiotic prescribing with no restrictions to study designs or healthcare setting. PARTICIPANTS: Adults (aged ≥ 18 years) with RT-PCR confirmed diagnosis of COVID-19, regardless of study setting. METHODS: Systematic review and meta-analysis. Proportion (prevalence) data was pooled using random effects meta-analysis approach; and stratified based on region and study design. RESULTS: A total of 1058 studies were screened, of which 22, hospital-based studies were eligible, compromising 76,176 of COVID-19 patients. Pooled estimates for the prevalence of bacterial co-infection and antibiotic use were 5.62% (95% CI 2.26-10.31) and 61.77% (CI 50.95-70.90), respectively. Sub-group analysis by region demonstrated that bacterial co-infection was more prevalent in North American studies (7.89%, 95% CI 3.30-14.18). CONCLUSION: Prevalence of bacterial coinfection in COVID-19 is low, yet prevalence of antibiotic prescribing is high, indicating the need for targeted COVID-19 antimicrobial stewardship initiatives to reduce the global threat of AMR.


Subject(s)
Bacterial Infections , COVID-19 , Coinfection , Adult , Anti-Bacterial Agents/therapeutic use , Bacteria , Bacterial Infections/drug therapy , Bacterial Infections/epidemiology , Bacterial Infections/microbiology , COVID-19/drug therapy , COVID-19/epidemiology , Coinfection/drug therapy , Coinfection/epidemiology , Coinfection/microbiology , Humans , Prevalence
10.
Rev Argent Microbiol ; 54(3): 247-257, 2022.
Article in English | MEDLINE | ID: covidwho-1977764

ABSTRACT

Bacterial co-pathogens are commonly identified in viral respiratory infections and are important causes of morbid-mortality. The prevalence of Chlamydia (C.) pneumoniae infection in patients infected with SARS-CoV-2 has not been sufficiently studied. The objective of the present review was to describe the prevalence of C. pneumoniae in patients with coronavirus disease 2019 (COVID-19). A search in MEDLINE and Google Scholar databases for English language literature published between January 2020 and August 2021 was performed. Studies evaluating patients with confirmed COVID-19 and reporting the simultaneous detection of C. pneumoniae were included. Eleven articles were included in the systematic review (5 case cross-sectional studies and 6 retrospective studies). A total of 18450 patients were included in the eleven studies. The detection of laboratory-confirmed C. pneumoniae infection varied between 1.78 and 71.4% of the total number of co-infections. The median age of patients ranged from 35 to 71 years old and 65% were male. Most of the studies reported one or more pre-existing comorbidities and the majority of the patients presented with fever, cough and dyspnea. Lymphopenia and eosinopenia were described in COVID-19 co-infected patients. The main chest CT scan showed a ground glass density shadow, consolidation and bilateral pneumonia. Most patients received empirical antibiotics. Bacterial co-infection was not associated with increased ICU admission and mortality. Despite frequent prescription of broad-spectrum empirical antimicrobials in patients with coronavirus 2-associated respiratory infections, there is a paucity of data to support the association with respiratory bacterial co-infection. Prospective evidence generation to support the development of an antimicrobial policy and appropriate stewardship interventions specific for the COVID-19 pandemic are urgently required.


Subject(s)
Anti-Infective Agents , Bacterial Infections , COVID-19 , Chlamydophila pneumoniae , Coinfection , Adult , Aged , Anti-Bacterial Agents , Bacterial Infections/epidemiology , Coinfection/epidemiology , Cross-Sectional Studies , Female , Humans , Male , Middle Aged , Pandemics , Prospective Studies , Retrospective Studies , SARS-CoV-2
11.
Turk J Pediatr ; 64(3): 549-557, 2022.
Article in English | MEDLINE | ID: covidwho-1975713

