Akkermansia muciniphila might improve anti-PD-1 therapy against HCC by changing host bile acid metabolism.

PD-1 monoclonal antibodies (mAb) have demonstrated remarkable efficacy in a variety of cancers, including Hepatocellular carcinoma (HCC). However, the patient response rates remain suboptimal, and a significant proportion of initial responders may develop resistance to this therapeutic approach. Akkermansia muciniphila (AKK), a microorganism implicated in multiple human diseases, has been reported to be more abundant in patients who exhibit favorable responses to PD-1mAb. However, the underlying mechanism has yet to be elucidated. In our study, we found that AKK could enhance the efficacy of PD-1mAb against HCC in a tumor-bearing mouse model. It promotes HCC tumor cells apoptosis and raise the CD8+ T proportion in the tumor microenvironment. Additionally, AKK downregulates PD-L1 expression in tumor cells. Furthermore, the analysis of metabonomics demonstrates that AKK induces alterations in the host's bile acid metabolism, leading to a significant increase in serum TUDCA levels. Considering the immunosuppresive roles of TUDCA in HCC development, it is plausible to speculate that AKK may reinforce the immunotherapy of PD-1mAb against HCC through its impact on bile acid metabolism.

Development and evaluation of an artificial intelligence for bacterial growth monitoring in clinical bacteriology.

In clinical bacteriology laboratories, reading and processing of sterile plates remain a significant part of the routine workload (30%-40% of the plates). Here, an algorithm was developed for bacterial growth detection starting with any type of specimens and using the most common media in bacteriology. The growth prediction performance of the algorithm for automatic processing of sterile plates was evaluated not only at 18-24 h and 48 h but also at earlier timepoints toward the development of an early growth monitoring system. A total of 3,844 plates inoculated with representative clinical specimens were used. The plates were imaged 15 times, and two different microbiologists read the images randomly and independently, creating 99,944 human ground truths. The algorithm was able, at 48 h, to discriminate growth from no growth with a sensitivity of 99.80% (five false-negative [FN] plates out of 3,844) and a specificity of 91.97%. At 24 h, sensitivity and specificity reached 99.08% and 93.37%, respectively. Interestingly, during human truth reading, growth was reported as early as 4 h, while at 6 h, half of the positive plates were already showing some growth. In this context, automated early growth monitoring in case of normally sterile samples is envisioned to provide added value to the microbiologists, enabling them to prioritize reading and to communicate early detection of bacterial growth to the clinicians.

Spectrum and antimicrobial resistance in acute exacerbation of chronic obstructive pulmonary disease with pneumonia: a cross-sectional prospective study from Vietnam.

BACKGROUND: Respiratory infections have long been recognized as a primary cause of acute exacerbation of chronic obstructive pulmonary disease (AE-COPD). Additionally, the emergence of antimicrobial resistance has led to an urgent and critical situation in developing countries, including Vietnam. This study aimed to investigate the distribution and antimicrobial resistance of bacteria in patients with AE-COPD using both conventional culture and multiplex real-time PCR. Additionally, associations between clinical characteristics and indicators of pneumonia in these patients were examined. METHODS: This cross-sectional prospective study included 92 AE-COPD patients with pneumonia and 46 without pneumonia. Sputum specimens were cultured and examined for bacterial identification, and antimicrobial susceptibility was determined for each isolate. Multiplex real-time PCR was also performed to detect ten bacteria and seven viruses. RESULTS: The detection rates of pathogens in AE-COPD patients with pneumonia were 92.39%, compared to 86.96% in those without pneumonia. A total of 26 pathogenic species were identified, showing no significant difference in distribution between the two groups. The predominant bacteria included Klebsiella pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, and Streptococcus pneumoniae, followed by Acinetobacter baumannii and Streptococcus mitis. There was a slight difference in antibiotic resistance between bacteria isolated from two groups. The frequency of H. influenzae was notably greater in AE-COPD patients who experienced respiratory failure (21.92%) than in those who did not (9.23%). S. pneumoniae was more common in patients with stage I (44.44%) or IV (36.36%) COPD than in patients with stage II (17.39%) or III (9.72%) disease. ROC curve analysis revealed that C-reactive protein (CRP) levels could distinguish patients with AE-COPD with and without pneumonia (AUC = 0.78). CONCLUSION: Gram-negative bacteria still play a key role in the etiology of AE-COPD patients, regardless of the presence of pneumonia. This study provides updated evidence for the epidemiology of AE-COPD pathogens and the appropriate selection of antimicrobial agents in Vietnam.

