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1.
PLoS Negl Trop Dis ; 15(11): e0009921, 2021 11.
Article in English | MEDLINE | ID: covidwho-1523404

ABSTRACT

Coronavirus Disease 2019 (COVID-19), during the second wave in early 2021, has caused devastating chaos in India. As daily infection rates rise alarmingly, the number of severe cases has increased dramatically. The country has encountered health infrastructure inadequacy and excessive demand for hospital beds, drugs, vaccines, and oxygen. Adding more burden to such a challenging situation, mucormycosis, an invasive fungal infection, has seen a sudden surge in patients with COVID-19. The rhino-orbital-cerebral form is the most common type observed. In particular, approximately three-fourths of them had diabetes as predisposing comorbidity and received corticosteroids to treat COVID-19. Possible mechanisms may involve immune and inflammatory processes. Diabetes, when coupled with COVID-19-induced systemic immune change, tends to cause decreased immunity and an increased risk of secondary infections. Since comprehensive data on this fatal opportunistic infection are evolving against the backdrop of a major pandemic, prevention strategies primarily involve managing comorbid conditions in high-risk groups. The recommended treatment strategies primarily included surgical debridement and antifungal therapy using Amphotericin B and selected azoles. Several India-centric clinical guidelines have emerged to rightly diagnose the infection, characterise the clinical presentation, understand the pathogenesis involved, and track the disease course. Code Mucor is the most comprehensive one, which proposes a simple but reliable staging system for the rhino-orbital-cerebral form. A staging system has recently been proposed, and a dedicated registry has been started. In this critical review, we extensively analyse recent evidence and guidance on COVID-19-associated mucormycosis in India.


Subject(s)
COVID-19/complications , COVID-19/epidemiology , Mucormycosis/epidemiology , Mucormycosis/virology , Antifungal Agents/therapeutic use , COVID-19/microbiology , Coinfection/drug therapy , Coinfection/microbiology , Comorbidity , Diabetes Complications/microbiology , Humans , India/epidemiology , Mucormycosis/drug therapy , Risk Factors
2.
Genome Med ; 13(1): 182, 2021 11 17.
Article in English | MEDLINE | ID: covidwho-1523323

ABSTRACT

BACKGROUND: Clinical metagenomics (CMg) has the potential to be translated from a research tool into routine service to improve antimicrobial treatment and infection control decisions. The SARS-CoV-2 pandemic provides added impetus to realise these benefits, given the increased risk of secondary infection and nosocomial transmission of multi-drug-resistant (MDR) pathogens linked with the expansion of critical care capacity. METHODS: CMg using nanopore sequencing was evaluated in a proof-of-concept study on 43 respiratory samples from 34 intubated patients across seven intensive care units (ICUs) over a 9-week period during the first COVID-19 pandemic wave. RESULTS: An 8-h CMg workflow was 92% sensitive (95% CI, 75-99%) and 82% specific (95% CI, 57-96%) for bacterial identification based on culture-positive and culture-negative samples, respectively. CMg sequencing reported the presence or absence of ß-lactam-resistant genes carried by Enterobacterales that would modify the initial guideline-recommended antibiotics in every case. CMg was also 100% concordant with quantitative PCR for detecting Aspergillus fumigatus from 4 positive and 39 negative samples. Molecular typing using 24-h sequencing data identified an MDR-K. pneumoniae ST307 outbreak involving 4 patients and an MDR-C. striatum outbreak involving 14 patients across three ICUs. CONCLUSION: CMg testing provides accurate pathogen detection and antibiotic resistance prediction in a same-day laboratory workflow, with assembled genomes available the next day for genomic surveillance. The provision of this technology in a service setting could fundamentally change the multi-disciplinary team approach to managing ICU infections. The potential to improve the initial targeted treatment and rapidly detect unsuspected outbreaks of MDR-pathogens justifies further expedited clinical assessment of CMg.