ABSTRACT

BACKGROUND: Cystic fibrosis (CF) is a degenerative disease distinguished by progressive epithelial secretory gland dysfunction associated with recurrent respiratory tract infections. Despite that bacteria have previously been studied as the main cause of CF airway damage, a strong effect of respiratory viral infections is also now recognized. We aimed to detect the relationship between viral infection and exacerbation in children with cystic fibrosis. METHODS: This is a cross sectional observational study recruiting 60 patients diagnosed as CF following in Cystic Fibrosis Clinic, Children`s Hospital, Cairo University, throughout a period of 7 months. Their age ranged from 6 months to 13 years. Patients had nasal swabs and sputum samples obtained when they developed respiratory exacerbations. Multiplex PCR (polymerase chain reaction) technique was used to detect respiratory viruses from nasal swabs. RESULTS: We detected viruses in 48 patients during exacerbation (80%), the most common virus was rhinovirus in 43.4% of patients, followed by bocavirus in 20%, adenovirus in 13.3%, enterovirus in 10% and human metapneumovirus in 6.7%. Co-infection with double viruses was detected in 10 patients. Bacterial infection was present in 56.7% of patients; the most common organism was Pseudomonas in 20% of patients, followed by Staphylococcus aureus, methicillin resistant Staphylococcus aureus, Klebsiella and Haemophilus influenzae. CRP was positive in 53.3% of patients. There was a significant relationship between sputum positive bacterial culture and each of influenza A virus, enterovirus and human metapneumovirus. CONCLUSIONS: This study demonstrated that exacerbation in cystic fibrosis may be exaggerated by viral infections such as influenza A and enterovirus necessitating hospitalization which shows the important protective role of vaccination. Also, a strong relationship was detected between some viruses such as enterovirus, human metapneumovirus and influenza and between bacterial infection.


Subject(s)
Bacterial Infections , Cystic Fibrosis , Influenza, Human , Methicillin-Resistant Staphylococcus aureus , Respiratory Tract Infections , Virus Diseases , Viruses , Bacteria , Bacterial Infections/complications , Bacterial Infections/epidemiology , Child , Cross-Sectional Studies , Cystic Fibrosis/complications , Humans , Infant , Influenza, Human/complications , Influenza, Human/diagnosis , Prospective Studies , Respiratory Tract Infections/complications , Respiratory Tract Infections/epidemiology , Virus Diseases/complications , Virus Diseases/epidemiology
12.
J Infect Dev Ctries ; 16(7): 1131-1137, 2022 07 28.
Article in English | MEDLINE | ID: covidwho-1974973

ABSTRACT

INTRODUCTION: Secondary Bacterial Infections (SBIs) of the respiratory system are one of the biggest medical concerns in patients undergoing hospitalization with a diagnosis of COVID-19. This study aims to provide relevant data for the initiation of appropriate empirical treatment after examining the etiology and antimicrobial resistance of SBIs in COVID-19 patients under care in the Intensive Care Units (ICUs) in the largest pandemic hospital of our country. METHODOLOGY: Between March 16, 2020 and December 31, 2021, 56,993 COVID patients were hospitalized, of which 7684 were admitted to ICUs. A total of 1513 patients diagnosed with SBIs have been included in this study. During the course of the study, demographic data, clinical course, etiology and antimicrobial resistance data of all patients were collected. RESULTS: The most common causative agents of SBIs were inferred as Acinetobacter baumanii (35.1%), Staphylococcus aureus (15.2%), Klebsiella pneumoniae (12.3%) and Pseudomonas aeruginosa (10.4%). The isolation rates of carbapenem-resistant and colistin-resistant A. baumannii, K. pneumoniae and P. aeruginosa were 83.7%; 42.7%, 79.2%, and 5.6%, 42.7%, 1.7%, respectively. Acinetobacter pittii clustering was seen in one of the ICUs in the hospital. Multidrug resistant 92 (5.4%) Corynebacterium striatum isolates were also found as a causative agent with increasing frequency during the study period. CONCLUSIONS: SBI of the respiratory system is one of the major complications in patients hospitalized with COVID-19. The antimicrobial resistance rates of the isolated bacteria are generally high, which indicates that more accurate use of antibacterial agents is necessary for SBIs in patients hospitalized with COVID-19 diagnosis.


Subject(s)
Acinetobacter baumannii , Bacterial Infections , COVID-19 , Coinfection , Staphylococcal Infections , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/therapeutic use , Bacterial Infections/drug therapy , Bacterial Infections/epidemiology , COVID-19/epidemiology , COVID-19 Testing , Coinfection/drug therapy , Drug Resistance, Multiple, Bacterial , Humans , Klebsiella pneumoniae , Microbial Sensitivity Tests , Pseudomonas aeruginosa , Respiratory System , Staphylococcal Infections/drug therapy
13.
Infection ; 50(4): 1013-1017, 2022 Aug.
Article in English | MEDLINE | ID: covidwho-1971886

