Increasing proportions of extended-spectrum ß-lactamase-producing isolates among Escherichia coli from urine and bloodstream infections: results from a nationwide surveillance network, Finland, 2008 to 2019.

BackgroundEscherichia coli is the leading cause of urinary tract infections (UTI) and bloodstream infections (BSI), and the emergence of antimicrobial resistance (AMR) in E. coli causes concern.AimTo investigate changes in the proportion of extended-spectrum ß-lactamase (ESBL) producing isolates among E. coli isolated from urine and blood in Finland during 2008-2019.MethodsSusceptibility testing of 1,568,488 urine (90% female, 10% male) and 47,927 blood E. coli isolates (61% female, 39% male) from all Finnish clinical microbiology laboratories during 2008-2019 was performed according to guidelines from the Clinical and Laboratory Standard Institute during 2008-2010 and the European Committee on Antimicrobial Susceptibility Testing during 2011-2019. A binomial regression model with log link compared observed trends over time and by age group and sex.ResultsThe annual proportion of ESBL-producing E. coli isolates among E. coli from blood cultures increased from 2.4% (23/966) to 8.6% (190/2,197) among males (average annual increase 7.7%; 95% CI: 4.4-11.0%, p < 0.01) and from 1.6% (28/1,806) to 6.4% (207/3,218) among females (9.3%; 95% CI: 4.8-14.0%, p < 0.01). In urine cultures, the proportion of ESBL-producing E. coli isolates increased from 2.2% (239/10,806) to 7.2% (1,098/15,297) among males (8.8%; 95% CI: 6.5-11.3%, p < 0.01) and from 1.0% (1,045/108,390) to 3.1% (3,717/120,671) among females (8.6%; 95% CI: 6.3-11.0%, p < 0.01). A significant increase was observed within most age groups.ConclusionsConsidering the ageing population and their risk of E. coli BSI and UTI, the increase in the annual proportions of ESBL-producing E. coli is concerning, and these increasing trends should be carefully monitored.

External Quality Assessment of SARS-CoV-2 Sequencing: an ESGMD-SSM Pilot Trial across 15 European Laboratories.

This first pilot trial on external quality assessment (EQA) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) whole-genome sequencing, initiated by the European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Genomic and Molecular Diagnostics (ESGMD) and the Swiss Society for Microbiology (SSM), aims to build a framework between laboratories in order to improve pathogen surveillance sequencing. Ten samples with various viral loads were sent out to 15 clinical laboratories that had free choice of sequencing methods and bioinformatic analyses. The key aspects on which the individual centers were compared were the identification of (i) single nucleotide polymorphisms (SNPs) and indels, (ii) Pango lineages, and (iii) clusters between samples. The participating laboratories used a wide array of methods and analysis pipelines. Most were able to generate whole genomes for all samples. Genomes were sequenced to various depths (up to a 100-fold difference across centers). There was a very good consensus regarding the majority of reporting criteria, but there were a few discrepancies in lineage and cluster assignments. Additionally, there were inconsistencies in variant calling. The main reasons for discrepancies were missing data, bioinformatic choices, and interpretation of data. The pilot EQA was overall a success. It was able to show the high quality of participating laboratories and provide valuable feedback in cases where problems occurred, thereby improving the sequencing setup of laboratories. A larger follow-up EQA should, however, improve on defining the variables and format of the report. Additionally, contamination and/or minority variants should be a further aspect of assessment.

Common cold in Team Finland during 2018 Winter Olympic Games (PyeongChang): epidemiology, diagnosis including molecular point-of-care testing (POCT) and treatment.

