Peptoniphilus faecalis sp. nov., isolated from swine faeces.

An obligately anaerobic, Gram-positive, non-motile, coccus-shaped bacterial strain designated AGMB00490T was isolated from swine faeces. 16S rRNA gene sequence-based phylogenetic analysis indicated that the isolate belongs to the genus Peptoniphilus and that the most closely related species is Peptoniphilus gorbachii WAL 10418T (=KCTC 5947T, 97.22 % 16S rRNA gene sequence similarity). Whole genome sequence analysis determined that the DNA G+C content of strain AGMB00490T was 31.2 mol% and moreover that the genome size and numbers of tRNA and rRNA genes were 2 129 517 bp, 34 and 10, respectively. Strain AGMB00490T was negative for oxidase and urease; positive for catalase, indole production, arginine arylamidase, leucine arylamidase, tyrosine arylamidase and histidine arylamidase; and weakly positive for phenylalanine arylamidase and glycine arylamidase. The major cellular fatty acids (>10 %) of the isolate were determined to be C16 : 0 and C18 : 1 ω9c. Strain AGMB00490T produced acetic acid as a major end product of metabolism. Accordingly, phylogenetic, physiologic and chemotaxonomic analyses revealed that strain AGMB00490T represents a novel species for which the name Peptoniphilus faecalis sp. nov. is proposed. The type strain is AGMB00490T (=KCTC 15944T=NBRC 114159T).

In vitro susceptibility of ceftaroline against clinically important Gram-positive cocci, Haemophilus species and Klebsiella pneumoniae in Taiwan: Results from the Antimicrobial Testing Leadership and Surveillance (ATLAS) in 2012-2018.

BACKGROUND/PURPOSE: Ceftaroline, with a unique activity against methicillin-resistant Staphylococcus aureus (MRSA), was not launched in Taiwan before 2019. The in vitro susceptibility data of ceftaroline against important Taiwanese pathogens are lacking. METHODS: The in vitro susceptibility of ceftaroline against important pathogens collected from 2012 through 2018 were extracted from the Antimicrobial Testing Leadership and Surveillance program. Broth microdilution method was used to determine the minimum inhibitory concentrations (MICs) to ceftaroline against all isolates. RESULTS: During the study period, the in vitro data regarding isolates of S. aureus (n = 2049), Staphylococcus epidermidis (n = 185), Streptococcus pneumoniae (n = 334), Streptococcus pyogenes (n = 170), Haemophilus influenzae (n = 75), Haemophilus parainfluenzae (n = 10) and Klebsiella pneumoniae (n = 680) regardless of hospital sites of collection were analyzed. Among the S. aureus isolates studied, 19.4% showed MICs of 1 mg/L to ceftaroline, and 4.4% showed in vitro susceptible-dose dependent to ceftaroline (all MICs, 2 mg/L). Most of other Gram-positive cocci, all H. influenzae and H. parainfluenzae isolates were susceptible to ceftaroline. By contrast, about one-third (35.9%) of K. pneumoniae isolates, irrespective of infection sources, exhibited non-susceptibility to ceftaroline (MIC range, 0.015-256 mg/L; MIC50 and MIC90 values, 0.12 and 256 mg/L, respectively). CONCLUSIONS: From the pharmacodynamic perspectives, the ceftaroline dosage of 600 mg as a 2-h intravenous infusion every 8 h is effective against all S. aureus and other Gram-positive isolates regardless of acquisition sites in Taiwan. Before ceftaroline is prescribed in treatment of the patient with Gram-negative infection, a cautious evaluation about patient's healthcare-associated factor is warranted.

Rapid multiplex detection of the resistance genes mecA, vanA and vanB from Gram-positive cocci-positive blood cultures using a PCR-dipstick technique.