ABSTRACT

PURPOSE: SARS-CoV-2 infection produces lymphopenia and CD4+ T-cell decrease, which could lead to a higher risk of bacterial co-infection or impair immunological evolution in people living with HIV (PLWH). METHODS: We investigated the rate of co-infection and superinfection, and the evolution of CD4+ count and CD4+/CD8+ ratio, in hospitalized PLWH with COVID-19. RESULTS: From March to December 2020, 176 PLWH had symptomatic COVID-19 and 62 required hospitalization (median age, 56 years, 89% males). At admission, 7% and 13% of patients had leukocytosis or increased procalcitonin values and 37 (60%) received empiric antibiotic therapy, but no bacterial co-infection was diagnosed. There were seven cases of superinfection (12%), and one case of P. jiroveci pneumonia during ICU stay. No significant change in CD4+ count or CD4+/CD8+ ratio was observed after discharge. CONCLUSION: Bacterial co-infection is not frequent in PLWH with COVID-19. Immune recovery is observed in most of patients after the disease.


Subject(s)
COVID-19 , HIV Infections , Bacterial Infections/epidemiology , COVID-19/epidemiology , COVID-19/immunology , Coinfection/epidemiology , Female , HIV Infections/epidemiology , HIV Infections/immunology , Humans , Immunosuppression Therapy/statistics & numerical data , Male , Middle Aged , Opportunistic Infections/epidemiology , Risk Assessment
14.
J Prev Med Hyg ; 63(1): E19-E26, 2022 Mar.
Article in English | MEDLINE | ID: covidwho-1955102

ABSTRACT

Introduction: Secondary bacterial infections have been reported in majority of patients hospitalized with coronavirus disease 2019 (COVID-19). A study of the antimicrobial susceptibility profiles of these bacterial strains revealed that they were multidrug resistant, demonstrating their resistance to at least three classes of antimicrobial agents including beta-lactams, fluoroquinolones and aminoglycosides. Bacterial co-infection remains as an important cause for high mortality in patients hospitalized with COVID-19. Methods: In our study, we conducted a retrospective comparative analysis of bacterial co-infections and the antimicrobial resistance profile of bacterial isolates obtained from inpatients admitted in COVID-19 and non-COVID-19 intensive care units. The goal was to obtain the etiology and antimicrobial resistance of these infections for more accurate use of antimicrobials in clinical settings. This study involved a total of 648 samples collected from 356 COVID-19 positive patients and 292 COVID-19 negative patients admitted in the intensive care unit over a period of six months from May to October 2020. Results: Among the co-infections found, maximum antimicrobial resistance was found in Acinetobacter species followed by Klebsiella species in both the ICU's. Incidence of bacterial co-infection was found to be higher in COVID-19 intensive care patients and most of these isolates were multidrug resistant strains. Conclusion: Therefore, it is important that co-infections should not be underestimated and instead be made part of an integrated plan to limit the global burden of morbidity and mortality during the SARS-CoV-2 pandemic and beyond.


Subject(s)
Bacterial Infections , COVID-19 , Coinfection , Bacteria , Bacterial Infections/drug therapy , Bacterial Infections/epidemiology , COVID-19/epidemiology , Coinfection/drug therapy , Coinfection/epidemiology , Drug Resistance, Multiple, Bacterial , Humans , Intensive Care Units , Microbial Sensitivity Tests , Prevalence , Retrospective Studies , SARS-CoV-2
15.
Front Cell Infect Microbiol ; 12: 784130, 2022.
Article in English | MEDLINE | ID: covidwho-1902923

ABSTRACT

Data on the prevalence of bacterial co-infections and secondary infection among adults with COVID-19 admitted to the intensive care unit (ICU) are rare. We aimed to determine the frequency of secondary bacterial infection, antibiotic use, and clinical characteristics in patients admitted to the ICU with severe SARS-CoV-2 pneumonia. This was a retrospective cohort study of adults with severe COVID-19 admitted to two ICUs from March 6 to September 7, 2020 in an academic medical center in Isfahan, Iran. To detect COVID-19, reverse transcription real-time polymerase chain reaction was performed and also typical pattern of CT scan was used for the diagnosis of COVID-19. Data collection included the age, gender, main symptoms, history of underlying disease, demographics, hospital stay, outcomes, and antibiotic regimen of the patient. Antimicrobial susceptibility testing was carried out according to the CLSI guidelines. During the study period, 553 patients were referred to the both ICUs for COVID-19 with severe pneumonia. Secondary bacterial infection was detected in 65 (11.9%) patients. The median age was 69.4 (range 21-95) years; 42 (63.6%) were men. Notably, 100% (n = 65) of the patients with superinfection were prescribed empirical antibiotics before first positive culture, predominantly meropenem (86.2%) with a median duration of 12 (range 2-32) days and levofloxacin (73.8%) with a median duration of nine (range 2-24) days. Most prevalent causative agents for secondary bacterial infection were Klebsiella pneumoniae (n = 44) and Acinetobacter baumannii (n = 33). Most patients with secondary bacterial infection showed extensive drug-resistance. The mortality among patients who acquired superinfections was 83% against an overall mortality of 38.1% in total admitted COVID-19 patients. We found a high prevalence of carbapenem-resistant Gram-negative bacilli in COVID-19 patients admitted to our ICUs, with a high proportion of K. pneumoniae followed by A. baumannii. These findings emphasize the importance of implementation of strict infection control measures and highlight the role of antimicrobial stewardship during a pandemic.