Subject(s)
COVID-19/pathology , Cross Infection/transmission , Metagenomics , Anti-Bacterial Agents/therapeutic use , COVID-19/virology , Coinfection/drug therapy , Coinfection/microbiology , Corynebacterium/genetics , Corynebacterium/isolation & purification , Cross Infection/microbiology , DNA, Bacterial/chemistry , DNA, Bacterial/metabolism , Drug Resistance, Multiple, Bacterial/genetics , Female , Humans , Intensive Care Units , Klebsiella pneumoniae/genetics , Klebsiella pneumoniae/isolation & purification , Male , Middle Aged , Polymorphism, Single Nucleotide , SARS-CoV-2/isolation & purification , Sequence Analysis, DNA , beta-Lactamases/genetics
4.
BMC Microbiol ; 21(1): 277, 2021 10 11.
Article in English | MEDLINE | ID: covidwho-1463230

ABSTRACT

BACKGROUND: Fusobacterium nucleatum (F. n) is an important opportunistic pathogen causing oral and gastrointestinal disease. Faecalibacterium prausnitzii (F. p) is a next-generation probiotic and could serve as a biomarker of gut eubiosis/dysbiosis to some extent. Alterations in the human oral and gut microbiomes are associated with viral respiratory infection. The aim of this study was to characterise the oral and fecal bacterial biomarker (i.e., F. n and F. p) in COVID-19 patients by qPCR and investigate the pharyngeal microbiome of COVID-19 patients through metagenomic next-generation sequencing (mNGS). RESULTS: Pharyngeal F. n was significantly increased in COVID-19 patients, and it was higher in male than female patients. Increased abundance of pharyngeal F. n was associated with a higher risk of a positive SARS-CoV-2 test (adjusted OR = 1.32, 95% CI = 1.06 ~ 1.65, P < 0.05). A classifier to distinguish COVID-19 patients from the healthy controls based on the pharyngeal F. n was constructed and achieved an area under the curve (AUC) of 0.843 (95% CI = 0.688 ~ 0.940, P < 0.001). However, the level of fecal F. n and fecal F. p remained unaltered between groups. Besides, mNGS showed that the pharyngeal swabs of COVID-19 patients were dominated by opportunistic pathogens. CONCLUSIONS: Pharyngeal but not fecal F. n was significantly increased in COVID-19 patients, clinicians should pay careful attention to potential coinfection. Pharyngeal F. n may serve as a promising candidate indicator for COVID-19.


Subject(s)
COVID-19/microbiology , Feces/microbiology , Fusobacterium Infections/microbiology , Fusobacterium nucleatum/genetics , Pharynx/microbiology , Adult , Biomarkers/analysis , COVID-19/virology , Carrier State/microbiology , Coinfection/microbiology , Coinfection/virology , Dysbiosis , Female , Fusobacterium Infections/virology , High-Throughput Nucleotide Sequencing , Humans , Male , Metagenomics , Microbiota , Middle Aged , Pharynx/virology , Sex Factors
5.
J Infect Dev Ctries ; 15(8): 1104-1106, 2021 08 31.
Article in English | MEDLINE | ID: covidwho-1405470

ABSTRACT

Brucellosis is a common zoonotic infection. Brucellosis typically presents with fever, weakness, night sweats, and arthralgias. Symptoms associated with Coronavirus Disease 2019 (COVID-19) and infection with Brucella spp. are similar to one another, which may lead to delayed diagnosis of the latter condition. There are no previous reports of brucellosis in a patient previously diagnosed with COVID-19. We present here the case of a 20-year-old male who we diagnosed with brucellosis after joint pains and fever that persisted after resolution of COVID-19.


Subject(s)
Brucellosis/diagnosis , COVID-19/complications , Coinfection/diagnosis , Zoonoses/diagnosis , Animals , Arthralgia/microbiology , Brucellosis/physiopathology , COVID-19/diagnostic imaging , Coinfection/microbiology , Coinfection/virology , Diagnosis, Differential , Fever/microbiology , Humans , Male , Tomography, X-Ray Computed , Young Adult , Zoonoses/microbiology
6.
J Laryngol Otol ; 135(11): 981-986, 2021 Nov.
Article in English | MEDLINE | ID: covidwho-1402000

ABSTRACT

BACKGROUND: Treatment of coronavirus disease 2019 infection can result in immunosuppression. Rhino-orbital-cerebral mucormycosis is a frequent co-infection, even after recovery. METHODS: An ambispective interventional study was conducted of 41 coronavirus patients with rhino-orbital-cerebral mucormycosis at a tertiary care centre from March to May 2021. RESULTS: There were 28 males and 13 females with a mean age of 48.2 years (range, 21-68 years). Twelve had long-standing diabetes mellitus and 28 had been recently diagnosed. Thirty-six had received systemic corticosteroids for coronavirus disease 2019. Nasal signs were present in 95 per cent of patients, ophthalmic symptoms and signs in 87 per cent, palatal necrosis in 46.3 per cent, facial signs in 24.3 per cent, nerve palsies in 60.9 per cent, and intracranial involvement in 21.9 per cent. Treatment with amphotericin B was based on clinical features and co-morbidities. Endonasal debridement was performed in 51.2 per cent of patients, total maxillectomy in 14.6 per cent and orbital exenteration in 9.7 per cent. At the last follow up, 37 patients (90.24 per cent) were on antifungal therapy; 4 (9.75 per cent) did not survive. CONCLUSION: Early detection may improve survival. Follow up of high-risk patients after coronavirus disease 2019 infection is paramount.