Impact of sample refrigeration and freezing on the bacteriological counts of different bedding materials for dairy cows.

BACKGROUND: Different organic and inorganic bedding materials can be used in dairy farms. Among organic materials, there is an increasing interest in alternative substrates based on recycled manure solids (RMS). Microbiological analyses are crucial to monitor the microbial load and evaluate the presence of pathogens impacting animal welfare and health. However, logistic factors may hamper the possibility of immediately sending fresh samples to the laboratory, requiring storage in cooled conditions before analysis. METHODS: We assessed the impact of sample refrigeration and freezing of different organic and inorganic bedding substrates including separated raw manure solids (SRMS), anaerobically digested manure solids (ADMS), and new sand (NS), on the total bacterial count (TBC) and on different microbial classes. RESULTS: The TBC was higher in fresh NS and ADMS than in refrigerated and frozen samples of the same substrates; in addition, the TBC of ADMS was higher in refrigerated than frozen samples. The TBC of SRMS did not change significantly with refrigeration and freezing. Freezing reduced the total Gram-negative bacterial count more than refrigeration in all substrates. In fresh NS, Gram-negatives were higher than in both refrigerated and frozen NS. Escherichia coli counts were significantly lower in frozen than in refrigerated SRMS. However, both refrigeration and freezing of ADMS resulted in no E. coli growth. The coliform counts were also lower in frozen than refrigerated NS and SRMS. Frozen NS and ADMS showed lower counts compared to refrigeration for Gram-negative bacteria other than E. coli and coliforms. On the other hand, cold storage did not significantly impact the streptococci and streptococcus-like organisms (SSLO) count of all evaluated bedding substrates. CONCLUSION: Refrigeration and freezing affect the bacteriological results of bedding substrates, with freezing generally leading to lower counts than refrigeration. Whenever possible, preference should be given to analyzing fresh bedding samples, however, when necessary, refrigeration would be recommended over freezing, while acknowledging that the measured bacterial load might underestimate the actual microbial content.

Diversity of Strains in the Pseudomonas syringae Complex Causing Bacterial Stem Blight of Alfalfa (Medicago sativa) in the United States.

Alfalfa growers in the Intermountain West of the United States have recently seen an increased incidence in bacterial stem blight (BSB), which can result in significant herbage yield losses from the first harvest. BSB has been attributed to Pseudomonas syringae pv. syringae and P. viridiflava; however, little is known about the genetic diversity and pathogenicity of these bacteria or their interaction with alfalfa plants. Here, we present a comprehensive phylogenetic and phenotypic analysis of P. syringae and P. viridiflava strains causing BSB on alfalfa. A multilocus sequence analysis found that they grouped exclusively with P. syringae PG2b and P. viridiflava PG7a. Alfalfa symptoms caused by both bacterial groups were indistinguishable, although there was a large range in mean disease scores for individual strains. Overall, PG2b strains incited significantly greater disease scores than those caused by PG7a strains. Inoculated plants showed browning in the xylem and collapse of epidermal and pith parenchyma cells. Inoculation with a mixture of PG2b and PG7a strains did not result in synergistic activity. The populations of PG2b and PG7a strains were genetically diverse within their clades and did not group by location or haplotype. The PG2b strains had genes for production of the phytotoxin coronatine, which is unusual in PG2b strains. The results indicate that both pathogens are well established on alfalfa across a wide geographic range and that a recent introduction or evolution of more aggressive strains as the basis for emergence of the disease is unlikely.

Epizootic of enterocolitis and clostridial overgrowth in NSG and NSG-related mouse strains.

