Standard Microbiological Culture Research Articles

Aerobic vaginitis, bacterial vaginosis, and vaginal candidiasis among women of reproductive age in Arba Minch, southern Ethiopia

Reproductive tract infections (RTIs) are a persistent public health threat worldwide, particularly among women in low-income countries of Africa, including Ethiopia, where drug resistance is also a growing problem. It is crucial to address this problem to ensure women's health and well-being. A cross-sectional study was carried out among a cohort of 398 women of reproductive age who sought medical attention at the Gynecology Department of the Arba Minch General Hospital, southern Ethiopia, from January to June 2020. They were chosen through systematic random sampling, and a pre-tested structured questionnaire was used to collect the data. The collection of vaginal and/or cervical swabs were done to diagnose bacterial vaginosis (BV) and aerobic vaginitis (AV) using Nugent and AV score analyses, respectively. The swabs were subjected to standard microbiological culture techniques to detect the isolates causing AV and vaginal candidiasis (VC). The susceptibility profiles of the causative agents of AV were checked by the Kirby-Bauer disc diffusion technique. Descriptive and inferential statistical analyses were also done. Aerobic vaginitis was the predominantly diagnosed RTI (n = 122, 30.7%), followed by BV (n = 117, 29.4%) and VC (n = 111, 27.9%). The prominent bacteria of AV were Escherichia coli (n = 36, 34.2%) and Klebsiella pneumoniae (n = 30, 28.5%). The overall rate of multidrug-resistant (MDR) bacteria was 65.71% (n = 69). History of abortion (p = 0.01; AOR = 4.0, 95% CI = 2.1, 7.7) and the habit of using vaginal pH-altering contraceptives (p = 0.01; AOR = 4.7, 95% CI = 2.5, 8.8) have the greatest odds of RTI. The high prevalence of RTIs in our study warrants an urgent intervention to minimize the associated morbidities and complications. The overall rate of MDR bacterial isolates necessitates the implementation of an effective surveillance program in the study setting.

Phenotypic and molecular characterization of β-lactamase-producing Klebsiella species among children discharged from hospital in Western Kenya

BackgroundThe emergence and spread of β-lactamase-producing Klebsiella spp. has been associated with a substantial healthcare burden resulting in therapeutic failures. We sought to describe the proportion of phenotypic resistance to commonly used antibiotics, characterize β-lactamase genes among isolates with antimicrobial resistance (AMR), and assess the correlates of phenotypic AMR in Klebsiella spp. isolated from stool or rectal swab samples collected from children being discharged from hospital.MethodsWe conducted a cross-sectional study involving 245 children aged 1–59 months who were being discharged from hospitals in western Kenya between June 2016 and November 2019. Whole stool or rectal swab samples were collected and Klebsiella spp. isolated by standard microbiological culture. β-lactamase genes were detected by PCR whilst phenotypic antimicrobial susceptibility was determined using the disc diffusion technique following standard microbiology protocols. Descriptive analyses were used to characterize phenotypic AMR and carriage of β-lactamase-producing genes. The modified Poisson regression models were used to assess correlates of phenotypic beta-lactam resistance.ResultsThe prevalence of β-lactamase carriage among Klebsiella spp. isolates at hospital discharge was 62.9% (154/245). Antibiotic use during hospitalization (adjusted prevalence ratio [aPR] = 4.51; 95%CI: 1.79–11.4, p < 0.001), longer duration of hospitalization (aPR = 1.42; 95%CI: 1.14–1.77, p < 0.002), and access to treated water (aPR = 1.38; 95%CI: 1.12–1.71, p < 0.003), were significant predictors of phenotypically determined β-lactamase. All the 154 β-lactamase-producing Klebsiella spp. isolates had at least one genetic marker of β-lactam/third-generation cephalosporin resistance. The most prevalent genes were blaCTX-M 142/154 (92.2%,) and blaSHV 142/154 (92.2%,) followed by blaTEM 88/154 (57.1%,) and blaOXA 48/154 (31.2%,) respectively.ConclusionCarriage of β-lactamase producing Klebsiella spp. in stool is common among children discharged from hospital in western Kenya and is associated with longer duration of hospitalization, antibiotic use, and access to treated water. The findings emphasize the need for continued monitoring of antimicrobial susceptibility patterns to inform the development and implementation of appropriate treatment guidelines. In addition, we recommend measures beyond antimicrobial stewardship and infection control within hospitals, improved sanitation, and access to safe drinking water to mitigate the spread of β-lactamase-producing Klebsiella pathogens in these and similar settings.