OBJECTIVES: The common cold is the main cause of medical time loss in elite sport. Rapid diagnosis has been a challenge that may be amenable to molecular point-of-care testing (POCT). METHODS: We performed a prospective observational study of the common cold in Team Finland during the 2018 Winter Olympic Games. There were 44 elite athletes and 68 staff members. The chief physician recorded the symptoms of the common cold daily on a standardised form. Two nasal swabs were taken at the onset of symptoms. One swab was analysed within 45 min using a molecular POCT for respiratory syncytial virus and influenza A and B viruses. After the Games, the other swab was tested for 16 possible causative respiratory viruses using PCR in laboratory-based testing. RESULTS: 20 out of 44 (45%) athletes and 22 out of 68 (32%) staff members experienced symptoms of the common cold during a median stay of 21 days. Eleven (26%) samples tested virus-positive using POCT. All subjects with influenza (n=6) and 32 close contacts were treated with oseltamivir. The aetiology of the common cold was finally detected in 75% of the athletes and 68 % of the staff members. Seven virus clusters were identified. They were caused by coronaviruses 229E, NL63 and OC43, influenza B virus, respiratory syncytial virus A, rhinovirus and human metapneumovirus. The virus infections spread readily within the team, most commonly within the same sport discipline. CONCLUSIONS: The cold was indeed a common illness in Team Finland during the Winter Olympic Games. POCT proved to be clinically valuable, especially for influenza. The aetiology of the common cold was identified in most cases.

Chlamydia trachomatis samples testing falsely negative in the Aptima Combo 2 test in Finland, 2019.

Since February 2019, over 160 Chlamydia trachomatis (CT) cases testing negative or equivocal by Aptima Combo 2 (AC2) but positive by Aptima CT test run with Panther instruments occurred in Finland. The AC2 test targets chlamydial 23S rRNA while the CT test targets 16S rRNA. Sequencing of 10 strains revealed a nucleotide substitution in 23S rRNA. The significance of this for the failure of the AC2 test to detect the variant is not yet known.

Antibiotic susceptibility of intestinal Escherichia coli in men undergoing transrectal prostate biopsies: a prospective, registered, multicentre study.

OBJECTIVES: To determine, in a prospective, multicentre setting, the prevalence of fluoroquinolone-resistant (FQ-R) and extended-spectrum ß-lactamase (ESBL)-producing Escherichia coli (E. coli) strains in men undergoing transrectal ultrasonography-guided prostate biopsy (TRUS-Bx) in Finland; and to survey the associated risk factors for having the previously mentioned strains. PATIENTS AND METHODS: This is a substudy of the trial investigating the role of magnetic resonance imaging (MRI) in prostate cancer diagnosis (Improved Prostate Cancer Diagnosis - Combination of Magnetic Resonance Imaging Targeted Biopsies and Biomarkers Multi-institutional Study [multi-IMPROD], NCT02241122). In all, 359 patients from four study centres were recruited to this prospective study. After having signed the informed consent form, these men with suspicion of prostate cancer completed a detailed questionnaire on their medical, smoking, and travelling history, as well as their recent use of antibiotics. After the bi-parametric MRI scan, TRUS-Bx was taken and a rectal swab sample was collected and cultured for determining the antimicrobial susceptibility profile of E. coli strains. The potential risk factors for having FQ-R or third-generation cephalosporin-resistant (3GC-R) E. coli strains were analysed using univariate and multivariate logistic regression analysis. RESULTS: The percentage of FQ-R and 3GC-R E. coli strains amongst the study population was 13% and 8%, respectively. Amongst patients having E. coli strains, the rate of FQ-R and 3GC-R strains was 14% and 8%, respectively. Of the 3GC-R E. coli strains, 62% proved to be ESBL-producers and 88% were also FQ-R. In multivariate analysis, international travel during the preceding year significantly increased the risk of having a FQ-R E. coli strain (odds ratio [OR] 3.592, P = 0.001) and, unexpectedly, use of antibiotics during the previous year significantly decreased this risk (OR 0.442, P = 0.035). No significant risk factors for having 3GC-R E. coli were identified. CONCLUSION: The occurrence of intestinal FQ-R and/or 3GC-R (potentially ESBL-producing) E. coli strains in men undergoing TRUS-Bx in Finland is notable. The finding is consistent with the global increase in antimicrobial resistance. International travel appears to be an indisputable risk factor for having intestinal FQ-R E. coli strains. The contemporary antimicrobial resistance situation should be taken into account in the care of post-TRUS-Bx infections.

Cefotaxime-resistant Salmonella enterica in travelers returning from Thailand to Finland.