Subject(s)
Bacterial Infections , COVID-19 , Coinfection , Adult , Aged , Aged, 80 and over , Bacterial Infections/epidemiology , COVID-19/epidemiology , Coinfection/epidemiology , Hospitals , Humans , Intensive Care Units , Iran/epidemiology , Male , Middle Aged , Pandemics , Retrospective Studies , SARS-CoV-2 , Young Adult
16.
Pediatr Infect Dis J ; 41(9): e365-e368, 2022 09 01.
Article in English | MEDLINE | ID: covidwho-1891101

ABSTRACT

BACKGROUND: Infants with COVID-19 can often present with fever without source, which is a challenging situation in infants <90 days old. The "step-by-step" algorithm has been proposed to identify children at high risk of bacterial infection. In the context of the COVID-19 pandemic, we aimed to reassess the diagnostic performance of this algorithm. METHODS: We performed a multicentric retrospective study in 3 French pediatric emergency departments between 2018 and 2020. We applied the "step-by-step" algorithm to 4 clinical entities: COVID-19, febrile urinary tract infections (FUTI), invasive bacterial infection (IBI), and enterovirus infections. The main outcome was the proportion of infants classified at high risk (ill-appearing, ≤21 days old, with leukocyturia or procalcitonin level ≥0.5 ng/mL). RESULTS: Among the 199 infants included, 40 had isolated COVID-19, 25 had IBI, 60 had FUTI, and 74 had enterovirus infection. All but 1 infant with bacterial infection were classified at high risk (96% for IBI and 100% for FUTI) as well as 95% with enterovirus and 82% with COVID-19. Infants with COVID-19 were classified at high risk because an ill-appearance (72%), an age ≤21 days (27%), or leukocyturia (19%). All these infants had procalcitonin values <0.5 ng/mL and only 1 had C-reactive protein level >20 mg/L. CONCLUSIONS: The "step-by-step" algorithm remains effective to identify infants with bacterial infection but misclassifies most infants with COVID-19 as at high risk of bacterial infection leading to unnecessary cares. An updated algorithm based adding viral testing may be needed to discriminate fever related to isolated COVID-19 in infants <90 days old.


Subject(s)
Bacterial Infections , COVID-19 , Urinary Tract Infections , Bacterial Infections/epidemiology , COVID-19/epidemiology , Child , Fever/microbiology , Humans , Infant , Pandemics , Procalcitonin , Prospective Studies , Retrospective Studies , Urinary Tract Infections/microbiology
17.
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
18.
Microbiol Spectr ; 10(3): e0195621, 2022 06 29.
Article in English | MEDLINE | ID: covidwho-1846337

