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1.
PLoS One ; 16(12): e0261849, 2021.
Article in English | MEDLINE | ID: covidwho-1623664

ABSTRACT

BACKGROUND: Tuberculosis (TB) and COVID-19 pandemics are both diseases of public health threat globally. Both diseases are caused by pathogens that infect mainly the respiratory system, and are involved in airborne transmission; they also share some clinical signs and symptoms. We, therefore, took advantage of collected sputum samples at the early stage of COVID-19 outbreak in Ghana to conduct differential diagnoses of long-standing endemic respiratory illness, particularly tuberculosis. METHODOLOGY: Sputum samples collected through the enhanced national surveys from suspected COVID-19 patients and contact tracing cases were analyzed for TB. The sputum samples were processed using Cepheid's GeneXpert MTB/RIF assay in pools of 4 samples to determine the presence of Mycobacterium tuberculosis complex. Positive pools were then decoupled and analyzed individually. Details of positive TB samples were forwarded to the NTP for appropriate case management. RESULTS: Seven-hundred and seventy-four sputum samples were analyzed for Mycobacterium tuberculosis in both suspected COVID-19 cases (679/774, 87.7%) and their contacts (95/774, 12.3%). A total of 111 (14.3%) were diagnosed with SARS CoV-2 infection and six (0.8%) out of the 774 individuals tested positive for pulmonary tuberculosis: five (83.3%) males and one female (16.7%). Drug susceptibility analysis identified 1 (16.7%) rifampicin-resistant tuberculosis case. Out of the six TB positive cases, 2 (33.3%) tested positive for COVID-19 indicating a coinfection. Stratifying by demography, three out of the six (50%) were from the Ayawaso West District. All positive cases received appropriate treatment at the respective sub-district according to the national guidelines. CONCLUSION: Our findings highlight the need for differential diagnosis among COVID-19 suspected cases and regular active TB surveillance in TB endemic settings.


Subject(s)
COVID-19/diagnosis , COVID-19/epidemiology , Coinfection/diagnosis , Coinfection/epidemiology , Mycobacterium tuberculosis/genetics , Pandemics/prevention & control , SARS-CoV-2/genetics , Tuberculosis, Pulmonary/diagnosis , Tuberculosis, Pulmonary/epidemiology , Antibiotics, Antitubercular/pharmacology , COVID-19/prevention & control , COVID-19/virology , Coinfection/virology , Diagnosis, Differential , Drug Resistance, Bacterial/drug effects , Female , Ghana/epidemiology , Humans , Male , Microbial Sensitivity Tests , Mycobacterium tuberculosis/drug effects , Rifampin/pharmacology , Sputum/microbiology , Tuberculosis, Pulmonary/microbiology
2.
Viruses ; 13(12)2021 12 16.
Article in English | MEDLINE | ID: covidwho-1580428

ABSTRACT

BACKGROUND: We aimed to compare the clinical severity in patients who were coinfected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and rhinovirus or monoinfected with a single one of these viruses. METHODS: The study period ranged from 1 March 2020 to 28 February 2021 (one year). SARS-CoV-2 and other respiratory viruses were identified by real-time reverse-transcription-PCR as part of the routine work at Marseille University hospitals. Bacterial and fungal infections were detected by standard methods. Clinical data were retrospectively collected from medical files. This study was approved by the ethical committee of our institute. RESULTS: A total of 6034/15,157 (40%) tested patients were positive for at least one respiratory virus. Ninety-three (4.3%) SARS-CoV-2-infected patients were coinfected with another respiratory virus, with rhinovirus being the most frequent (62/93, 67%). Patients coinfected with SARS-CoV-2 and rhinovirus were significantly more likely to report a cough than those with SARS-CoV-2 monoinfection (62% vs. 31%; p = 0.0008). In addition, they were also significantly more likely to report dyspnea than patients with rhinovirus monoinfection (45% vs. 36%; p = 0.02). They were also more likely to be transferred to an intensive care unit and to die than patients with rhinovirus monoinfection (16% vs. 5% and 7% vs. 2%, respectively) but these differences were not statistically significant. CONCLUSIONS: A close surveillance and investigation of the co-incidence and interactions of SARS-CoV-2 and other respiratory viruses is needed. The possible higher risk of increased clinical severity in SARS-CoV-2-positive patients coinfected with rhinovirus warrants further large scale studies.


