David Llewellyn Gordon

Several studies report the diversity, and population structure of Escherichia coli (E. coli) in the human gut, but most used faecal specimens as the source of E. coli for analysis. In the present study, we collected mucosal biopsies from three different locations: the terminal ileum, transverse colon, and rectum from 46 individuals. To identify unique strains, we fingerprinted about 3300 isolates of E. coli via the multiple-locus variable-number tandem-repeat analysis (MLVA) technique. An example of each strain per individual then underwent PCR for phylogrouping, and specific phylogrouped strains were further screened to determine whether they belonged to one of four common human-associated sequence types (ST69, ST73, ST95, and ST131), and to identify B2-subtypes. We detected on average 2.5 unique strains per individual. The frequency of unique strain(s) appeared in individuals as follows: 35% (16/46) had only one strain, 22% (10/46) had two strains, 24% (11/46) had three strains and 4% (2/46), 9% (4/46) and 7% (3/46) had 4, 5 and 6 strains, respectively. Strain richness did not depend on gender, age, or disease status. The most abundant phylogroup in all gut locations was B2 followed by A, B1, and D. Strain richness overall and across gut locations was decreased if an individual’s dominant strain belonged to phylogroup B2. ST95, ST131, and ST73 constituted more than half of the total B2 strains. Analysis of B2 sub-types revealed that sub-types IX (STc95) and I (STc131) were more common than other sub-types. The phylogroup and ST of strains at different gut locations did not vary significantly. However, there were multiple examples of individuals who carried strains detected only in one gut location. The present study suggests that particular phylogroups and STs are likely to dominate in different locations in the lower gut of humans.

Aging-associated cognitive decline affects more than half of those in long-term residential aged care. Emerging evidence suggests that gut microbiome–host interactions influence the effects of modifiable risk factors. We investigated the relationship between gut microbiome characteristics and severity of cognitive impairment (CI) in 159 residents of long-term aged care. Severe CI was associated with a significantly increased abundance of proinflammatory bacterial species, including Methanobrevibacter smithii and Alistipes finegoldii, and decreased relative abundance of beneficial bacterial clades. Severe CI was associated with increased microbial capacity for methanogenesis, and reduced capacity for synthesis of short-chain fatty acids, neurotransmitters glutamate and gamma-aminobutyric acid, and amino acids required for neuroprotective lysosomal activity. These relationships were independent of age, sex, antibiotic exposure, and diet. Our findings implicate multiple gut microbiome–brain pathways in aging-associated cognitive decline, including inflammation, neurotransmission, and autophagy, and highlight the potential to predict and prevent cognitive decline through microbiome-targeted strategies.

Background: Nocardia is a gram‐positive bacterium capable of causing both local and systemic infections, typically in immunocompromised patients. The most common clinical presentation is pulmonary infection. Muscle abscess due to Nocardia infection without disseminated nocardiosis is rare. Case Report: In this report, we describe the case of a 67‐year‐old male kidney transplant recipient who developed a swelling of the right biceps muscle. CT imaging showed an intramuscular abscess, which was subsequently surgically drained. The drained fluid grew Nocardia pseudobrasiliensis , which was resistant to imipenem but susceptible to trimethoprim/sulfamethoxazole (TMP‐SMX), ciprofloxacin and linezolid. The patient was initially treated with TMP‐SMX and ciprofloxacin. Treatment was changed to 6 months of ciprofloxacin and azithromycin due to intolerance to TMP‐SMX which resulted in a good clinical response and no recurrence for 3 years. We also review all previously reported N. pseudobrasiliensis infections and cases of nocardiosis presenting as intramuscular infections. Conclusion: Given its prevalence amongst immunocompromised patients, Nocardiosis requires consideration in the differential diagnosis for the cause of atypical infections in transplant recipients. The antimicrobial susceptibilities of Nocardia are variable depending on species. Of key note, carbapenem resistance has been recently described in N. pseudobrasiliensis . This development should be considered when initiating antimicrobial therapy to ensure good patient response to treatment.

Aim: Severe dengue is correlated with a decrease in the circulating complement regulator, factor H (FH) and prior work has shown that dengue virus (DENV) infection induces FH mRNA but not FH protein release. Here, the mechanisms of this phenomenon were defined. Methods: HEK293 cells were infected with DENV-2 and changes in FH mRNA and protein were analyzed by real time reverse transcription-polymerase chain reaction (RT-PCR), enzyme-linked immunosorbent assay (ELISA), and fluorescent microscopy. Additionally, cells were stimulated with size fractionated supernatants from DENV-infected cells, supernatant containing DENV non-structural protein-1 (NS1) without virus particles, and infections performed with or without the toll-like receptor-4 (TLR4) antagonist, TAK-242. Mass spectrometry was used to define the protein content of the fractionated supernatant, and treatment of cells with sialidase or heparinase was used to define cell-associated FH protein. Results: DENV-infection induced full-length FH mRNA and cell-associated FH protein. Microscopy demonstrated membrane and intracellular-associated FH with a cytoskeletal and perinuclear localisation, in both DENV positive and uninfected neighboring bystander cells. Fractionation of cultured supernatant from DENV-infected cells demonstrated that secreted factors > 50 (kilodaltons) kDa induced FH mRNA and this could be blocked with TAK-242 but was not simulated by the TLR4 agonist, DENV NS1. Mass spectrometry detected DENV envelope, membrane and NS1, complement component 5 (C5), and complement FB, and indicated a > 20-fold increase in C4, inter-alpha-trypsin inhibitor heavy chain H2 (ITIH2), and alpha-2-macroglobulin in the > 50 kDa fraction from DENV-infected compared with conditioned media from uninfected cells. Sialic acid levels were unchanged and cleavage did not affect release of FH from DENV-infected compared to uninfected cells. In contrast, sulphated glycosaminoglycans (GAGs) were reduced in the cultured supernatant and cell lysates following DENV-infection, and heparinase cleavage released significantly more FH from DENV-compared with uninfected cells. Conclusions: Following DENV-infection, secreted molecules induce FH that remains intracellular and with increased binding to cell surface heparan sulphate. The mediators of induction of FH mRNA act in trans and via TLR4 but this is not likely to be via DENV NS1. The retention of FH in the local environment of the infected cell could benefit the virus by negating local complement killing of cells, and/or benefit the host by inhibition of heparan sulphate-mediated DENV infection to restrict viral spread.

