Routine Bacterial Culture Research Articles

Real-time metagenomics-based diagnosis of community-acquired meningitis: A prospective series, southern France.

SummaryBackgroundPoint-Of-Care (POC) diagnosis of life-threatening community-acquired meningitis currently relies on multiplexed RT-PCR assays, that lack genotyping and antibiotic susceptibility profiling. We assessed the usefulness of real-time metagenomics (RTM) directly applied to the cerebrospinal fluid (CSF) for the identification, typing and susceptibility profiling of pathogens responsible for community-acquired meningitis.MethodsA series of 52 CSF samples from patients suspected of having community-acquired meningitis, were investigated at POC by direct RTM in parallel to routine real-time multiplex PCR (RT-PCR) and bacterial culture, for the detection of pathogens. RTM-generated sequences were blasted in real-time against an in-house database incorporating the panel of 12 most prevalent pathogens and against NCBI using EPI2ME online software, for pathogen identification. In-silico antibiogram and genotype prediction were determined using the ResFinder bio-tool and MLST online software.FindingsOver eight months, routine multiplex RT-PCR yielded 49/52 positive CSFs, including 21 Streptococcus pneumoniae, nine Neisseria meningitidis, eight Haemophilus influenzae, three Streptococcus agalactiae, three Herpesvirus-1, two Listeria monocytogenes, and one each of Escherichia coli, Staphylococcus aureus and Varicella-Zoster Virus. Parallel RTM agreed with the results of 47/52 CSFs and revealed two discordant multiplex RT-PCR false positives, one H. influenzae and one S. pneumoniae. Both multiplex RT-PCR and RTM agreed on the negativity of three CSFs. While multiplex RT-PCR routinely took 90 min, RTM took 120 min, although the pipeline analysis detected the pathogen genome after 20 min of sequencing in 33 CSF samples; and after two hours in 14 additional CSFs; yielding > 50% genome coverage in 19 CSFs. RTM identified 14 pathogen genotypes, including a majority of H. influenzae b, N. meningitidis B and S. pneumoniae 11A and 3A. In all 16 susceptible cultured bacteria, the in-silico antibiogram agreed with the in-vitro antibiogram in 10 cases, available within 48 h in routine bacteriology.InterpretationIn addition to pathogen detection, RTM applied to CSF samples offered supplementary information on bacterial profiling and genotyping. These data provide the proof-of-concept that RTM could be implemented in a POC laboratory for one-shot diagnostic and genomic surveillance of pathogens responsible for life-threatening meningitis.FundingThis work was supported by the French Government under the Investments in the Future programme managed by the National Agency for Research reference: Méditerranée Infection 10-IAHU-03.

Microbiological and drug resistance patterns of bronchoalveolar lavage samples taken from hospitalized patients in Iran.

Pulmonary diseases are amongst the most common causes of premature death and distressing disorders worldwide. This study aimed to detect the fastidious and routine infectious agents, and their drug resistance patterns in bronchoalveolar lavage (BAL) samples. A total of 44 BAL samples were collected by bronchoscopy from patients with respiratory disorders hospitalized at 2 teaching hospitals in Ilam, Iran. The samples were cultured on routine bacterial culture media to identify the bacterial agents and calculate the colony count. Antibiotic susceptibility was determined by disk diffusion method according to the CLSI protocol. PCR was used to detect the fastidious bacteria Mycoplasma pneumoniae and Chlamydia pneumoniae using the 16srRNA specific primers and Legionella pneumophila using the mip specific primers. Overall, 100 bacterial isolates were isolated by culture from the 44 BAL samples including: Staphylococcus aureus (24, 31.2%), Streptococcus pyogenes (18, 23.4%), Enterococcus spp. (11, 14.3%), Acinetobacter baumannii (11, 14.3%), Pseudomonas aeruginosa (11, 14.3%), Enterococcus spp. (10, 13%), Micrococcus spp. (5, 6.5%), Staphylococcus epidermidis (5, 6.5%) and Klebsiella pneumoniae (5, 6.5%). PCR detected 4 positive samples (9.1%) for Chlamydia pneumoniae but no positive cases for Mycoplasma pneumoniae and Legionella pneumophila. Acinetobacter baumannii showed the highest resistance rate (81.8%) to aztreonam and ceftazidime. Seventy-five percent of the Staphylococcus aureus isolates were resistant to cefoxitin (MRSA) and 83.3% had the mecA gene. Vancomycin resistance was observed in 27.3% of the Enterococcus species (VRE). Resistance to piperacillin, cefotaxime, ciprofloxacin and imipenem was observed in 54.5%, 45.5%, and 36.4% of the Pseudomonas aeruginosa isolates, respectively. The frequency of organisms isolated from the ICU was higher (46%) than from other wards. The presence of MRSA, cephalosporins-resistant Enterobacteriaceae as well as Pseudomonas aeruginosa and Acinetobacter baumannii resistant against piperacillin, imipenem, cefotaxime, aztreonam and ciprofloxacin amongst different wards, especially the ICU ward of the surveyed hospitals, is a major healthcare concern and it is necessary to wisely scrutinize the preventive strategies for antibiotic resistant infections.