Antimicrobial resistance profiles of Escherichia coli derived from an integrated agroforestry-livestock system in Deli Serdang Regency, Indonesia

Background and Aim: Antimicrobial resistance (AMR) has become a significant global concern. Epidemiological data do not provide a robust description of the potential risks associated with AMR in the integrated agroforestry-livestock systems in Indonesia. Thus, the present study investigated the phenotypic and multidrug resistance (MDR) profiles of Escherichia coli strains isolated from the feces of livestock raised in the agro-silvopastoral system in Deli Serdang Regency, North Sumatra Province. Materials and Methods: A standard microbiological culture procedure was followed to isolate the organism and test antibiotic susceptibility using the Kirby-Bauer disk diffusion protocol. Furthermore, the multiple antibiotic resistance index was determined. Univariate analysis was conducted to identify the risk factors associated with AMR. Results: The vast majority (77.5%) of livestock farmers were aged &gt;30 years. All farmers were men and had no higher education (100% of them). The majority of the animal species managed were cattle and goats (37.5% each) and the livestock grazing pasture system (67.5%). In addition, the majority of farmers reported high antimicrobial use on their farms (87.5%). Of the samples (n = 142) analyzed, n = 70 were positive, with an overall prevalence of 44.4%. The species-specific prevalences of E. coli were 32.5%, 47.8%, and 50% in buffalo, goat, and cattle, respectively. Ampicillin and tetracyclines exhibited high resistance levels among the studied animal species. A relatively lower MDR for E. coli was associated with grazing on the pasture. Conclusion: The findings from the current study provide baseline epidemiological information for future robust studies aimed at elucidating the drivers and patterns of AMR in agro-silvopastoral systems in the study area or elsewhere. Keywords: agro-silvopastoral, antimicrobial Resistance, Escherichia coli,Indonesia, livestock, multidrug resistance.

Comparison of the VITEK® 2 System with Conventional Methods for Species Identification and Antimicrobial Susceptibility Pattern of Staphylococcal Carrier Isolates

Staphylococcus aureus, an opportunistic pathogen that inhabits 20% to 70% of human anterior nares and can cause infections, ranging from mild, superficial infections of the skin and soft tissues to severe conditions like sepsis, necrotizing pneumonia and toxic shock syndrome. Healthcare workers are potential asymptomatic nasal carriers, contribute to major infection transmission. The emergence of multidrug-resistant strains necessitates advanced treatment approaches. The study aimed to identify staphylococcal nasal carriers among dental students, and to compare the results obtained from automated identification system, VITEK® 2 with conventional methods for identifying Staphylococcus species and determining antibiotic susceptibility patterns. Anterior nasal swabs were collected from 42 study participants were processed as per standard microbiological culture techniques. All the conventionally identified S. aureus isolates were subjected to a further analysis using an automated VITEK® 2 SYSTEM. Surprisingly, the automated identification system classified all conventionally proven S. aureus isolates as other Staphylococci species (S. epidermidis (60%), S. warneri, and S. lentus), raising concerns about potential misdiagnosis. Overall, there was a 97.5% categorical agreement between VITEK® 2 system and the reference method, with minimal errors (0.8% very major, 0.6% major, and 1.17% minor). These discrepancies underscore the importance of accurate species identification and highlight the necessity for advanced techniques in infection control strategies, emphasizing the potential impact on decolonization decisions.

Antibiogram of selected bacteria isolated from urine polluted environment in Benue State Campus, Makurdi

Urine contaminated soil contains various potential hazardous components which create an environment for bacteria to adapt, multiply and share their resistant genes. This study aimed to determine the antibiogram of selected bacteria isolated from urine polluted environment. Urine contaminated soil were randomly sampled from four different sites in Benue State University, Makurdi metropolis. Standard microbiological cultures, biochemical tests, modified Kirby-Bauer techniques and Clinical and Laboratory Standard Institute (CLSI) were used to isolate, identify, and determine the antibiotic susceptibility profiles of the bacteria at a 0.5 scale Mcfarland’s standard (1.5x 108 cells/ml). Bacteria insolated include Bacillus sp. (25), E. coli (13), Klebsiella sp. (10), Staphylococcus sp. (8) Salmonella sp. (7). The colony and colony forming unit (CFU) of eastern wing campus (7.85 X 107) was slightly higher compared to western wing campus (7.05 x 107). Escherichia coli (100 %) was resistant to all the antibiotics (Imipinem, Oxacillin, Ciprofloxacin, and Gentamicin), Staphylococcus spp isolates obtained were resistant to all the antibiotics except 50 % that were susceptible to Gentamicin, while 50 % of Bacillus spp on the other hand was susceptible to Imipenem, all were susceptible to Gentamicin and Ciprofloxacin (100 %); and all were however resistant to Oxacillin (100.00 %). Salmonella spp and Klebsiella spp showed similar pattern of susceptibility. All the isolates of the two organisms were susceptible to Imipenem, Gentamicin and Ciprofloxacin (100 %). All the isolates were resistant to Oxacillin. All the selected bacteria showed resistance to at least one antibiotic (P˂0.05) Unavailability of good toilet systems has contributed to the open urination and environmental contamination. Provision of more and adequate toilet facilities within the university premises and good antibiotic misuse orientation should be giving priority to prevent excessive contamination of soil with urine and antibiotic resistance.