During 1993-2011, cefotaxime resistance among Salmonella enterica isolates from patients in Finland increased substantially. Most of these infections originated in Thailand; many were qnr positive and belonged to S. enterica serovar Typhimurium and S. enterica monophasic serovar 4,[5],12:i:-. Although cefotaxime-resistant salmonellae mainly originate in discrete geographic areas, they represent a global threat.

Evaluation of the Carba NP test for carbapenemase detection.

The Carba NP test was evaluated against a panel of 61 carbapenemase-producing bacterial species (15 producing class A carbapenemases, 15 producing class D carbapenemases, and 31 producing metallo-ß-lactamases) and against 111 isolates with non-wild-type carbapenem susceptibility but not producing carbapenemase. Carbapenemase production was verified by PCR and UV-spectrophotometric measurement of imipenem hydrolysis. No false positives were seen, but there were consistent problems with the detection of OXA-48-like enzymes and also some rarer class A enzymes.

High-throughput DNA extraction strategy for fecal microbiome studies.

Microbiome studies are becoming larger in size to detect the potentially small effect that environmental factors have on our gut microbiomes, or that the microbiome has on our health. Therefore, fast and reproducible DNA isolation methods are needed to handle thousands of fecal samples. We used the Chemagic 360 chemistry and Magnetic Separation Module I (MSMI) instrument to compare two sample preservatives and four different pre-treatment protocols to find an optimal method for DNA isolation from thousands of fecal samples. The pre-treatments included bead beating, sample handling in tube and plate format, and proteinase K incubation. The optimal method offers a sufficient yield of high-quality DNA without contamination. Three human fecal samples (adult, senior, and infant) with technical replicates were extracted. The extraction included negative controls (OMNIgeneGUT, DNA/RNA shield fluid, and Chemagic Lysis Buffer 1) to detect cross-contamination and ZymoBIOMICS Gut Microbiome Standard as a positive control to mimic the human gut microbiome and assess sensitivity of the extraction method. All samples were extracted using Chemagic DNA Stool 200 H96 kit (PerkinElmer, Finland). The samples were collected in two preservatives, OMNIgeneGUT and DNA/RNA shield fluid. DNA quantity was measured using Qubit-fluorometer, DNA purity and quality using gel electrophoresis, and taxonomic signatures with 16S rRNA gene-based sequencing with V3V4 and V4 regions. Bead beating increased bacterial diversity. The largest increase was detected in gram-positive genera Blautia, Bifidobacterium, and Ruminococcus. Preservatives showed minor differences in bacterial abundances. The profiles between the V3V4 and V4 regions differed considerably with lower diversity samples. Negative controls showed signs from genera abundant in fecal samples. Technical replicates of the Gut Standard and stool samples showed low variation. The selected isolation protocol included recommended steps from manufacturer as well as bead beating. Bead beating was found to be necessary to detect hard-to-lyse bacteria. The protocol was reproducible in terms of DNA yield among different stool replicates and the ZymoBIOMICS Gut Microbiome Standard. The MSM1 instrument and pre-treatment in a 96-format offered the possibility of automation and handling of large sample collections. Both preservatives were feasible in terms of sample handling and had low variation in taxonomic signatures. The 16S rRNA target region had a high impact on the composition of the bacterial profile. IMPORTANCE: Next-generation sequencing (NGS) is a widely used method for determining the composition of the gut microbiota. Due to the differences in the gut microbiota composition between individuals, microbiome studies have expanded into large population studies to maximize detection of small effects on microbe-host interactions. Thus, the demand for a rapid and reliable microbial profiling is continuously increasing, making the optimization of high-throughput 96-format DNA extraction integral for NGS-based downstream applications. However, experimental protocols are prone to bias and errors from sample collection and storage, to DNA extraction, primer selection and sequencing, and bioinformatics analyses. Methodological bias can contribute to differences in microbiome profiles, causing variability across studies and laboratories using different protocols. To improve consistency and confidence of the measurements, the standardization of microbiome analysis methods has been recognized in many fields.

Appendicolith classification: physical and chemical properties of appendicoliths in patients with CT diagnosed acute appendicitis - a prospective cohort study.