Case report of arthritis caused by Legionella anisa and review of the literature

BackgroundLegionella spp. is recognized as a common cause of community acquired pneumonia, with Legionella pneumophila serogroup 1 being the most prevalent. At least 70 species are described so far but few are identified in pathogenic conditions. Data on extrapulmonary infections are scarce.Case presentationA 73-yar-old male with chronic lymphoid leukemia was hospitalized for an insidious wrist arthritis. Ultrasound of the wrist showed a carpal and radiocarpal fluid effusion with positive Doppler signal. While routine bacterial cultures remained sterile, 16S rRNA PCR identified Legionella anisa. Ciprofloxacin 500 mg twice a day for a period of six weeks improved arthritis with full recovery at the end of the treatment.ConclusionLegionella non pneumophila are a rare cause of septic arthritis especially found in immunosuppressed patients and identification of species could help clinician to adapt antibiotherapy.

Evaluation of the clinical sensitivity and specificity of the BD Max™ Enteric Bacterial Panel for molecular detection of pathogens for acute gastroenteritis in the Singaporean population

PurposeAcute gastroenteritis (AGE) is caused by a wide range of pathogens. Culture methods for the detection of bacterial pathogens is time consuming and labour intensive. This study compared a same-day-to-result commercial molecular method using BD Max™ Enteric Bacterial Panel against conventional culture and laboratory-developed PCR assays (LDTs), and characterised the epidemiology of bacterial AGE in Singapore. MethodologyPCRs for Campylobacter spp., Salmonella spp., Shigella spp./Enteroinvasive Escherichia coli (EIEC) and Shiga toxin-producing E. coli (STEC)/Shigella dysenteriae were performed on the BD Max™ platform. Concurrent routine bacterial culture (“reference standard”) was performed for Campylobacter, Salmonella, Shigella, Vibrio and Aeromonas spp. In the event of a discrepancy, an “expanded reference standard” (bacterial culture with LDT) was used. ResultsThere were 299 stool specimens in the study, with no bacterial pathogens detected in 190 samples (63.5%). The positive samples (n = 109,36.5%) were detected with Salmonella (n = 57,19.1%), Campylobacter (n = 28,9.4%), Vibrio parahaemolyticus (n = 6,2.0%), Shigella/EIEC (n = 6,2.0%), ETEC (n = 4,1.3%), STEC (n = 2,0.7%), Aeromonas (n = 2,0.7%), Plesiomonas shigelloides (n = 1,0.3%) and 3(1.0%) co-infections. Compared to the “expanded reference standard”, conventional culture missed 38/112 (33.9%) pathogens. Conversely, testing by BD Max™ alone failed to detect 17 pathogens. BD Max™ reported seven (2.3%) false-positive results. ConclusionsBD Max™ increased the detection rate of bacterial AGE pathogens in the panel, but was limited by the absence of detection capability for Vibrio and Aeromonas spp.

Serologic testing for Bartonella in Manitoba, Canada, 2010-2020: a retrospective case series.

Background:Bartonella are gram-negative bacilli not identified by routine bacterial culture. The objectives of this study were to review the results of all serologic testing for Bartonella ordered in Manitoba, Canada, and to review cases with positive test results among adults to assess species identification, risk factors, clinical manifestations and outcomes.Methods:This retrospective study included all Bartonella serologic tests ordered in Manitoba and performed at the National Microbiology Laboratory, Winnipeg, from Jan. 1, 2010, until Dec. 31, 2020. We analyzed the aggregate data for all serologic tests for Bartonella for patients of all ages. We reviewed the charts of adult (age ≥ 18 yr) patients with serologic positivity for Bartonella who had a medical chart at 1 of Winnipeg’s 2 largest hospitals (Health Sciences Centre and St. Boniface Hospital) to extract clinical and demographic data and create a case series. Descriptive statistics were performed.Results:During the study period, 1014 Bartonella serologic tests were ordered in adult and pediatric patients, of which 24 (2.4%) gave a positive result. Sixteen adults (12 men and 4 women; mean age 48 yr) seen at a participating hospital had a positive result. Molecular species-level identification occurred on explanted cardiac valves in 5 (31%) of the 16 cases; B. quintana was identified in all 5. Six patients (38%) were diagnosed with probable B. quintana infection, for a total of 11 B. quintana cases (69%); 8 (73%) of the 11 had endocarditis. Four cases of B. quintana infection (36%) were associated with rural residence. Four cases (25%) of probable B. henselae were identified; 2 patients had fever and lymphadenopathy, and 2 had endocarditis. The remaining patient was deemed to have a false-positive result as his B. henselae titre was at the threshold for positivity, his B. quintana serologic test gave a negative result, and his clinical syndrome was not suggestive of Bartonella infection. Two patients died; both had multivalvular B. quintana endocarditis with ruptured intracranial mycotic aneurysms.Interpretation:Bartonella quintana was a common cause of Bartonella serologic positivity among adults in Manitoba in 2010–2020 and was associated with endocarditis and systemic embolization. As B. quintana is transmitted by body lice, active case finding for people who lack suitable housing, both in urban and rural settings, should prioritize those with elevated Bartonella titres to receive echocardiography and detect endocarditis before systemic embolization occurs.