Subject(s)
COVID-19/epidemiology , Coinfection/epidemiology , Coinfection/virology , Picornaviridae Infections/epidemiology , Adolescent , Adult , Aged , COVID-19/diagnosis , Child , Coinfection/diagnosis , Female , Humans , Incidence , Male , Middle Aged , Picornaviridae Infections/diagnosis , Picornaviridae Infections/virology , Real-Time Polymerase Chain Reaction , Respiratory Tract Infections/epidemiology , Respiratory Tract Infections/virology , Retrospective Studies , Rhinovirus , SARS-CoV-2 , Severity of Illness Index , Young Adult
3.
J Med Virol ; 93(12): 6798-6802, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1530182

ABSTRACT

Viral infections have been on the rise for the past decades. The impact of the viruses worsened amidst the pandemic burdening the already overwhelmed health care system in African countries. This article sheds light on how the coronavirus together with the already existing viral infections, some of which re-emerged, impacted the continent. The strategies in place such as immunization, education, will have to be strengthened in all African countries to reduce the burden. Furthermore, governments can further collaborate with other countries in creating guidelines to reduce co-infection of the diseases.


Subject(s)
COVID-19/enzymology , COVID-19/virology , Coinfection/epidemiology , Coinfection/virology , Virus Diseases/epidemiology , Africa/epidemiology , COVID-19/immunology , Coinfection/immunology , Humans , Pandemics/prevention & control , SARS-CoV-2/immunology , Vaccination/methods , Virus Diseases/immunology , Virus Diseases/virology
4.
Virol J ; 18(1): 159, 2021 08 03.
Article in English | MEDLINE | ID: covidwho-1496199

ABSTRACT

BACKGROUND: The multifaceted non-pharmaceutical interventions (NPIs) taken during the COVID-19 pandemic not only decrease the spreading of the SARS-CoV-2, but have impact on the prevalence of other viruses. This study aimed to explore the prevalence of common respiratory viruses among hospitalized children with lower respiratory tract infections (LRTI) in China during the COVID-19 pandemic. METHODS: Respiratory specimens were obtained from children with LRTI at Children's Hospital of Fudan University for detection of respiratory syncytial virus (RSV), adenovirus (ADV), parainfluenza virus (PIV) 1 to 3, influenza virus A (FluA), influenza virus B (FluB), human metapneumovirus (MPV) and rhinovirus (RV). The data were analyzed and compared between the year of 2020 (COVID-19 pandemic) and 2019 (before COVID-19 pandemic). RESULTS: A total of 7107 patients were enrolled, including 4600 patients in 2019 and 2507 patients in 2020. Compared with 2019, we observed an unprecedented reduction of RSV, ADV, FluA, FluB, and MPV infections in 2020, despite of reopening of schools in June, 2020. However, the RV infection was significantly increased in 2020 and a sharp increase was observed especially after reopening of schools. Besides, the PIV infection showed resurgent characteristic after September of 2020. The mixed infections were significantly less frequent in 2020 compared with the year of 2019. CONCLUSIONS: The NPIs during the COVID-19 pandemic have great impact on the prevalence of common respiratory viruses in China. Meanwhile, we do need to be cautious of a possible resurgence of some respiratory viruses as the COVID-19 restrictions are relaxed.