While the immunodeficient status of NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) and NSG-related mice provides utility for numerous research models, it also results in increased susceptibility to opportunistic pathogens. Over a 9-week period, a high rate of mortality was reported in a housing room of NSG and NSG-related mice. Diagnostics were performed to determine the underlying etiopathogenesis. Mice submitted for evaluation included those found deceased (n = 2), cage mates of deceased mice with or without diarrhea (n = 17), and moribund mice (n = 8). Grossly, mice exhibited small intestinal and cecal dilation with abundant gas and/or digesta (n = 18), serosal hemorrhage and congestion (n = 6), or were grossly normal (n = 3). Histologically, there was erosive to ulcerative enterocolitis (n = 7) of the distal small and large intestine or widespread individual epithelial cell death with luminal sloughing (n = 13) and varying degrees of submucosal edema and mucosal hyperplasia. Cecal dysbiosis, a reduction in typical filamentous bacteria coupled with overgrowth of bacterial rods, was identified in 18 of 24 (75%) mice. Clostridium spp. and Paeniclostridium sordellii were identified in 13 of 23 (57%) and 7 of 23 (30%) mice, respectively. Clostridium perfringens (7 of 23, 30%) was isolated most frequently. Toxinotyping of C. perfringens positive mice (n = 2) identified C. perfringens type A. Luminal immunoreactivity to several clostridial species was identified within lesioned small intestine by immunohistochemistry. Clinicopathologic findings were thus associated with overgrowth of various clostridial species, though direct causality could not be ascribed. A diet shift preceding the mortality event may have contributed to loss of intestinal homeostasis.

Embolic necrosuppurative pneumonia in domestic cats induced by a novel Neisseria species.

Three cats, aged 2 to 11 years, presented to the University of Minnesota Veterinary Diagnostic Laboratory over a 3-year period following euthanasia or death due to respiratory distress. Thoracic radiographs revealed nodular, soft tissue opacities throughout the lung fields in all cases. On postmortem examination, approximately 60% to 80% of the lung parenchyma were expanded by multifocal to coalescing, well-demarcated, beige, semi-firm nodules. Histologically, large numbers of neutrophils, fewer macrophages, fibrin, and cellular and karyorrhectic debris effaced the pulmonary parenchyma. The inflammatory foci contained aggregates of gram-negative cocci. 16s rRNA Sanger sequencing and whole-genome sequencing identified the bacteria isolated from the lung of all cats under aerobic conditions as a novel Neisseria spp. Based on whole-genome sequence analysis, all 3 sequences shared 92.71% and 92.67% average nucleotide identity with closely related Neisseria animaloris NZ LR134440T and Neisseria animaloris GCA 002108605T, respectively. The in silico DNA-DNA hybridization identity compared to our isolates was 46.6% and 33.8% with strain DSM Neisseria zoodegmatis 21642 and strain DSM 21643, respectively. All 3 sequences have less than 95% average nucleotide identity and less than 70% DNA-DNA hybridization identity, suggesting that the 3 isolates are a novel species of the genus Neisseria. Infection with Neisseria spp. induces an embolic pneumonia in cats that radiographically and pathologically resembles a metastatic neoplastic process and should be considered among the etiologic differential diagnoses in cases of infectious pulmonary disease with a disseminated, nodular lung pattern.

Testing a health baseline during a bivalve mollusc mortality event: An investigation into die-offs of pipi Paphies australis from Aotearoa New Zealand.

Disease is a major threat to the economic, ecological and cultural services provided by wild bivalve populations. Over the past decade anecdotal reports on declining health of native bivalve populations around Aotearoa New Zealand have been supported by increasing observations of mass die-offs. Causes of declining health and mass die-offs of wild bivalves are not clear and could be due to a number of interactive and cumulative factors, including declining water quality, climate change, or disease. Pipi/kokota (Paphies australis) within the Whangarei area (northern New Zealand) have suffered repeated die-offs and declining health since at least 2009. Baseline health data for wild native bivalve populations are scarce making it difficult to identify changes in pathogen infection prevalence and intensity and infer their importance to host health. This research aimed to examine and document the health of pipi in Whangarei with the objective of identifying factors that may contribute to their ill health and lack of population recovery. We sampled pipi from four sites within Whangarei, eight times across two years (total n = 640) to establish a health baseline using histopathology, general bacteriology, and qPCR for the intracellular bacteria Endozoicomonas spp. Three pipi mass die-offs occurred during the sampling window that were opportunistically sampled to compare against the health baseline established using healthy pipi. An increase in bacterial growth and a decrease in the abundance of Endozoicomonas spp. in mortality pipi was observed compared with the health baseline. Establishing a health baseline for pipi from Whangarei provided a benchmark to assess changes in a pipi population experiencing high mortality. Such data can help identify factors contributing to die-offs and to help inform what mitigation, if any, is possible in wild shellfish populations.