Isolation of obligate anaerobes from clinical samples received for routine bacterial culture and sensitivity: a cross sectional study.

Background and Objectives:Obligate anaerobic bacteria are known to cause various infections in human beings. We aimed to determine the prevalence and spectrum of obligate anaerobes encountered in pus aspirate, sterile fluids and tissue samples received for routine bacterial culture and sensitivity.Materials and Methods:A total of 160 samples including tissue, sterile body fluids and pus aspirate were collected, analysed for prevalence and spectrum of obligate anaerobes. Identification of obligate and facultative anaerobes was done by automated MALDI-TOF and Vitek 2 method.Results:Among 160 samples, 75 samples (46.8%) yielded obligate anaerobes out of which 41 samples (26%) yielded obligate anaerobes along with facultative anaerobes which was significant (p value=0.031) and 34 samples (21%) yielded only obligate anaerobes. 90 obligate anaerobes were isolated from 75 samples among which only 34 (37.7%) samples yielded only obligate anaerobes and 56 (62.2%) yielded both obligate and facultative anaerobes. Gram stain with polymicrobial appearance (p value 0.02) was found to be significantly associated with growth of obligate anaerobes. Clinical conditions where obligate anaerobes were commonly associated were appendicular abscess, empyema, fournier’s gangrene, diabetic foot, ludwigs angina and deep abscess. Out of 75 positive samples 30 (40%) patients had predisposing conditions like diabetes mellitus, hypertension etc. Total of 90 obligate anaerobes and 49 facultative anaerobes were isolated. The common obligate anaerobes were Bacteroides fragilis 18 (20%), Prevotella spp. 20 (22.2%), and Clostridium spp. 8 (8.88%). Facultative anaerobes like Escherichia coli 25 (34.7%), Klebsiella species 15 (20.8%), Enterococcus faecalis 19 (26.3%) were isolated. Antibiotic sensitivity was performed for facultative anaerobes by Kirby bauer disc diffusion method. Out of 15 Escherichia coli isolates resistance was commonly seen for ampicillin 13 (86.6%), cephalosporins 11 (73.3%), ciprofloxacin 10 (66.6%) and Piperacillin tazobactum 8 (53.3%). In Klebsiella species resistance were commonly seen to Ampicillin 6 (100%), cephalosporins 2 (33.3%) and ciprofloxacin 2 (33.3%).Conclusion:There was significant isolation of obligate anaerobes along with facultative anaerobes in clinical samples received for aerobic culture and sensitivity. There is a need for isolation of these bacteria routinely and a scope for doing antibiotic susceptibility testing, which will help in evidence-based medicine and a better clinical outcome by giving appropriate therapy.

Evaluation of the Potential Impact of a Multiplex Rapid Diagnostic Panel in Critically Ill Patients With Hospital-Acquired Pneumonia.

BackgroundRapid diagnostic tools have emerged as valuable assets assisting clinicians in decision-making regarding patient management in the hospital setting. Our study sought to identify the potential impact of the BioFire® FilmArray® Pneumonia Panel (FP Panel) (BioFire Diagnostics, Salt Lake City, UT, USA) in patients with hospital-acquired pneumonia (HAP).MethodsRespiratory samples obtained by bronchoalveolar lavage (BAL) or tracheal aspiration (TA) from ICU patients with a diagnosis of HAP were tested by the FP panel in addition to routine bacterial cultures. In addition, the electronic health records of these patients were reviewed to determine what potential changes in antimicrobial therapy could have been implemented if the panel results were known to the treatment team in real-time. A cost analysis was also performed incorporating the cost of the pneumonia panel and the savings associated with the potential decrease of antibiotic use and avoidance of the rapid viral diagnostic panel. ResultsFifty-six patients met the study criteria. The FP panel results could have prompted a change in therapy in 36 (64.3%) patients, with an anticipated mean reduction in time to optimized therapy of approximately 51 hours. In addition, the panel identified three cases where antimicrobials should have been altered because patients were not receiving empiric therapy with activity against the causative pathogen and 34 opportunities for antibiotic de-escalation. The cost analysis calculated an additional cost of $10 per patient associated with using the FP panel. ConclusionsThe FP panel could have prompted a change in therapy in about two-thirds of patients studied. Its potential benefits include a more rapid time to optimized therapy, reduced exposure to and cost of broad-spectrum antimicrobials, and reduced cost of other rapid diagnostic tests.