Subject(s)
COVID-19/epidemiology , Respiratory Tract Infections/epidemiology , Respiratory Tract Infections/virology , Age Distribution , COVID-19/prevention & control , Child , Child, Preschool , China/epidemiology , Coinfection/epidemiology , Coinfection/virology , Female , Hospitalization , Hospitals, Pediatric , Humans , Infant , Male , Prevalence , SARS-CoV-2 , Seasons , Viruses/classification , Viruses/isolation & purification
5.
Viruses ; 12(8)2020 08 18.
Article in English | MEDLINE | ID: covidwho-1453290

ABSTRACT

Enteric viral co-infections, infections involving more than one virus, have been reported for a diverse group of etiological agents, including rotavirus, norovirus, astrovirus, adenovirus, and enteroviruses. These pathogens are causative agents for acute gastroenteritis and diarrheal disease in immunocompetent and immunocompromised individuals of all ages globally. Despite virus-virus co-infection events in the intestine being increasingly detected, little is known about their impact on disease outcomes or human health. Here, we review what is currently known about the clinical prevalence of virus-virus co-infections and how co-infections may influence vaccine responses. While experimental investigations into enteric virus co-infections have been limited, we highlight in vivo and in vitro models with exciting potential to investigate viral co-infections. Many features of virus-virus co-infection mechanisms in the intestine remain unclear, and further research will be critical.


Subject(s)
Coinfection/virology , Gastroenteritis/virology , Virus Diseases/physiopathology , Viruses/classification , Viruses/pathogenicity , Animals , Asymptomatic Infections , Disease Models, Animal , Feces/virology , Humans , Intestines/virology , Mice , Primates
7.
Microbiol Spectr ; 9(2): e0083121, 2021 10 31.
Article in English | MEDLINE | ID: covidwho-1476399

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of coronavirus disease 2019 (COVID-19), has infected all age groups and disproportionately impacted vulnerable populations globally. Polymicrobial infections may play an important role in the development of SARS-CoV-2 infection in susceptible hosts. These coinfections may increase the risk of disease severity and pose challenges to the diagnosis, treatment, and prognosis of COVID-19. There have been limited SARS-CoV-2 coinfection studies. In this retrospective study, residual nucleic acid extracts from 796 laboratory-confirmed COVID-19-positive specimens, collected between March 2020 and February 2021, were analyzed using a Luminex NxTAG respiratory pathogen panel (RPP). Of these, 745 returned valid results and were used for analysis; 53 (7.1%) were positive for one or more additional pathogens. Six different respiratory viruses were detected among the 53 SARS-CoV-2-positive patient specimens, and 7 of those specimens tested positive for more than one additional respiratory virus. The most common pathogens include rhinovirus/enterovirus (RV/EV) (n = 22, 41.51%), human metapneumovirus (hMPV) (n = 18, 33.9%), and adenovirus (n = 12, 22.6%). Interestingly, there were no SARS-CoV-2 coinfections involving influenza A or influenza B in the study specimens. The median age of the SARS-CoV-2-positive patients with coinfections was 38 years; 53% identified as female, and 47% identified as male. Based on our retrospective analysis, respiratory coinfections associated with SARS-CoV-2-positive patients were more common in young children (≤9 years old), with white being the most common race. Our findings will likely prompt additional investigation of polymicrobial infection associated with SARS-CoV-2 during seasonal respiratory pathogen surveillance by public health laboratories. IMPORTANCE This examination of respiratory pathogen coinfections in SARS-CoV-2 patients will likely shed light on our understanding of polymicrobial infection associated with COVID-19. Our results should prompt public health authorities to improve seasonal respiratory pathogen surveillance practices and address the risk of disease severity.


Subject(s)
COVID-19/complications , Coinfection/virology , Respiratory Tract Infections/complications , Respiratory Tract Infections/virology , Adenoviridae/genetics , Adenoviridae/isolation & purification , Adolescent , Adult , Aged , Aged, 80 and over , Child , Enterovirus/genetics , Enterovirus/isolation & purification , Female , Humans , Male , Metapneumovirus/genetics , Metapneumovirus/isolation & purification , Middle Aged , Retrospective Studies , Rhinovirus/genetics , Rhinovirus/isolation & purification , SARS-CoV-2/genetics , Wisconsin , Young Adult
8.
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
9.
Nat Commun ; 12(1): 5819, 2021 10 05.
Article in English | MEDLINE | ID: covidwho-1454763