OBJECTIVE: Appendicoliths are associated with a more complicated course of acute appendicitis and failure of non-operative treatment. We aimed to update the appendicolith classification originally described in 1966 and to assess the association of appendicolith characteristics with appendicitis severity. DESIGN: This prospective predefined MAPPAC-trial (ClinicalTrials.gov NCT03257423) substudy included patients with CT diagnosed appendicitis presenting with an appendicolith. CT visible appendicoliths were harvested at surgery, measured and characterised by morphological examination complemented with micro-CT and micro-X-ray fluorescence spectroscopy. Patients were categorised into two groups: appendicolith appendicitis without other complications and appendicolith appendicitis with complications (appendiceal gangrene, perforation and/or abscess). The association of appendicolith classification and characteristics with appendicitis severity was evaluated. RESULTS: Of 78 patients with a CT appendicolith, 41 appendicoliths were collected and classified based on the degree of hardness into three classes. The hardest appendicoliths (class 3) were less common (19.5%) presenting with a stone-hard outer layer and concentrically layered inner structure around a core. The layered inner structure was also observed in class 2 appendicoliths, but was absent in soft, class 1 appendicoliths. Appendicolith hardness or measures (maximum length, diameter and weight) were not associated with appendicitis severity. The spatial distribution of the main inorganic elements of calcium and phosphorus varied within most appendicoliths. CONCLUSION: This updated classification confirms categorisation of CT visible appendicoliths into three classes based on their physical and chemical characteristics. The data on clinical and aetiopathological characteristics of appendicoliths is scarce and using this systematic classification would add to this understanding.

Differences in Gut Microbiota Profiles and Microbiota Steroid Hormone Biosynthesis in Men with and Without Prostate Cancer.

Background: Although prostate cancer (PCa) is the most common cancer in men in Western countries, there is significant variability in geographical incidence. This might result from genetic factors, discrepancies in screening policies, or differences in lifestyle. Gut microbiota has recently been associated with cancer progression, but its role in PCa is unclear. Objective: Characterization of the gut microbiota and its functions associated with PCa. Design setting and participants: In a prospective multicenter clinical trial (NCT02241122), the gut microbiota profiles of 181 men with a clinical suspicion of PCa were assessed utilizing 16S rRNA sequencing. Outcome measurements and statistical analysis: Sequences were assigned to operational taxonomic units, differential abundance analysis, and α- and ß-diversities, and predictive functional analyses were performed. Plasma steroid hormone levels corresponding to the predicted microbiota steroid hormone biosynthesis profiles were investigated. Results and limitations: Of 364 patients, 181 were analyzed, 60% of whom were diagnosed with PCa. Microbiota composition and diversity were significantly different in PCa, partially affected by Prevotella 9, the most abundant genus of the cohort, and significantly higher in PCa patients. Predictive functional analyses revealed higher 5-α-reductase, copper absorption, and retinol metabolism in the PCa-associated microbiome. Plasma testosterone was associated negatively with the predicted microbial 5-α-reductase level. Conclusions: Gut microbiota of the PCa patients differed significantly compared with benign individuals. Microbial 5-α-reductase, copper absorption, and retinol metabolism are potential mechanisms of action. These findings support the observed association of lifestyle, geography, and PCa incidence. Patient summary: In this report, we found that several microbes and potential functions of the gut microbiota are altered in prostate cancer compared with benign cases. These findings suggest that gut microbiota could be the link between environmental factors and prostate cancer.

High-throughput screening of colonization samples for methicillin-resistant Staphylococcus aureus.

BACKGROUND: We present here the first application of 2-photon excited fluorescence detection (TPX) technology for the direct screening of clinical colonization samples for methicillin-resistant Staphylococcus aureus (MRSA). METHODS: A total of 125 samples from 14 patients with previously identified MRSA carriage and 16 controls from low-prevalence settings were examined. RESULTS: The results were compared to those obtained by both standard phenotypic and molecular methods. In identifying MRSA carriers, i.e. persons with at least 1 MRSA positive colonization sample by standard methods, the sensitivity of the TPX technique was 100%, the specificity 78%, the positive predictive value 75%, and the negative predictive value 100%. The TPX assay sensitivity per colonization sample was 89%, the specificity 93%, the positive predictive value 84%, and the negative predictive value 95%. The median time for a true-positive test result was 3 h and 26 min; negative test results are available after 13 h. The assay capacity was 48 samples per test run. CONCLUSIONS: The TPX MRSA technique could provide early preliminary results for clinicians, while simultaneously functioning as a selective enrichment step for further conventional testing. Costs and workload associated with hospital infection control can be reduced using this high-throughput, point-of-care compatible methodology.