Investigation of Bacterial Community Using 16s rRNA Amplicon Sequencing for Children with Otitis Media Effusion in Korea.

Recently, microbiome of otitis media with effusion (OME) was investigated using high throughput sequencing (HTS) in children to discover unbiased causal bacteria and natural otitis media microbiomes. However, there are very few studies in the Asian population, and there are no studies in Koreans yet. We investigated bacterial community of OME from 27 Korean children. Routine bacterial culture, PCR targeting six frequent bacteria, and 16S rRNA amplicon sequencing were performed on effusion samples. Medical records of patients were reviewed. The most common bacteria found in culture and PCR were coagulase negative Staphylococci and Hemophilus influenza, respectively. The most abundant taxon in 16S rRNA amplicon sequencing was Hemophilus. The bacteria that showed positive PCR were found to be the most abundant taxon in 16S rRNA amplicon sequencing. Alloiococcus was not found in all three methods. Our findings will contribute to a better understanding of causative agents of otitis media in children. The technical advancement of HTS in the clinical field will help further understanding.

Routine bacterial culture of proximal bone specimens during minor amputation in patients with diabetes-related foot infections has little clinical utility in predicting re-operation or ulcer healing

BackgroundTrans-phalangeal and trans-metatarsal amputation, collectively termed ‘minor amputations’ are important procedures for managing infections of diabetes-related foot ulcers (DFU). Following minor amputation, international guidelines recommend a prolonged course of antibiotics if residual infected bone on intra-operative bone samples are identified, but the quality of the evidence underpinning these guidelines is low. In this study, we examined the concordance of microbiological results from proximal bone cultures compared to results from superficial wound swabs in relation to patient outcomes; with the aim of determining the utility of routinely obtaining marginal bone specimens.MethodsData was retrospectively collected on 144 individuals who underwent minor amputations for infected DFU at a large Australian tertiary hospital. Concordance was identified for patients with both superficial wound swabs and intra-operative bone samples available. Patient outcomes were monitored up to 6 months post-amputation. The primary outcome was complete healing at 6 months; and secondary outcome measures included further surgery and death. Mann Whitney U testing was performed for bivariate analyses of continuous variables, Chi-Squared testing used for categorical variables and a logistic regression was performed with healing as the dependent variable.ResultsA moderate-high degree of concordance was observed between microbiological samples, with 38/111 (35%) of patients having discordant wound swab and bone sample microbiology. Discordant results were not associated with adverse outcomes (67.2% with concordant results achieved complete healing compared with 68.6% patients with discordant results; P = 0.89). Revascularisation during admission (0.37 [0.13–0.96], P = 0.04) and amputation of the 5th ray (0.45 [0.21–0.94], P = 0.03) were independent risk factors for non-healing.ConclusionThere was a moderate-high degree of concordance between superficial wound swab results and intra-operative bone sample microbiology in this patient cohort. Discordance was not associated with adverse outcomes. These results suggest there is little clinical utility in routinely collecting proximal bone as an adjunct to routine wound swabs for culture during minor amputation for an infected DFU.

Next-generation sequencing as an advanced supplementary tool for the diagnosis of pathogens in lower respiratory tract infections: An observational trial in Xi'an, China.

The application of next-generation sequencing (NGS) in routine clinical analysis is still limited. The significance of NGS in the identification of pathogens of lower respiratory tract infection should be assessed as part of routine clinical bacterial examinations and chest imaging results. In the present study, the alveolar lavage fluid samples of 30 patients (25 males and 5 females, aged 19-92 years old, with a median age of 62) were examined by routine bacterial culture and NGS, and the results of pathogen detection and identification were compared. Chest imaging showed consolidation in all 30 patients (100%), and pleural effusion in 13 of the 30 patients (43.33%). The routine bacterial culture of the lavage solution was only positive in 14 of the 30 patients (46.6%), and negative in 16 patients (53.33%). However, the positive rate of NGS test results of the lavage fluid was 100%. A total of 12 cases (40%) were completely consistent with the routine bacterial culture test, with 56 other pathogens of mixed infection detected, accounting for the short comings of the routine bacterial examination. Although NGS cannot distinguish between live and dead bacteria, it is still a useful detection technology for accurate diagnosis of clinical infectious diseases. It is worthy of adaptation in the clinic for more effective clinical management and treatment of the lower respiratory airway infection in addition to the routine bacterial culture testing.