ABSTRACT

Coronavirus disease 2019 (COVID-19) is a respiratory infectious disease responsible for many infections worldwide. Differences in respiratory microbiota may correlate with disease severity. Samples were collected from 20 severe and 51 mild COVID-19 patients. High-throughput sequencing of the 16S rRNA gene was used to analyze the bacterial community composition of the upper and lower respiratory tracts. The indices of diversity were analyzed. When one genus accounted for >50% of reads from a sample, it was defined as a super dominant pathobiontic bacterial genus (SDPG). In the upper respiratory tract, uniformity indices were significantly higher in the mild group than in the severe group (P < 0.001). In the lower respiratory tract, uniformity indices, richness indices, and the abundance-based coverage estimator were significantly higher in the mild group than in the severe group (P < 0.001). In patients with severe COVID-19, SDPGs were detected in 40.7% of upper and 63.2% of lower respiratory tract samples. In patients with mild COVID-19, only 10.8% of upper and 8.5% of lower respiratory tract samples yielded SDPGs. SDPGs were present in both upper and lower tracts in seven patients (35.0%), among which six (30.0%) patients possessed the same SDPG in the upper and lower tracts. However, no patients with mild infections had an SDPG in both tracts. Staphylococcus, Corynebacterium, and Acinetobacter were the main SDPGs. The number of SDPGs identified differed significantly between patients with mild and severe COVID-19 (P < 0.001). SDPGs in nasopharyngeal microbiota cause secondary bacterial infection in COVID-19 patients and aggravate pneumonia. IMPORTANCE The nasopharyngeal microbiota is composed of a variety of not only the true commensal bacterial species but also the two-face pathobionts, which are one a harmless commensal bacterial species and the other a highly invasive and deadly pathogen. In a previous study, we found that the diversity of nasopharyngeal microbiota was lost in severe influenza patients. We named the genus that accounted for over 50% of microbiota abundance as super dominant pathobiontic genus, which could invade to cause severe pneumonia, leading to high fatality. Similar phenomena were found here for SARS-CoV-2 infection. The diversity of nasopharyngeal microbiota was lost in severe COVID-19 infection patients. SDPGs in nasopharyngeal microbiota were frequently detected in severe COVID-19 patients. Therefore, the SDPGs in nasopharynx microbiota might invade into low respiratory and be responsible for secondary bacterial pneumonia in patients with SARS-CoV-2 infection.


Subject(s)
Bacterial Infections , COVID-19 , Coinfection , Microbiota , Bacteria/genetics , Bacterial Infections/epidemiology , Coinfection/microbiology , Humans , Microbiota/genetics , Nasopharynx , RNA, Ribosomal, 16S/genetics , SARS-CoV-2
19.
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
20.
Infection ; 50(5): 1243-1253, 2022 Oct.
Article in English | MEDLINE | ID: covidwho-1821023

ABSTRACT

OBJECTIVE: The aim of our study was to build a predictive model able to stratify the risk of bacterial co-infection at hospitalization in patients with COVID-19. METHODS: Multicenter observational study of adult patients hospitalized from February to December 2020 with confirmed COVID-19 diagnosis. Endpoint was microbiologically documented bacterial co-infection diagnosed within 72 h from hospitalization. The cohort was randomly split into derivation and validation cohort. To investigate risk factors for co-infection univariable and multivariable logistic regression analyses were performed. Predictive risk score was obtained assigning a point value corresponding to ß-coefficients to the variables in the multivariable model. ROC analysis in the validation cohort was used to estimate prediction accuracy. RESULTS: Overall, 1733 patients were analyzed: 61.4% males, median age 69 years (IQR 57-80), median Charlson 3 (IQR 2-6). Co-infection was diagnosed in 110 (6.3%) patients. Empirical antibiotics were started in 64.2 and 59.5% of patients with and without co-infection (p = 0.35). At multivariable analysis in the derivation cohort: WBC ≥ 7.7/mm3, PCT ≥ 0.2 ng/mL, and Charlson index ≥ 5 were risk factors for bacterial co-infection. A point was assigned to each variable obtaining a predictive score ranging from 0 to 5. In the validation cohort, ROC analysis showed AUC of 0.83 (95%CI 0.75-0.90). The optimal cut-point was ≥2 with sensitivity 70.0%, specificity 75.9%, positive predictive value 16.0% and negative predictive value 97.5%. According to individual risk score, patients were classified at low (point 0), intermediate (point 1), and high risk (point ≥ 2). CURB-65 ≥ 2 was further proposed to identify patients at intermediate risk who would benefit from early antibiotic coverage. CONCLUSIONS: Our score may be useful in stratifying bacterial co-infection risk in COVID-19 hospitalized patients, optimizing diagnostic testing and antibiotic use.


Subject(s)
Bacterial Infections , COVID-19 , Coinfection , Adult , Aged , Anti-Bacterial Agents/therapeutic use , Bacterial Infections/diagnosis , Bacterial Infections/epidemiology , COVID-19/diagnosis , COVID-19/epidemiology , COVID-19 Testing , Cohort Studies , Coinfection/diagnosis , Coinfection/epidemiology , Female , Hospitalization , Humans , Male , Retrospective Studies
SELECTION OF CITATIONS
SEARCH DETAIL