Extra-urogenital infection by Mycoplasma hominis in transplant patients: two case reports and literature review.

BACKGROUND: Mycoplasma hominis is a facultative anaerobic bacterium commonly present in the urogenital tract. In recent years, M. hominis has increasingly been associated with extra-urogenital tract infections, particularly in immunosuppressed patients. Detecting M. hominis in a diagnostic laboratory can be challenging due to its slow growth rate, absence of a cell wall, and the requirements of specialized media and conditions for optimal growth. Consequently, it is necessary to establish guidelines for the detection of this microorganism and to request the appropriate microbiological work-up of immunosuppressed patients. CASE PRESENTATION: We hereby present two cases of solid organ transplant patients who developed M. hominis infection. Microscopic examination of the bronchial lavage and pleural fluid showed no microorganisms. However, upon inoculating the specimens onto routine microbiology media, the organism was successfully identified and confirmation was performed using 16S rDNA sequencing. Both patients received appropriate treatment resulting in the resolution of M. hominis infection. CONCLUSIONS: The prompt detection of M. hominis in a clinical specimen can have a significant impact on patient care by allowing for early intervention and ultimately resulting in more favorable clinical outcomes, especially in transplant patients.

Fluorescence - modern method of the diagnosis of chronic wounds on the example of venous leg ulcer.

Introduction: Fluorescence imaging has become a method for bacterial visualisation in chronic wounds for the last few years. MolecuLight i:X (MolecuLight, Inc, ON, Canada) is a handheld device, which enables quick diagnostics to determine both the type and location of pathogens present in the wound and on the skin. By means of fluorescent light illumination the tissues populated by pathogenic bacteria emit red or cyan fluorescent signatures, depending on the type of the pathogen: red fluorescence signal is emitted by Staphylococcus and Escherichia coli among others, while Pseudomonas aeruginosa produce cyan fluorescence. The fluorescence image also presents the spatial pattern of bacterial load, which creates bacterial mapping of the wound and may be used by a clinician for targeted sampling or debridement, among others. Aim: This study presents the method of microbiological fluorescent imaging and two case studies of patients with venous leg ulcers. Material and methods: In both cases, the sample for microbiological testing was obtained by means of a swab stick. Results: The results obtained from fluorescent imaging showed moderate-to-heavy bacterial load, which corresponded with the results from microbiology laboratory. Thanks to quick diagnostics with the use of MolecuLight i:X device, instant implementation of targeted topical actions such as wound hygiene, skin disinfection, appropriate dressing choice and curative treatment among others was possible. Conclusions: Our observations are consistent with the reports from other facilities.

Do we overtreat patients with presumed neutropenic sepsis?

PURPOSE: Many aspects of the management of neutropenic sepsis remain controversial. These include the choice of empiric antibiotic, the duration of antibiotic therapy and the possibility that very low-risk cases may be managed safely with oral rather than intravenous therapy. STUDY DESIGN: Retrospective cohort study conducted in a district general hospital serving a population of 148 000 in south west Scotland. RESULTS: Fifty one patients with cancer, whose neutrophil count was less than 1.0×109/L within 21 days of their last chemotherapy, were admitted as a medical emergency in 2019. All received antibiotic because of presumed neutropenic sepsis. A total of 4 patients had positive blood cultures (group 1), 12 patients had a clinical focus of infection but no clear pathogen (group 2), while 35 patients had neither (group 3). Group 3 patients were more likely to have a solid tumour, less likely to be febrile, had shorter time to neutrophil recovery and higher Multinational Association of Supportive Care in Cancer scores, though not all of these comparisons achieved statistical significance. Median intravenous plus oral antibiotic duration in group 3 patients was 9 days with median hospital stay of 7 days, raising the possibility of overtreatment. Retrospectively, 23 (66%) group 3 patients had MASSC Risk Index greater than 21 suggesting they were at low risk of complications. CONCLUSIONS: It seems likely that many low-risk neutropenic cancer patients with solid tumours could be managed as effectively and as safely with shorter courses of antibiotic, with oral rather than intravenous antibiotic, as outpatients rather than inpatients and with an overall positive impact on antimicrobial stewardship.

A Rapid and Specific Real-Time PCR Assay for the Detection of Clinically Relevant Mucorales Species.

