Genetic Diversity, Antimicrobial Resistance Pattern, and Biofilm Formation in Klebsiella pneumoniae Isolated from Patients with Coronavirus Disease 2019 (COVID-19) and Ventilator-Associated Pneumonia.

INTRODUCTION: Patients with acute respiratory distress syndrome caused by coronavirus disease 2019 (COVID-19) are at risk for superadded infections, especially infections caused by multidrug resistant (MDR) pathogens. Before the COVID-19 pandemic, the prevalence of MDR infections, including infections caused by MDR Klebsiella pneumoniae (K. pneumoniae), was very high in Iran. This study is aimed at assessing the genetic diversity, antimicrobial resistance pattern, and biofilm formation in K. pneumoniae isolates obtained from patients with COVID-19 and ventilator-associated pneumonia (VAP) hospitalized in an intensive care unit (ICU) in Iran. METHODS: In this cross-sectional study, seventy K. pneumoniae isolates were obtained from seventy patients with COVID-19 hospitalized in the ICU of Shahid Beheshti hospital, Kashan, Iran, from May to September, 2020. K. pneumoniae was detected through the ureD gene. Antimicrobial susceptibility testing was done using the Kirby-Bauer disc diffusion method, and biofilm was detected using the microtiter plate assay method. Genetic diversity was also analyzed through polymerase chain reaction based on enterobacterial repetitive intergenic consensus (ERIC-PCR). The BioNumerics software (v. 8.0, Applied Maths, Belgium) was used for analyzing the data and drawing dendrogram and minimum spanning tree. Findings. K. pneumoniae isolates had varying levels of resistance to antibiotics meropenem (80.4%), cefepime-aztreonam-piperacillin/tazobactam (70%), tobramycin (61.4%), ciprofloxacin (57.7%), gentamicin (55.7%), and imipenem (50%). Around 77.14% of isolates were MDR, and 42.8% of them formed biofilm. Genetic diversity analysis revealed 28 genotypes (E1-E28) and 74.28% of isolates were grouped into ten clusters (i.e., clusters A-J). Clusters were further categorized into three major clusters, i.e., clusters E, H, and J. Antimicrobial resistance to meropenem, tobramycin, gentamicin, and ciprofloxacin in cluster J was significantly higher than cluster H, denoting significant relationship between ERIC clusters and antimicrobial resistance. However, there was no significant difference among major clusters E, H, and J respecting biofilm formation. CONCLUSION: K. pneumoniae isolates obtained from patients with COVID-19 have high antimicrobial resistance, and 44.2% of them have genetic similarity and can be clustered in three major clusters. There is a significant difference among clusters respecting antimicrobial resistance.

Timing and causes of death in severe COVID-19 patients.

BACKGROUND: Previous studies reporting the causes of death in patients with severe COVID-19 have provided conflicting results. The objective of this study was to describe the causes and timing of death in patients with severe COVID-19 admitted to the intensive care unit (ICU). METHODS: We performed a retrospective study in eight ICUs across seven French hospitals. All consecutive adult patients (aged ≥ 18 years) admitted to the ICU with PCR-confirmed SARS-CoV-2 infection and acute respiratory failure were included in the analysis. The causes and timing of ICU deaths were reported based on medical records. RESULTS: From March 1, 2020, to April 28, 287 patients were admitted to the ICU for SARS-CoV-2 related acute respiratory failure. Among them, 93 patients died in the ICU (32%). COVID-19-related multiple organ dysfunction syndrome (MODS) was the leading cause of death (37%). Secondary infection-related MODS accounted for 26% of ICU deaths, with a majority of ventilator-associated pneumonia. Refractory hypoxemia/pulmonary fibrosis was responsible for death in 19% of the cases. Fatal ischemic events (venous or arterial) occurred in 13% of the cases. The median time from ICU admission to death was 15 days (25th-75th IQR, 7-27 days). COVID-19-related MODS had a median time from ICU admission to death of 14 days (25th-75th IQR: 7-19 days), while only one death had occurred during the first 3 days since ICU admission. CONCLUSIONS: In our multicenter observational study, COVID-19-related MODS and secondary infections were the two leading causes of death, among severe COVID-19 patients admitted to the ICU.

Lung ultrasound score to monitor COVID-19 pneumonia progression in patients with ARDS.