Prevalence and phenotypic characteristics of Acinetobacter baumannii isolated from critically ill patients in two healthcare facilities in Ebonyi State, Nigeria

Background: The intrinsic property of Acinetobacter baumannii to survive in harsh conditions on environmental surfaces and its ability to resist commonly used antibiotics in hospitals make this pathogen to be one of the most prevalent causes of hospital infections. The present study was aimed at determining the prevalence of A. baumannii among critically ill patients in two tertiary hospitals; Alex Ekwueme-Federal University Teaching Hospital, Abakaliki (AE-FUTHA) and Mater Misericodiae Hospital Afikpo (MMHA) in Ebonyi State, southeast Nigeria. Methodology: This was a hospital-based cross-sectional study of 300 consecutively selected critically ill hospitalized patients in the two hospitals over a period of 6 months, from whom a total of 300 different clinical samples were collected. The specimens were processed by standard microbiological culture methods at the Applied Microbiology Laboratory Unit of Ebonyi State University (EBSU), Abakaliki. All isolated bacteria from cultures were phenotypically screened for A. baumannii by conventional biochemical test scheme and antibiotic susceptibility of test (AST) of confirmed isolates was done using the Kirby–Bauer disc diffusion technique, with AST results interpreted according to the Clinical and Laboratory Standards Institute (CLSI) guideline. Results: Of the 300 critically ill patients, clinical samples of 21 (7.0%) were positive for A. baumannii, with 20 (10.0%) of 220 samples from AE-FUTHA and 1 (1.3%) of 80 samples from MMHA. Analysis of the different isolation sites showed that catheter urine (16.0%, 11/70) from AE-FUTHA and (2.0%, 1/50) from MMHA was the most frequent site of A. baumannii isolation. A. baumannii isolates showed high resistance rates to tetracycline (100.0%), trimethoprim- sulphamethoxazole (100.0%), ceftriaxone (81.0%) and amikacin (81.0%), while low resistance rate was demonstrated to meropenem (14.3%), imipenem (19.0%) and polymyxin B (33.3%). The multiple antibiotic resistance index (MARI) of the A. baumannii isolates was 12.1, with average MARI value of 0.57. Conclusion: Early diagnosis of infection caused by A. baumannii and its treatment with meropenem, imipenem or polymyxin B can reduce the risks of mortality and morbidity in A. baumannii infection of critically ill patients.

Evaluation of pulmonary abnormalities in recipients of hematopoietic cell transplants and cellular therapies.

Hematopoietic cell transplant (HCT) and chimeric antigen receptor T-cell (CAR-T) therapy recipients are susceptible to multiple pulmonary complications that are caused by infectious and noninfectious processes. Numerous variables can be associated with specific pulmonary diseases including time from transplantation, presence of graft versus host disease (GVHD), underlying disease, and prolonged neutropenia and lymphocytopenia. Most pulmonary complications are infectious in origin, with bacterial pneumonia remaining the most common pulmonary infection, particularly before neutrophil engraftment. Invasive fungal infections continue to affect this patient population even when antifungal prophylaxis is used. Noninfectious pulmonary complications include a wide differential of pathologies in this population, and as clinical presentations of these various pulmonary disorders often overlap, clinicians frequently will use a multidisciplinary approach in diagnosing these abnormalities. Radiography, particularly with chest computed tomography (CT) imaging, is an essential tool in identifying pulmonary pathology and potential sources. While standard microbiological cultures of respiratory specimens are still utilized, their role is limited by low sensitivity and diagnostic yield. The likelihood of obtaining a diagnosis can be improved by using other microbiological assays, including fungal antigen tests and molecular diagnostic methods, particularly if specimens are collected via bronchoscopy. This review will highlight the more common causes of pulmonary diseases encountered after HCT and CAR-T and will examine the different methods in their diagnosis.