Infections triggered by filamentous fungi placed in the order Mucorales, phylum Zygomycota, can cause serious harm to immunocompromised patients. Since there is lack of a standardized PCR (polymerase chain reaction) assay for early diagnosis of this fungal infection, this work was aimed to develop a new PCR assay able to detect the presence of Mucorales genera in clinical specimens. Here, we describe a novel diagnostic TaqMan MGB probe assay for precise and rapid detection of the most common clinical species of Mucorales. Zygomycete-specific oligonucleotides were designed to specifically amplify and bind highly conserved sequences of fungal 28S rRNA gene. Additionally, we succeeded in differentiating Mucorales species (i.e., Rhizopus, Lichtheimia, Mucor, and Rhizomucor) in artificially infected serum samples, suggesting that the quantitative capability of this real-time PCR assay could potentially optimize the diagnosis of mucormycosis.

Deep Neural Networks Offer Morphologic Classification and Diagnosis of Bacterial Vaginosis.

Bacterial vaginosis (BV) is caused by the excessive and imbalanced growth of bacteria in vagina, affecting 30 to 50% of women. Gram staining followed by Nugent scoring based on bacterial morphotypes under the microscope is considered the gold standard for BV diagnosis; this method is often labor-intensive and time-consuming, and results vary from person to person. We developed and optimized a convolutional neural network (CNN) model and evaluated its ability to automatically identify and classify three categories of Nugent scores from microscope images. The CNN model was first established with a panel of microscopic images with Nugent scores determined by experts. The model was trained by minimizing the cross-entropy loss function and optimized by using a momentum optimizer. The separate test sets of images collected from three hospitals were evaluated by the CNN model. The CNN model consisted of 25 convolutional layers, 2 pooling layers, and a fully connected layer. The model obtained 82.4% sensitivity and 96.6% specificity with the 5,815 validation images when altered vaginal flora and BV were considered the positive samples, which was better than the rates achieved by top-level technologists and obstetricians in China. The capability of our model for generalization was so strong that it exhibited 75.1% accuracy in three categories of Nugent scores on the independent test set of 1,082 images, which was 6.6% higher than the average of three technologists, who are hold bachelor's degrees in medicine and are qualified to make diagnostic decisions. When three technologists ran one specimen in triplicate, the precision of three categories of Nugent scores was 54.0%. One hundred three samples diagnosed by two technologists on different days showed a repeatability of 90.3%. The CNN model outperformed human health care practitioners in terms of accuracy and stability for three categories of Nugent score diagnosis. The deep learning model may offer translational applications in automating diagnosis of bacterial vaginosis with proper supporting hardware.

Assessment of nasopharyngeal Streptococcus pneumoniae colonization does not permit discrimination between Canadian children with viral and bacterial respiratory infection: a matched-cohort cross-sectional study.

BACKGROUND: Readily-available diagnostics do not reliably discriminate between viral and bacterial pediatric uncomplicated pneumonia, both of which are common. Some have suggested that assessment of pneumococcal carriage could be used to identify those children with bacterial pneumonia. The objective of this study was to determine if nasopharyngeal pneumococcal colonization patterns differed between children with definite viral disease, definite bacterial disease, and respiratory disease of indeterminate etiology. METHODS: Three groups of subjects were recruited: children with critical respiratory illness, previously healthy children with respiratory illness admitted to the ward, and previously healthy children diagnosed in the emergency department with non-severe pneumonia. Subjects were categorized as follows: a) viral infection syndrome (eg. bronchiolitis), b) bacterial infection syndrome (ie. pneumonia complicated by effusion/empyema), or c) 'indeterminate' pneumonia. Subjects' nasopharyngeal swabs underwent quantitative PCR testing for S. pneumoniae. Associations between categorical variables were determined with Fisher's exact, chi-square, or logistic regression, as appropriate. Associations between quantitative genomic load and categorical variables was determined by linear regression. RESULTS: There were 206 children in Group 1, 122 children in Group 2, and 179 children in Group 3. Only a minority (227/507, 45%) had detectable pneumococcal carriage; in those subjects, there was no association of quantitative genomic load with age, recruitment group, or disease category. In multivariate logistic regression, pneumococcal colonization > 3 log copies/mL was associated with younger age and recruitment group, but not with disease category. CONCLUSIONS: The nasopharyngeal S. pneumoniae colonization patterns of subjects with definite viral infection were very similar to colonization patterns of those with definite bacterial infection or indeterminate pneumonia. Assessment and quantification of nasopharyngeal pneumococcal colonization does not therefore appear useful to discriminate between acute viral and bacterial respiratory disease; consequently, this diagnostic testing is unlikely to reliably determine which children with indeterminate pneumonia have a bacterial etiology and/or require antibiotic treatment.