COVID-19 pneumonia typically begins with subpleural ground glass opacities with progressive extension on computerized tomography studies. Lung ultrasound is well suited to this interstitial, subpleural involvement, and it is now broadly used in intensive care units (ICUs). The extension and severity of lung infiltrates can be described numerically with a reproducible and validated lung ultrasound score (LUSS). We hypothesized that LUSS might be useful as a tool to non-invasively monitor the evolution of COVID-19 pneumonia at the bedside. LUSS monitoring was rapidly implemented in the management of our COVID-19 patients with RT-PCR-documented COVID-19. The LUSS was evaluated repeatedly at the bedside. We present a graphic description of the course of LUSS during COVID-19 in 10 consecutive patients admitted in our intensive care unit with moderate to severe ARDS between March 15 and 30th. LUSS appeared to be closely related to the disease progression. In successfully extubated patients, LUSS decreased and was lower than at the time of intubation. LUSS increased inexorably in a patient who died from refractory hypoxemia. LUSS helped with the diagnosis of ventilator-associated pneumonia (VAP), showing an increased score and the presence of new lung consolidations in all 5 patients with VAPs. There was also a good agreement between CT-scans and LUSS as for the presence of lung consolidations. In conclusion, our early experience suggests that LUSS monitoring accurately reflect disease progression and indicates potential usefulness for the management of COVID-19 patients with ARDS. It might help with early VAP diagnosis, mechanical ventilation weaning management, and potentially reduce the need for X-ray and CT exams. LUSS evaluation is easy to use and readily available in ICUs throughout the world, and might be a safe, cheap and simple tool to optimize critically ill COVID-19 patients care during the pandemic.

Impact of respiratory viruses in hospital-acquired pneumonia in the intensive care unit: A single-center retrospective study.

BACKGROUND: Data on the frequency and role of respiratory viruses (RVs) in hospital-acquired pneumonia (HAP) are still scarce. OBJECTIVES: We assessed the proportion of RVs and their impact on the outcome of hospital-acquired pneumonia (HAP) in the intensive care unit (ICU). STUDY DESIGN: Cases of HAP were retrospectively selected among patients who underwent screening for RVs by multiplex PCR (mPCR) in the ICU of a French tertiary care hospital from May 2014 to April 2016. ICU length of stay and in-hospital mortality were compared between four groups defined according to the identified pathogens: virus only (V), virus/bacteria (V/B), bacteria only (B) and no pathogen (Neg). When available, previous mPCR was retrieved in order to assess possible chronic viral carriage. RESULTS: Overall, 95/999 (10%) ICU patients who underwent mPCR had HAP (V(17,18%), V/B(13,14%), B(60,63%), Neg(5,5%)). Median age was 61 years and 45 (47%) were immunocompromised. Influenza (27%) and rhinovirus (27%) were the most common RVs. V/B group had higher mortality rate than B and V groups (62% vs. 40% and 35%, p=0.3) and a significantly longer length of stay (31days (18-48)) than V group (5days (3-11), p=0.0002)) and B group (14.5days (5.5-25.5), p=0.007)). Among the 15 patients with available mPCR tests before viral HAP, seven were negative and eight were positive corresponding to long-term carriage of community-acquired viruses. DISCUSSION: RVs were detected in 32% of HAP patients who underwent mPCR. Two situations were encountered: (i) acute acquired viral infection; (ii) long-term viral carriage (mostly rhinovirus) especially in immunocompromised patients complicated by a virus/bacteria coinfection. The latter was associated with a longer length of stay and a trend toward a higher mortality.

Mimivirus is not a frequent cause of ventilator-associated pneumonia in critically ill patients.

Acanthamoeba polyphaga mimivirus (APMV) belongs to the amoebae-associated microorganisms. Antibodies to APMV have been found in patients with pneumonia suggesting a potential role as a respiratory pathogen. In addition, positive serology for APMV was associated with an increased duration of mechanical ventilation and intensive care unit stay in patients with ventilator-associated pneumonia. The aim of the present study was to assess the presence of APMV in bronchoalveolar lavage fluid samples of critically ill patients suspected of ventilator-associated pneumonia. The study was conducted in the intensive care unit of the Maastricht University Medical Centre. All consecutive bronchoalveolar lavage fluid samples obtained between January 2005 and October 2009 from patients suspected of ventilator-associated pneumonia were eligible for inclusion. All samples were analyzed by real-time PCR targeting the APMV. A total of 260 bronchoalveolar lavage fluid samples from 214 patients (139 male, 75 female) were included. Bacterial ventilator-associated pneumonia was confirmed microbiologically in 105 out of 260 (40%) suspected episodes of ventilator-associated pneumonia (86 patients). The presence of APMV DNA could not be demonstrated in the bacterial ventilator-associated pneumonia positive or in the bacterial ventilator-associated pneumonia negative bronchoalveolar lavage fluid samples. Although suspected, APMV appeared not to be present in critically ill patients suspected of ventilator-associated pneumonia, and APMV does not seem to be a frequent cause of ventilator-associated pneumonia.

