Community-acquired bacteria frequently detected by means of quantitative polymerase chain reaction in nosocomial early-onset ventilator-associated pneumonia*

Guidelines for Antibiotics Prescription in Critically Ill Patients

How to cite this article: Khilnani GC, Tiwari P, Mittal S, Kulkarni AP, Chaudhry D, Zirpe KG, et al. Guidelines for Antibiotics Prescription in Critically Ill Patients. Indian J Crit Care Med 2024;28(S2):S104-S216.

M. pneumoniae and C. pneumoniae are no relevant pathogens in critically ill patients with hospital-acquired respiratory tract infections

PURPOSE

To assess the incidence of Mycoplasma pneumoniae and Chlamydia pneumoniae in the pathogenesis of hospital-acquired respiratory tract infections (RTIs) in critically ill patients.

METHODS

This is a retrospective cohort study of all ICU-patients ≥ 18 years with RTI who underwent conventional culture techniques and PCR testing for both M. pneumoniae and C. pneumoniae from respiratory tract specimens (bronchoalveolar lavage or tracheobronchial aspirates) between January 2013 to May 2017 at the Jena University Hospital.

RESULTS

In total, 314 patients were included in the analysis. Of these, 210 (66.9%) patients were diagnosed with HAP, 65 (20.7%) with VAP and 39 (12.4%) with VAT. Overall, 73 (30.7%) patients were on mechanical ventilation on the day of microbiological examination. PCR-testing for M. pneumoniae was positive in two patients (0.6%) and for C. pneumoniae in zero patients.

CONCLUSIONS

Our study shows that the incidence of M. pneumoniae and C. pneumoniae in the pathogenesis of hospital-acquired RTIs in critically ill patients is negligible. The results support the recommendations of the guidelines not to perform empiric therapy covering these pathogens.

A study of community-acquired Mycoplasma pneumoniae in Yantai, China

Introduction:

Community-acquired pneumonia (CAP) is a global disease responsible for a large number of deaths, with significant economic impact. As diagnostic tools have increased in sensitivity, understanding of the etiology of CAP has begun to change. Mycoplasma pneumoniae is one of the major pathogens causing CAP. Macrolides and related antibiotics are first-line treatments for M. pneumoniae. Macrolide resistance has been spreading for 15 years and now occurs in worldwide. We undertook the first study on macrolide resistance of M. pneumoniae in Yantai. This may be helpful to determine the appropriate therapy for CAP in this population.

Objective:

To investigate the rate and mechanism of macrolide resistance in Yantai.

Methods:

Pharyngeal swab samples were collected from adult CAP patients. Samples were assayed by polymerase chain reaction (PCR) and cultivated to test for M. pneumoniae. Nested PCR was used to specifically amplify M. pneumoniae 23S rRNA gene fragments containing mutations, and amplicons were analyzed by CE-SSCP for macrolide resistance mutations. Results were confirmed by sequencing. Twenty-seven strains of M. pneumoniae were isolated and the activities of nine antibiotics against M. pneumoniae were tested in vitro.

Results:

Out of 128 samples tested, 27 were positive for M. pneumoniae. Mycoplasma 100% macrolides resistance to Mycoplasma pneumoniae. The mechanism of macrolides resistance was A2063G point mutation in the sequence directly binding to macrolides in the 23S rRNA V domain in vitro. The mean pyretolytic time for the fluoroquinolone group was 4.7 ±2.9 d, which was significantly shorter than 8.2 ±4.1 d for the azithromycin group.

Conclusions:

Macrolides are not the first-line treatment for M. pneumoniae respiratory tract infections in Yantai.

Increased rates of intensive care unit admission in patients with Mycoplasma pneumoniae: a retrospective study