Subject(s)
COVID-19/epidemiology , Coinfection/epidemiology , Epidemics , Mucorales , Mucormycosis/epidemiology , SARS-CoV-2 , Adult , Aged , Antifungal Agents/therapeutic use , Brain Diseases/epidemiology , Brain Diseases/microbiology , COVID-19/microbiology , Coinfection/microbiology , Debridement , Eye Infections, Fungal/epidemiology , Eye Infections, Fungal/microbiology , Female , Humans , Male , Middle Aged , Mucormycosis/microbiology , Orbital Diseases/epidemiology , Orbital Diseases/microbiology , Rhinitis/epidemiology , Rhinitis/microbiology , Young Adult
9.
Cell Rep ; 36(9): 109637, 2021 08 31.
Article in English | MEDLINE | ID: covidwho-1356160

ABSTRACT

Research conducted on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pathogenesis and coronavirus disease 2019 (COVID-19) generally focuses on the systemic host response, especially that generated by severely ill patients, with few studies investigating the impact of acute SARS-CoV-2 at the site of infection. We show that the nasal microbiome of SARS-CoV-2-positive patients (CoV+, n = 68) at the time of diagnosis is unique when compared to CoV- healthcare workers (n = 45) and CoV- outpatients (n = 21). This shift is marked by an increased abundance of bacterial pathogens, including Pseudomonas aeruginosa, which is also positively associated with viral RNA load. Additionally, we observe a robust host transcriptional response in the nasal epithelia of CoV+ patients, indicative of an antiviral innate immune response and neuronal damage. These data suggest that the inflammatory response caused by SARS-CoV-2 infection is associated with an increased abundance of bacterial pathogens in the nasal cavity that could contribute to increased incidence of secondary bacterial infections.


Subject(s)
Bacteria/classification , Bacterial Infections/microbiology , COVID-19 , Microbiota , Adult , Aged , Aged, 80 and over , Bacteria/isolation & purification , COVID-19/complications , COVID-19/immunology , COVID-19/microbiology , Coinfection/microbiology , Coinfection/virology , Cross-Sectional Studies , DNA, Bacterial/genetics , Female , Humans , Immunity, Innate , Inflammation , Male , Middle Aged , Nose/microbiology , Pseudomonas Infections/microbiology , Pseudomonas aeruginosa/isolation & purification , RNA, Ribosomal, 16S/genetics , RNA, Viral/genetics , RNA-Seq , Transcriptome , Viral Load , Young Adult
10.
Ann Clin Microbiol Antimicrob ; 20(1): 51, 2021 Aug 05.
Article in English | MEDLINE | ID: covidwho-1346234

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.


Subject(s)
Bacterial Infections/microbiology , COVID-19/microbiology , Coinfection/microbiology , Drug Resistance, Bacterial/drug effects , Adolescent , Adult , Aged , Aged, 80 and over , Anti-Bacterial Agents/pharmacology , Bacterial Infections/drug therapy , Bacterial Infections/epidemiology , COVID-19/epidemiology , COVID-19 Nucleic Acid Testing , Child , Child, Preschool , Coinfection/epidemiology , Female , Humans , Infant , Male , Microbial Sensitivity Tests , Middle Aged , Retrospective Studies , Turkey/epidemiology , Young Adult
11.
Int J Antimicrob Agents ; 58(4): 106409, 2021 Oct.
Article in English | MEDLINE | ID: covidwho-1330851