Bacterial and viral etiology of childhood diarrhea in Ouagadougou, Burkina Faso.

BACKGROUND: Diarrhea is the most frequent health problem among children in developing countries. This study investigated the bacterial and viral etiology and related clinical and epidemiological factors in children with acute diarrhea in Ouagadougou, Burkina Faso. METHODS: Stool specimens were collected from 283 children under 5 years of age visiting hospital due to acute diarrhea and from 60 healthy controls of similar age. Pathogens were investigated by using conventional culture techniques, PCR and immunochromatographic testing. Salmonella and Shigella strains were serotyped and their susceptibility to 23 antimicrobial agents was determined by the agar dilution method. RESULTS: At least one pathogen was detected in 64% of the 283 patients and in 8% of the 60 controls (p < 0.001). Rotavirus was found in 30% of the patients, followed by diarrheagenic Escherichia coli (24%), Salmonella enterica ssp. enterica (9%), Shigella spp. (6%), adenovirus (5%) and Campylobacter spp. (2%). Multiple pathogens were found in 11% of the patients and in 2% of the controls (p = 0.028). Viruses were found mainly in children of ≤ 2 years of age, whereas bacteria were equally prevalent among all the age groups. Viral infections occurred mostly during the cool dry season and the bacterial infections during the rainy season. Fever (64%) and vomiting (61%) were the most common symptoms associated with diarrhea. Only one Salmonella strain was resistant to nalidixic acid and ciprofloxacin. Of the Shigella strains, one was resistant to nalidixic acid but 81% to trimethoprim- sulfamethoxazole, 63% to streptomycin and 50% to ampicillin. Most of all the other Salmonella and Shigella strains were sensitive to all antimicrobials tested. CONCLUSION: Rotaviruses and diarrheal E. coli were the most predominant pathogens associated with acute diarrhea in Burkinabe children. Constant antimicrobial surveillance is warranted to observe for the emergence of enteric bacteria resistant to antimicrobials that are important in treatment also of severe infections.

Diagnostic Performance and Tolerability of Saliva and Nasopharyngeal Swab Specimens in the Detection of SARS-CoV-2 by RT-PCR.

Saliva is a promising alternative for a nasopharyngeal swab (NPS) in specimen collection to detect SARS-CoV-2. We compared the diagnostic performance and tolerability of saliva collection versus NPS in a clinical setting. Paired NPS and saliva specimens were collected sequentially from participants (n = 250) at the Turku University Hospital drive-in coronavirus testing station in the spring of 2022, with Omicron BA.2 as the dominant SARS-CoV-2 variant. Discomfort and preference for the sampling method were assessed. The specimens were analyzed for SARS-CoV-2 using real-time multiplex reverse transcriptase PCR (RT-PCR) with a laboratory-developed test (LDT) and two commercial kits (PerkinElmer SARS-CoV-2 and PerkinElmer SARS-CoV-2 Plus) for several target genes. Among the 250 participants, 246 had respiratory symptoms. With LDT, SARS-CoV-2 was detected in 135 and 134 participants from NPS and saliva, respectively. Of the 250 specimens, 11 gave a discordant outcome, resulting in excellent agreement between the specimen types (Cohen's kappa coefficient of 0.911; P = 0.763). The cycle threshold (CT) values of LDT and commercial kit target genes were significantly lower from NPS than from saliva. A total of 172 (69%) participants assessed saliva sampling as more tolerable than NPS (P < 0.0001). Our findings present saliva as an applicable alternative for SARS-CoV-2 diagnostics. However, the lower CT values obtained from NPS indicate that NPS may be a slightly more sensitive specimen type. Participants preferred saliva sampling, although delivering an adequate volume of saliva was challenging for some participants. IMPORTANCE The extensive testing of SARS-CoV-2 is vital in controlling the spread of COVID-19. The reference standard for specimen collection is a nasopharyngeal swab (NPS). However, the discomfort of NPS sampling, the risk of nosocomial infections, and global material shortages have accelerated the development of alternative testing methods. Our study demonstrates that patients tolerate saliva sampling better than NPS. Of importance, although the RT-PCR qualitative test results seem to correspond between NPS and saliva, we show significantly lower CT values for NPS, compared to saliva, thus contradicting the suggested superiority of the saliva specimen over NPS in the detection of the Omicron variants of SARS-CoV-2. Future research is still required to enable individual planning for specimen collection and to determine the effects of different SARS-CoV-2 variants on the sensitivity of the saliva matrix.