Symptoms, risk factors, diagnosis and treatment of urinary tract infections.

Urinary tract infection (UTI) is a common microbial infection found in all ages and sexes which involves inflammation of the urinary tract. These infections can range from simple bladder inflammation, that is, cystitis, to severe cases of uroseptic shock. UTI ranks as the number 1 infection that leads to a prescription of antibiotics after a doctor's visit. These infections are sometimes distressing and even life threatening, and both males (12%) and females (40%) have at least one symptomatic UTI throughout their lives. Diagnostic failures in case of bacterial infections are the main contributing factor in improper use of antibiotics, delay in treatment and low survival rate in septic conditions. So, early diagnosis and appropriate therapy with antibiotics are the most significant requirements for preventing complicated UTI conditions such as urosepsis. This review article summarises the symptoms of the UTIs and the associated risk factors to it. The various conventional and recent diagnostic methods were also discussed in this review, along with treatment therapies with or without antibiotics.

The impact of diagnostic microbiology on de-escalation of antimicrobial therapy in hospitalised adults.

BACKGROUND: Minimising antimicrobial overuse is needed to limit antimicrobial resistance. There is little evidence on how often microbiological testing informs antimicrobial de-escalation (e.g. stopping, shortening duration, switching to narrower spectrum or intravenous to oral switch) at 48-72 h "review and revise". We performed a patient level analysis of diagnostic microbiology and antimicrobial prescribing to determine the impact of microbiology results on antimicrobial review outcomes. METHODS: Antimicrobial prescribing data were collected for hospitalised adults from across Brighton and Sussex University Hospitals NHS Trust using routine monthly audits of prescribing practice from July 2016 to April 2017. Microbiology testing data for cultures of blood, urine, sputum and cerebrospinal fluid (CSF) were gathered from the hospital pathology database and linked to prescriptions with matching patient identification codes. Antimicrobial prescriptions were grouped into "prescription episodes" (PEs), defined as one or more antimicrobials prescribed to the same patient for the same indication. Medical records were reviewed for all PEs with positive microbiology and a randomised sample of those with negative results to assess the impact of the microbiology result on the antimicrobial prescription(s). RESULTS: After excluding topical and prophylactic prescriptions, data were available for 382 inpatient antimicrobial prescriptions grouped into 276 prescription episodes. 162/276 (59%) had contemporaneous microbiology sent. After filtering likely contaminants, 33/276 (12%) returned relevant positive results, of which 20/33 (61%) had antimicrobials changed from empiric therapy as a result with 6/33 (18%) prompting de-escalation. Positive blood and CSF tended to have greater impact than urine or sputum cultures. 124/276 (45%) PEs returned only negative microbiology, and this was documented in the medical notes less often (9/40, 23%) than positive results (28/33, 85%). Out of 40 reviewed PEs with negative microbiology, we identified just one (~ 3%) in which antimicrobials were unambiguously de-escalated following the negative result. CONCLUSIONS: The majority of diagnostic microbiology tests sent to inform clinical management yielded negative results. However, negative microbiology contributed little to clinical decision making about antimicrobial de-escalation, perhaps reflecting a lack of trust in negative results by treating clinicians. Improving the negative predictive value of currently available diagnostic microbiology could help hospital prescribers in de-escalating antimicrobial therapy.

Added Value of Xpert MTB/RIF Ultra for Diagnosis of Pulmonary Tuberculosis in a Low-Prevalence Setting.