Introduction. Among the causative agents of bloodstream infections (BSIs), methicillin-resistant Staphylococcus aureus (MRSA) or vancomycin-resistant Enterococcus (VRE) are the key causative pathogens. Their rapid detection directly from Gram-positive cocci-positive blood culture specimens will promote timely treatment and help to implement effective infection control measures.Aim. We aim to develop a PCR-dipstick technique for the rapid detection of MRSA and VRE directly from positive blood culture specimens.Methodology. PCR-dipstick is a PCR-based multiplex detection technique where DNA-DNA hybridization is employed, and the results are interpreted with the naked eye. It was designed to target three drug resistance genes: mecA in MRSA and vanA/vanB in VRE from positive blood culture specimens. A total of 120 clinical isolates were used to evaluate the sensitivity and specificity of PCR-dipstick. Then, PCR-dipstick was examined for MRSA and VRE detection directly from positive blood cultures.Results. PCR-dipstick showed 100 % sensitivity and specificity in detecting mecA, vanA and vanB genes directly from bacterial colonies in comparison with multiplex PCR for genomic DNA followed by agarose gel electrophoresis. Further, it could differentially detect multiple resistant genes in pooled bacterial colonies (n=10). Ultimately, PCR-dipstick could detect MRSA and VRE in positive blood cultures in ~3 h.Conclusion. The results of the current study substantiate that PCR-dipstick can be used as an efficient detection system for MRSA and VRE directly from Gram-positive cocci-positive blood cultures. Its affordability and rapidity indicate that PCR-dipstick can be an effective tool for controlling nosocomial pathogens.

Surgical site infection after hip replacement due to a novel Peptoniphilus species, provisionally named 'Peptoniphilus nemausus' sp. nov.

We report a case of surgical site infection after total hip prosthesis replacement due to an ofloxacin-resistant Peptoniphilus isolate belonging to an unknown species for which the name 'Peptoniphilus nemausus' sp. nov. is proposed. Follow-up was favourable under clindamycin and rifampin for 3 months in this patient whom had a Proteus mirabilis infection treated by fluoroquinolone.

Comparison of two methods skipping cell lysis and protein extraction for identification of bacteria from blood cultures by matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry / Comparación de dos métodos que eluden la lisis celular y la extracción de proteínas para la identificación de bacterias crecidas en hemocultivos mediante espectrometría de masas MALDI-TOF

OBJECTIVE: Matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry (MALDI-TOF MS) is widely used for fast identification of bacteria from blood cultures (BC). We compared the performance of two procedures, one including a pre-enrichment step in brain heart infusion and the other a direct method using vacutainer separator gel tubes (DI), for identification of bacteria from blood cultures by MALDI-TOF MS. MATERIAL AND METHODS: We first prepared a training set of 20 simulated bacteremia specimens, including 10 Gram-negative and 10 Gram-positive species. A total of 145 non-consecutive BCs flagged as positive (68 Gram-negative rods, and 77 Gram-positive cocci) were prospectively analyzed (validation set). RESULTS: A total of 82% and 49% of isolates were correctly identified to the species level by the respective methods. CONCLUSION: The pre-enrichment method outperformed the DI method for identification of virtually all bacterial species included in the panels

OBJETIVO: La espectrometría de masas MALDI-TOF se utiliza comúnmente para la identificación rápida de bacterias crecidas en hemocultivos (HC). Hemos comparado el rendimiento de dos procedimientos, uno que incluye un paso previo del enriquecimiento en caldo corazón-cerebro y el otro un método directo que usa tubos vacutainer con gel separador (DI), para la identificación de bacterias a partir de hemocultivos mediante MALDI-TOF MS. MATERIAL Y MÉTODOS: Analizamos prospectivamente un total de 145 HC no consecutivos (68 con crecimiento de bacterias gramnegativas y 77 de cocos grampositivos). RESULTADOS: Un total de 82% y 49% de los aislamientos fueron identificados correctamente a nivel de especie por los dos métodos, respectivamente. CONCLUSIÓN: El rendimiento del método de pre-enriquecimiento en caldo corazón-cerebro fue mejor que el del método DI para la identificación de la práctica totalidad de las especies bacterianas incluidas en el panel de estudio

Comparison of two methods skipping cell lysis and protein extraction for identification of bacteria from blood cultures by matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry.

OBJECTIVE: Matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry (MALDI-TOF MS) is widely used for fast identification of bacteria from blood cultures (BC). We compared the performance of two procedures, one including a pre-enrichment step in brain heart infusion and the other a direct method using vacutainer separator gel tubes (DI), for identification of bacteria from blood cultures by MALDI-TOF MS. METHODS: We first prepared a training set of 20 simulated bacteremia specimens, including 10 Gram-negative and 10 Gram-positive species. A total of 145 non-consecutive BCs flagged as positive (68 Gram-negative rods, and 77 Gram-positive cocci) were prospectively analyzed (validation set). RESULTS: A total of 82% and 49% of isolates were correctly identified to the species level by the respective methods. CONCLUSIONS: The pre-enrichment method outperformed the DI method for identification of virtually all bacterial species included in the panels.