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the ongoing coronavirus disease 2019 (COVID-19) pandemic. The continued spread of SARS-CoV-2 increases the probability of influenza/SARS-CoV-2 coinfection, which may result in severe disease. In this study, we examine the disease outcome of influenza A virus (IAV) and SARS-CoV-2 coinfection in K18-hACE2 mice. Our data indicate enhance susceptibility of IAV-infected mice to developing severe disease upon coinfection with SARS-CoV-2 two days later. In contrast to nonfatal influenza and lower mortality rates due to SARS-CoV-2 alone, this coinfection results in severe morbidity and nearly complete mortality. Coinfection is associated with elevated influenza viral loads in respiratory organs. Remarkably, prior immunity to influenza, but not to SARS-CoV-2, prevents severe disease and mortality. This protection is antibody-dependent. These data experimentally support the necessity of seasonal influenza vaccination for reducing the risk of severe influenza/COVID-19 comorbidity during the COVID-19 pandemic.


Subject(s)
COVID-19/immunology , COVID-19/virology , Coinfection/immunology , Coinfection/virology , Immunity , Orthomyxoviridae Infections/immunology , Orthomyxoviridae Infections/virology , SARS-CoV-2/immunology , Angiotensin-Converting Enzyme 2/metabolism , Animals , Antibodies, Viral/immunology , COVID-19/pathology , Cell Line , Disease Models, Animal , Female , Humans , Inflammation/genetics , Lung/pathology , Lung/virology , Male , Mice, Inbred C57BL , Mice, Transgenic , Up-Regulation/genetics , Viral Load/immunology
10.
Ghana Med J ; 54(4 Suppl): 121-124, 2020 Dec.
Article in English | MEDLINE | ID: covidwho-1436206

ABSTRACT

Coronavirus disease 2019 (COVID-19) is especially severe in patients with underlying chronic conditions, with increased risk of mortality. There is concern that people living with HIV (PLWH), especially those with severe immunosuppression, and COVID-19 may have severe disease and a negative clinical outcome. Most studies on COVID-19 in PLWH are from Asia, Europe and America where population dynamics, antiretroviral treatment coverage and coexisting opportunistic infections may differ from that in sub-Saharan Africa. We report on the clinical profile and outcome of three cases of PLWH co-infected with SARS-CoV-2. They all presented with fever, cough and breathlessness and also had advanced HIV infection as evidenced by opportunistic infections, high HIV viral loads and low CD4 counts. The patients responded favourably to the standard of care and were discharged home. Our findings suggest that PLWH with advanced immunosuppression may not necessarily have an unfavourable disease course and outcome. However, case-controlled studies with a larger population size are needed to better understand the impact of COVID-19 in this patient population. Funding: Not declared.


Subject(s)
COVID-19/virology , Coinfection/virology , HIV Infections/virology , HIV , Opportunistic Infections/virology , SARS-CoV-2 , Adult , Africa South of the Sahara , COVID-19/complications , Coinfection/complications , Female , HIV Infections/complications , Humans , Male , Middle Aged , Opportunistic Infections/complications , Viral Load
11.
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
12.
Biomed Res Int ; 2021: 5313832, 2021.
Article in English | MEDLINE | ID: covidwho-1394270