Diagnostic accuracy of the BioFire® FilmArray® pneumonia panel in COVID-19 patients with ventilator-associated pneumonia

BackgroundVentilator-Associated pneumonia (VAP) is one of the leading causes of morbidity and mortality in critically ill COVID-19 patients in lower-and-middle-income settings, where timely access to emergency care and accurate diagnostic testing is not widely available. Therefore, rapid microbiological diagnosis is essential to improve effective therapy delivery to affected individuals, preventing adverse outcomes and reducing antimicrobial resistance.MethodsWe conducted a cross-sectional study of patients with suspected VAP and COVID-19, evaluating the diagnostic performance of the BioFire® FilmArray® Pneumonia Panel (FA-PP). Respiratory secretion samples underwent standard microbiological culture and FA-PP assays, and the results were compared.ResultsWe included 252 samples. The traditional culture method detected 141 microorganisms, and FA-PP detected 277, resulting in a sensitivity of 95% and specificity of 60%, with a positive predictive value of 68% and negative predictive value of 93%. In samples with high levels of genetic material (> 10^5 copies/mL), the panel had a sensitivity of 94% and specificity of 86%. In addition, 40% of the culture-negative samples had positive FA-PP® results, of which 35% had > 10^5 copies/mL of genetic material. The most prevalent bacteria were Gram-negative bacilli, followed by Gram-positive cocci. The panel identified 98 genes associated with antimicrobial resistance, predominantly extended-spectrum beta-lactamases (28%).ConclusionThe FA-PP is a sensitive assay for identifying bacteria causing VAP in patients with COVID-19, with a greater capacity to detect bacteria than the conventional method. The timely microbiological recognition offered by this panel could lead to optimized decision-making processes, earlier tailored treatment initiation, and improved antibiotic stewardship practices.

Distribution and Antibiotic Resistance Profile of Extended Spectrum Beta-Lactamase Producing Escherichia coli from Fish Farms within Abakaliki Metropolis

Background and Objectives: The emergence of antibiotic resistant determinant in fish farms and its spread is on the increase and has evolved into strains that are resistant to many classes of antibiotics. Thus, it is critical to identify the distribution and antibiotic resistance profile of Extended Spectrum Beta-lactamase (ESBL) producing Escherichia coli from fish farms within Abakaliki Metropolis.&#x0D; Methodology: Aseptically, fifty (50) milliliters of fishpond water was collected from twenty locations in fifteen (15) fish farms and were analyze using standard microbiological culture and identification of Escherichia coli. Detection of phenotypic extended spectrum β-lactamases production was performed using Double-Disk Synergy Test (DDST). Antibiotic susceptibility studies of extended spectrum β-lactamases producing Escherichia coli was determined using the Kirby–Bauer disk diffusion method and the results were construed using the Clinical Laboratory Standard Institute (CLSI) zone diameter breakpoints.&#x0D; Results: Extended spectrum beta-lactamase producing Escherichia coli distribution from fishpond water revealed overall occurrence rate of 34(11.3 %). The proportion of ESBL producing Escherichia coli was 5(25.0 %) from fish farm L followed by Farm A, Farm E, Farm G, which both accounted for 20.0 % respectively while the least occurrence of 1(5.0 %) was recorded against Farm I. ESBL-producing E. coli were resistant to cephalosporin particularly Ceftriaxone (88.2%), Ceftazidime (91.2 %), Cefotaxime (94.1) and Cefepime (85.3 %). This was followed by Amoxicillin-Clavulanate (91. 2 %), Azetronam (97.1 %). In all, Ciprofloxacin (82.4 %), Imipenem (97.1 %), and Meropenem (100 %) were the most effective antibiotic against ESBL-producing E. coli isolate.&#x0D; Conclusion: This study reveals the prevalence of the ESBL phenotype in fish farms. The increasing prevalence of resistance to routinely used antibiotics in medical and veterinary therapies among the study isolates from aquaculture products poses a significant challenge to the treatment of human and animal diseases. As a result, adequate antibiotic intervention is essential to ensure the continued efficacy of antibiotics for aquaculture and human health, as well as the industry's viability.

Characterization of cerebrospinal fluid (CSF) microbiota at the time of initial surgical intervention for children with hydrocephalus.