Gut microbiota development of preterm infants hospitalised in intensive care units.

Gut microbiome development affects infant health and postnatal physiology. The gut microbe assemblages of preterm infants have been reported to be different from that of healthy term infants. However, the patterns of ecosystem development and inter-individual differences remain poorly understood. We investigated hospitalised preterm infant gut microbiota development using 16S rRNA gene amplicons and the metabolic profiles of 268 stool samples obtained from 17 intensive care and 42 term infants to elucidate the dynamics and equilibria of the developing microbiota. Infant gut microbiota were predominated by Gram-positive cocci, Enterobacteriaceae or Bifidobacteriaceae, which showed sequential transitions to Bifidobacteriaceae-dominated microbiota. In neonatal intensive care unit preterm infants (NICU preterm infants), Staphylococcaceae abundance was higher immediately after birth than in healthy term infants, and Bifidobacteriaceae colonisation tended to be delayed. No specific NICU-cared infant enterotype-like cluster was observed, suggesting that the constrained environment only affected the pace of transition, but not infant gut microbiota equilibrium. Moreover, infants with Bifidobacteriaceae-dominated microbiota showed higher acetate concentrations and lower pH, which have been associated with host health. Our data provides an in-depth understanding of gut microbiota development in NICU preterm infants and complements earlier studies. Understanding the patterns and inter-individual differences of the preterm infant gut ecosystem is the first step towards controlling the risk of diseases in premature infants by targeting intestinal microbiota.

Clinical and microbiological features of bacteraemia with Gram-positive anaerobic cocci: a population-based retrospective study.

OBJECTIVES: Gram-positive, anaerobic cocci (GPAC) can cause infections in humans. Only a few cases of bacteraemia with GPAC have been reported. We describe the clinical and microbiological characteristics of GPAC bacteraemia. METHODS: A retrospective population-based study of GPAC bacteraemia 2012-2016 in southern Sweden was performed. GPAC were identified using matrix-associated laser desorption ionization time-of-flight mass spectrometry or 16S rRNA gene sequencing. Etests were used to determine antibiotic susceptibilities. Data on patient and infection characteristics, treatment, and outcome were collected from the medical records. RESULTS: A total of 226 episodes of GPAC bacteraemia in adults were studied; this corresponds to an annual incidence of 3.4 cases per 100,000 persons per year. The bacteria identified were Anaerococcus spp. (n = 43), Atopobium spp. (n = 7), Blautia spp. (n = 1), Finegoldia spp. (n = 15), Parvimonas spp. (n = 100), Peptoniphilus spp. (n = 52), Peptostreptococcus spp. (n = 2), and Ruminococcus spp. (n = 9) of which 200 isolates were identified to the species level. Resistance to imipenem and piperacillin was not identified, whereas resistance among the 229 isolates to penicillin was detected in four, to metronidazole in six, and clindamycin in 16 isolates. The median age of patients was 73 years (55-83, IQR), 57% were male and comorbidities were common. Fifty-one per cent of infections were polymicrobial. In 60% of cases a focus of infection was identified. Forty per cent of patients had either organ dysfunction or shock. The 30-day mortality was 11%, and nosocomial infections were over-represented among the deceased. CONCLUSIONS: GPAC bacteraemia is much more common than previously reported. GPAC-bacteraemia is a condition with significant mortality mainly affecting elderly persons with comorbidities.

Asymptomatic carriage of antibiotic-resistant Gram-positive cocci among different background populations in East Timor, Southeast Asia.

Dissemination of pathogenic multiresistant bacteria is of public health concern. Reliable data can be difficult to obtain, especially in developing countries. This work aimed to characterize the skin and oropharyngeal microbiota, as well as their antimicrobial resistance profiles, of East-Timor populations to identify potentially pathogenic Gram-positive cocci. In order to assess the prevalence of pathogenic bacteria in East-Timor, the oropharyngeal and skin microbiota of 74 individuals was characterized. Gram-positive cocci were evaluated and their antimicrobial resistance profiles were determined. A total of 228 oropharyngeal and 278 skin samples were obtained. The population consisted of 36.5% of asymptomatic carriers of Gram-positive cocci. Kocuria rosea (n = 7, 19.4%), Staphylococcus spp. (n = 6, 16.7%), and Micrococcus luteus (n = 6, 16.7%) were isolated, among others. Antimicrobial resistance levels ranged between 0% and 36.1%, and a multiresistance profile was observed in one third of the isolates. Gram-positive cocci colonization was associated with age group. Prevalence of multiresistant isolates was higher in males who were sampled at the refugee camp. Results show that the prevalence of antimicrobial resistance on East Timor may be underestimated. This study represents the first step toward the full characterization of potential pathogenic Gram-positive cocci present in the populations from East Timor.