Inaccuracy of the disk diffusion method compared with the agar dilution method for susceptibility testing of Campylobacter spp.

The agar dilution method has been standardized by the CLSI for the susceptibility testing of Campylobacter species, and according to these standards, the disk diffusion method should be used only in screening for macrolide and ciprofloxacin resistance. Nevertheless, the disk diffusion test is currently widely used, since it is easy to perform in clinical microbiology laboratories. In this study, the disk diffusion method was compared to the agar dilution method by analyzing the in vitro activities of seven antimicrobial agents against 174 Campylobacter strains collected in Finland between 2003 and 2008. Recommendations of the CLSI were followed using Mueller-Hinton agar plates with 5% of sheep blood. For each strain, the disk diffusion tests were performed two to four times. Of the 33 erythromycin-resistant strains (MIC, ≥16 µg/ml), 24 (73%) constantly showed a 6-mm erythromycin inhibition zone (i.e., no inhibition), while for seven strains the inhibition zone varied from 6 to 44 mm in repeated measurements. Among the 141 erythromycin-susceptible strains (MIC, <16 µg/ml), erythromycin inhibition zones varied between 6 and 61 mm. Of the 87 ciprofloxacin-resistant strains, 47 (54%) showed 6-mm inhibition zones, while 40 strains showed inhibition zones between 6 and 60 mm. Significant differences between the repetitions were observed in the disk diffusion for all antimicrobial agents and all strains except for the macrolide-resistant strains regarding the macrolides. For 17 (10%) strains, the variation in repeated measurements was substantial. These results show that the disk diffusion method may not be a reliable tool for the susceptibility testing of Campylobacter spp. Further studies are needed to assess whether the disk diffusion test could be improved or whether all susceptibilities of campylobacters should be tested using an MIC-based method.

Carbapenemase-producing Enterobacteriaceae in Finland: the first years (2008-11).

OBJECTIVES: Carbapenemase-producing Enterobacteriaceae (CPE) are becoming a global problem; they are often resistant to nearly all available antibiotics. Here we report details on all Finnish CPE isolates found until the end of 2011: carbapenemase genes, travel history and multilocus sequence typing (MLST) data. METHODS: Enterobacteriaceae sent to the Antimicrobial Resistance Unit of the National Institute for Health and Welfare were tested for susceptibility to carbapenems, screened for carbapenemases by PCR and isolates with decreased susceptibility to carbapenems were tested for hydrolysis of imipenem. Carbapenemase-producing Escherichia coli and Klebsiella pneumoniae isolates were typed by MLST. RESULTS: In all, 26 CPE strains were found from 25 patients: 10 with OXA-48-like enzymes, 5 with KPC, 4 with VIM, 3 with NDM, 3 with IMI/NMC-A and 1 with GES-14. The species were K. pneumoniae (n = 16), E. coli (n = 6), Enterobacter cloacae (n = 3) and Raoultella planticola (n = 1). Of the 25 patients, 18 had a known travel history/hospital transfer from abroad. Local spread/transmission was suspected in 2011, but there were no hospital outbreaks. The K. pneumoniae multilocus sequence types ST258, ST182, ST147, ST244, ST14, ST13, ST383, ST101 and ST15, and the E. coli sequence types ST38 and ST90 were found. Many of these are global epidemic clones. CONCLUSIONS: CPE strains are increasingly found in Finland, but still at a very low prevalence.