708. Evaluation of Fungal Culture versus Bacterial Culture for the Identification of Various Mold Species

BackgroundInvasive mold infections are challenging to diagnose and in part relies on fungal cultures. A large proportion of mold isolates are recovered on routine bacterial cultures in our medical center, thus we sought to define the utility of bacterial versus fungal cultures for isolation of mold from clinical specimens. MethodsRoutine bacterial and fungal culture results from wound, tissue, body fluid, and respiratory specimens from Jan 2019-Dec 2020 from Keck Medical Center of USC (Los Angeles, CA) were retrospectively reviewed. Cases were excluded if specimens were collected specifically for dermatophyte recovery or for blood culture. Cultures in which mold, including dimorphic fungi, were isolated were included in the evaluation. ResultsMold was isolated from 612 specimens from 408 patients, with recovery from 329 bacterial and 450 fungal cultures. Among the 329 bacterial cultures, fungal cultures were not requested in 119 (36.2%) while the remaining 210 had concurrent fungal cultures which recovered mold in 167 cases (79.5%). Of 450 fungal cultures recovering mold, a corresponding bacterial culture was performed in 445, isolating mold in 181 (38.8%) of these cases. Two or more molds were found in 28 fungal cultures and in 5 bacterial cultures. Of positive specimens with both fungal and bacterial cultures performed (n=488), mold was isolated in fungal cultures in 446 (91.4%) and in bacterial cultures in 209 (42.9%) (Table).Yield of molds in 488 specimens with concomitant bacterial and fungal cultures ConclusionAlthough a significant number of molds are recovered in routine bacterial cultures, over half would be missed without concomitant fungal cultures. Conversely, recovery of clinically relevant mold species was optimal when both bacterial and fungal cultures were requested on a specimen. This may be related to increased specimen sampling and incubation conditions allowing for broader organism recovery. Disclosures All Authors: No reported disclosures

Significant bacteriuria among requested repeat urine samples and its clinical correlation

Background and Objectives:Urinary tract infections (UTI) are the most common bacterial infections in both outpatient and inpatient department received for routine bacterial culture and sensitivity. We looked for significant bacteriuria in requested repeat urine sample after primary urine culture yielded significant growth (>105 CFU/ml) of ≥3 types of colonies. Also studied, different isolates grown with their sensitivity pattern and contamination rates of urine samples from different departments.Materials and Methods:In routine, primary urine cultures yielding ≥3 types of colonies on Cystine Lactose Electrolyte Deficient (C.L.E.D) were requested for repeat samples, collected with aseptic precautions after proper instructions. Data was analyzed for the Microbiological profile and its clinical correlation.Results:Among 617 received requested urine samples, 292 (47.3%) yielded significant bacteriuria. Clinical details were available for 252 cases out of which 100 (39.7%) showed asymptomatic bacteriuria, 87 (34.5%) complicated UTI and 65 (25.7%) uncomplicated UTI. Null hypothesis was rejected as 292 (47.3%) of the received repeat samples showed significant bacteriuria and 325 (53%) showed normal flora/no growth i.e. there is a 50% chance of getting either a positive culture or normal flora/no growth in repeat urine samples after the primary urine culture showed ≥3 types of colonies. It indicates the importance of requesting repeat urine samples for an accurate urine culture report. Male patients were significantly associated with significant bacteriuria and complicated UTI (p= 0.001). Escherichia coli (n=112, 28%) was the most common followed by Klebsiella species (n=66, 16.4%) and Enterococcus species (n=69, 17.2%). 183 (45.6%) isolates were Multi-Drug Resistant (MDR) Gram Negative Bacilli (GNBs), Escherichia coli (50.3%) being most common. Vancomycin Resistant Enterococcus (VRE) (n=8, 2.0%) was also isolated.Conclusion:Our study justifies the rationale for asking a repeat urine samples which helps in providing an appropriate microbiological report with antibiotic sensitivity pattern, hence preventing unwanted reporting of commensals/contaminants facilitating evidence based therapy.

Bacterial Profile, Antimicrobial Susceptibility Pattern, and Associated Factors of Community- and Hospital-Acquired Urinary Tract Infection at Dessie Referral Hospital, Dessie, Northeast Ethiopia.