Mycoplasma pneumoniae is a leading cause of respiratory disease. In the Intensive Care Unit (ICU) setting M. pneumoniae is not considered a common pathogen. In 2010-13 an epidemic of M. pneumoniae-associated infections was reported and we observed an increase of M. pneumoniae patients admitted to ICU. We analysed the cohort of all M. pneumoniae-positive patients' admissions during 2007 to 2012 at the Hadassah-Hebrew University Medical Centre (a 1100-bed tertiary medical centre). Mycoplasma pneumoniae diagnosis was made routinely using PCR on throat swabs and other respiratory samples. Clinical parameters were retrospectively extracted. We identified 416 M. pneumoniae-infected patients; of which 68 (16.3%) were admitted to ICU. Of these, 48% (173/416) were paediatric patients with ICU admission rate of 4.6% (8/173). In the 19- to 65-year age group ICU admission rate rose to 18% (32/171), and to 38.8% (28/72) for patients older than 65 years. The mean APACHE II score on ICU admission was 20, with a median ICU stay of 7 days, and median hospital stay of 11.5 days. Of the ICU-admitted patients, 54.4% (37/68) were mechanically ventilated upon ICU admission. In 38.2% (26/68), additional pathogens were identified mostly later as secondary pathogens. A concomitant cardiac manifestation occurred in up to 36.8% (25/68) of patients. The in-hospital mortality was 29.4% (20/68) and correlated with APACHE II score. Contrary to previous reports, a substantial proportion (16.3%) of our M. pneumoniae-infected patients required ICU admission, especially in the adult population, with significant morbidity and mortality.

Comprehensive Molecular Testing for Respiratory Pathogens in Community-Acquired Pneumonia

Background. The frequent lack of a microbiological diagnosis in community-acquired pneumonia (CAP) impairs pathogen-directed antimicrobial therapy. This study assessed the use of comprehensive multibacterial, multiviral molecular testing, including quantification, in adults hospitalized with CAP.

Methods. Clinical and laboratory data were collected for 323 adults with radiologically-confirmed CAP admitted to 2 UK tertiary care hospitals. Sputum (96%) or endotracheal aspirate (4%) specimens were cultured as per routine practice and also tested with fast multiplex real-time polymerase-chain reaction (PCR) assays for 26 respiratory bacteria and viruses. Bacterial loads were also calculated for 8 bacterial pathogens. Appropriate pathogen-directed therapy was retrospectively assessed using national guidelines adapted for local antimicrobial susceptibility patterns.

Results. Comprehensive molecular testing of single lower respiratory tract (LRT) specimens achieved pathogen detection in 87% of CAP patients compared with 39% with culture-based methods. Haemophilus influenzae and Streptococcus pneumoniae were the main agents detected, along with a wide variety of typical and atypical pathogens. Viruses were present in 30% of cases; 82% of these were codetections with bacteria. Most (85%) patients had received antimicrobials in the 72 hours before admission. Of these, 78% had a bacterial pathogen detected by PCR but only 32% were culture-positive (P < .0001). Molecular testing had the potential to enable de-escalation in number and/or spectrum of antimicrobials in 77% of patients.

Conclusions. Comprehensive molecular testing significantly improves pathogen detection in CAP, particularly in antimicrobial-exposed patients, and requires only a single LRT specimen. It also has the potential to enable early de-escalation from broad-spectrum empirical antimicrobials to pathogen-directed therapy.

Rapid quantification of Staphylococcus aureus from endotracheal aspirates of ventilated patients: a proof-of-concept study

Major concern for intubated patients is ventilator-associated pneumonia (VAP). Early detection of VAP and its causative microorganism(s) is a key challenge for clinicians. Diagnosis is based on clinical, radiological, and microbiological elements, the latter being provided 24-48h after sampling. According to practices, clinicians can sample endotracheal aspirates (ETAs) so as to check for patient colonization or perform ETA in case of VAP suspicion. In this proof-of-concept study, we report the evaluation of a semiautomated molecular method to rapidly quantify Staphylococcus aureus, one of the most involved microorganisms in VAP, directly from raw ETA samples. After evaluation using artificial ETA samples, our method was applied on 40 clinical ETA samples. All S. aureus-positive samples were successfully detected and quantified. Our method can provide an efficient sample preparation protocol for all raw ETA samples, combined with an accurate quantification of the bacterial load, in less than 3h 30min.

Design and construction of a single tube, quantitative endpoint, LATE-PCR multiplex assay for ventilator-associated pneumonia

AIMS

The goal of this study was to develop a molecular diagnostic multiplex assay for the quantitative detection of microbial pathogens commonly responsible for ventilator-associated pneumonia (VAP) and their antibiotic resistance using linear-after-the-exponential polymerase chain reaction (LATE-PCR).

METHOD AND RESULTS

This multiplex assay was designed for the quantitative detection and identification of pathogen genomic DNA of methicillin-resistant Staphylococcus aureus (MRSA), Acinetobacter baumannii, Pseudomonas aeruginosa, plus a control target from Lactococcus lactis. After amplification, the single-stranded amplicons were detected simultaneously in the same closed tube by hybridization to low-temperature molecular beacon probes labelled with four differently coloured fluorophores. The resulting hybrids were then analysed by determining the fluorescence intensity of each of the four fluorophores as a function of temperature.