ABSTRACT

Since the start of the COVID-19 pandemic, there has been concern about the concomitant rise of antimicrobial resistance. While bacterial co-infections seem rare in COVID-19 patients admitted to hospital wards and intensive care units (ICUs), an increase in empirical antibiotic use has been described. In the ICU setting, where antibiotics are already abundantly-and often inappropriately-prescribed, the need for an ICU-specific antimicrobial stewardship programme is widely advocated. Apart from essentially warning against the use of antibacterial drugs for the treatment of a viral infection, other aspects of ICU antimicrobial stewardship need to be considered in view of the clinical course and characteristics of COVID-19. First, the distinction between infectious and non-infectious (inflammatory) causes of respiratory deterioration during an ICU stay is difficult, and the much-debated relevance of fungal and viral co-infections adds to the complexity of empirical antimicrobial prescribing. Biomarkers such as procalcitonin for the decision to start antibacterial therapy for ICU nosocomial infections seem to be more promising in COVID-19 than non-COVID-19 patients. In COVID-19 patients, cytomegalovirus reactivation is an important factor to consider when assessing patients infected with SARS-CoV-2 as it may have a role in modulating the patient immune response. The diagnosis of COVID-19-associated invasive aspergillosis is challenging because of the lack of sensitivity and specificity of the available tests. Furthermore, altered pharmacokinetic/pharmacodynamic properties need to be taken into account when prescribing antimicrobial therapy. Future research should now further explore the 'known unknowns', ideally with robust prospective study designs.


Subject(s)
Anti-Bacterial Agents/therapeutic use , Antimicrobial Stewardship/methods , COVID-19 , Cross Infection/diagnosis , Anti-Bacterial Agents/pharmacokinetics , Antimicrobial Stewardship/organization & administration , Biomarkers/analysis , COVID-19/drug therapy , Coinfection/drug therapy , Coinfection/microbiology , Cross Infection/drug therapy , Cytomegalovirus Infections/drug therapy , Cytomegalovirus Infections/virology , Humans , Intensive Care Units , Invasive Pulmonary Aspergillosis/diagnosis , Invasive Pulmonary Aspergillosis/drug therapy , Virus Activation/drug effects
12.
Emerg Med J ; 38(9): 685-691, 2021 Sep.
Article in English | MEDLINE | ID: covidwho-1320447

ABSTRACT

BACKGROUND: Guidelines recommend maximal efforts to obtain blood and sputum cultures in patients with COVID-19, as bacterial coinfection is associated with worse outcomes. The aim of this study was to evaluate the yield of bacteriological tests, including blood and sputum cultures, and the association of multiple biomarkers and the Pneumonia Severity Index (PSI) with clinical and microbiological outcomes in patients with COVID-19 presenting to the emergency department (ED). METHODS: This is a substudy of a large observational cohort study (PredictED study). The PredictED included adult patients from whom a blood culture was drawn at the ED of Haga Teaching Hospital, The Netherlands. For this substudy, all patients who tested positive for SARS-CoV-2 by PCR in March and April 2020 were included. The primary outcome was the incidence of bacterial coinfection. We used logistic regression analysis for associations of procalcitonin, C reactive protein (CRP), ferritin, lymphocyte count and PSI score with a severe disease course, defined as intensive care unit admission and/or 30-day mortality. The area under the receiver operating characteristics curve (AUC) quantified the discriminatory performance. RESULTS: We included 142 SARS-CoV-2 positive patients. On presentation, the median duration of symptoms was 8 days. 41 (29%) patients had a severe disease course and 24 (17%) died within 30 days. The incidence of bacterial coinfection was 2/142 (1.4%). None of the blood cultures showed pathogen growth while 6.3% was contaminated. The AUCs for predicting severe disease were 0.76 (95% CI 0.68 to 0.84), 0.70 (0.61 to 0.79), 0.62 (0.51 to 0.74), 0.62 (0.51 to 0.72) and 0.72 (0.63 to 0.81) for procalcitonin, CRP, ferritin, lymphocyte count and PSI score, respectively. CONCLUSION: Blood cultures appear to have limited value while procalcitonin and the PSI appear to be promising tools in helping physicians identify patients at risk for severe disease course in COVID-19 at presentation to the ED.