To characterize the microbiota of the cerebrospinal fluid (CSF) from children with hydrocephalus at the time of initial surgical intervention. CSF was obtained at initial surgical intervention. One aliquot was stored in skim milk-tryptone-glucose-glycerol (STGG) medium and the second was unprocessed; both were then stored at -70°C. Bacterial growth for CSF samples stored in STGG were subsequently characterized using aerobic and anaerobic culture on blood agar and MALDI-TOF sequencing. All unprocessed CSF samples underwent 16S quantitative polymerase chain reaction (qPCR) sequencing, and a subset underwent standard clinical microbiological culture. CSF with culture growth (either after storage in STGG or standard clinical) were further analyzed using whole-genome amplification sequencing (WGAS). 11/66 (17%) samples stored in STGG and 1/36 (3%) that underwent standard clinical microbiological culture demonstrated bacterial growth. Of the organisms present, 8 were common skin flora and 4 were potential pathogens; only 1 was also qPCR positive. WGAS findings and STGG culture findings were concordant for only 1 sample, identifying Staphylococcus epidermidis. No significant difference in time to second surgical intervention was observed between the STGG culture-positive and negative groups. Using high sensitivity methods, we detected the presence of bacteria in a subset of CSF samples at the time of first surgery. Therefore, the true presence of bacteria in CSF of children with hydrocephalus cannot be ruled out, though our findings may suggest these bacteria are contaminants or false positives of the detection methods. Regardless of origin, the detection of microbiota in the CSF of these children may not have any clinical significance.

Profile of Cutaneous Bacterial Flora in Pemphigus Patients.

Objectives Pemphigus, a group of autoimmune bullous diseases, can be fatal, resulting from overwhelming opportunistic infection of lesions secondary to cutaneous bacterial infections. This study aimed to look into the cutaneous bacterial infection profile of pemphigus patients as timely identification and appropriate treatment can play a major role in reducing mortality. Materials and Methods Pus samples/swabs received from patients with pemphigus over a 2-year period from July 2018 to June 2020 were subjected to standard microbiological culture techniques and susceptibility testing. The frequency of isolation and susceptibility profile of the different bacterial pathogens toward various antimicrobial agents were interpreted and analyzed as per the Clinical and Laboratory Standards Institute's guidelines. Results Samples from 315 patients were received during the study period comprising of 203 (64.4%) males and 112 (35.5%) females. Of 211 samples which were culture-positive, a total of 245 bacterial isolates were obtained, comprising of 158 Gram-positive cocci and 87 Gram-negative bacilli. Staphylococcus aureus (138, 56.3%) was the most common isolate followed by Pseudomonas aeruginosa (41, 16.7%) and Escherichia coli (16, 6.5%). Methicillin resistance was observed in 24.6% Staphylococcus aureus isolates and carbapenem resistance in 9.5 to 14.6% Gram-negative bacilli. Conclusions Study findings emphasize the need for continuous monitoring of cutaneous pemphigus lesions for appropriate choice of antimicrobial therapy.

Phenotypic Detection of AmpC \(\beta\)-lactamase Producing Escherichia coli among Patients in Hospital Wards

Background and Objectives: AmpC β-lactamase producing Escherichia coli has emerged in hospital environments as an important health issue that is of a global health concern as drug-resistant pathogenic bacteria that has evolved into strains that are resistant to many classes of antibiotics. However, awareness of the prevalence of AmpC β-lactamase producing microorganisms such as E. coli could be very valuable for achieving more accurate epidemiological results, as well as controlling their spread in the different hospital wards.&#x0D; Methodology: A total of four hundred (400) clinical samples comprising of two hundred and seventy-nine (279) urine samples and one hundred and Twenty-one (121) wound samples were collected from patients in different ward at AE-FUTHA. The clinical samples were analyze using standard microbiological culture and identification of Escherichia coli. Detection of phenotypic AmpC β-lactamases production was performed using Cefoxitin-Cloxacillin Double-Disk Synergy Test (CC-DDST). Antibiotic susceptibility studies of AmpC β-lactamases producing Escherichia coli was determined using the Kirby–Bauer disk diffusion method and the results were construed using the Clinical Laboratory Standard Institute (CLSI) zone diameter breakpoints.&#x0D; Results: Phenotypic AmpC β-lactamases producing E. coli accounted overall prevalence rate of 94.1%. The frequency of AmpC β-lactamases producing E. coli in urine samples were 57(93.4%) comprising of high occurrence rate in Surgical ward 15(100%) followed by medical ward 24(88.9%) but also accounted for overall prevalence rate of 38(95.0%) in wound samples consisting of 9(100 %) from children ward and medical ward 10(100%) followed by Orthopedic ward 13(86.7%) with the least prevalence rate. The AmpC β-lactamases producing E. coli exhibited high percentage of resistance within the range of 50-100% against ceftriaxone, ceftazidime, cefepime, azetronam, Trimethoprim-Sulfamethoxazole Ticarcillin-clavulanic acid but were susceptible to ofloxacin 70.0%, Imipenem 83.3% and amikacin 100%.&#x0D; Conclusion: The findings of this study is a proof of the occurrence of AmpC β-lactamase producing Escherichia coli among patients admitted to hospital wards and there’s an urgent need for controlling and managing the development of MDR genotype strain. Moreover, to prevent the spread of resistance among AmpC β-lactamase producing Escherichia coli to other strains and improve the effectiveness of antibiotics, it is suggested to establish a precise schedule for antibiotic use in each region based on their antibiotic resistance pattern.