CONCLUSIONS

This LATE-PCR single tube multiplex assay generated endpoint fluorescent contours that allowed identification of all microbial pathogens commonly responsible for VAP, including MRSA. The assay was quantitative, identifying the pathogens present in the sample, no matter whether there were as few as 10 or as many 100 000 target genomes.

SIGNIFICANCE AND IMPACT OF THE STUDY

This assay is rapid, reliable and sensitive and is ready for preclinical testing using samples recovered from patients suffering from ventilator-associated pneumonia.

We should be measuring genomic bacterial load and virulence factors

OBJECTIVE

To describe relevant pathogen-related characteristics and their impact on sepsis pathogenesis and prognosis.

DATA SOURCE

Current literature regarding genomic bacterial load and virulence factors, with an emphasis on the impact of these factors on pathophysiology and prognosis of sepsis.

DATA EXTRACTION AND SYNTHESIS

The current paradigm on sepsis pathophysiology and management overlooks aspects concerning the nature and characteristics of the infecting pathogen. Our findings suggest that evaluation of genomic bacterial load might be useful to assess severity and predict prognosis in septic patients; its use during treatment for monitoring clinical response is another interesting potential application. Virulence factors identification might help to develop pathogen-specific therapeutic strategies for higher-risk septic patients.

CONCLUSIONS

The recognition of the importance of quantifying the pathogen has major clinical implications and will open up a new field of exploration of therapies targeted at anticipating development and appropriate treatment in severe sepsis. The improved detection and understanding of bacterial virulence factors may lead to specific therapies.

Novel toxin assays implicate Mycoplasma pneumoniae in prolonged ventilator course and hypoxemia

BACKGROUND

Community-acquired respiratory distress syndrome (CARDS) toxin is a unique Mycoplasma pneumoniae virulence factor. Molecular assays targeting this toxin are more sensitive than existing diagnostics, but these assays have not been used to investigate the role of M pneumoniae as a nosocomial infection in critical illness. We sought to determine the incidence of M pneumoniae among mechanically ventilated subjects using these novel assays and to investigate the impact of this pathogen on pulmonary outcomes.

METHODS

We conducted a prospective observational study enrolling subjects with suspected ventilator-associated pneumonia (VAP) undergoing BAL in the surgical trauma ICU at a level I trauma center. Lavage fluid and serum samples were tested for M pneumoniae using assays to detect CARDS toxin gene sequences, protein, or antitoxin antibodies.

RESULTS

We collected samples from 37 subjects, with 41% (15 of 37) testing positive using these assays. The positive and negative groups did not differ significantly in baseline demographic characteristics, including age, sex, injury severity, or number of ventilator days before bronchoscopy. The positive group had significantly fewer ventilator-free days (P = .04) and lower average oxygenation (P = .02). These differences were most pronounced among subjects with ARDS.

CONCLUSIONS

Evidence is provided that M pneumoniae is present in a substantial number of subjects with suspected VAP. Subjects testing positive experience a significantly longer ventilator course and worse oxygenation compared with subjects testing negative.

Rapid identification of penicillin and macrolide resistance genes and simultaneous quantification of Streptococcus pneumoniae in purulent sputum samples by use of a novel real-time multiplex PCR assay

We evaluated a real-time quantitative PCR combined with a multiplex PCR assay for the quantification of Streptococcus pneumoniae and the simultaneous detection of drug-resistant genes by gel-based PCR, using purulent sputum samples. This assay correctly quantified S. pneumoniae and identified their penicillin and erythromycin susceptibilities directly from samples within 3 h.

