It’s with great sadness to let you know that Itzhak passed away peacefully on Jan 10, 2025 from cancer, surrounded by his family at home. We miss Itzhak dearly; you can read more about his life here.
The blog explains the microbiology, diagnosis, and treatment of infections caused by anaerobic bacteria. It was was created by Itzhak Brook MD.
Infections caused by anaerobic bacteria are common, and may be serious and life-threatening. Anaerobes predominant in the bacterial flora of normal human skin and mucous membranes, and are a common cause of bacterial infections of endogenous origin. Infections due to anaerobes can evolve all body systems and sites. The predominate ones include: abdominal, pelvic, respiratory, and skin and soft tissues infections. Because of their fastidious nature, they are difficult to isolate and are often overlooked. Failure to direct therapy against these organisms often leads to clinical failures. Their isolation requires appropriate methods of collection, transportation and cultivation of specimens. Treatment of anaerobic bacterial infection is complicated by the slow growth of these organisms, which makes diagnosis in the laboratory only possible after several days, by their often polymicrobial nature and by the growing resistance of anaerobic bacteria to antimicrobial agents.
The site is made of a home page that presents new developments and pages dedicated to infectious site entities.
Sunday, May 4, 2025
Monday, November 6, 2023
Intracranial Pyogenic Complications of Sinusitis in Children , a 20-year Study
Intracranial pyogenic complications of sinusitis in children can lead to serious sequelae. Smiljkovic and colleagues from the Hospital for Sick Children, Toronto, Canada; characterized the clinical, epidemiologic and microbiologic characteristics of children with such complications over a 20-year period.
One hundred and four cases of complicated sinusitis were included after review. The most frequent complications were epidural empyema (n = 50, 48%), subdural empyema (n = 46, 44%) and Pott's puffy tumor (n = 27, 26%). 52% (n = 54) underwent neurosurgery and 46% (n = 48) underwent otolaryngological surgery. The predominant pathogen isolated from sterile site specimens was Streptococcus anginosus (n = 40, 63%), but polymicrobial growth was common (n = 24; 38%). The median duration of intravenous antibiotic therapy was 51 days (IQR 42-80). Persistent neurological sequelae (or death, n = 1) were found in 24% (n = 25) and were associated with the presence of cerebritis and extensive disease on neuroimaging (P = 0.02 and P = 0.04, respectively).
The authors concluded that Intracranial complications of sinusitis continue to cause significant morbidity in children. Polymicrobial aerobic anaerobic infections are common, which reinforces the need for broad-spectrum empiric antibiotic therapy and cautious adjustment of the antibiotic regimen based primarily on sterile site cultures. The association of neurologic sequelae with the presence of cerebritis and extensive intracranial involvement on neuroimaging suggest that delayed diagnosis may be a contributor to adverse outcome.
Tuesday, January 24, 2023
Changes in Penile Microbiome Following Pediatric Circumcision
Mishra and colleges from several medical centers in the USA, Italy and India studied the characterization of Changes in Penile Microbiome Following Pediatric Circumcision. While microbiome and host regulation contribute independently to many disease states, it is unclear how circumcision in pediatric population influences subsequent changes in penile microbiome.
They analyzed 11 paired samples, periurethral collection,
before and after circumcision, to generate microbiome and mycobiome profiling.
Sample preparation of 16S ribosomal RNA and internal transcribed spacer
sequencing was adapted from the methods developed by the National Institutes of
Health Human Microbiome Project.
Several notable microbiome and mycobiome compositional differences were observed between pre- and postcircumcision patients. Pairwise comparisons across taxa revealed a significant decrease (p < 0.05, false discovery rate corrected) of microbiome organisms (Clostridiales, Bacteroidales, and Campylobacterales) and mycobiome (Saccharomycetales and Pleosporales) following circumcision. A total of 14 pathways were found to differ in abundance between the pre- and postcircumcision groups (p < 0.005, false discovery rate <0.1 and linear discriminant analysis score >3; five enriched and nine depleted). The pathways reduced after circumcision were mostly involved with amino acid and glucose metabolism, while pathways prior to circumcision were enriched in genetic information processing and transcription processes.
The study found that bacteria and fungi involved in chronic
inflammation appear to be more prevalent in uncircumcised boys. The
investigators concluded that circumcision may reduce the risk of chronic
inflammation of the penis later in life.
The study was published in European Urology Focus on
December 2022. https://pubmed.ncbi.nlm.nih.gov/36566099/
Friday, October 21, 2022
Anti-anaerobic antibacterials may increase risk of adverse clinical outcomes in critically ill patients
Critically ill patients routinely receive antibiotics with
activity against anaerobic gut bacteria. Yet in other disease states and animal
models, gut anaerobes are protective against pneumonia, organ failure, and
mortality.
Rishi Chanderraj et al. from the University of Michigan
Medical School, Ann Arbor, MI; designed a translational series of analyses and
experiments to determine the effects of anti-anaerobic antibiotics on the risk
of adverse clinical outcomes among critically ill patients. Their finding were
published in the Eur Respir J in October 2022.