ABSTRACT

Background: Coinfections have a potential role in increased morbidity and mortality rates during pandemics. Our investigation is aimed at evaluating the viral coinfection prevalence in COVID-19 patients. Methods: We systematically searched scientific databases, including Medline, Scopus, WOS, and Embase, from December 1, 2019, to December 30, 2020. Preprint servers such as medRxiv were also scanned to find other related preprint papers. All types of studies evaluating the viral coinfection prevalence in COVID-19 patients were considered. We applied the random effects model to pool all of the related studies. Results: Thirty-three studies including 10484 patients were identified. The viral coinfection estimated pooled prevalence was 12.58%; 95% CI: 7.31 to 18.96). Blood viruses (pooled prevalence: 12.48%; 95% CI: 8.57 to 16.93) had the most frequent viral coinfection, and respiratory viruses (pooled prevalence: 4.32%; 95% CI: 2.78 to 6.15) had less frequent viral coinfection. The herpesvirus pooled prevalence was 11.71% (95% CI: 3.02 to 24.80). Also, the maximum and minimum of viral coinfection pooled prevalence were in AMRO and EMRO with 15.63% (95% CI: 3.78 to 33.31) and 7.05% (95% CI: 3.84 to 11.07), respectively. Conclusion: The lowest rate of coinfection belonged to respiratory viruses. Blood-borne viruses had the highest coinfection rate. Our results provide important data about the prevalence of blood-borne viruses among COVID-19 patients which can be critical when it comes to their treatment procedure.


Subject(s)
COVID-19/epidemiology , Coinfection/epidemiology , Coinfection/virology , Humans , Pandemics/prevention & control , Prevalence , SARS-CoV-2/pathogenicity , Virus Diseases/epidemiology , Virus Diseases/virology , Viruses/pathogenicity
14.
Rev Esp Quimioter ; 33(6): 444-447, 2020 Dec.
Article in Spanish | MEDLINE | ID: covidwho-1390020

ABSTRACT

OBJECTIVE: Co-circulation of the two Influenza B lineages hinders forecast of strain to include in trivalent vaccine. Autonomous Communities such as Cantabria continue without supplying tetravalent vaccine. The aim of this study was to analyse epidemiological characteristics of influenza type B in Cantabria (2019-2020 season) as well as to establish the predominant lineage and its relation to the recommended vaccine. METHODS: Retrospective study whereby flu diagnosis and lineage analysis were determined by RT-PCR. RESULTS: All samples belonged to the Victoria lineage. Most prevalent viral co-infection was due to SARS-CoV-2. The population affected by influenza B was mainly paediatric and non-vaccinated patients more frequently required hospital admittance. CONCLUSIONS: Influenza type B has a higher incidence in the paediatric population and type A affects more the adult population. Only 28.8% of patients with Influenza B that presented with some underlying condition or risk factor were vaccinated. This shows the need to increase coverage with tetravalent vaccines in order to reduce the burden of disease associated with the Influenza B virus.


Subject(s)
COVID-19/epidemiology , Influenza B virus , Influenza, Human/epidemiology , Pandemics , SARS-CoV-2 , Adult , COVID-19/virology , Chi-Square Distribution , Child , Coinfection/epidemiology , Coinfection/virology , Epidemics , Female , Hospitalization/statistics & numerical data , Humans , Influenza Vaccines/administration & dosage , Influenza, Human/prevention & control , Influenza, Human/virology , Male , Retrospective Studies , Seasons , Spain/epidemiology , Statistics, Nonparametric
16.
Korean J Parasitol ; 59(4): 399-402, 2021 Aug.
Article in English | MEDLINE | ID: covidwho-1381388

ABSTRACT

The COVID-19 pandemic continues to be a major health problem worldwide. Timely diagnosis of co-infections mimicking COVID-19, such as malaria, might be challenging particularly in non-endemic areas. We report the first case of COVID-19 and Plasmodium ovale malaria co-infection from our region aiming to highligt the importance of travel history and prophylaxis in malaria management in the context of pandemic. The galloping sound can sometimes be a harbinger of zebra besides the horse.


Subject(s)
COVID-19/virology , Coinfection/parasitology , Coinfection/virology , Malaria/parasitology , Plasmodium ovale/physiology , Adult , Humans , Male , Plasmodium ovale/genetics , SARS-CoV-2/genetics , SARS-CoV-2/physiology
17.
J Acquir Immune Defic Syndr ; 85(1): 6-10, 2020 09 01.
Article in English | MEDLINE | ID: covidwho-1373693