A complex ePrescribing antimicrobial stewardship-based (ePAMS+) intervention for hospitals: mixed-methods feasibility trial results.

BACKGROUND: Antibiotic resistant infections cause over 700,000 deaths worldwide annually. As antimicrobial stewardship (AMS) helps minimise the emergence of antibiotic resistance resulting from inappropriate use of antibiotics in healthcare, we developed ePAMS+ (ePrescribing-based Anti-Microbial Stewardship), an ePrescribing and Medicines Administration (EPMA) system decision-support tool complemented by educational, behavioural and organisational elements. METHODS: We conducted a non-randomised before-and-after feasibility trial, implementing ePAMS+ in two English hospitals using the Cerner Millennium EPMA system. Wards of several specialties were included. Patient participants were blinded to whether ePAMS+ was in use; prescribers were not. A mixed-methods evaluation aimed to establish: acceptability and usability of ePAMS+ and trial processes; feasibility of ePAMS+ implementation and quantitative outcome recording; and a Fidelity Index measuring the extent to which ePAMS+ was delivered as intended. Longitudinal semi-structured interviews of doctors, nurses and pharmacists, alongside non-participant observations, gathered qualitative data; we extracted quantitative prescribing data from the EPMA system. Normal linear modelling of the defined daily dose (DDD) of antibiotic per admission quantified its variability, to inform sample size calculations for a future trial of ePAMS+ effectiveness. RESULTS: The research took place during the SARS-CoV-2 pandemic, from April 2021 to November 2022. 60 qualitative interviews were conducted (33 before ePAMS+ implementation, 27 after). 1,958 admissions (1,358 before ePAMS+ implementation; 600 after) included 24,884 antibiotic orders. Qualitative interviews confirmed that some aspects of ePAMS+ , its implementation and training were acceptable, while other features (e.g. enabling combinations of antibiotics to be prescribed) required further development. ePAMS+ uptake was low (28 antibiotic review records from 600 admissions; 0.047 records per admission), preventing full development of a Fidelity Index. Normal linear modelling of antibiotic DDD per admission showed a residual variance of 1.086 (log-transformed scale). Unavailability of indication data prevented measurement of some outcomes (e.g. number of antibiotic courses per indication). CONCLUSIONS: This feasibility trial encountered unforeseen circumstances due to contextual factors and a global pandemic, highlighting the need for careful adaptation of complex intervention implementations to the local setting. We identified key refinements to ePAMS+ to support its wider adoption in clinical practice, requiring further piloting before a confirmatory effectiveness trial. TRIAL REGISTRATION: ISRCTN Registry ISRCTN13429325, 24 March 2022.

Whole Genome Sequencing: Applications in Clinical Bacteriology.

The success in determining the whole genome sequence of a bacterial pathogen was first achieved in 1995 by determining the complete nucleotide sequence of Haemophilus influenzae Rd using the chain-termination method established by Sanger et al. in 1977 and automated by Hood et al. in 1987. However, this technology was laborious, costly, and time-consuming. Since 2004, high-throughput next-generation sequencing technologies have been developed, which are highly efficient, require less time, and are cost-effective for whole genome sequencing (WGS) of all organisms, including bacterial pathogens. In recent years, the data obtained using WGS technologies coupled with bioinformatics analyses of the sequenced genomes have been projected to revolutionize clinical bacteriology. WGS technologies have been used in the identification of bacterial species, strains, and genotypes from cultured organisms and directly from clinical specimens. WGS has also helped in determining resistance to antibiotics by the detection of antimicrobial resistance genes and point mutations. Furthermore, WGS data have helped in the epidemiological tracking and surveillance of pathogenic bacteria in healthcare settings as well as in communities. This review focuses on the applications of WGS in clinical bacteriology.

Complete Circularized Genome Resources of Seven Strains of Xylella fastidiosa subsp. fastidiosa Using Hybrid Assembly Reveals Unknown Plasmids.