Characterization of a novel Gram-stain-positive anaerobic coccus isolated from the female genital tract: Genome sequence and description of Murdochiella vaginalis sp. nov.

Strain Marseille-P2341T , a nonmotile, nonspore-forming, Gram-stain-positive anaerobic coccus, was isolated in the vaginal specimen of a patient with bacterial vaginosis using culturomics. Its growth occurred at temperatures ranging from 25 to 42°C, with pH between 6.5 and 8.5, and at NaCl concentrations lower than 5%. The major fatty acids were C18:1n9 (27.7%) and C16:0 (24.4%). Its genome is 1,671,491 bp long with 49.48 mol% of G+C content. It is composed of 1,501 genes: 1,446 were protein-coding genes and 55 were RNAs. Strain Marseille-P2341T shared 97.3% of 16S rRNA gene sequence similarity with Murdochiella asaccharolytica, the phylogenetically closest species. These results enabled the classification of strain Marseille-P2341T as a new species of the genus Murdochiella for which we proposed the name Murdochiella vaginalis sp. nov. The type strain is strain Marseille-P2341T (=DSM 102237, =CSUR P2341).

Is it possible to perform bacterial identification and antimicrobial susceptibility testing with a positive blood culture bottle for quick diagnosis of bloodstream infections?

INTRODUCTION: Bloodstream infections can be fatal, and timely identification of the etiologic agent is important for treatment. METHODOLOGY: An alternative method, consisting of direct identification and susceptibility testing of blood culture bottles using the automated VITEK 2® system, was assessed. RESULTS: All 37 of the Gram-negative bacilli (GNB) identifications and 57.1% of the 28 Gram-positive cocci (GPC) identifications matched those obtained with standard methods. In susceptibility testing, the agreement was greater than 90%. CONCLUSIONS: This alternative methodology may assist in the early identification and susceptibility testing of GNB. Further research is necessary to develop appropriate methods for GPC.

Is it possible to perform bacterial identification and antimicrobial susceptibility testing with a positive blood culture bottle for quick diagnosis of bloodstream infections?

Abstract INTRODUCTION: Bloodstream infections can be fatal, and timely identification of the etiologic agent is important for treatment. METHODOLOGY: An alternative method, consisting of direct identification and susceptibility testing of blood culture bottles using the automated VITEK 2® system, was assessed. RESULTS: All 37 of the Gram-negative bacilli (GNB) identifications and 57.1% of the 28 Gram-positive cocci (GPC) identifications matched those obtained with standard methods. In susceptibility testing, the agreement was greater than 90%. CONCLUSIONS: This alternative methodology may assist in the early identification and susceptibility testing of GNB. Further research is necessary to develop appropriate methods for GPC.

Pan-genome analysis of the genus Finegoldia identifies two distinct clades, strain-specific heterogeneity, and putative virulence factors.

Finegoldia magna, a Gram-positive anaerobic coccus, is an opportunistic pathogen, associated with medical device-related infections. F. magna is the only described species of the genus Finegoldia. We report the analysis of 17 genomes of Finegoldia isolates. Phylogenomic analyses showed that the Finegoldia population can be divided into two distinct clades, with an average nucleotide identity of 90.7%. One clade contains strains of F. magna, whereas the other clade includes more heterogeneous strains, hereafter tentatively named "Finegoldia nericia". The latter species appears to be more abundant in the human microbiome. Surface structure differences between strains of F. magna and "F. nericia" were detected by microscopy. Strain-specific heterogeneity is high and previously identified host-interacting factors are present only in subsets of "F. nericia" and F. magna strains. However, all genomes encode multiple host factor-binding proteins such as albumin-, collagen-, and immunoglobulin-binding proteins, and two to four copies of CAMP (Christie-Atkins-Munch-Petersen) factors; in accordance, most strains show a positive CAMP reaction for co-hemolysis. Our work sheds new light of the genus Finegoldia and its ability to bind host components. Future research should explore if the genomic differences identified here affect the potential of different Finegoldia species and strains to cause opportunistic infections.

Characterization and susceptibility of streptococci and enterococci isolated from Nile tilapia (Oreochromis niloticus) showing septicaemia in aquaculture and wild sites in Egypt.