Evaluation and improvement of real-time PCR assays targeting lytA, ply, and psaA genes for detection of pneumococcal DNA

The accurate diagnosis of pneumococcal disease has frequently been hampered not only by the difficulties in obtaining isolates of the organism from patient specimens but also by the misidentification of pneumococcus-like viridans group streptococci (P-LVS) as Streptococcus pneumoniae. This is especially critical when the specimen comes from the respiratory tract. In this study, three novel real-time PCR assays designed for the detection of specific sequence regions of the lytA, ply, and psaA genes were developed (lytA-CDC, ply-CDC, and psaA, respectively). These assays showed high sensitivity (<10 copies for lytA-CDC and ply-CDC and an approximately twofold less sensitivity for psaA). Two additional real-time PCR assays for lytA and ply described previously for pneumococcal DNA detection were also evaluated. A panel of isolates consisting of 67 S. pneumoniae isolates (44 different serotypes and 3 nonencapsulated S. pneumoniae isolates from conjunctivitis outbreaks) and 104 nonpneumococcal isolates was used. The 67 S. pneumoniae isolates were reactive in all five assays. The new real-time detection assays targeting the lytA and psaA genes were the most specific for the detection of isolates confirmed to be S. pneumoniae, with lytA-CDC showing the greatest specificity. Both ply PCRs were positive for all isolates of S. pseudopneumoniae, along with 13 other isolates of other P-LVS isolates confirmed to be non-S. pneumoniae by DNA-DNA reassociation. Thus, the use of the ply gene for the detection of pneumococci can lead to false-positive reactions in the presence of P-LVS. The five assays were applied to 15 culture-positive cerebrospinal fluid specimens with 100% sensitivity; and serum and ear fluid specimens were also evaluated. Both the lytA-CDC and psaA assays, particularly the lytA-CDC assay, have improved specificities compared with those of currently available assays and should therefore be considered the assays of choice for the detection of pneumococcal DNA, particularly when upper respiratory P-LVS might be present in the clinical specimen.

Ertapenem versus cefepime for initial empirical treatment of pneumonia acquired in skilled-care facilities or in hospitals outside the intensive care unit

The study presented here compared the efficacy and safety of ertapenem and cefepime as initial treatment for adults with pneumonia acquired in skilled-care facilities or in hospital environments outside the intensive care unit (ICU). Non-ventilated patients developing pneumonia in hospital environments outside the ICU, in nursing homes, or in other skilled-care facilities were enrolled in this double-blind non-inferiority study, stratified by APACHE II score (<or=15 vs >15) and randomized (1:1) to receive cefepime (2 g every 12 h with optional metronidazole 500 mg every 12 h) or ertapenem (1 g daily). After 3 days of parenteral therapy, participants demonstrating clinical improvement could be switched to oral ciprofloxacin or another appropriate oral agent. Probable pathogens were identified in 162 (53.5%) of the 303 randomized participants. The most common pathogens were Enterobacteriaceae, Streptococcus pneumoniae, and Staphylococcus aureus, isolated from 59 (19.5%), 39 (12.9%), and 35 (11.6%) participants, respectively. At the test-of-cure assessment 7-14 days after completion of all study therapy, pneumonia had resolved or substantially improved in 89 (87.3%) of 102 clinically evaluable ertapenem recipients and 80 (86%) of 93 clinically evaluable cefepime recipients (95% confidence interval for the difference, -9.4 to 11.8%), fulfilling pre-specified criteria for statistical non-inferiority. The frequency and severity of drug-related adverse events were generally similar in both treatment groups. In this study population, ertapenem was as well-tolerated and efficacious as cefepime for the initial treatment of pneumonia acquired in skilled-care facilities or in hospital environments outside the ICU.

[Mycoplasma pneumoniae infections: retrospective study in Basse-Normandie, 1997-2005. Epidemiology--diagnostic utility of serology and PCR for a rapid diagnostic]

But de l'étude

L'objectif de cette étude est de décrire l'épidémiologie des infections à Mycoplasma pneumoniae (Mpn) en Basse-Normandie par une analyse rétrospective des résultats sérologiques et PCR, et de valider ces deux outils pour un diagnostic précoce de ces infections.

Patients et méthodes

De 1997 à août 2005, 6156 sérums et 6123 prélèvements respiratoires ont été réalisés chez des patients hospitalisés et analysés pour une recherche d'infection à Mpn, soit par PCR, soit par sérologie Elisa, soit par les deux. Pendant la période épidémique (2004–2005), les résultats de 1489 patients ont été analysés.

Résultats

Sur les neuf années, la séroprévalence moyenne se chiffre à 40,4 % et 525 cas d'infection ont été diagnostiqués par PCR et/ou sérologie, se profilant nettement sous l'aspect de deux pics épidémiques espacés de sept ans. Pendant la période épidémique, la séroprévalence augmente (50,2 %) et l'incidence est de 8,3 %. L'analyse des caractéristiques épidémiologiques des 124 cas diagnostiqués montre : une prédominance chez l'enfant et l'adulte jeune, une fréquence saisonnière estivohivernale, l'existence de co-infection virale. L'analyse des résultats chez 36 patients ayant bénéficié des deux tests diagnostiques, PCR et sérologie, montre une concordance dans seulement 41,7 % des cas.