Xylella fastidiosa is a vascular plant pathogenic bacterium native to the Americas that is causing significant epidemics and economic losses in olive and almonds in Europe, where it is a quarantine pathogen. Since its first detection in 2013 in Italy, mandatory surveys across Europe revealed the presence of the bacterium also in France, Spain, and Portugal. Combining Oxford Nanopore Technologies and Illumina sequencing data, we assembled high-quality complete genomes of seven X. fastidiosa subsp. fastidiosa strains isolated from different plants in Spain, the United States, and Mexico. Comparative genomic analyses discovered differences in plasmid content among strains, including plasmids that had been overlooked previously when using the Illumina sequencing platform alone. Interestingly, in strain CFBP8073, intercepted in France from plants imported from Mexico, three plasmids were identified, including two (plasmids pXF-P1.CFBP8073 and pXF-P2.CFBP8073) not previously described in X. fastidiosa and one (pXF5823.CFBP8073) almost identical to a plasmid described in a X. fastidiosa strain from citrus. Plasmids found in the Spanish strains here were similar to those described previously in other strains from the same subspecies and ST1 isolated in the Balearic Islands and the United States. The genome resources from this work will assist in further studies on the role of plasmids in the epidemiology, ecology, and evolution of this plant pathogen.

Bacterium detected by gram stain and drug sensitivity in Chinese children with acute sinusitis.

BACKGROUND: Acute rhinosinusitis (ARS) is one of the common diseases of upper respiratory tract infection in children. Bacterial infection is a significant aggravating factor in pediatric ARS. In this research, our goal was to detected the bacterial flora and antibiotic sensitivity of ARS in Chinese children. METHODS: We recruited 133 children with ARS between January 2020 and January 2022 from our hospital. Sinus secretion were collected and cultured for Gram stain as well as antimicrobial susceptibility tests. RESULTS: Moraxella catarrhalis, Staphylococcus aureus, Haemophilus influenzae, Streptococcus pneumoniae and Pseudomonas aeruginosa were detected in order in children with ARS, of which 25% were negative for bacterial culture and 10% were positive for two strains. Amoxicillin and clavulanate potassium were useful for Haemophilus influenzae, Streptococcus pneumoniae and Moraxella catarrhalis. Quinolones are useful for Staphylococcus aureus, Haemophilus influenzae, Streptococcus pneumoniae and Pseudomonas aeruginosa. CONCLUSIONS: This research updates the proportion of ARS bacterial infection in children in southern China and the antibiotic sensitivity.

Ion-Powered Rotary Motors: Where Did They Come from and Where They Are Going?

Molecular motors are found in many living organisms. One such molecular machine, the ion-powered rotary motor (IRM), requires the movement of ions across a membrane against a concentration gradient to drive rotational movement. The bacterial flagellar motor (BFM) is an example of an IRM which relies on ion movement through the stator proteins to generate the rotation of the flagella. There are many ions which can be used by the BFM stators to power motility and different ions can be used by a single bacterium expressing multiple stator variants. The use of ancestral sequence reconstruction (ASR) and functional analysis of reconstructed stators shows promise for understanding how these proteins evolved and when the divergence in ion use may have occurred. In this review, we discuss extant BFM stators and the ions that power them as well as recent examples of the use of ASR to study ion-channel selectivity and how this might be applied to further study of the BFM stator complex.

Bacteriology and trends of antimicrobial resistance of Pseudomonas aeruginosa and methicillin-resistant Staphylococcus aureus in otitis media: A retrospective data analysis.