Xpert MTB/RIF (Xpert) for direct molecular detection of Mycobacterium tuberculosis and rifampin resistance from clinical specimens has dramatically improved the diagnosis of tuberculosis (TB). Xpert MTB/RIF Ultra (Ultra) is proposed as a substitute of Xpert with increased sensitivity and improved rifampin resistance detection. We evaluated the diagnostic performance of Ultra and Xpert for pulmonary TB diagnosis in a low-TB-burden setting. Performance of Ultra and Xpert were compared to culture on respiratory specimens from patients with suspected pulmonary TB (November 2016 to August 2018; n = 196) in Lausanne (Switzerland). Clinical data were used to investigate discrepant results. Correlation between semiquantitative result of Ultra and smear microscopy status for the detection of acid-fast bacilli (AFB) was established. The sensitivities of Xpert and Ultra were 82.9% (39/47) and 95.8% (45/47), respectively, when considering all culture-positive specimens, 100% (23/23) for both assays on smear-positive specimens, and 66.7% (16/24) and 91.7% (22/24) on smear-negative specimens. Using culture as gold standard, the specificities of Xpert and Ultra were 97.3% (145/149) and 96.64% (144/149), respectively. All the patients with Ultra-positive results with the new category "trace" were diagnosed with active TB based on clinical findings and microbiological culture. The semiquantitative results of both Xpert and of Ultra positively correlated with the semiquantitative result of AFB detection. Our data support an increased sensitivity of Ultra compared to Xpert in a low-prevalence setting. Correlation between the Ultra semiquantitative result and AFB burden can help in evaluating a patient's transmission potential.

Japan nosocomial infections surveillance (JANIS): a model of sustainable national antimicrobial resistance surveillance based on hospital diagnostic microbiology laboratories.

BACKGROUND: Antimicrobial resistance (AMR) is now recognized as a major threat to public health, and surveillance of AMR is essential for successful containment. In 2000, Japan Nosocomial Infections Surveillance (JANIS) Clinical Laboratory (CL) division has been launched as a voluntary AMR surveillance funded by the Ministry of Health, Labour and Welfare and managed by the National Institute of Infectious Diseases. In this study, we aimed to propose a model of sustainable national AMR surveillance which provides not only national AMR surveillance reports but also benchmarking reports to each hospital to facilitate infection control practices. METHODS: JANIS CL division collects comprehensive specimen-based data complies with JANIS data format from participating hospitals each month. It had targeted only blood and cerebrospinal fluid samples but was expanded to all types of specimens in 2007 at revision of JANIS. The JANIS system interprets the antimicrobial susceptibility according to the same criteria and conducts removal of duplicates to allow accurate comparison between hospitals. Monthly feedback reports are created automatically within 48 h, while quarterly and annual reports are generated after data validation. RESULTS: At the beginning, 468 hospitals were enrolled in the JANIS CL division, but the number of hospitals that submitted data decreased to 210 (45%) in 2006. After surveillance revision in 2007, annual recruitment of hospitals was initiated and as of 2015, 1475 hospitals participated, and 1461 (99%) of them submitted data throughout the year. Nationwide surveillance data collected over the past decade revealed that the prevalence of methicillin-resistant Staphylococcus aureus has decreased since 2008, and that its prevalence is higher in the western part of Japan, where the number of hospitals per capita is higher than in the eastern part. CONCLUSIONS: JANIS CL division serves a model of sustainable national AMR surveillance system. Comprehensive data for all specimens promotes understanding of the sampling frequency and prevalence of AMR. As a well-established system for providing rich information to guide action both locally and nationally, JANIS may also be utilized for sharing AMR data globally.

Deployed military general internal physician's toolkit: the recent past and near future.

INTRODUCTION: The role of the military physician in Deployed Hospital Care involves the diagnosis and management of a wide variety of disease states. Broad clinical skills need to be complemented by judicious use of a limited array of investigations. No study has specifically quantified what investigations physicians use on operations. METHODS: A retrospective cross-sectional study was performed to ascertain what investigations were undertaken on all patients managed by the General Internal Medicine teams over a 14 month period during a recent enduring operation in Afghanistan. A record was also made of investigations that were unavailable but considered desirable by the treating physician in order to inform clinical or occupational decisions. RESULTS: 676 patients were admitted during the study period. Blood tests were performed in 96% of patients, plain radiographs in 50%, CT in 12% and ultrasound in 12%. An ECG was performed in over half (57%) and a peak flow in 11%. The most desirable, but unavailable, investigations were cardiac monitoring and echocardiography (24% and 12% of patients, respectively). DISCUSSION: The data produced by this study both identified and quantified the investigations used by physicians during a mature operational deployment. This can be used in addition to accurate medical intelligence to inform and rationalise the diagnostic requirements for future operations as well as the provision of training. Technological advancements, particularly in weight and portability, are likely to enable more complex investigational modalities to be performed further forward on military deployments.

Determining clinical decision thresholds for HIV-positive patients suspected of having tuberculosis.