Klebsiella infections in a pediatric intensive care unit: incidence, antimicrobial susceptibility, and resistance genes

BackgroundInfections with multidrug-resistant K. pneumoniae is associated with high morbidity and mortality especially among critically ill patients. This was the main principle to conduct a detailed study about this organism, its resistance pattern, and type of its resistance genesSubjects and methodsA cross-sectional study was carried out in a pediatric intensive care unit on patients with age range from 1 month to 12 years over a period of 1 year with positive K. pneumoniae using standard microbiological culture and antibiogram sensitivity testing. All collected samples were processed using multiplex PCR technique to identify the most relevant resistant genes.ResultsForty-four patients had 54 positive cultures for K. pneumoniae, out of which 17 patients (38.6%) passed away. The most prevalent-resistant gene was New Delhi metallo-beta lactamase (NDM) gene (65.4%) followed by cefotaximase (CTX-M) gene (57.7%). Extensively drug-resistant K. pneumoniae was detected in (15.9%) of the results and was proved to be independent risk factor increasing mortality odds 139 folds.ConclusionThe evolution of resistance of Klebsiella pneumoniae was proved to be associated with a high mortality rate. Continuous widespread surveillance of Klebsiella pathogen focusing on identification of resistance genes and antibiotic resistance pattern is highly recommended.

Perinatal bacterial colonization and neonatal early-onset sepsis: A case-control study.

The utility of determining maternal-neonatal surface colonization as detected by standard microbiological cultures around the time of birth is unclear. The aim of this study is to evaluate the association between maternal and neonatal surface colonization at birth and neonatal early onset sepsis (EOS). To investigate the association of white matter hyperintensities (WMHs) present in the brain with AD CSF biomarker levels. We conducted a case-control study of newborns admitted to the neonatal department of a referral women's and children's hospital from 2009 to 2017. Cases were infants with blood-culture-confirmed EOS (<3 days of life), and controls were infants without EOS randomly chosen based on the cases' date of birth. Maternal genitourinary and neonatal ear swab cultures were used to determine bacterial surface colonization status. Fifty-one infants were diagnosed with EOS during the study period, where Escherichia coli (45%), and Group B Streptococcus (23%) accounted for 68% of infecting organisms. Compared to infants without EOS, those infected were more likely to have surface colonization of the mothers (60% vs 40%, p = 0.048) and infants (90% vs 11%, p < 0.001). In univariate analysis, chorioamnionitis [7.1 (95% CI 2.9, 16.8)], small-for-gestational-age [OR 0.08 (95% CI 0.02, 0.4)], exposure to antibiotics around time of birth [2.3 (95% CI 1.0, 5.1)], maternal surface colonization [2.2 (95% CI 1.0, 4.9)] and neonatal surface colonization [23.5 (95% CI 7.3, 76.1)] were significantly associated with EOS. Adjusting for potential confounders, neonatal colonization remained significantly associated with neonatal EOS [AOR 15.0 (95% CI 3.5, 64.2), p < 0.001]. In our setting with predominant Gram-negative EOS, neonatal colonization but not maternal colonization was significantly associated with EOS in the newborn.

Characterization of the urogenital microbiome in patients with urinary tract infections

Standard microbiological culture techniques can only identify a fraction of the urogenital microbiome. Meanwhile, identifying and characterizing infectious microorganisms are very important for the success of diagnosis and treatments, especially for Urinary Tract Infection (UTI) patients. This study aimed to characterize the urogenital microbiome of UTI patients using 16S rRNA gene sequencing. We sequenced two pooled DNA samples from voided urine of UTI patients (21 females and 13 males). To determine the structure and composition of taxa in the samples, 16S rRNA gene sequencing was performed using the Illumina Mi‐Seq paired‐end platform. The most abundant genera were Burkholderia‐Caballeronia‐Paraburkholderia (71%) followed by Prevotella (33%), Escherichia‐Shigella (24%), Klebsiella (23%) and Sneathia (10%). The female microbiome was dominated by Prevotella bivia (28%), Escherichia coli (24%), Sneathia sanguinegens (7%) and Klebsiella pneumoniae (4%). On the other hand, the male microbiome was dominated by K. pneumoniae (23%) and E. coli (2%). K. pneumoniae and E. coli were the most abundant species found in both microbiomes. The 16S rRNA gene sequencing used in this study successfully uncovered the composition of the urogenital microbiome, which might not have been possible with conventional culture methods.