Cytomegalovirus and herpes simplex virus effect on the prognosis of mechanically ventilated patients suspected to have ventilator-associated pneumonia.

OBJECTIVE: Cytomegalovirus (CMV) and herpes simplex virus (HSV) are common viruses that can affect critically ill patients who are not immunocompromised. The aim of this study was to determine whether the identification of CMV and/or HSV in mechanically ventilated critically ill patients suspected of having pneumonia was associated with an increased mortality. DESIGN: Prospective epidemiological study. SETTING: Medical intensive care unit of a tertiary medical center. PATIENTS: Ninety-three patients with suspected pneumonia. INTERVENTIONS: Patients with suspected pneumonia had bronchoalveolar lavage and blood samples taken to confirm the diagnosis. Antigenemia was used to detect CMV in the blood. Bronchoalveolar lavage samples were submitted to testing using quantitative real-time Polymerase Chain Reaction. MEASUREMENTS AND MAIN RESULTS: We identified 22 patients with a CMV infection, 26 patients with an HSV infection and 45 patients without CMV or HSV infection (control group). Mortality at day 60 was higher in patients with a CMV infection than in patients from the control group (55% vs. 20%, P<0.01). Mortality at day 60 was not significantly increased in the group with HSV infection. Duration of ICU stay and ICU mortality were significantly higher in patients with CMV infections when compared to patients from the control group, whereas ventilator free days were significantly lower in patients with CMV infections when compared to patients from the control group. CONCLUSIONS: In critically ill patients, a CMV infection is associated with an increased mortality. Further interventional studies are needed to evaluate whether treatment could improve the prognosis.

Viral ventilator-associated pneumonia: uncovering tip of the iceberg.

CONTEXT: Hospital-acquired infections are frequently encountered by the physicians for ailments demanding prolonged hospitalization, especially in intensive care units, where patients are often mechanically ventilated. The organisms most often implicated are bacteria; viral etiology is infrequent. AIMS: The study aims at reviewing lung pathology at autopsy in mechanically ventilated children admitted in pediatric intensive care unit (PICU) to assess the incidence of viral ventilator-associated pneumonias (VAP). SETTING AND DESIGN: Retrospective analysis. MATERIALS AND METHODS: Among the 275 children who had been autopsied, 13 who had been admitted in the PICU satisfied the criteria for VAP. These cases were analyzed on the basis of clinical data and pulmonary pathology. Depending on the overall histology, the cases were classified as being viral or bacterial in etiology. Immunohistochemistry (IHC) for detection of viral antigens was also performed. RESULTS: Of the 13 children, nine (five males and four females) had shown the histomorphologic features, suggesting viral inflammation. The mean age was 33 months. Falling oxygen saturation and increasing respiratory distress had necessitated ventilator support. Acute lymphocytic bronchiolitis, interstitial pneumonitis, diffuse alveolar damage, and necrotizing pneumonia were the histological features. The viruses identified in five patients were adenovirus, respiratory syncytial virus and cytomegalovirus. CONCLUSION: This communication, though not representing the true incidence, emphasizes that a proportion of nosocomial infections is due to viral infections. This should alert the treating intensivists to actively pursue investigations to confirm viral etiology.

[Acute viral infections in immunocompetent patients]. / Infecciones virales graves en pacientes inmunocompetentes.

Viruses play a significant role in serious infections in adults and sometimes lead to the need for hospitalization and admission to intensive care units, especially in cases of severe respiratory distress or encephalopathy. Influenza and parainfluenza viruses, syncytial respiratory virus, herpes viruses and adenovirures are the most frequent causes of these severe infections. A review of the literature has been performed in order to update the epidemiology, pathogenesis and therapeutic approach of viral infections affecting immunocompetent patients. Furthermore, ventilator-associated pneumonia (VAP) is the most frequent nosocomial infection in intensive care units and has a high morbidity and mortality rate. It is mainly a bacterial disease, although the potential role of viruses as pathogens or copathogens in VAP is under discussion. Therefore, a brief review of the potential pathogenic role of viruses in VAP has also been performed.

The role of viruses in nosocomial pneumonia.