Conclusion

Les infections à Mpn surviennent sur un mode endémo-épidémique, avec une incidence élevée lors des pics épidémiques, particulièrement chez l'enfant. Nous disposons actuellement d'outils bactériologiques performants permettant de réaliser un diagnostic précoce et fiable. Chez l'enfant, il convient d'associer une sérologie (IgM) et une PCR sur un prélèvement nasopharyngé ; chez l'adulte il faudra privilégier la PCR.

Nosocomial pneumonia

PURPOSE OF REVIEW

This review describes the most recent advances in the management and prevention of nosocomial pneumonia. The new ATS guidelines in particular are most likely to affect clinical practice outside the USA.

RECENT FINDINGS

The problem of multidrug-resistant bacteria causing nosocomial pneumonia seems to be increasing. This is particularly true for methicillin-resistant Staphylococcus aureus. While the diagnosis of ventilator associated pneumonia remains a conflictive issue, serial tracheobronchial aspirates may improve the selection of adequate antimicrobial treatment. Combined beta-lactam and aminoglycoside therapy is inferior to beta-lactam monotherapy, both in terms of clinical outcome and in the prevention of resistance during treatment; in addition, it carries an increased risk of nephrotoxicity.

SUMMARY

The updated ATS guidelines will considerably impact clinical approaches to nosocomial and healthcare-related pneumonia. Serial tracheobronchial aspirates can be used to guide selection of antimicrobial treatment in ventilator associated pneumonia. The combination of beta-lactams and aminoglycosides is likely to be abandoned in the future. New potent treatment options for pneumonia due to nonfermenters are urgently needed.

Nosocomial pneumonia: aetiology, diagnosis and treatment

PURPOSE OF REVIEW

This review highlights recent advances in the aetiology of nosocomial pneumonia, and in strategies to increase accuracy of diagnosis and antibiotic prescription while limiting unnecessary antibiotic consumption.

RECENT FINDINGS

Bacterial pathogens still cause the bulk of nosocomial pneumonia and are of concern because of ever-rising antimicrobial resistance. Yet, the pathogenic role of fungal and viral organisms is increasingly recognized. Since early appropriate antimicrobial therapy is the cornerstone of an effective treatment, further studies have been conducted to improve appropriateness of early antibiotic therapy. De-escalation strategies combine initial broad-spectrum antibiotics to maximize early antibiotic coverage with a subsequent focusing of the antibiotic spectrum when the cause is identified. Invasive techniques probably do not alter the immediate outcome but have the potential to reduce unnecessary antibiotic exposure. Decisions to stop or change antibiotic therapy are hampered due to a lack of reliable parameters to assess the resolution of pneumonia.

SUMMARY

Increasing antimicrobial resistance in nosocomial pneumonia both challenges treatment and mandates limitation of selection pressure by reducing antibiotic burden. Treating physicians should be both aggressive in initiating antimicrobials when suspecting nosocomial pneumonia but willing to discontinue antimicrobials when diagnostic results point to an alternative diagnosis. Efforts should be made to limit duration of antibiotic therapy when possible.

Quantitative detection of Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis in lower respiratory tract samples by real-time PCR

The limitation of polymerase chain reaction (PCR) in diagnosis of lower respiratory tract infections (LRTIs) caused by Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis has been a distinguishing colonization from infection. We assess here the usefulness of real-time quantitative PCR (RQ-PCR) performed on lower respiratory tract samples to overcome this problem. Consecutive respiratory tract samples from patients with and without signs of infection (n = 203) were subjected to RQ-PCR, targeting the genes pneumolysin (S. pneumoniae), fumarate reductase (H. influenzae), and outer membrane protein B (M . catarrhalis). DNA from positive controls with predefined colony forming units (CFUs) per milliliter were included to allow estimation of CFU per milliliter for the test samples. In parallel, assessment of quantitative cultures from all samples was performed. In the group of patients with LRTI, significant pathogens (>/=10(5) CFU/mL) were found in 32/135 samples (23.7%) with culture, in 51/135 (37.7%) with RQ-PCR, and in 59/135 (43.7%) when combining the methods.