OBJECTIVES: Otitis media (OM) has a high prevalence worldwide and the treatment is crucial because hearing loss in children can lead to growth disorders such as language development disorders. The aim of this study is to analyse the changes in bacterial strains and the trends of antibiotic susceptibility in otitis media with effusion (OME), chronic otitis media (COM) and cholesteatomatous otitis media (Chole OM). DESIGN: This retrospective study involved 2926 patients diagnosed with OME, COM, or Chole OM between January 2000 and December 2020. The clinical data were collected and analysed through chart review from May 2021 to July 2021. SETTING: Two tertiary medical centres. PARTICIPANTS: The 2926 OM patients. MAIN OUTCOMES AND MEASURES: An otorrhea sample was collected on the first day of their hospital visit. Middle ear fluid samples for bacterial culture and antibiotics susceptibility test were collected from patients during middle ear surgery, including ventilation tube insertion. In each type of OM, the distribution of bacterial strains in the 2000s and the 2010s was compared. In addition, changes in the detection rate of methicillin-resistant Staphylococcus aureus (MRSA) and Pseudomonas aeruginosa (PA) and trends in their antibiotic susceptibility over the last 10 years were analysed. RESULTS: The most frequently detected bacterial strains in OME, COM and Chole OM over the study period were coagulase-negative Staphylococcus (CNS) (29.6%), MRSA (24.1%), and PA (20.1%). Compared to the 2000s, the proportion of non-typable Haemophilus influenzae in OME and MRSA in COM increased in the 2010s (27.4%-31.6% and 1.5%-29.5%, respectively). In total three types of OM, although there was no significant trend of change in detection rates of MRSA, PA, and multidrug resistant-P. aeruginosa (MDR-PA) during the last 10 years, resistance to the Quinolone class of MRSA and PA tended to increase (P < .05). CONCLUSIONS: The composition of bacterial strains in each types of OM has changed over the past 20 years. Additionally, the antibiotic resistance of MRSA and PA has increased in the last decade. Therefore, when using empirical antibiotics in necessary situations, it is necessary to change to an appropriate antibiotic through a bacterial culture test and antimicrobial susceptibility test.

Genomic Analysis of a Strain Collection Containing Multidrug-, Extensively Drug-, Pandrug-, and Carbapenem-Resistant Modern Clinical Isolates of Acinetobacter baumannii.

In this study, we characterize a new collection that comprises multidrug-resistant (MDR), extensively drug-resistant (XDR), pandrug-resistant (PDR), and carbapenem-resistant modern clinical isolates of Acinetobacter baumannii collected from hospitals through national microbiological surveillance in Belgium. Bacterial isolates (n = 43) were subjected to whole-genome sequencing (WGS), combining Illumina (MiSeq) and Nanopore (MinION) technologies, from which high-quality genomes (chromosome and plasmids) were de novo assembled. Antimicrobial susceptibility testing was performed along with genome analyses, which identified intrinsic and acquired resistance determinants along with their genetic environments and vehicles. Furthermore, the bacterial isolates were compared to the most prevalent A. baumannii sequence type 2 (ST2) (Pasteur scheme) genomes available from the BIGSdb database. Of the 43 strains, 40 carried determinants of resistance to carbapenems; blaOXA-23 (n = 29) was the most abundant acquired antimicrobial resistance gene, with 39 isolates encoding at least two different types of OXA enzymes. According to the Pasteur scheme, the majority of the isolates were globally disseminated clones of ST2 (n = 25), while less frequent sequence types included ST636 (n = 6), ST1 (n = 4), ST85 and ST78 (n = 2 each), and ST604, ST215, ST158, and ST10 (n = 1 each). Using the Oxford typing scheme, we identified 22 STs, including two novel types (ST2454 and ST2455). While the majority (26/29) of blaOXA-23 genes were chromosomally carried, all blaOXA-72 genes were plasmid borne. Our results show the presence of high-risk clones of A. baumannii within Belgian health care facilities with frequent occurrences of genes encoding carbapenemases, highlighting the crucial need for constant surveillance.

Supercharged MPNs? Automated Determination of High-Throughput Most Probable Number (htMPN) Using Chip-Based 3D Digital PCR.

Surface plating on agar and most probable number (MPN) are the standard methods for determining bacterial viability but both have limitations. Here we present a novel cell count method, high-throughput MPN (htMPN), that uses a chip-based digital PCR instrument to accelerate and to improve the quantification of viable or sublethally injured cells. This method tracks growth of up to 20,000 individual bacterial cells on a single chip. Single cells were grown in the individual wells of the chip at their optimal temperature until the cell density was high enough to detect the fluorescent signal with cell-permeant or cell-impermeant DNA-intercalating fluorescent dyes. This method based on microfluidic devices implemented in digital PCR equipment was equivalent to surface plating in determining cell counts of Escherichia coli, Salmonella enterica serovar Typhimurium, Fructilactobacillus sanfranciscensis, Pseudomonas putida, and vegetative cells but not spores of Bacillus subtilis. Viable E. coli could be enumerated within 7 h. Culture of strict aerobes was restricted to strains that are capable of nitrate respiration; organisms requiring complex media that also contain double-stranded DNA were detected after treatment of growth media with DNase before inoculation. Our approach not only monitors the frequency distribution of bacterial growth and determines cell counts with high reliability but also detected heat-injured cells of S. Typhimurium that escaped detection by the surface plating. Overall, the method accelerates detection of viable bacterial cells, facilitates automation, and offers new possibilities for the analysis of individual bacterial cells. IMPORTANCE htMPN uses chip-based fluorescence acquisition and is a simple and compact tool for automatic viable cell enumeration with applications in microbiological research. This method applies to a wide range of anaerobic or facultative anaerobic species and improves accuracy by reducing the number of pipetting steps. In addition, the method offers an additional tool for single-cell microbiology. The single cell time-to-detection times have been used as an important criterion for the physiological state of bacterial cells after sublethal stress, and htMPNs support the acquisition of such data with an unprecedented number of cells. In particular, htMPN provides an anaerobic environment and enables a long incubation time to increase the recovery rate of sublethally injured cells. Given its reproducibility and reliability, our approach can potentially be applied to quantify viable cells in samples from environmental, clinical, or food samples to reduce the risk of underestimation of the number of viable bacterial cells.