BACKGROUND: The present investigation was an endeavor into the elucidation of the disease-causing pathogen of streptococcosis in Nile tilapia (Oreochromis niloticus) in Egypt affecting adult fish cultured and wild fish in the Nile river. Fish were obtained from commercial fishermen, collected as part of their routine fishing activities. The researchers observed the routine fishing process and selected fish for use in the study, at the point of purchase from the fisherman. RESULTS: Diseased fish showed exophthalmia with accumulation of purulent and haemorrhagic fluid around eyes, and ventral petechial haemorrhages. The Post mortem examination revealed, abdominal fat haemorrhage, pericarditis and enlargement of the liver, spleen and kidney. Gram-stained smears revealed the presence of Gram-positive cocci, ß-hemolytic, oxidase and catalase negative. Analysis of the 16S rRNA gene confirmed that the 17 tilapia isolates studied were 6/17 Enterococcus faecalis, 2/17 Enterococcus gallinarum, 3/17 Streptococcus pluranimalium, 2/17 Aerococcus viridans, 1/17 isolate of each Streptococcus dysgalactiae, Streptococcus anginosus, Lactococcus garvieae and Granulicetella elegans/Leuconostoc mesenteroides cremoris. It should be noted that there was no mixed infection. Multiple resistance was observed and the most frequent antibiotic combination was penicillin, ampicillin, vancomycin, chloramphenicol, rifampicin, ofloxacin, clindamycin, erythromycin and tetracycline representing eight classes. CONCLUSIONS: Consequently, we concluded that Streptococcus species are an emerging pathogen for Nile tilapia aquaculture in Egypt and to be considered as a new candidate in the warm water fish diseases in Egypt with special reference to L. garvieae, S. dysgalactiae in addition to L. mesenteroides cremoris which was not reported before from tilapia and taking into consideration their zoonotic implications for public health.

[Characterization of microbial flora in patients suspected of having urogenital tuberculosis].

INTRODUCTION: In the structure of tuberculosis morbidity, urogenital tuberculosis (UGT) ranks second or third only to pulmonary tuberculosis. Every fourth patient has the stage of cavern formation at first presentation. Seventy five percent of nephrotuberculosis cases co-occur with nonspecific pyelonephritis, which excludes "sterile pyuria". We aimed to determine the microbial spectrum of urine and gonadal appendages in patients with suspected UGT and to investigate the susceptibility of the isolated microorganisms to the main antibacterial drugs. MATERIAL AND METHODS: The study investigated the spectrum of pathogenic microflora isolated from patients admitted to the urogenital clinic of the TB Research Institute from January 1, 2012 to September 30, 2016 to rule out UGT. Microorganism species were identified by time-of-flight mass spectrometry using the microbiological analyzer Phoenix 100 (Becton Dickinson, USA). Antibiotic resistance was determined using the Phoenix 100 microbiological analyzer (Becton Dickinson, USA). RESULTS: A total of 3004 bacteriological tests for nonspecific microflora were performed during the analyzed period. In the structure of pathogens, E. coli comprised about half of the cases thus confirming its role as the leading uropathogen. Only piperacillin/tazobactam and nitrofurantoin provided relatively plausible antimicrobial resistance rates, for other antibacterial drugs the rates of susceptible strains progressively decreased and by 2016 dropped to 40% and lower. CONCLUSION: Our findings cannot be extrapolated to the entire population since patients presenting for differential diagnosis receive multiple courses of treatment with various antibacterial drugs, which led to the selection of resistant strains. The findings emphasize the need for a strict selection of antibiotics for urogenital infection empirical therapy. In the absence of response, the patient should be immediately examined for tuberculosis using molecular and genetic diagnostic techniques.

Evaluation of Three Bacterial Identification Systems for Species Identification of Bacteria Isolated from Bovine Mastitis and Bulk Tank Milk Samples.