Clinical decision thresholds may aid the evaluation of diagnostic tests but have rarely been determined for tuberculosis (TB). We presented clinicians with six web-based clinical scenarios, describing patients with HIV and possible TB at various sites and with a range of clinical stability. The probability of disease was varied randomly and clinicians asked to make treatment decisions; threshold curves and therapeutic thresholds were calculated. Test and treatment thresholds were calculated using Bayes theorem and the diagnostic accuracy of Xpert MTB/RIF. We received 165 replies to our survey. Therapeutic thresholds vary depending on the clinical stability and site of suspected disease. For inpatients, it ranges from 3.4% in unstable to 79.6% in stable patients. For TB meningitis, it ranges from 0% in unstable to 51.4% in stable patients and for pulmonary TB in outpatients it ranges from 29.1% in unstable to 74.5% in the stable patients. Test and treatment thresholds vary in a similar way with test thresholds ranging from 0 in unstable patients with suspected meningitis to 8.2% for stable inpatients. Treatment thresholds vary from 0 for unstable patients with suspected meningitis to 97% for stable inpatients. Therapeutic thresholds for TB can be determined by presenting clinicians with patient scenarios with random probabilities of disease and can be used to calculate test and treatment thresholds using Bayes theorem. Thresholds are lower when patients are more clinically unstable and when the implications of inappropriately withholding therapy are more serious. These results can be used to improve use and evaluation of diagnostic tests.

Enteric fever in a British soldier from Sierra Leone.

Enteric fever (typhoid and paratyphoid) remains a threat to British troops overseas and causes significant morbidity and mortality. We report the case of a soldier who developed typhoid despite appropriate vaccination and field hygiene measures, which began 23 days after returning from a deployment in Sierra Leone. The incubation period was longer than average, symptoms started 2 days after stopping doxycycline for malaria chemoprophylaxis and initial blood cultures were negative. The Salmonella enterica serovar Typhi eventually isolated was resistant to amoxicillin, co-amoxiclav, co-trimoxazole and nalidixic acid and had reduced susceptibility to ciprofloxacin. He was successfully treated with ceftriaxone followed by azithromycin, but 1 month later he remained fatigued and unable to work. The clinical and laboratory features of enteric fever are non-specific and the diagnosis should be considered in troops returning from an endemic area with a febrile illness. Multiple blood cultures and referral to a specialist unit may be required.

Characterization of amygdalin-degrading Lactobacillus species.

AIMS: Cyanogenic glycosides are phytotoxic secondary metabolites produced by some crop plants. The aim of this study was to identify lactic acid bacteria (LAB) capable of catabolizing amygdalin, a model cyanogenic glycoside, for use in the biodetoxification of amygdalin-containing foods and feeds. METHODS AND RESULTS: Amygdalin-catabolizing lactobacilli were characterized using a combination of cultivation-dependent and molecular assays. Lactobacillus paraplantarum and Lactobacillus plantarum grew robustly on amygdalin (Amg(+)), while other LAB species typically failed to catabolize amygdalin (Amg(-)). Interestingly, high concentrations of amygdalin and two of its metabolic derivatives (mandelonitrile and benzaldehyde) inhibited the growth of Lact. plantarum RENO 0093. The differential regulation of genes tentatively involved in cyanohydrin metabolism illustrated that the metabolism of amygdalin- and glucose-grown cultures also differed significantly. CONCLUSIONS: Amygdalin fermentation was a relatively uncommon phenotype among the LAB and generally limited to strains from the Lact. plantarum group. Phenotype microarrays (PM) enabled strain-level discrimination between closely related strains within a species and suggested that phenotypic differences might affect niche specialization. SIGNIFICANCE AND IMPACT OF THE STUDY: Amygdalin-degrading lactobacilli with practical application in the biodetoxification of amygdalin were characterized. These strains show potential for use as starter cultures to improve the safety of foods and feeds.

Identification of lymphogranuloma venereum-associated Chlamydia trachomatis serovars by fluorescence in situ hybridisation--a proof-of-principle analysis.

We describe a proof-of-principle evaluation of a fluorescence in situ hybridisation (FISH) procedure to identify Chlamydia trachomatis serovars L1-L3, the causative agents of lymphogranuloma venereum, in cell cultures based on newly designed DNA probes. Rapid and easy-to-perform FISH could facilitate the diagnosis of lymphogranuloma venereum without nucleic acid amplification or serotyping, but requires broader evaluation studies, for example, in tropical high-endemicity regions.