Background Bacterial urinary tract infection is among the most common community and hospital-acquired infections. Therefore, to know the status of the community and hospital-acquired urinary tract infection, antimicrobial susceptibility patterns, and associated factors among urinary tract infection profiles are essential to physicians and health workers to implement appropriate intervention. Methods An institution-based cross-sectional study was conducted among 422 urinary tract infection suspected patients. All isolates were identified by standard microbiological techniques, and their antibiotic susceptibility was done by the Kirby–Bauer disc diffusion method. Data were entered using EpiData version 3.1 and analyzed by SPSS software version 20. P value < 0.05 at 95% CI was considered statistically significant. Result Of 422 urine samples processed, 100 (23.7%) yielded bacterial isolates. About 50(30.7%) and 50(19.3%) were bacterial isolates from the community and hospitalized patients, respectively. E. coli 44/103(42.7%) predominated across the two groups, followed by S. aureus 25/103(24.3%), CONs, 14/103(13.5%), Klebsiella spp. 7/103(6.78), Proteus spp. 3/103(2.91), and Enterococcus spp. 3/103 (2.91%). Pseudomonas spp. 3/103 (2.91), Citrobacter spp. 2/103(1.94%), and Acinetobacter spp. 1/103(0.999), which were isolated from only the hospitalized patients. Meropenem susceptibly was 100% in both study groups and Ampicillin resistance was documented as 83.3% to 100% and 76.9% to 100% in hospitalized and community-acquired samples, respectively. Conclusion This study found a high prevalence of bacterial urinary tract infection in the study area and a high rate of bacterial resistance was observed to most antimicrobial drugs tested. Meropenem and nitrofurantoin were the most active drugs for urinary tract infections. Therefore, expanding routine bacterial culture and identification with antimicrobial susceptibility testing and strengthening regular surveillance systems are essential for appropriate patient care.

Metagenomic Next Generation Sequencing in the Detection of Pathogens in Cerebrospinal Fluid of Patients After Alternative Donor Transplantation: A Feasibility Analysis.

Central nervous system (CNS) complications can occur in 9%–15% of patients after allogeneic hematopoietic stem cell transplantation (allo-HSCT). The clinical manifestations of the CNS complications are non-specific, with most of them being disturbances of consciousness, convulsions, headaches, fever, and epilepsy, making it difficult to infer the cause of the complications based on clinical manifestations. We retrospectively analyzed the sensitivity and feasibility of metagenomic next generation sequencing (mNGS) in the diagnosis of CNS infections after allo-HSCT. Lumbar punctures were performed on 20 patients with CNS symptoms after receiving alternative donor HSCT(AD-HSCT) at the Affiliated Cancer Hospital of Zhengzhou University from February 2019 to December 2020, and their cerebrospinal fluid (CSF) was collected. The mNGS technique was used to detect pathogens in the CSF. Routine CSF testing, biochemical analyses, G experiments, GM experiments, ink staining, acid-fast staining, and bacterial cultures were carried out, and quantitative PCR (qPCR) tests were used to detect cytomegalovirus (CMV), Epstein-Barr virus (EBV), BK polyomavirus (BKPyV), and human alphaherpesvirus (HHV). A total of 29 tests were performed with 21 of them being positive. Of the five negative patients, three were diagnosed with a posterior reversible encephalopathy syndrome, one as having transplantation-associated thrombotic microangiopathy, and one with transient seizure caused by hypertension. Fifteen patients tested positive, of which four had single infections and eleven had mixed infections. Five cases of fungal infections, six cases of bacterial infections, and 13 cases of viral infections were detected. Among the 13 cases of viral infections, ten cases were CMV(HHV-5); three were BKPyV; two were Torque teno virus (TTV); Two were HHV-1,two were EBV(HHV4), and one each of HpyV5 and HHV-6B. Thirteen patients tested positive for virus while the qPCR detection method of 6 identical specimens were below the minimum detection limit(<1×103 U/ml). The mNGS technique is highly sensitive, and it can be used to diagnose CNS infections after allo-HSCT.

Diagnosing pulmonary aspergillosis is much easier than it used to be: a new diagnostic landscape.

Significant innovations in the past decade have resulted in more sensitive and faster diagnosis of allergic, chronic and invasive pulmonary aspergillosis, as well as Aspergillus bronchitis and Aspergillus nodules. This new diagnostic landscape has revealed that the incidence and prevalence of aspergillosis is substantially higher than previously understood, and is summarised in this review. Oral and intravenous antifungal treatment offers good clinical response rates for affected patients. Nevertheless, missed diagnoses mean that patients are over-treated with antibacterial agents, corticosteroids and anti-TB drugs, resulting in continuing illness and often death. The clinical introduction of several high performing diagnostic tests is helping to redefine patient management. It is well-known that Aspergillus antigen can be detected in 70-95% of bronchoscopy samples in patients with invasive and chronic aspergillosis in less than 1 hour. Aspergillus immunoglobulin G (IgG) (precipitins) is >90% sensitive and >85% specific for chronic and allergic aspergillosis. High-volume respiratory fungal culture and Aspergillus polymerase chain reaction have 3-5-fold higher sensitivity than routine bacterial culture. Aspergillus IgE (or skin prick testing) diagnoses Aspergillus sensitisation in asthma, cystic fibrosis, chronic obstructive pulmonary disease and post-TB, and correlates well with poorer lung function and/or exacerbations. Clinicians and laboratorians across the world need to mainstream these excellent new tools to improve clinical outcomes by delivering results in a more timely and accurate fashion.