The authors conducted a retrospective single-center cohort
study of 3032 critically ill patients, comparing patients who did and did not
receive early anti-anaerobic antibiotics. The investigators retrospectively compared ICU
outcomes (ventilator-associated pneumonia-free survival, infection-free
survival, overall survival) in all patients, and changes in gut microbiota in a
116-patient subcohort. They also studied in murine models, the effects of
anaerobe depletion in infectious (K. pneumoniae and S. aureus pneumonia) and
noninfectious (hyperoxia) injury models.
The investigators found that early administration of
anti-anaerobic antibiotics was associated with decreased VAP-free survival,
infection-free survival, and overall survival. Patients who received
anti-anaerobic antibiotics had decreased initial gut bacterial density
(p=0.00038), increased microbiome expansion during hospitalization (p=0.011),
and domination by Enterobacteriaceae spp. (p=0.045). Enterobacteriaceae were
also enriched among respiratory pathogens in anti-anaerobic treated patients.
In murine models, treatment with anti-anaerobic antibiotics increased
susceptibility to Enterobacteriaceae pneumonia (p<0.05) and increased the
lethality of hyperoxia (p=0.0002).
The investigators concluded that in critically ill patients,
early treatment with anti-anaerobic antibiotics is associated with increased
mortality. Mechanisms may include enrichment of the gut with respiratory
pathogens, but increased mortality is incompletely explained by infections
alone. Given consistent clinical and experimental evidence of harm, the
widespread use of anti-anaerobic antibiotics should be reconsidered. Since the current study was retrospective, prospective studies are warranted to further evaluate this issue.
Wednesday, June 1, 2022
Oral Microbiome and SARS-CoV-2: Beware of Lung Co-infection
Bao et al. Sichuan University, Chengdu, China; presented a review on the role of the oral microbiome in the current global pandemic.
The new coronavirus SARS-CoV-2, the cause of COVID-19, has become a public health emergency of global concern. Like the SARS and influenza pandemics, there have been a large number of cases coinfected with other viruses, fungi, and bacteria, some of which originate from the oral cavity. Capnocytophaga, Veillonella, and other oral opportunistic pathogens were found in the BALF of the COVID-19 patients by mNGS. Risk factors such as poor oral hygiene, cough, increased inhalation under normal or abnormal conditions, and mechanical ventilation provide a pathway for oral microorganisms to enter the lower respiratory tract and thus cause respiratory disease. Lung hypoxia, typical symptoms of COVID-19, would favor the growth of anaerobes and facultative anaerobes originating from the oral microbiota. SARS-CoV-2 may aggravate lung disease by interacting with the lung or oral microbiota via mechanisms involving changes in cytokines, T cell responses, and the effects of host conditions such as aging and the oral microbiome changes due to systemic diseases. Because the oral microbiome is closely associated with SARS-CoV-2 co-infections in the lungs, effective oral health care measures are necessary to reduce these infections, especially in severe COVID-19 patients.
Monday, February 14, 2022
Porphyromonas pasteri and Prevotella nanceiensis in the sputum are associated with increased decline in lung function in individuals with cystic fibrosis
The role of
anaerobic bacteria in disease
progression in cystic fibrosis (CF) was studied by Webb et al. from UnitedKingdom. The authors hypothesized that
the presence and relative abundance of the most prevalent, live, anaerobic
bacteria in sputum of adults with CF were associated with adverse clinical
outcomes.
The
investigators performed 16S rRNA analysis using a viability quantitative PCR
technique on sputum samples obtained from a prospective cohort of 70 adults
with CF and collected clinical data over an 8 year follow-up period. They
examined the associations of the ten most abundant obligate anaerobic bacteria
present in the sputum with annual rate of FEV1 change. The presence of Porphyromonas
pasteri and Prevotella nanceiensis were associated with a greater
annual rate of FEV1 change. Similarly, the relative abundance of these live
organisms were associated with a greater annual rate of FEV1 decline of -3.7 ml
yr-1 and -5.3 ml yr-1 for each log 2
increment of abundance, respectively.
The authors
concluded that the presence and relative abundance of certain anaerobes in the
sputum of adults with CF are associated with a greater rate of long-term lung
function decline.
Monday, October 18, 2021
Diagnosis of orthopaedic-implant-associated infections caused by slow-growing Gram-positive anaerobed
Slow-growing Gram-positive anaerobic bacteria (SGAB) such as Cutibacterium acnes are increasingly recognized as causative agents of implant-associated infections (IAIs) in orthopaedic surgeries. SGAB IAIs are difficult to diagnose because of their non-specific clinical and laboratory findings as well as the fastidious growth conditions required by these bacteria. A high degree of clinical suspicion and awareness of the various available diagnostic methods is therefore important. A review by Ponraj et al. overviews the current knowledge regarding SGAB IAI, providing details about clinical features and available diagnostic methodologies. In recent years, new methods for the diagnosis of IAI were developed, but there is limited knowledge about their usefulness in SGAB IAI. The authors conclude that further studies are required to determine the ideal diagnostic methodology to identify these infections so that they are not overlooked and mistakenly classified as aseptic failure.
Cutibacterium acnes gram stain



