Subject(s)
Bacterial Infections/diagnosis , Bacteriological Techniques/methods , COVID-19/diagnosis , Coinfection/diagnosis , Adult , Aged , Aged, 80 and over , Bacterial Infections/blood , Bacterial Infections/complications , Bacterial Infections/microbiology , Bacteriological Techniques/statistics & numerical data , C-Reactive Protein/analysis , COVID-19/blood , COVID-19/complications , COVID-19/virology , COVID-19 Nucleic Acid Testing , Coinfection/blood , Coinfection/epidemiology , Coinfection/microbiology , Emergency Service, Hospital , Female , Ferritins/blood , Humans , Incidence , Lymphocyte Count , Male , Middle Aged , Netherlands/epidemiology , Procalcitonin/blood , Prognosis , ROC Curve , Retrospective Studies , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Severity of Illness Index
13.
Microbiol Spectr ; 9(1): e0016321, 2021 09 03.
Article in English | MEDLINE | ID: covidwho-1319383

ABSTRACT

Emerging evidence indicates that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected individuals are at an increased risk for coinfections; therefore, physicians need to be cognizant about excluding other treatable respiratory pathogens. Here, we report coinfection with SARS-CoV-2 and other respiratory pathogens in patients admitted to the coronavirus disease (COVID) care facilities of an Indian tertiary care hospital. From June 2020 through January 2021, we tested 191 patients with SARS-CoV-2 for 33 other respiratory pathogens using an fast track diagnostics respiratory pathogen 33 (FTD-33) assay. Additionally, information regarding other relevant respiratory pathogens was collected by reviewing their laboratory data. Overall, 13 pathogens were identified among patients infected with SARS-CoV-2, and 46.6% (89/191) of patients had coinfection with one or more additional pathogens. Bacterial coinfections (41.4% [79/191]) were frequent, with Staphylococcus aureus being the most common, followed by Klebsiella pneumoniae. Coinfections with SARS-CoV-2 and Pneumocystis jirovecii or Legionella pneumophila were also identified. The viral coinfection rate was 7.3%, with human adenovirus and human rhinovirus being the most common. Five patients in our cohort had positive cultures for Acinetobacter baumannii and K. pneumoniae, and two patients had active Mycobacterium tuberculosis infection. In total, 47.1% (90/191) of patients with coinfections were identified. The higher proportion of patients with coinfections in our cohort supports the systemic use of antibiotics in patients with severe SARS-CoV-2 pneumonia with rapid de-escalation based on respiratory PCR/culture results. The timely and simultaneous identification of coinfections can contribute to improved health of COVID-19 patients and enhanced antibiotic stewardship during the pandemic. IMPORTANCE Coinfections in COVID-19 patients may worsen disease outcomes and need further investigation. We found that a higher proportion of patients with COVID-19 were coinfected with one or more additional pathogens. A better understanding of the prevalence of coinfection with other respiratory pathogens in COVID-19 patients and the profile of pathogens can contribute to effective patient management and antibiotic stewardship during the current pandemic.


Subject(s)
COVID-19/epidemiology , Coinfection/epidemiology , Coinfection/microbiology , Coinfection/virology , Acinetobacter baumannii , Adenoviruses, Human , Adolescent , Adult , Aged , Aged, 80 and over , Anti-Bacterial Agents , Antimicrobial Stewardship , COVID-19/diagnosis , Coinfection/drug therapy , Enterovirus , Female , Humans , India/epidemiology , Klebsiella pneumoniae , Male , Middle Aged , Mycobacterium tuberculosis , Pandemics , SARS-CoV-2 , Tuberculosis/epidemiology , Young Adult
14.
mBio ; 12(4): e0047321, 2021 08 31.
Article in English | MEDLINE | ID: covidwho-1318003

ABSTRACT

The coronavirus disease 2019 (COVID-19) pandemic is a challenge for ongoing efforts to combat antimicrobial-resistant (AMR) bacterial infections. As we learn more about COVID-19 disease and drug stewardship evolves, there is likely to be a lasting impact of increased use of antimicrobial agents and antibiotics, as well as a lack of consistent access to health care across many populations. Sexually transmitted infections have been underreported during the pandemic and are often caused by some of the most drug-resistant pathogens. In their recent article in mBio, Parzych et al. (E. M. Parzych, S. Gulati, B. Zheng, M. A. Bah, et al., mBio 12:e00242-21, 2021, https://doi.org/10.1128/mBio.00242-21) focus on protection against Neisseria gonorrhoeae infection via in vivo delivery of an antigonococcal DNA-encoded antibody that has been modified for increased complement activation. Nucleic acid approaches are highly adaptable and could be tremendously beneficial for personalized strategies to combat AMR pathogens.