Prevalence and Predictors of Bacterial Contamination in Excisional Lymph Node Biopsies: Implications for Diagnosis and Management.

Routine tissue handling exposes lymph node specimens to microbial contamination that can confound microbiological culture results and interfere with diagnosis. The scope and impact of this problem remain poorly understood. We combined over 13 years of lymph node pathology, culture data, and patient records to define the prevalence, predisposing factors, microbiology, and clinical management of false-positive lymph node cultures at a large academic medical center. Nearly one third (31.9%) of 216 cultured lymph nodes yielded bacterial growth. Approximately 90% of positive bacterial cultures grew 1 of 2 common skin-resident taxa-coagulase-negative Staphylococcus and Cutibacterium acnes-with well-documented predispositions for contamination in other clinical settings. Lymph nodes excised from axillary, cervical, and inguinal regions yielded higher positive culture rates than nodes excised from the mediastinum, suggesting proximity to the skin surface may increase contamination risk. Accordingly, cultures from thoracoscopic pulmonary resections displayed contamination rates over 5-fold lower than those from percutaneously accessed lymph nodes. Lymph nodal tissue allocated for culture in the operating room yielded unexpectedly high contamination rates, significantly higher than cultures sent from the frozen section processing area. A significant minority of contamination events were noted in the clinical record and prompted antibiotic therapy on multiple occasions. Collectively, our results illuminate the risk factors contributing to bacterial contamination and argue that routine lymph node bacterial cultures provide minimal clinical benefit for adult patients. This widespread bacterial contamination also warrants cautious implementation of increasingly sensitive molecular microbiology tools for excised tissues.

Systemic Erysipelothrix rhusiopathiae in seven free-ranging delphinids stranded in England and Wales.

Microbiology records for 1127 cetaceans stranded on English and Welsh beaches and examined at the Institute of Zoology between 1990 and 2019 were reviewed to identify cases of Erysipelothrix rhusiopathiae, an uncommon but potentially fatal zoonotic pathogen. Once cases were identified, prevalence was calculated, corresponding postmortem reports were reviewed, common gross and histopathological findings were identified, and antibiotic susceptibilities were determined. Overall prevalence for E. rhusiopathiae was 0.62% (7/1127; 95% CI: 0.30-1.28%). It was isolated from 3 bottlenose dolphins Tursiops truncatus, 3 harbor porpoises Phocoena phocoena, and 1 short-beaked common dolphin Delphinus delphis, with a prevalence of 21.4% (3/14; 95% CI: 7.6-47.9%), 0.39% (3/779; 95% CI: 0.13-1.13%), and 0.47% (1/212; 95% CI: 0.08-2.62%) for each species, respectively. E. rhusiopathiae resulted in septicemia in all cases from which it was isolated. Gross necropsy findings included pulmonary edema (5/7), hemorrhage (5/7) and/or congestion of various organs (4/7), and serosanguineous effusion (3/7; pericardial: 3/7, pleural: 2/6, abdominal: 2/6). Congestion (5/5), bacterial emboli (4/5), and hemorrhage (4/5) were commonly observed on histopathology, and acute renal tubular injury (2/5) and pulmonary edema (2/5) were occasionally observed. Routine bacterial cultures were vital in identifying E. rhusiopathiae, since gross lesions were often subtle and nonspecific. The liver, kidney, and brain were key organs from which E. rhusiopathiae was consistently isolated. Antibiotic resistance was uncommon and was only observed for amikacin and trimethoprim sulfonamide. Penicillins were consistently effective, along with fluoroquinolones, macrolides, clindamycin, cephalexin, and oxytetracycline.

Nosocomial Outbreak of Port-site Infection due to Atypical Mycobacteria following Laparoscopy: Suggested Infection Control Strategies

Introduction: Atypical mycobacteria can survive in conditions that make them hard to eradicate, despite using the standard decontamination procedures and protocols. Thus, errors in sterilisation techniques for laparoscopic instruments can be responsible for outbreaks caused by such bacteria and make it a problem mainly affecting developing countries including India. Aim: To investigate the outbreak of postlaparoscopic wound infection caused by atypical mycobacteria. Materials and Methods: An institution based cross-sectional study was conducted over a two-month period from January 2020 to February 2020. A total of 14 patients presented with postlaparoscopic surgical site wound infections were evaluated with Ziehl-Neelsen (ZN) staining and pus culture on Lowenstein Jensen (LJ) medium and subsequently treated with appropriate antibiotics. For further investigation of the outbreak, environmental samples were collected and isolation rates (percentage) of atypical mycobacteria from these samples were analysed. Results: All the patients included in the study were diagnosed with postlaparoscopic surgical site wound infections caused by atypical mycobacteria. Infection control investigation of the Operation Theatres (OTs) revealed multiple sources of atypical mycobacterial contamination viz., laparoscopic surgical instruments, used disinfectant (gluteraldehyde disinfectant solution) and tap aerators. Conclusion: Negative routine bacterial culture report of samples collected from port-sites should be further investigated for other aetiology e.g., atypical mycobacteria which do not grow on routine bacterial culture. Since high indices of suspicion followed by timely and efficient management of patients with postlaparoscopic surgical site infection are of critical importance.