ABSTRACT

BACKGROUND: SARS-CoV-2 infection continues to cause significant morbidity and mortality worldwide. Preliminary data on SARS-CoV-2 infection suggest that some immunocompromised hosts experience worse outcomes. We performed a retrospective matched cohort study to characterize outcomes in HIV-positive patients with SARS-CoV-2 infection. METHODS: Leveraging data collected from electronic medical records for all patients hospitalized at NYU Langone Health with COVID-19 between March 2, 2020, and April 23, 2020, we matched 21 HIV-positive patients with 42 non-HIV patients using a greedy nearest-neighbor algorithm. Admission characteristics, laboratory test results, and hospital outcomes were recorded and compared between the 2 groups. RESULTS: Although there was a trend toward increased rates of intensive care unit admission, mechanical ventilation, and mortality in HIV-positive patients, these differences were not statistically significant. Rates for these outcomes in our cohort are similar to those previously published for all patients hospitalized with COVID-19. HIV-positive patients had significantly higher admission and peak C-reactive protein values. Other inflammatory markers did not differ significantly between groups, although HIV-positive patients tended to have higher peak values during their clinical course. Three HIV-positive patients had superimposed bacterial pneumonia with positive sputum cultures, and all 3 patients died during hospitalization. There was no difference in frequency of thrombotic events or myocardial infarction between these groups. CONCLUSIONS: This study provides evidence that HIV coinfection does not significantly impact presentation, hospital course, or outcomes of patients infected with SARS-CoV-2, when compared with matched non-HIV patients. A larger study is required to determine whether the trends we observed apply to all HIV-positive patients.


Subject(s)
Betacoronavirus , Coinfection/virology , Coronavirus Infections/complications , HIV Infections/complications , Pneumonia, Viral/complications , Adult , Aged , Aged, 80 and over , COVID-19 , Case-Control Studies , Cohort Studies , Coinfection/mortality , Coronavirus Infections/mortality , Critical Care , Female , HIV Infections/mortality , Hospitalization , Humans , Male , Middle Aged , Pandemics , Pneumonia, Viral/mortality , Respiration, Artificial , Retrospective Studies , SARS-CoV-2 , Treatment Outcome
18.
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
19.
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
20.
J Clin Lab Anal ; 35(8): e23868, 2021 Aug.
Article in English | MEDLINE | ID: covidwho-1312737

ABSTRACT

BACKGROUND: Studies have reported coinfection of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the cause of coronavirus disease-2019 (COVID-19), with other viruses that cause respiratory tract infections (RTIs). We investigated the coinfection rate of SARS-CoV-2 and other RTI-causing viruses, and whether the cycle threshold (Ct) value of a real-time reverse transcriptase PCR (RT-PCR) differed when the coinfection occurred during the first wave of COVID-19 in Daegu, Republic of Korea, in 2020. METHODS: After performing PCR for SARS-CoV-2, we additionally tested for the presence of RTI-causing viruses to check for coinfection. Subsequently, we identified the specific coexisting respiratory viruses and calculated the coinfection rate. In addition, based on the coinfection status, we compared the Ct values obtained from RT-PCR for SARS-CoV-2 in patients who tested positive for COVID-19 PCR. RESULTS: Of 13,717 patients, 123 had positive results on COVID-19 PCR testing and six tested positive for an RTI-causing virus. Thus, the coinfection rate was 4.9%. There were no statistically significant differences in the mean Ct values of SARS-CoV-2 RT-PCR between coinfected and non-coinfected patients. CONCLUSION: This study computed the coinfection rate of SARS-CoV-2 and RTI-causing viruses and revealed that the mean Ct values in SARS-CoV-2 real-time RT-PCR did not differ according to the coinfection status.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/epidemiology , Coinfection/epidemiology , Coinfection/virology , Respiratory Tract Infections/epidemiology , Aged , Aged, 80 and over , Female , Humans , Male , Middle Aged , Real-Time Polymerase Chain Reaction , Republic of Korea/epidemiology , Respiratory Tract Infections/etiology , Respiratory Tract Infections/virology , SARS-CoV-2/genetics , Tertiary Care Centers/statistics & numerical data
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