Subject(s)
Anti-Bacterial Agents/therapeutic use , Antimicrobial Stewardship/methods , COVID-19/pathology , Drug Resistance, Multiple, Bacterial/genetics , Coinfection/drug therapy , Coinfection/microbiology , Gonorrhea/drug therapy , Health Services Accessibility , Humans , Microbial Sensitivity Tests , Neisseria gonorrhoeae/drug effects , Neisseria gonorrhoeae/genetics , Precision Medicine , SARS-CoV-2
15.
Mycoses ; 64(10): 1253-1260, 2021 Oct.
Article in English | MEDLINE | ID: covidwho-1307862

ABSTRACT

IMPORTANCE: Coronavirus disease (COVID-19) causes an immunosuppressed state and increases risk of secondary infections like mucormycosis. We evaluated clinical features, predisposing factors, diagnosis and outcomes for mucormycosis among patients with COVID-19 infection. METHODS: This prospective, observational, multi-centre study included 47 consecutive patients with mucormycosis, diagnosed during their course of COVID-19 illness, between January 3 and March 27, 2021. Data regarding demography, underlying medical conditions, COVID-19 illness and treatment were collected. Clinical presentations of mucormycosis, imaging and biochemical characteristics and outcome were recorded. RESULTS: Of the 2567 COVID-19 patients admitted to 3 tertiary centres, 47 (1.8%) were diagnosed with mucormycosis. Mean age was 55 ± 12.8years, and majority suffered from diabetes mellitus (n = 36, 76.6%). Most were not COVID-19 vaccinated (n = 31, 66.0%) and majority (n = 43, 91.5%) had developed moderate-to-severe pneumonia, while 20 (42.6%) required invasive ventilation. All patients had received corticosteroids and broad-spectrum antibiotics while most (n = 37, 78.7%) received at least one anti-viral medication. Mean time elapsed from COVID-19 diagnosis to mucormycosis was 12.1 ± 4.6days. Eleven (23.4%) subjects succumbed to their disease, mostly (n = 8, 72.7%) within 7 days of diagnosis. Among the patients who died, 10 (90.9%) had pre-existing diabetes mellitus, only 2 (18.2%) had received just one vaccine dose and all developed moderate-to-severe pneumonia, requiring oxygen supplementation and mechanical ventilation. CONCLUSIONS: Mucormycosis can occur among COVID-19 patients, especially with poor glycaemic control, widespread and injudicious use of corticosteroids and broad-spectrum antibiotics, and invasive ventilation. Owing to the high mortality, high index of suspicion is required to ensure timely diagnosis and appropriate treatment in high-risk populations.


Subject(s)
Adrenal Cortex Hormones/adverse effects , COVID-19/epidemiology , Mucormycosis/epidemiology , Respiration, Artificial/adverse effects , Adrenal Cortex Hormones/therapeutic use , Antifungal Agents/therapeutic use , Antiviral Agents/therapeutic use , COVID-19/drug therapy , COVID-19/mortality , Coinfection/microbiology , Diabetes Complications , Diabetes Mellitus/pathology , Humans , India/epidemiology , Middle Aged , Mucormycosis/drug therapy , Mucormycosis/mortality , Prospective Studies , Ventilators, Mechanical/adverse effects
16.
Pediatr Infect Dis J ; 40(8): e313-e316, 2021 08 01.
Article in English | MEDLINE | ID: covidwho-1305446

ABSTRACT

Masking and social distancing have been adopted to mitigate the severe acute respiratory syndrome coronavirus 2 pandemic. We evaluated the indirect impact of severe acute respiratory syndrome coronavirus 2 prevention strategies on invasive Staphylococcus aureus, Streptococcus pneumoniae (pneumococcus) and Group A Streptococcus in Houston area children. We observed a decline in invasive pneumococcal disease and invasive Group A Streptococcus temporally associated with social distancing/masking/school closures.


Subject(s)
COVID-19/epidemiology , Pneumococcal Infections/epidemiology , Staphylococcal Infections/epidemiology , Streptococcal Infections/epidemiology , COVID-19/microbiology , COVID-19/prevention & control , Child , Coinfection/epidemiology , Coinfection/microbiology , Coinfection/virology , Hospitalization , Humans , Pandemics , Pneumococcal Infections/prevention & control , Pneumococcal Infections/virology , Prospective Studies , SARS-CoV-2/isolation & purification , Staphylococcal Infections/prevention & control , Staphylococcal Infections/virology , Staphylococcus aureus/isolation & purification , Streptococcal Infections/prevention & control , Streptococcal Infections/virology , Streptococcus pneumoniae/isolation & purification , Streptococcus pyogenes/isolation & purification
17.
J Infect Dev Ctries ; 15(6): 761-765, 2021 06 30.
Article in English | MEDLINE | ID: covidwho-1304764

