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Serology assays against spike, receptor binding domain (RBD) and nucleocapsid proteins of the severe acute respiratory syndrome coronavirus 2 are essential for serosurveillance. We performed a comparison of four medium-to-high throughput commercial assays [Abbott Laboratories, Ortho Clinical Diagnostics, Meso Scale Diagnostics (MSD)], one point-of-care test (ZEKMED) and a laboratory-developed plaque reduction neutralization test using a reference panel and clinical specimens. Overall, the assays showed a high positive percent agreement of ≥85% and negative percent agreement of ≥90%, with the MSD anti-spike IgG assay having the best performance (100% in both). Notably, Abbott anti-nucleocapsid IgG, MSD anti-spike IgG and ZEKMED anti-spike RBD IgM/IgG combined assays were able to detect antibodies from individuals infected with all different variants tested - Alpha, Beta, Gamma, Delta and Omicron. The limit of detection (LOD) of the assays ranged from 9.9 to 62.0 BAU ml^-1, with the Abbott anti-spike RBD having the lowest LOD. The COVID-19 serology assays will continue to be useful in determining seroprevalence from infection and vaccination.

Tuberculosis (TB) is a preventable and usually curable disease but remains a major health problem worldwide, particularly in developing countries. TB of the lumbosacral junction is rare and occurs in only 1-2% of all cases of spinal TB. Moreover, isolated sacrococcygeal TB is extremely rare. We present a case of a 64-year-old patient with a history of diabetes who presented with chronic back pain and cough. Physical examinations revealed a perianal fistula and left elbow joint arthritis. The patient is diagnosed with disseminated TB with coccygeal involvement. Diagnosis was achieved non-invasively using Xpert MTB/RIF, confirming Mycobacterium tuberculosis infection. The patient experienced complete resolution of symptoms following the commencement of anti-TB therapy. We highlight the importance of this case due to the rare coccygeal localization of TB in an immunocompetent patient, diagnosed through non-invasive means.

[This corrects the article DOI: 10.1099/acmi.0.000918.v4.].

Rice (Oryza sativa L.) is a vital global crop with a predominant presence in Asia, including Thailand. However, it faces a significant threat from bacterial blight disease, primarily caused by Xanthomonas oryzae pv. oryzae (Xoo). This research aims to provide valuable insights into the genetic virulence factors and genomic variations of Xoo strains isolated in Thailand. Furthermore, we present the first complete genomic database of Thai Xoo, offering a comprehensive resource for studying pathogen diversity, tracking virulence evolution and supporting disease management strategies in rice production. Our phylogenetic analysis unveils that the 20 Thai strains align with the Asian strains, setting them apart from African and US strains. Remarkably, the average nt identity values, in comparison with Xanthomonas oryzae type strain 35933 (XO35933), consistently exceed 99%. These strains can be classified into three assigned ribosomal sequence types. Our investigation into the pangenome and the phylogenetic relationships of these 20 Xoo genomes reveals a diverse genetic landscape, with the pangenome comprising 11,872 orthologous gene clusters, of which roughly 30% form the core genome. Notably, all of these genomes exhibit a clustered regularly interspaced short palindromic repeats-Cas I-C array, indicative of their adaptive immune mechanisms. All strains belonged to BXO1 type LPS cassette with high identity. Furthermore, our analysis identifies two distinct types of plasmids, namely, Xanthomonas oryzae pv. oryzicola strain GX01 plasmid pXOCgx01 (A46, A57, A83, A112, D and E) and the X. oryzae strain AH28 plasmid pAH28 (A97). This genomic resource will be valuable for advancing research on surveillance, prevention, management and comparative studies of this critical pathogen in the future.