PURPOSE OF REVIEW: The frequency and impact of viruses among intensive care unit (ICU) nonimmunocompromised patients remains controversial. This review analyzes their place as causal pathogens in ventilator-associated pneumonia, as well as their effects on ICU patients' outcomes. RECENT FINDINGS: Herpesviruses, namely herpes simplex virus (HSV) and cytomegalovirus (CMV), are the most frequent viruses detected among nonimmunosuppressed ICU patients, as confirmed by recent prospective studies. Patients infected with these viruses show increased morbidity and, especially for CMV, mortality. An increase of bacterial or fungal superinfections was observed in ICU patients with CMV reactivation. A therapeutic trial of acyclovir (HSV antiviral) in ICU patients was negative. Concerning CMV, pathogenicity was suggested by histologic assessment in ICU patients, and recent murine models with a positive effect of prophylaxis with ganciclovir that prevented postseptic CMV reactivation and secondary lung damage. SUMMARY: Using efficient and rapid virologic diagnostic tests (antigenemia or PCR), the identification of viruses in ICU patients is frequent. Their role in the occurrence of ventilator-acquired pneumonia and their impact on patient outcome depend on the virus. There is sufficient evidence suggesting CMV pathogenicity to conduct an interventional randomized trial using anti-CMV drugs.

Herpes simplex virus: a marker of severity in bacterial ventilator-associated pneumonia.

PURPOSE: Ventilator-associated pneumonia (VAP) is the most frequent nosocomial infection in intensive care units and has a high morbidity and mortality rate. It is mainly a bacterial disease, although the potential role of viruses as pathogens or copathogens in VAP is under discussion. Our study aims were to determine the incidence of herpes simplex virus (HSV) in the lower respiratory tract (LRT) secretions in patients with bacterial VAP and to assess its potential clinical relevance. MATERIAL AND METHODS: This is a prospective observational study carried out over a 14-month period. All LRT samples of adult patients with VAP were sent for bacterial culture and virus isolation. We compared patients with bacterial VAP with isolation of HSV and those without. RESULTS: One-hundred seventy-seven patients had confirmed bacterial VAP. Herpes simplex virus was present in 13.4% of them. Patients with HSV had more severe underlying conditions and worse outcome. They consumed more antibiotics for the VAP episode, had more Clostridium difficile infection, spent a longer time on mechanical ventilation, had a longer intensive care unit and hospital stay, and had greater mortality than those without. CONCLUSIONS: Herpes simplex virus excretion in LRT secretions is not infrequent in VAP, and it is associated with greater severity and worse prognosis.

Monitoring of herpes simplex virus in the lower respiratory tract of critically ill patients using real-time PCR: a prospective study.

Herpes simplex virus (HSV) has increasingly been associated with pulmonary disease in critically ill patients. However, the clinical relevance of HSV is still a topic of debate. Monitoring of HSV in a quantitative way could potentially give relevant information on its role in the pathogenesis of lower respiratory tract infection. A fast and reliable quantitative real-time PCR (Q-PCR) for the quantitative detection of HSV-1 and HSV-2 DNA was developed. A prospective observational study was performed in an intensive-care unit (ICU) to monitor the HSV viral load in lower respiratory tract aspirates of long-term mechanically ventilated patients. HSV was common in the lower respiratory tract (LRT) of critically ill patients with mechanical ventilation for at least 48 h (62%, n = 65/105). Detection of HSV was significantly associated with prolonged mechanical ventilation (p <0.01), prolonged ICU stay (p <0.01), and development of ventilator-associated pneumonia (p = 0.02). Corticosteroid administration (p <0.01) in the ICU and anti-HSV IgG seropositivity (p <0.01) were risk factors for the occurrence of HSV in the LRT. The fact that no HSV-seronegative patient became positive suggests that all HSV DNA-positive patients had HSV reactivations. Monitoring the HSV viral load in the LRT of critically ill patients showed a typical homogeneous pattern of HSV kinetics. HSV emerged in tracheal and bronchial aspirates after a median of 7 days of intubation (5-11 days), and this was followed by an exponential increase (c. 1 log copies/mL/day) to reach very high HSV peaks (10(6)-10(10) copies/mL) in 78% of the HSV DNA-positive patients.

Clinical significance of a positive serology for mimivirus in patients presenting a suspicion of ventilator-associated pneumonia.