Feasibility and acceptability of frequent vaginal self-sampling at home by Rwandan women at high risk of urogenital tract infections.

OBJECTIVES: To establish temporal links between vaginal microbiota (VMB) data and incident clinical events, frequent longitudinal vaginal sampling is required. Self-collection of swabs at the participant's home may be useful to avoid overburdening research clinics and participants. One-off vaginal self-sampling for STI or cervical cancer screening programmes has been shown to be feasible and acceptable to women in multiple studies, including in sub-Saharan Africa, but the feasibility and acceptability of frequent longitudinal vaginal sampling in the context of VMB sequencing studies is unknown. METHODS: Twelve participants of a randomised clinical trial in Kigali, Rwanda, self-collected vaginal swabs three times a week for a month. We studied feasibility by comparing DNA concentrations, proportions of samples with >1000 16S rRNA amplicon sequencing reads and VMB composition outcomes of self-collected swabs with clinician-collected swabs. We evaluated the acceptability of self-collection using structured face-to-face interviews and a focus group discussion. RESULTS: The participants collected vaginal swabs at 131 different time points. One woman stopped self-sampling after one try due to a social harm. All self-sampled swabs generated >1000 rRNA amplicon sequencing reads, and the DNA concentration of self-sampled swabs and clinician-sampled swabs did not differ significantly (Kruskal-Wallis p=0.484). Self-sampled and clinician-sampled swabs generated similar VMB composition data. Participants reported feeling very comfortable during self-sampling (11/12; 91.7%) and that self-sampling had become easier over time (12/12; 100%). They mentioned reduced travel time and travel costs as advantages of self-sampling at home. CONCLUSIONS: Frequent longitudinal vaginal sampling at home is feasible and acceptable to participants, even in the context of a low-resource setting, as long as adequate counselling is provided. TRIAL REGISTRATION NUMBER: NCT02459665.

Comprehensive characterization of sortase A-dependent surface proteins in Streptococcus mutans.

Streptococcus mutans, a cariogenic pathogen, adheres to the tooth surface and forms a biofilm. Bacterial cell surface proteins are associated with adherence to substrates. Sortase A (SrtA) mediates the localization of proteins with an LPXTG motif-containing proteins to the cell surface by covalent binding to peptidoglycan. In S. mutans UA159, six SrtA-dependent proteins, SpaP, WapA, WapE, DexA, FruA, and GbpC, were identified. Although some of these proteins were characterized, a comprehensive analysis of the six proteins has not been reported. In this study, we constructed mutants deficient in each of these proteins and the SrtA-deficient mutant. The SrtA-deficient mutant showed drastically decreased binding to salivary components, biofilm formation, bacterial coaggregation activity, hydrophobicity, and cellular matrix binding (collagen type I, fibronectin, and laminin). The SpaP-deficient mutant showed significantly reduced binding to salivary components and partially increased coaggregation with Porphyromonas gingivalis, and decreased hydrophobicity, and collagen binding. The WapA-deficient mutant showed slightly decreased coaggregation with Fusobacterium nucleatum. Although the SrtA-deficient mutant showed drastically altered phenotypes, all SrtA-dependent protein-deficient mutants, except the SpaP-deficient mutant, did not show considerable alterations in binding to salivary components. These results indicate that the six proteins may coordinately contribute to these activities. In addition, using genomic data of 125 S. mutans strains, the amino acid sequences of each surface protein were compared and many variations were found among strains, which may affect the phenotype of cell surface proteins in S. mutans.