661. Futility of Bacterial Bone Marrow Cultures: Experience over a 19 Year Period

BackgroundBone marrow biopsies are often performed on patients with unclear diagnoses and cultures may be ordered for both routine bacterial, mycobacterial and fungal pathogens. They are performed in semi-sterile conditions and involve needle penetration through the skin, posing an increased risk of skin contamination. These cultures also require a substantial amount of laboratory personnel time.MethodsCultures collected from 2001-2020 were surveyed in the lab electronic record. We assessed the culture type (fungal, bacterial, mycobacterial), and the presence of pathogens and contaminants. An organism was deemed a contaminant if it was consistent with skin flora or listed as a contaminant in the report given to the physician. Organisms for which the role in bone marrow disease is unclear were included as possible pathogens. For questionable non-contaminant organisms, clinical significance was determined based on if patient was treated for the organism. For all bone marrow cultures, growth of the same organism within 1 month of the bone marrow specimen was surveyed to determine whether the organism would have been found by alternative methods.ResultsOf 483 bacterial bone marrow cultures, there were 110 (23%) positives, of which 76 (69%) were deemed contaminants. Twenty (18%) of the 76 contaminants grew in the routine bacterial culture. However, 49 (65%) contaminants grew in the AFB culture, of which 10 also grew in the bacterial culture. For the 34 non-contaminant organisms, 26 were determined to be clinically significant. Nineteen of the 26 had a matching culture (usually blood) growing the organism within 1 month. The majority of pathogens were mycobacteria (18 of the 34). Fungal organisms represented 5 cultures and 11 were bacterial. Of the 11 bacterial organisms, 1 was a Helicobacter species (grown in special media), and 4 had a matching positive blood culture. Only 4 (1% of 483) bacterial non-contaminants grew in the routine bacterial culture. Given an unknown number of true negatives, we can only conclude a positive predictive value (PPV) of 0.16 for routine bacterial cultures. Including AFB and fungal cultures, the PPV increased to 0.30.ConclusionOur findings indicate that routine bacterial bone marrow culture is unlikely to yield a novel result and is likely a poor use of lab resources.Disclosures All Authors: No reported disclosures

Bacterial Profiles and Antimicrobial Susceptibility Pattern of Isolates from Inanimate Hospital Environments at Tikur Anbessa Specialized Teaching Hospital, Addis Ababa, Ethiopia.

IntroductionMicrobial contamination of the hospital environment plays an important role in the spread of healthcare-associated infections (HCAIs). This study was conducted to determine bacterial contamination, bacterial profiles, and antimicrobial susceptibility pattern of bacterial isolates from environmental surfaces and medical equipment.MethodsA cross-sectional study was conducted at Tikur Anbessa Specialized Hospital (TASH) from June to September 2018. A total of 164 inanimate surfaces located at intensive care units (ICUs) and operation theaters (OTs) were swabbed. All isolates were identified by using routine bacterial culture, Gram staining, and a panel of biochemical tests. For each identified bacteria, antibiogram profiles were determined by the Kirby–Bauer disk diffusion method according to the guidelines of the Clinical and Laboratory Standards Institute (CLSI).ResultsOut of the 164 swabbed samples, 141 (86%) were positive for bacterial growth. The predominant bacteria identified from OTs and ICUs were Staphylococci aureus (23% vs 11.5%), Acinetobacter baumannii (3.8% vs 17.5%) and coagulase-negative Staphylococcus (CoNS) (12.6% vs 2.7%) respectively. Linens were the most contaminated materials among items studied at the hospital (14.8%). Gram-positive bacteria (GPB) had significantly high resistance levels to penicillin (92.8%), cefoxitin (83.5%), and erythromycin (53.6%). On the other hand, Gram-negative bacteria (GNB) revealed the highest resistance levels to ampicillin (97.5%), ceftazidime (91.3%), ceftriaxone (91.3%), and aztreonam (90%). However, a low resistance level was recorded for amikacin (25%) followed by Ciprofloxacin (37.5%). Of the 63 S. aureus isolates, 54 (85.7%) were methicillin-resistant S. aureus (MRSA).ConclusionThe inanimate surfaces and commonly touched medical equipment within OTs and ICUs are reservoirs of potentially pathogenic bacteria that could predispose critically ill patients to acquire HCAIs. The proportions of the antimicrobial resistance profile of the isolates are much higher from studied clean inanimate environments.