OBJECTIVE: A seroconversion to mimivirus has been observed in patients with community-acquired or nosocomial pneumonia. The aim of this study was to determine whether a positive serology for mimivirus was associated with increased morbidity and mortality in patients with a suspicion of ventilator-associated pneumonia (VAP). DESIGN: Prospective matched-cohort study. SETTING: A 12-bed medical intensive care unit (ICU) in a teaching hospital. PATIENTS: Patients ventilated for at least 2 days presenting with a suspicion of VAP. Patients with a positive serology for mimivirus were matched to seronegative patients. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: Matching criteria were: 1) the same main diagnosis on ICU admission, 2) the same age (+/- 10 yrs), 3) the same Simplified Acute Physiology II score (+/-10 points), 4) the same McCabe and Jackson comorbidity score, 5) admission within 1 year, and 6) diagnosis of at least one bacterial VAP during the ICU stay or not. A total of 55 pairs were submitted for analysis. The effectiveness of matching was 94.8%. Patients with a positive serology for mimivirus had longer duration of mechanical ventilation and ICU stay with median excesses of 7 days and 10 days, respectively. There was no difference in ICU mortality. The duration of mechanical ventilation before bronchoalveolar lavage (adjusted odds ratios [OR]1.08, p = 0.02), viral identification other than mimivirus during ICU stay (adjusted OR 0.32, p = 0.05), and enteral nutrition (adjusted OR 0.13, p = 0.01) were associated with positive serology for mimivirus. CONCLUSION: A positive serology for mimivirus is associated with a poorer outcome in mechanically ventilated ICU patients.

Etiology of viral pneumopathies in patients in intensive care unit under mechanical ventilation.

The objective of this work was to define the etiology of viral pneumopathies at the patients from reanimation section being under mechanical ventilation, making reference to viruses with respiratory tropism, and also to Chlamydia Pneumoniae and Mycoplasma pneumoniae. The subjects were 36 patients hospitalized into Service of Medical Reanimation from CHU Caen and who needed mechanical ventilation more than 48 hours. The samples from the patients were mostly nasal aspirate, 1 bronchial aspirate and 2 tracheal aspirates. The diagnosis tests were: the test of direct immunofluorescence (DIF) from the samples (for Influenza viruses A and B, Parainfluenza 1,2,3, Adenovirus and Respiratory Syncytial Virus (RSV), inoculation on the tissue culture of diploid cells MRC5, and at the appearance of cythopatic effect specific for Herpes Simplex Virus (HSV), it was made DIF for the detection of type 1 or 2, and also there were made 6 techniques of Polymerase Chain Reaction (PCR). The results of the tests were: at admission before installing the mechanical ventilation, 6 patients presented an infection with Rhinoviruses (RV), 3 with Influenza type A, 3 with HSV type 1 and 2 with Enterovirus. After a period of time from installing the mechanical ventilation, 8 patients presented an infection with HSV typel, among who 1 presented at admission an infection with RV, and 1 patient presented at 7 days from installing the mechanical ventilation an infection with RSV, and at 16 days an infection with HSV type 1. Thus, it could be concluded that in 25% from the cases of viral pneumopathies from patients being under mechanical ventilation it was an endogen reactivation of HSV type1 and only into a single case was diagnosed initially with an infection with RSV, after that it appeared also an infection with HSV typel.

Herpes simplex virus lung infection in patients undergoing prolonged mechanical ventilation.

RATIONALE: It is not known whether the isolation of herpes simplex virus (HSV) from lower respiratory tract samples of nonimmunocompromised ventilated patients corresponds to bronchial contamination from the mouth and/or throat, local tracheobronchial excretion of HSV, or true HSV lung involvement (bronchopneumonitis) with its own morbidity/mortality. OBJECTIVES: This prospective, single-center, observational study was conducted to define the frequency, risk factors, and relevance of HSV bronchopneumonitis. METHODS: All consecutive nonimmunocompromised patients receiving mechanical ventilation for 5 days or more were evaluated. Bronchoalveolar lavage, oropharyngeal swabs, and bronchial biopsies (presence of macroscopic bronchial lesions) were obtained for all who deteriorated clinically with suspected lung infection. HSV bronchopneumonitis was defined as this deterioration, associated with HSV in bronchoalveolar lavage and HSV-specific nuclear inclusions in cells recovered during lavage or bronchial biopsies. MEASUREMENTS AND MAIN RESULTS: HSV bronchopneumonitis was diagnosed in 42 (21%) of the 201 patients who deteriorated clinically, with a mean mechanical ventilation duration before diagnosis of 14 +/- 6 days. Risk factors associated with HSV bronchopneumonitis were oral-labial lesions, HSV in the throat, and macroscopic bronchial lesions seen during bronchoscopy. Patients with HSV bronchopneumonitis were comparable to those without at admission, but their courses were more complicated, with longer duration of mechanical ventilation and intensive care unit stays. CONCLUSIONS: HSV bronchopneumonitis is common in nonimmunocompromised patients with prolonged mechanical ventilation, is associated with HSV reactivation or infection of the mouth and/or throat, and seems to be associated with poorer outcome.