Risk Factors and Outcome of Sepsis in Traumatic Patients and Pathogen Detection Using Metagenomic Next-Generation Sequencing.

Objective Sepsis, a life-threatening clinical syndrome, is a leading cause of mortality after experiencing multiple traumas. Once diagnosed with sepsis, patients should be given an appropriate empiric antimicrobial treatment followed by the specific antibiotic therapy based on blood culture due to its rapid progression to tissue damage and organ failure. In this study, we aimed to analyze the risk factors and outcome of sepsis in traumatic patients and to investigate the performance of metagenomic next-generation sequencing (mNGS) compared with standard microbiological diagnostics in post-traumatic sepsis. Methods The study included 528 patients with multiple traumas among which there were 142 cases with post-traumatic sepsis. Patients' demographic and clinical data were recorded. The outcome measures included mortality during the emergency intensive care unit (EICU), EICU length of stay (LOS), all-cause 28-day mortality, and total ventilator days in 28 days after admission. A total of 89 blood samples from 89 septic patients underwent standard microbiological blood cultures and 89 samples of peripheral blood (n = 21), wound secretion (n = 41), bronchoalveolar lavage fluid (BALF) (19), ascites (n = 5), and sputum (n = 3) underwent mNGS. Pathogen detection was compared between standard microbiological blood cultures and mNGS. Results The sepsis group and non-sepsis group exhibited significant differences regarding shock on admission, blood transfusion, mechanical ventilation, body temperature, heart rate, WBC count, neutrophil count, hematocrit, urea nitrogen, creatinine, CRP, D-D dimer, PCT, scores of APACHE II, sequential organ failure assessment (SOFA), and Injury Severity Score (ISS) on admission to the EICU, and Multiple Organ Dysfunction Syndromes (MODS) (P < 0.05). Multivariate logistic regression analysis showed that scores of APACHE II, SOFA, and ISS on admission, and MODS were independent risk factors for the occurrence of sepsis in patients with multiple traumas. The 28-day mortality was higher in the sepsis group than in the non-sepsis group (45.07% vs. 19.17%, P < 0.001). The mortality during the EICU was higher in the sepsis group than in the non-sepsis group (P=0.002). The LOS in the EICU in the sepsis group was increased compared with the non-sepsis group (P=0.004). The total ventilator days in 28 days after admission in the sepsis group was increased compared with the non-sepsis group (P < 0.001). Multivariate logistic regression analysis showed that septic shock, APACHE II score on admission, SOFA score, and MODS were independent risk factors of death for patients with post-traumatic sepsis. The positive detection rate of mNGS was 91.01% (81/89), which was significantly higher than that of standard microbiological blood cultures (39.33% (35/89)). Standard microbiological blood cultures and mNGS methods demonstrated double positive results in 33 (37.08%) specimens and double-negative results in 8 (8.99%) specimens, while 46 (51.69%) samples and 2 (2.25%) samples had positive results only with mNGS or culture alone, respectively. Conclusion Our study identifies risk factors for the incidence and death of sepsis in traumatic patients and shows that mNGS may serve as a better diagnostic tool for the identification of pathogens in post-traumatic sepsis than standard microbiological blood cultures.

Nasal carriage of Staphylococcus aureus in children with grass pollen-induced allergic rhinitis and the effect of polyvalent mechanical bacterial lysate immunostimulation on carriage status: A randomized controlled trial.

ABSTRACTBackgroundNumerous studies indicate that Staphylococcus aureus (S. aureus) colonizing the nasal cavity plays a role in the pathogenesis of allergic rhinitis (AR). This bacterium is able to produce a variety of toxins with superantigenic properties that can exacerbate allergic inflammation.ObjectiveThe objective of the study was to evaluate the ability of polyvalent mechanical bacterial lysate (PMBL) to eliminate S. aureus nasal carriage in children with grass pollen‐induced AR.MethodsThis randomized, double‐blind, placebo‐controlled study included 80 children aged 5–17 years with seasonal AR (SAR). At the randomization visit and after 12 weeks of the study, a swab was taken from the region of the middle nasal meatus. Standard microbiology culture and identification techniques were used to analyze the swab contents.ResultsNasal colonization by S. aureus was confirmed in 29 children (42%), with Moraxella catarrhalis in three participants (4.4%). Physiological flora was detected in 37 children. No statistically significant differences were observed between the two measurement points in both the PMBL and placebo groups with respect to the number of patients whose nasal swab cultures showed a growth of S. aureus (p = 1). Both groups also showed no significant changes in the mean number of S. aureus colonies in nasal swab cultures taken at baseline and after 12 weeks of the study (PMBL group p = .41; placebo group p = .16).ConclusionAlmost every second child with SAR is S. aureus nasal carrier. Sublingual administration of PMBL in children with grass pollen‐induced AR did not affect S. aureus nasal colonization. Therefore, PMBL should not be used for the eradication of S. aureus from the nasal cavity.