Background: Data on the health-related quality of life (HRQoL) for invasive meningococcal disease (IMD) survivors, particularly among adolescents and young adults (AYAs), are limited. This study aimed to investigate the in-depth experiences and impacts of IMD on AYAs. Methods: Participants were recruited from two Australian states, Victoria and South Australia. We conducted qualitative, semi-structured interviews with 30 patients diagnosed with IMD between 2016 and 2021. The interview transcripts were analyzed thematically. Results: Of the participants, 53% were aged 15–19 years old, and 47% were aged 20–24. The majority (70%) were female. Seven themes relating to the participants’ experience of IMD were identified: (1) underestimation of the initial symptoms and then rapid escalation of symptoms; (2) reliance on social support for emergency care access; (3) the symptoms prompting seeking medical care varied, with some key symptoms missed; (4) challenges in early medical diagnosis; (5) traumatic and life-changing experience; (6) a lingering impact on HRQoL; and (7) gaps in the continuity of care post-discharge. Conclusion: The themes raised by AYA IMD survivors identify multiple areas that can be addressed during their acute illness and recovery. Increasing awareness of meningococcal symptoms for AYAs may help reduce the time between the first symptoms and the first antibiotic dose, although this remains a challenging area for improvement. After the acute illness, conducting HRQoL assessments and providing multidisciplinary support will assist those who require more intensive and ongoing assistance during their recovery.

A cluster of deep sternal wound infections caused by Candida spp. occurred at our institution. Investigation did not disclose a common environmental source. We postulate that broad spectrum antibiotic surgical prophylaxis and liberal use of antibiotics contributed to these infections.

Escherichia coli (E. coli) is an important commensal in the human gut; however, it is unknown whether strains show site-specificity in the lower gut. To investigate this, we assessed genotypic and phenotypic differences in 37 clone pairs (two strains with very similar multiple locus variable-number-tandem-repeat analysis [MLVA] profiles) of E. coli isolated from mucosal biopsies of two different gut locations (terminal ileum and rectum). The clone pairs varied at the genomic level; single nucleotide polymorphisms (SNPs) were common, multiple nucleotide polymorphisms (MNPs) were observed but less common, and few indels (insertions and deletions) were detected. The variation was higher in clone pairs that are associated with non-human-associated sequence types (ST) compared to human-associated STs, such as ST95, ST131, and ST73. No gene(s) with non-synonymous mutations were found to be commonly associated with either the terminal ileum or the rectal strains. At the phenotypic level, we identified the metabolic signatures for some STs. Rectum strains of some STs showed consistently higher metabolic activity with particular carbon sources. Clone pairs belonging to specific STs showed distinct growth patterns under different pH conditions. Overall, this study showed that E. coli may exhibit genomic and phenotypic variability at different locations in the gut. Although genomics did not reveal significant information suggesting the site-specificity of strains, some phenotypic studies have suggested that strains may display site-specificity in the lower gut. These results provide insights into the nature and adaptation of E. coli in the lower gut of humans. To the best of our knowledge, no study has investigated or demonstrated the site-specificity of commensal E. coli in the human gut.

Summary: We previously characterized the genetic diversity of Escherichia coli strains isolated from septic tanks in the Canberra region, Australia. In this study, we used repetitive element palindromic (REP) PCR fingerprinting to identify dominant REP‐types belonging to phylogroups A and B1 strains across septic tanks. Subsequently, 76 E . coli strains were selected for whole‐genome sequencing and phenotype microarrays. Comparative genome analysis was performed to compare septic tank E . coli genomes with a collection of 433 E . coli isolates from different hosts and freshwater. Clonal complexes (CCs) 10 ( n = 15) and 399 ( n = 10) along with sequence type (ST) 401 ( n = 9) were the common lineages in septic tanks. CC10 strains have been detected from animal hosts and freshwater, whereas CC399 and ST401 strains appeared to be associated with septic tanks as they were uncommon in isolates from other sources. Comparative genome analysis revealed that CC399 and ST401 were genetically distinct from other isolates and carried an abundance of niche‐specific traits involved in environmental adaptation. These strains also showed distinct metabolic characteristics, such as the ability to utilize pectin, which may provide a fitness advantage under nutrient‐limited conditions. The results of this study characterized the adaptive mechanisms allowing E . coli to persist in wastewater.