Appendiceal microbiome in uncomplicated and complicated acute appendicitis: A prospective cohort study.

BACKGROUND: Uncomplicated and complicated acute appendicitis seem to be two different forms of this common abdominal emergency. The contribution of appendiceal microbiota to appendicitis pathogenesis has been suggested, but differences between uncomplicated and complicated appendicitis are largely unknown. We compared the appendiceal microbiota in uncomplicated and complicated acute appendicitis. METHODS: This prospective single-center clinical cohort study was conducted as part of larger multicenter MAPPAC trial enrolling adult patients with computed tomography or clinically confirmed uncomplicated or complicated acute appendicitis. The microbial composition of the appendiceal lumen was determined using 16S rRNA gene amplicon sequencing. RESULTS: Between April 11, 2017, and March 29, 2019, 118 samples (41 uncomplicated and 77 complicated appendicitis) were available. After adjusting for age, sex, and BMI, alpha diversity in complicated appendicitis was higher (Shannon p = 0.011, Chao1 p = 0.006) compared to uncomplicated appendicitis. Microbial compositions were different between uncomplicated and complicated appendicitis (Bray-Curtis distance, P = 0.002). Species poor appendiceal microbiota composition with specific predominant bacteria was present in some patients regardless of appendicitis severity. CONCLUSION: Uncomplicated and complicated acute appendicitis have different appendiceal microbiome profiles further supporting the disconnection between these two different forms of acute appendicitis. STUDY REGISTRATION: ClinicalTrials.gov NCT03257423.

Blood culture positivity in patients with acute appendicitis: A propensity score-matched prospective cohort study.

BACKGROUND AND OBJECTIVE: The prevalence of bacteremia in acute appendicitis is unknown. We aimed to assess prevalence and predictive factors of bacteremia in adult patients with appendicitis. METHODS: In this prospective propensity score-matched cohort study, patients were recruited as part of one single-center prospective observational study assessing appendicitis microbiology in concurrence with two randomized controlled trials on non-operative treatment of uncomplicated acute appendicitis. All patients evaluated for enrollment in these three trials between April 2017 and December 2018 with both a confirmed diagnosis of appendicitis and available blood culture on admission were included in this study. Potential predictive factors of bacteremia (age, sex, body mass index (BMI), body temperature, C-reactive protein (CRP), leukocyte count, comorbidities, symptom duration, and appendicitis severity) were assessed. Prevalence of bacteremia was determined by all available blood cultures followed by propensity score matching using sex, age, BMI, CRP, leukocyte count, and body temperature of the patients without available blood culture. RESULTS: Out of the 815 patients with appendicitis, 271 patients had available blood culture and the prevalence of bacteremia was 12% (n = 33). Based on propensity score estimation, the prevalence of bacteremia in the whole prospective appendicitis cohort was 11.1%. Bacteremia was significantly more frequent in complicated acute appendicitis (15%; 29/189) compared with uncomplicated acute appendicitis (5%; 4/82) (p = 0.015). Male sex (p = 0.024) and higher body temperature (p = 0.0044) were associated with bacteremia. CONCLUSIONS: Estimated prevalence of bacteremia in patients with acute appendicitis was 11.1%. Complicated appendicitis, male sex, and higher body temperature were associated with bacteremia in acute appendicitis.

Antimicrobial resistance among bacteria isolated from urinary tract infections in females in Namibia, 2016-2017.