ABSTRACT

INTRODUCTION: The aim of this study is to determine the coinfections with other respiratory pathogens in SARS-CoV-2 infected children patients in a pediatric unit in Istanbul. METHODOLOGY: This retrospective descriptive study was conducted in a 1000-bedded tertiary education and research hospital in Istanbul. All children hospitalized with the diagnosis of SARS-CoV-2 infection had been investigated for respiratory agents in nasopharyngeal secretions. Laboratory confirmation of SARS-CoV-2 and the other respiratory pathogens were performed using reverse transcriptase-polymerase chain reaction (RT-PCR). RESULTS: A total of 209 hospitalized children with suspected SARS-CoV-2 infection between March 2020-May 2020 were enrolled in this study. Among 209 children, 93 (44.5%) were RT-PCR positive for SARS-CoV-2 infection, and 116 (55.5%) were RT-PCR negative. The most common clinical symptoms in all children with SARS-CoV-2 infection were fever (68.8%) and cough (57.0%). The other clinical symptoms in decreasing rates were headache (10.8%), myalgia (5.4%), sore throat (3.2%), shortness of breath (3.2%), diarrhea (2.2%) and abdominal pain in one child. In 7 (7.5%) patients with SARS-CoV-2 infection, coinfection was detected. Two were with rhinovirus/enterovirus, two were with Coronavirus NL63, one was with adenovirus, and one was with Mycoplasma pneumoniae. In one patient, two additional respiratory agents (rhinovirus/enterovirus and adenovirus) were detected. There was a significantly longer hospital stay in patients with coinfection (p = 0.028). CONCLUSIONS: Although the coinfection rate was low in SARS-CoV-2 infected patients in our study, we found coinfection as a risk factor for length of hospital stay in the coinfected patient group.


Subject(s)
COVID-19/microbiology , COVID-19/virology , Coinfection/microbiology , Coinfection/virology , Viruses/genetics , Adenoviridae/genetics , Adolescent , COVID-19/diagnosis , Child , Child, Preschool , Coinfection/diagnosis , Coinfection/epidemiology , Hospitalization/statistics & numerical data , Humans , Length of Stay/statistics & numerical data , Mycoplasma pneumoniae/genetics , Mycoplasma pneumoniae/isolation & purification , Nasopharynx/microbiology , Nasopharynx/virology , Qualitative Research , Respiratory System/microbiology , Respiratory System/virology , Retrospective Studies , SARS-CoV-2/genetics , Tertiary Care Centers/statistics & numerical data , Turkey/epidemiology , Viruses/classification , Viruses/isolation & purification
18.
Sci Rep ; 11(1): 12703, 2021 06 16.
Article in English | MEDLINE | ID: covidwho-1275958

ABSTRACT

Secondary bacterial infections are a potentially fatal complication of influenza infection. We aimed to define the impact of secondary bacterial infections on the clinical course and mortality in coronavirus disease 2019 (COVID-19) patients by comparison with influenza patients. COVID-19 (n = 642) and influenza (n = 742) patients, admitted to a large tertiary center in Israel and for whom blood or sputum culture had been taken were selected for this study. Bacterial culture results, clinical parameters, and death rates were compared. COVID-19 patients had higher rates of bacterial infections than influenza patients (12.6% vs. 8.7%). Notably, the time from admission to bacterial growth was longer in COVID-19 compared to influenza patients (4 (1-8) vs. 1 (1-3) days). Late infections (> 48 h after admission) with gram-positive bacteria were more common in COVID-19 patients (28% vs. 9.5%). Secondary infection was associated with a higher risk of death in both patient groups 2.7-fold (1.22-5.83) for COVID-19, and 3.09-fold (1.11-7.38) for Influenza). The association with death remained significant upon adjustment to age and clinical parameters in COVID-19 but not in influenza infection. Secondary bacterial infection is a notable complication associated with worse outcomes in COVID-19 than influenza patients. Careful surveillance and prompt antibiotic treatment may benefit selected patients.