Interactions between environmental protists and bacteria play a crucial role in shaping bacterial survival strategies and pathogenic potential. Certain bacteria have evolved mechanisms to resist predation by protists such as Acanthamoeba, allowing them to persist intracellularly and, in some cases, enhance their virulence. We hypothesize that Acanthamoeba species may also play a role in promoting antimicrobial resistance (AMR) in amoeba-resistant bacteria. This study investigated whether Acanthamoeba castellanii enhanced AMR development in Pseudomonas putida under lethal ciprofloxacin concentrations. P. putida was co-incubated with A. castellanii and maintained in ciprofloxacin concentrations starting at 2 µg ml^-1, four times the planktonic MIC, which was incrementally increased as resistance emerged. The survival of the co-incubated P. putida and the development of resistance were monitored, and antimicrobial susceptibility tests were conducted using multiple antibiotics. P. putida co-incubated with A. castellanii in the presence of ciprofloxacin became increasingly resistant in a dose-dependent manner, with the MIC increasing from 0.5 to 20 µg ml^-1 after 17 days. Contrastingly, the naïve strain did not survive sustained exposure at 2 µg ml^-1. Co-incubated bacteria maintained under ciprofloxacin pressure developed resistance to ciprofloxacin, chloramphenicol, azithromycin and enrofloxacin while retaining susceptibility to streptomycin and tetracycline. Co-incubation in the absence of ciprofloxacin did not promote resistance in P. putida, suggesting that the combination of extracellular drug pressure and intracellular survival is important in driving resistance. These findings indicate that intracellular survival within Acanthamoeba can significantly accelerate AMR development in P. putida under fluoroquinolone pressure. Further research into the molecular mechanisms involved is warranted to inform strategies for mitigating AMR emergence in clinical and environmental contexts.

Antibiotic-resistant infections cause an estimated 2.8 million illnesses and 35,900 deaths annually in the USA. Carbapenems are a class of antibiotics that are generally reserved to treat life-threatening invasive infections including sepsis. Accurate diagnosis of carbapenem-resistant infections is critical for early and appropriate treatment. bla _IMP encodes bacterial production of the IMP metallo-beta-lactamase (MBL), which can confer resistance to all the beta-lactams including carbapenems. Zinc is an essential co-factor in the IMP MBL enzymatic hydrolysis of carbapenems. Tests for the presence of IMP carbapenemase, such as the Carba NP, include zinc sulphate (ZnSO₄) although broth dilution methods for determining MIC for carbapenems may vary. We hypothesized that ZnSO₄ availability would improve the accuracy of carbapenem MIC determination for bacteria expressing bla _IMP. Thus, the objective of this study was to determine if supplemental ZnSO₄ affects the carbapenem MICs of Enterobacterales, Alteromonadales and Moraxellales expressing bla _IMP. Isolates utilized for this study were originally recovered from environmental samples collected at farms, wastewater treatment plants and surface water. They were selected based on phenotypic non-susceptibility to carbapenems and genetic confirmation of bacterial carriage of bla _IMP. Cation-adjusted Mueller-Hinton broth suspensions of each isolate standardized to a 0.5 MacFarland standard were tested with and without ZnSO₄ added at 0.1 mmol l^-1 concentration to determine MICs using standard extended-spectrum beta-lactamase microbroth dilution MIC panels. Although we observed that Morganellaceae imipenem MICs were higher (P<0.001) than those from other bacteria harbouring bla _IMP, the inclusion of supplemental ZnSO₄ did not influence carbapenem MIC. This suggests that supplemental ZnSO₄ will not improve the accuracy of carbapenem MICs in environmental bacteria expressing IMP carbapenemase. Additional research will be required to identify important factors that may influence the expression of carbapenemase including IMP and the accurate determination of clinical MICs, which is critical to appropriate therapeutic decision-making.

Background. Blastocystis, the most prevalent microbial eukaryote in humans, has a global distribution. Studies have linked its presence with distinct gut microbiome and metabolome profiles compared to those where the organism is absent. However, the interplay of antibiotic administration, Blastocystis and the surrounding gut microbiome remains understudied. This case study aimed to explore antibiotic consumption and the presence of Blastocystis with subsequent changes in the gut microbiome and metabolome of an individual diagnosed with irritable bowel syndrome (IBS). Methods. Stool samples from an IBS patient, collected at 12 time points, were tested for the presence of Blastocystis using real-time PCR targeting the SSUrRNA gene, followed by sequencing of positive samples. Illumina sequencing determined the gut microbiome composition, while one-dimensional proton NMR spectroscopy was used to analyse the metabolome composition. Statistical analyses were conducted to identify relationships between antibiotic consumption, bacterial diversity, metabolome composition and Blastocystis presence. Results. Antibiotics significantly impacted the gut microbiome, with diversity declining early in the antibiotic course, then recovering later and post-course. Blastocystis was detected early, late and post-course but was not detectable mid-course, coinciding with the decline in bacterial diversity. Significant differences were observed between Blastocystis-positive and Blastocystis-negative samples, with bacterial composition significantly changing between samples collected before, early and after the antibiotic course compared to those collected mid-course. Metabolite groups, including short-chain fatty acids, amino acids and succinate, exhibited changes throughout the antibiotic course, indicating that gut metabolite composition is affected by antibiotic consumption. Discussion/Conclusion. While antibiotics did not significantly impact Blastocystis colonization, they did cause a mid-course decline in microbial diversity and Blastocystis presence. The study also revealed significant alterations in important metabolites such as short-chain fatty acids and amino acids throughout the antibiotic course, with an altered metabolome observed post-course. This case study underscores the complex interactions between antibiotics, gut microbiota and metabolites, highlighting the resilience of Blastocystis in the gut ecosystem.