The Bacteriology of Skin Lesions in Patients with Hidradenitis Suppurativa Is Associated with Previous Antibiotic Treatment in the Community Setting: A Referral Center Experience.

BACKGROUND: Hidradenitis suppurativa (HS) is a chronic skin disease characterized by inflammatory nodules and abscesses. The pathogenic role of bacteria is not fully understood. As the diagnosis is usually delayed, patients are often treated with several lines of antibiotics in a nonstandardized fashion. The aim of the study was to investigate and compare the bacteriology of active HS lesions in patients treated or not treated with antibiotics in the community setting before referral to a dedicated HS clinic. METHODS: Purulent skin lesions of patients with HS referred to the HS Clinic of Rabin Medical Center in 2009-2020 were cultured. Data were collected from the patients' medical files and microbiology reports. The correlation between the location of the skin lesion and the bacteriologic profile was analyzed, and the effects of previous antibiotic treatment on the bacteriologic profile of the lesions and susceptibility patterns of the cultured bacteria were evaluated. RESULTS: Pus (or tissue) from inflammatory lesions of 97 patients with HS was cultured. Mean (SD) patient age was 39.5 (13.0) years, and mean delay in diagnosis was 7.3 (8.3) years. Most patients (57.7%) had dominant involvement of one location, with the most active lesions concentrated in the genitalia, gluteal/perineal area, and axilla. Enterobacterales species were the most frequent isolates detected in all locations except the face and scalp. Seventy-eight patients (80.4%) had been treated in the community setting prior to referral with a median (range) of 2 (1-8) lines of antibiotics. The most commonly prescribed antibiotics were amoxicillin/clavulanate (22.0%), doxycycline/minocycline (16.8%), clindamycin (16.2%; monotherapy 8.1%, clindamycin with rifampicin 8.1%), and cephalexin (13.9%). Compared to the previously untreated patients, cultures of lesions from the previously treated patients yielded a higher percentage of gram-negative Enterobacterales (the most common isolates in this group) (31.3% vs. 10.3%) and a significantly higher median number of isolates per culture (2 vs. 1, p < 0.0001). Gram-positive bacteria, usually considered contaminants (mainly coagulase-negative staphylococci) accounted for 31.0% of the isolates in the previously treated group. Susceptibility testing for the entire cohort revealed 100% bacterial sensitivity to ciprofloxacin. Staphylococcus spp. were 100% sensitive to rifampicin. Both gram-positive and gram-negative bacteria had high sensitivity to trimethoprim and sulfamethoxazole. CONCLUSION: Nonstandardized antibiotic treatment of HS in the community setting can skew the microbiology of skin lesions toward gram-negative bacteria. Therefore, treatment with trimethoprim and sulfamethoxazole or ciprofloxacin, either alone or combined with rifampicin, may be considered.

Antifungal Peptides from a Burkholderia Strain Suppress Basal Stem Rot Disease of Oil Palm.

Basal stem rot (BSR) is the most common disease of oil palm (Elaeis guineensis) in Southeast Asia. BSR is caused by a white-rot fungus Ganoderma boninense. The disease is difficult to manage. Therefore, development of novel and environmentally safe approaches to control the disease is important. Species of Burkholderia are known to have diverse lifestyles, some of which can benefit plants by suppressing diseases or increasing plant growth. In the present study, antifungal peptides produced by a bacterial strain isolated from the rhizosphere of an oil palm tree, Burkholderia sp. strain CP01, exhibited strong growth inhibition on G. boninense. A loss-of-function mutant of CP01 was generated, and it has enabled the identification of a 1.2-kDa peptide and its variants as the active antifungal compounds. High-resolution mass spectrometry revealed six analogous compounds with monoisotopic masses similar to the previously reported cyclic lipopeptides occidiofungin and burkholdine. The antifungal compounds of CP01 were secreted into media, and we sought to use CP01 culture extract without living cells to control BSR disease. Glasshouse experiments showed that CP01 culture extract suppressed BSR disease in oil palm seedlings. The ability of CP01 to produce an antifungal substance and suppress plant disease suggests its potential applications as a biofungicide in agriculture.