Subject(s)
COVID-19/epidemiology , COVID-19/mortality , Coinfection/epidemiology , Gram-Negative Bacteria/isolation & purification , Gram-Negative Bacterial Infections/epidemiology , Gram-Positive Bacteria/isolation & purification , Gram-Positive Bacterial Infections/epidemiology , Influenza A virus/isolation & purification , Influenza, Human/epidemiology , Influenza, Human/mortality , Pandemics , SARS-CoV-2/isolation & purification , Adult , Aged , COVID-19/virology , Coinfection/microbiology , Female , Gram-Negative Bacterial Infections/microbiology , Gram-Positive Bacterial Infections/microbiology , Humans , Influenza, Human/virology , Israel/epidemiology , Length of Stay , Male , Middle Aged , Patient Admission , Retrospective Studies
19.
J Med Virol ; 93(7): 4564-4569, 2021 07.
Article in English | MEDLINE | ID: covidwho-1263107

ABSTRACT

Adverse outcomes in coronavirus infection disease-19 (COVID-19) patients are not always due to the direct effects of the viral infection, but often due to bacterial coinfection. However, the risk factors for such bacterial coinfection are hitherto unknown. A case-control study was conducted to determine risk factors for bacterial infection in moderate to critical COVID-19. Out of a total of 50 cases and 50 controls, the proportion of cases with severe/critical disease at presentation was 80% in cases compared to 30% in controls (p < 0.001). The predominant site was hospital-acquired pneumonia (72%) and the majority were Gram-negative organisms (82%). The overall mortality was 30%, with comparatively higher mortality among cases (42% vs. 18%; p = 0.009). There was no difference between procalcitonin levels in both groups (p = 0.883). In multivariable logistic regression analysis, significant independent association was found with severe/critical COVID-19 at presentation (AOR: 4.42 times; 95% CI: 1.63-11.9) and use of steroids (AOR: 4.60; 95% CI: 1.24-17.05). Notably, 64% of controls were administered antibiotics despite the absence of bacterial coinfection or secondary infection. Risk factors for bacterial infections in moderate to critically ill patients with COVID-19 include critical illness at presentation and use of steroids. There is widespread empiric antibiotic utilization in those without bacterial infection.


Subject(s)
Bacterial Infections/epidemiology , COVID-19/pathology , Coinfection/epidemiology , Healthcare-Associated Pneumonia/epidemiology , Aged , Antimicrobial Stewardship , Bacterial Infections/complications , COVID-19/etiology , Case-Control Studies , Coinfection/microbiology , Female , Humans , Male , Middle Aged , Pakistan/epidemiology , Risk Factors , SARS-CoV-2
20.
J Microbiol Methods ; 186: 106259, 2021 07.
Article in English | MEDLINE | ID: covidwho-1249029

ABSTRACT

The prevalence and microbiology of concomitant respiratory bacterial infections in patients with SARS-CoV-2 infection are not yet fully understood. In this retrospective study, we assessed respiratory bacterial co-infections in lower respiratory tract samples taken from intensive care unit-hospitalized COVID-19 patients, by comparing the conventional culture approach to an innovative molecular diagnostic technology. A total of 230 lower respiratory tract samples (i.e., bronchial aspirates or bronchoalveolar lavages) were taken from 178 critically ill COVID-19 patients. Each sample was processed by a semi-quantitative culture and by a multiplex PCR panel (FilmArray Pneumonia Plus panel), allowing rapid detection of a wide range of clinically relevant pathogens and a limited number of antimicrobial resistance markers. More than 30% of samples showed a positive bacterial culture, with Pseudomonas aeruginosa, Klebsiella pneumoniae and Staphylococcus aureus the most detected pathogens. FilmArray showed an overall sensitivity and specificity of 89.6% and 98.3%, respectively, with a negative predictive value of 99.7%. The molecular test significantly reduced the turn-around-time (TAT) and increased the rates of microbial detection. Most cases missed by culture were characterized by low bacterial loads (104-105 copies/mL). FilmArray missed a list of pathogens not included in the molecular panel, especially Stenotrophomonas maltophilia (8 cases). FilmArray can be useful to detect bacterial pathogens in lower respiratory tract specimens of COVID-19 patients, with a significant decrease of TAT. The test is particularly useful to rule out bacterial co-infections and avoid the inappropriate prescription of antibiotics.


Subject(s)
Bacteria/isolation & purification , Bacterial Typing Techniques , COVID-19/complications , COVID-19/microbiology , Multiplex Polymerase Chain Reaction , Respiratory Tract Infections/microbiology , Adult , Bacteria/classification , Coinfection/microbiology , Humans , Intensive Care Units , Respiratory Tract Infections/etiology , Retrospective Studies , Sensitivity and Specificity
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