Non-typeable Haemophilus influenzae (NTHi) is an early pathogen isolated from the lungs of children with cystic fibrosis (CF). However, its role in the progression of CF lung infection is poorly understood. Additionally, whether it forms biofilms in the lungs of people with CF is an open question. The development of synthetic CF sputum media (SCFM) has given key insights into the microbiology of later CF pathogens, Pseudomonas aeruginosa and Staphylococcus aureus, through replicating the chemical composition of CF sputum. However, the growth of NTHi in these media has not previously been reported. We show that NTHi grows poorly in three variants of SCFM commonly used to induce in vivo-like growth of P. aeruginosa and S. aureus (SCFM1, SCFM2 and SCFM3). The addition of NAD and haemin to SCFM1 and SCFM2 promoted the planktonic growth and biofilm formation of both laboratory and clinical NTHi isolates, and we were able to develop a modified variant of SCFM2 that allows culture of NTHis. We show that NTHi cannot be identified in an established ex vivo model of CF infection, which uses SCFM and porcine bronchiolar tissue. This may in part be due to the presence of endogenous bacteria on the pig lung tissue, which outcompete NTHi, but the lack of selective agar to isolate NTHi from endogenous bacteria, and the fact that NTHi is an exclusively human pathogen, makes it hard to conclude that this is the case. Through spiking modified SCFM2 with filter-sterilized lung homogenate, biofilm growth of clinical NTHi isolates was enhanced. Our results highlight that there are crucial components present in the lung tissue, which NTHi require for growth, which are not present in any published variant of SCFM from the Palmer et al. Endres and Konstan in JAMA (2022;137:191-1) lineage. Our results may inform future modifications to SCFM recipes to truly mimic the environment of CF lung sputum and thus, to facilitate the study of a wide range of CF pathogens.

Background. Salmonellosis most commonly presents clinically as typhoid fever or gastroenteritis. Pleuropulmonary infections due to Salmonella are still rare, even though they have often been described in immunocompromised patients. Case presentation. We report a rare case of purulent pleurisy caused by Salmonella enterica subsp. arizonae, occurring in a 50-year-old female with breast cancer who is currently treated with chemotherapy and radiotherapy along with chronic renal failure requiring haemodialysis, who presented with acute chest pain, dyspnoea and haemodynamic instability. After bacteriological identification of Salmonella enterica subsp. arizonae in pleural fluid, antibiotic susceptibility testing was performed. The patient was then started on a broad-spectrum antibiotic, which successfully improved her condition. Conclusion. Our case highlights the implication of Salmonella enterica subsp. arizonae in purulent pleurisy in an immunocompromised patient. An early diagnosis and a proper antibiotic therapy enabled us to reduce the morbidity and mortality risk in our patient.

Here, we report the draft 5.8 Mb genome sequence of a Flavobacterium aquidurense isolate from untreated wastewater in Liverpool, United Kingdom. The reported isolate has the potential to produce both flexirubin and β-carotene pigments, and contains an additional biosynthetic gene cluster for a putative novel β-lactone. The genome also contains a gene for a putative β-lactamase bla_JOHN-1 analogue, and there are multiple copies of a putative novel insertion sequence of the IS3 family. This genome adds to a growing resource of Flavobacterium spp. sequencing data which can be utilized to investigate microbial pigment production, antimicrobial resistance genes and mobile genetic elements within this genus.