A study was conducted to evaluate Sensititre® Automated Reading and Incubation System 2x System (ARIS), API® (API), and Bruker MALDI-TOF MS (MALDI) bacterial species identification systems using 132 diverse bacterial isolates from bovine milk samples and bulk tank milk received at the Penn State Animal Diagnostic Laboratory. The results were compared with 16S rRNA gene sequence analysis, which served as the reference method for species identification. The ARIS, API, and MALDI identified 0%, 40%, and 33.4% of species classified as Gram-positive rod isolates belonging to genera Arthrobacter, Bacillus, Brachybacterium, Brevibacterium, and Corynebacterium, respectively. It was observed that 76.5%, 93.9%, and 96.9% of catalase-negative, Gram-positive cocci (n = 33; Aerococcus, Enterococcus, Lactococcus, Streptococcus) were correctly identified to the species level by ARIS, API, and MALDI, respectively, while 33.4%, 84.5%, and 97.7% of catalase-positive, Gram-positive cocci (n = 45; Kocuria, Staphylococcus) were correctly identified to their species by ARIS, API, and MALDI, respectively. A total of 48 isolates (Acinetobacter, Citrobacter, Enterobacter, Escherichia, Klebsiella, Pantoea, Pasteurella, Providencia, Pseduomonas, Serratia) of Gram-negative bacteria were examined, of which 85.4%, 93.7%, and 95.8% of the isolates were correctly identified to the species level by ARIS, API, and MALDI, respectively. In our laboratory, the MALDI had the least costs associated with consumables and reagents compared to ARIS, API, and 16S rRNA identification methods. Identification of bacterial species was accomplished in <2 h using MALDI and 24 h for ARIS, API, and 16S rRNA identification systems.

Use of PNA FISH for blood cultures growing Gram-positive cocci in chains without a concomitant antibiotic stewardship intervention does not improve time to appropriate antibiotic therapy.

Peptide nucleic acid fluorescence in situ hybridization (PNA FISH) is a rapid diagnostic assay that can identify certain organisms growing in blood cultures 30-90 min from the time of positive Gram-stain. Existing studies have demonstrated a clinical utility with this assay when antibiotic stewardship programs assist clinicians with interpreting the results. However, the benefit of these rapid assays in the absence of concomitant antibiotic stewardship involvement is unclear. In this randomized study of 220 patients with enterococcal or streptococcal bacteremia, we found that PNA FISH, in the absence of concomitant input from an antibiotic stewardship program, had no impact on time to effective or optimal therapy, length of hospital stay, or in-hospital mortality. Our results suggest that in the absence of guidance from an antibiotic stewardship program, the clinical benefits of rapid diagnostic microbiological tools may be reduced.

Peptoniphilus catoniae sp. nov., isolated from a human faecal sample from a traditional Peruvian coastal community.

A novel Gram-stain-positive, coccus-shaped, obligately anaerobic bacterium was isolated from a faecal sample obtained from an individual in a traditional community located off the southern coast of Peru. Comparative 16S rRNA gene sequence analysis showed the novel bacterium belonged to the genus Peptoniphilus but showed no particular relationship with any species, demonstrating less than 91 % 16S rRNA gene sequence similarity with all members of the genus. The major cellular fatty acids of the novel isolate were determined to be C10 : 0, C14 : 0, C16 : 0, C18 : 1ω9c and C18 : 2ω6,9c/anteiso-C18 : 0. The DNA G+C content was 34.4 mol%. End-products of metabolism from peptone-yeast-glucose broth (PYG) were determined to be acetate and butyrate. Based on the phenotypic, chemotaxonomic and phylogenetic results, the organism represents a novel species of the genus Peptoniphilus, for which the name Peptoniphilus catoniae sp. nov. is proposed. The type strain is M6.X2DT ( = DSM 29874T = CCUG 66798T).

Urine flow cytometry can rule out urinary tract infection, but cannot identify bacterial morphologies correctly.

The diagnosis of urinary tract infection (UTI) by urine culture is a time-consuming and costly procedure. Usage of a screening method, to identify negative samples, would therefore affect time-to-diagnosis and laboratory cost positively. Urine flow cytometers are able to identify particles in urine. Together with the introduction of a cut-off value, which determines if a urine sample is subsequently cultured or not, the number of cultures can be reduced, while maintaining a low level of false negatives and a high negative predictive value. Recently, Sysmex developed additional software for their urine flow cytometers. Besides measuring the number of bacteria present in urine, information is given on bacterial morphology, which may guide the physician in the choice of antibiotic. In this study, we evaluated this software update. The UF1000i classifies bacteria into two categories: 'rods' and 'cocci/mixed'. Compared to the actual morphology of the bacterial pathogen found, the 'rods' category scores reasonably well with 91% chance of classifying rod-shaped bacteria correctly. The 'cocci/mixed' category underperforms, with only 29% of spherical-shaped bacteria (cocci) classified as such. In its current version, the bacterial morphology software does not classify bacteria, according to their morphology, well enough to be of clinical use in this study population.