Next- and Third-Generation Sequencing Outperforms Culture-Based Methods in the Diagnosis of Ascitic Fluid Bacterial Infections of ICU Patients.

Objectives: Infections of the ascitic fluid are serious conditions that require rapid diagnosis and treatment. Ascites is often accompanied by other critical pathologies such as gastrointestinal bleeding and bowel perforation, and infection increases the risk of mortality in intensive care patients. Owing to a relatively low success rate of conventional culture methods in identifying the responsible pathogens, new methods may be helpful to guide antimicrobial therapy and to refine empirical regimens. Here, we aim to assess outcomes and to identify responsible pathogens in ascitic fluid infections, in order to improve patients’ care and to guide empirical therapy. Methods: Between October 2019 and March 2021, we prospectively collected 50 ascitic fluid samples from ICU patients with suspected infection. Beside standard culture-based microbiology methods, excess fluid underwent DNA isolation and was analyzed by next- and third-generation sequencing (NGS) methods. Results: NGS-based methods had higher sensitivity in detecting additional pathogenic bacteria such as E. faecalis and Klebsiella in 33 out of 50 (66%) ascitic fluid samples compared with culture-based methods (26%). Anaerobic bacteria were especially identified by sequencing-based methods in 28 samples (56%), in comparison with only three samples in culture. Analysis of clinical data showed a correlation between sequencing results and various clinical parameters such as peritonitis and hospitalization outcomes. Conclusions: Our results show that, in ascitic fluid infections, NGS-based methods have a higher sensitivity for the identification of clinically relevant pathogens than standard microbiological culture diagnostics, especially in detecting hard-to-culture anaerobic bacteria. Patients with such infections may benefit from the use of NGS methods by the possibility of earlier and better targeted antimicrobial therapy, which has the potential to lower the high morbidity and mortality in critically ill patients with ascitic bacterial infection.

Rapid Assay for Sick Children with Acute Lung infection Study (RASCALS): diagnostic cohort study protocol

IntroductionLower respiratory tract infection (LRTI) is the most commonly treated infection in critically ill children. Pathogens are infrequently identified on routine respiratory culture, and this is a time-consuming process. A...

Improved diagnosis of gastrointestinal infections using a semi-automated multiplex real-time PCR for detection of enteropathogens.

Introduction. The identification of enteropathogens is critical for the clinical management of patients with suspected gastrointestinal infection. The FLOW multiplex PCR system (FMPS) is a semi-automated platform (FLOW System, Roche) for multiplex real-time PCR analysis.Hypothesis/Gap Statement. FMPS has greater sensitivity for the detection of enteric pathogens than standard methods such as culture, biochemical identification, immunochromatography or microscopic examination.Aim.The diagnostic performance of the FMPS was evaluated and compared to that of traditional microbiological procedures.Methodology. A total of 10 659 samples were collected and analysed over a period of 7 years. From 2013 to 2018 (every July to September), samples were processed using standard microbiological culture methods. In 2019, the FMPS was implemented using real-time PCR to detect the following enteropathogens: Shigella spp., Salmonella spp., Campylobacter spp., Giardia intestinalis, Entamoeba histolytica, Blastocystis hominis, Cryptosporidum spp., Dientamoeba fragilis, adenovirus, norovirus and rotavirus. Standard microbiological culture methods (2013-2018) included stool culture, microscopy and immunochromatography.Results. A total of 1078 stool samples were analysed prospectively using the FMPS from July to September (2019): bacterial, parasitic and viral pathogens were identified in 15.3, 9.71 and 5.29 % of cases, respectively. During the same period of 6 years (2013-2018), the proportion of positive identifications using standard microbiological methods from 2013 to 2018 was significantly lower. A major significant recovery improvement was observed for all bacteria species tested: Shigella spp./enteroinvasive Escherichia coli (EIEC) (P <0.05), Salmonella spp. (P <0.05) and Campylobacter spp. (P <0.05). Marked differences were also observed for the parasites G. intestinalis, Cryptosporidium spp. and D. fragilis.Conclusion. These results support the value of multiplex real-time PCR analysis for the detection of enteric pathogens in laboratory diagnosis with outstanding performance in identifying labile micro-organisms. The identification of unsuspected micro-organisms for less specific clinical presentations may also impact on clinical practice and help optimize patient management.