BACKGROUND: The emergence of antimicrobial resistance (AMR) among bacterial pathogens demands a local understanding of the epidemiological situation. This information is needed both for clinical treatment decision-making purposes as well as for the revision of current care guidelines. Clinical AMR data from Namibia is sparse, whilst urinary tract infections remain not only widespread but they disproportionally affect females. This paper aims to describe the national antimicrobial resistance situation of major bacterial uropathogens in females within the 14 Namibian regions. METHOD: Retrospective countrywide information on clinical urine cultures performed in females in Namibia in 2016-2017 was obtained from the national public health laboratory, Namibia Institute of Pathology (NIP). The data set included both microbiological findings as well as antimicrobial susceptibility test (AST) results. The AST was done as per the Clinical and Laboratory Standards Institute (CLSI) guidelines. Resistance to 3rd generation cephalosporins was indicative of Extended Spectrum-ß-lactamase (ESBL) production. Data analysis was done with WHONET using expert interpretation rules. RESULTS: In total, 22,259 urinary cultures were performed, of which 13,673 (61.4%) were culture positive. Gram-negative bacterial species accounted for 72.6% of the findings. The most common pathogens identified were Escherichia coli, Klebsiella pneumoniae and Proteus mirabilis. Most of these were from young females, with a median age ranging from 28 to 32 years for the various pathogens. Resistance to ampicillin was 77.7% in E. coli and 84.9% in K. pneumoniae. In E. coli, resistance to 1st line empiric therapy antibiotic, nitrofurantoin, was below 13%, except for one region that showed 59.2% resistance. Resistance to third generation cephalosporin (3GC) was used as a proxy for ESBL production. By year 2017, 3GC resistance was 22%, 31.4% and 8.3% for E. coli, K. pneumoniae and P. mirabilis, respectively. CONCLUSION: We report high resistance to ampicillin, quinolones and sulfamethoxazole-trimethoprim amongst E. coli. Resistance rates to third-generation cephalosporins was also concerningly high at 22%. Resistance to carbapenems was low. However, superiority of nitrofurantoin was found, which provides rational support for the usefulness of nitrofurantoin as an empiric therapy regimen for the treatment of urinary tract infections in this setting.

Ribosomal mutations as the main cause of macrolide resistance in Campylobacter jejuni and Campylobacter coli.

The aim of this study was to examine macrolide resistance mutations in Campylobacter species. In 76 strains studied, point mutation A to G at position 2059 of the 23S rRNA gene was detected in 30 of the 33 erythromycin-resistant strains. An amino acid insertion in the ribosomal protein L22 was found in one resistant strain without a 23S rRNA mutation. The A2059G mutation is the main cause of macrolide resistance in Campylobacter species.

Diagnostic Efficacy and Tolerability of Molded Plastic Nasopharyngeal Swab (FinSwab) Compared to Flocked Nylon Swab in Detection of SARS-CoV-2 and Other Respiratory Viruses.

The supply of testing equipment is vital in controlling the spread of SARS-CoV-2. We compared the diagnostic efficacy and tolerability of molded plastic (FinSwab; Valukumpu, Finland) versus flocked nylon (FLOQSwab; Copan, Italy) nasopharyngeal swabs in a clinical setting. Adults (n = 112) with suspected symptomatic COVID-19 infection underwent nasopharyngeal sampling with FinSwab and FLOQSwab from the same nostril at a drive-in coronavirus testing station. In a subset of 36 patients the samples were collected in a randomized order to evaluate the discomfort associated with sampling. SARS-CoV-2 and 16 other respiratory viruses, as well as human ß-actin mRNA were analyzed by using reverse transcriptase PCR (RT-PCR) assays. Among the 112 patients (mean age, 38 [standard deviation (SD), 14] years) ß-actin mRNA was found in all samples. There was no difference in the ß-actin mRNA cycle threshold (CT) values between FinSwab (mean, 22.3; SD, 3.61) and FLOQSwab (mean, 22.1; SD, 3.50; P = 0.46) swabs. There were 31 virus-positive cases (26 rhinovirus, 4 SARS-CoV-2, and 1 coronavirus-OC43), 24 of which were positive in both swabs; 3 rhinovirus positives were only found in the FinSwab, and similarly 4 rhinovirus positives were only found in the FLOQSwab. Rhinovirus CT values were similar between swab types. Of the 36 patients, 22 (61%) tolerated the sampling with the FinSwab better than with the FLOQSwab (P = 0.065). The molded plastic nasopharyngeal swab (FinSwab) was comparable to the standard flocked swab in terms of efficacy for respiratory virus detection and tolerability of sampling. IMPORTANCE We demonstrate that a molded plastic swab is a valid alternative to conventional brush-like swabs in collection of a nasopharyngeal sample for virus diagnostics.