- Volume 6, Issue 11, 2024

Introduction. Virological failure is one of the main causes of failing to treat, and better management of HIV infection requires understanding and controlling the factors that contribute to this phenomenon. The main objective was to characterize the patients of the active file of the Brazzaville Outpatient Treatment Center in virological failure to identify predictive factors leading to virological failure.

Methods. Conducted between June and December 2020, this was a cross-sectional study. Patients enrolled were HIV-1-infected patients from the Brazzaville Outpatient Treatment Center receiving a potent combination therapy for at least 6 months but experiencing virological failure. Viral load was measured using the automated Abbott Real-time HIV-1 m2000rt System. Sociodemographic and clinical data were collected from a computerized patient record software called Santia. For the identification of the independent predictors of virological failure, statistical analysis was performed.

Results. A total of 109 patients with virological failure were recruited. The median age of the patients was 45 years (interquartile range: 37–52 years) and women were more represented (74%). More than half of the patients had World Health Organization stage IV HIV and the median duration of antiretroviral treatment was 96 months. The most followed treatment regimen was AZT+3TC+EFV (or nevirapine) with 48%, while the median viral load was 12985 copies ml−1.

Conclusion. In our study, we did not identify any sociodemographic or clinical variables predictive of virological failure. However, we felt that it would be desirable to carry out a study with temporal follow-up and the possibility of sequencing in order to identify the different circulating genotypes and resistance mutations.

Introduction. Antimicrobial resistance (AMR) is a growing global concern. Clonal lineages of CTX-M β-lactamase-producing Escherichia coli (CTXE) and quinolone-resistant E. coli (QREC) were disseminated among the deer population in a famous tourist destination (Nara Park; NP) in Japan.

Hypothesis/gap statement. The molecular characteristics of CTXE or QREC isolates, which could pose a threat to public health, have not been elucidated.

Aim. This study aimed to characterize the genetic traits of CTXE and QREC isolates derived from NP deer and compare them with lineages prevalent worldwide.

Methodology. Sixteen CTXE and three QREC isolates recovered from NP deer faeces between 2018 and 2020 were analysed using whole-genome sequencing (WGS). For endemic lineages, phylogenetic trees were constructed against the isolates registered in the EnteroBase database using the core genome SNP scheme.

Results. The most prevalent lineage in NP deer was ST3580. Several pandemic lineages, such as sequence type (ST) 38, ST58 and ST117, were included. The QREC lineages prevalent among deer were designated as extra-intestinal pathogenic E. coli or uropathogenic E. coli (UPEC). Thirteen of the 24 antimicrobial resistance genes (ARGs) were considered high-risk ARG families. Chromosomal integration of bla CTX-M-15 was observed in all plasmid-negative isolates. Phylogenetic analysis suggested relationships between NP isolates and isolates sourced from the environment or poultry.

Conclusion. ST3580 has a high potential for clonal dissemination. Furthermore, multiple clinically relevant lineages of CTXE and QREC are endemic in NP deer; however, they could be less virulent than isolates belonging to the same lineages, which could cause severe infectious diseases. Further studies are required to investigate the relationship between chromosomal integration of plasmid-encoded genes and the stable propagation of AMR bacteria in wildlife and the environment.

Background. According to the World Health Organization, neglected tropical diseases (NTDs) affect over two billion people worldwide. While the links between nutrition and many diseases have become clear over recent decades, NTDs have lagged behind and the linkage with nutrition is largely unknown. We conducted this systematic review with meta-analysis to determine the current knowledge on the association between NTDs and malnutrition.

Methodology. PubMed, Embase, Scopus and African Journals Online databases were searched using predefined search terms. We included all original articles with a case–control design and at least one NTD. The studies had to compare nutritional parameters between infected cases and control participants. Articles that did not report original data were excluded. The quality of the studies was assessed using the Newcastle–Ottawa scale. Pooled estimates were conducted using the random effect model. The publication bias of the studies was determined by funnel plots. Q and I 2 statistics were used to assess the heterogeneity of the studies.

Results. After screening 1294 articles, only 16 qualified for the systematic review and 12 for meta-analysis. These predominately had a focus on soil-transmitted helminthiasis (ascariasis, hookworm diseases and trichuriasis) and schistosomiasis, with a minority concerning leishmaniasis and leprosy. Pooled estimates showed an association between intestinal parasites and stunting in children [odds ratio (OR) = 1.38, 95% confidence interval (CI): 1.14–1.66, I 2 = 0%, tau2 = 0]. We also identified a moderate association established between serum iron deficiency (OR = 4.67, 95% CI: 1.91–11.44, tau2 = 0) and intestinal parasites.

Conclusions/significance. Of the 20 NTDs, the links between diet and disease have been explored for only 4. There is a paucity of data from low- and middle-income countries and least-developed countries where the NTD burden is high. Therefore, more research into the role of malnutrition in NTDs other than intestinal parasites, leishmaniasis and leprosy is needed.

The Tol-Pal proteins stabilize the outer membrane during cell division in many Gram-negative bacteria, including Escherichia coli. Pal is an outer membrane lipoprotein that can bind peptidoglycan. It accumulates at the septum during division by a mobilization-and-capture mechanism. This work further substantiates and extends knowledge of Pal’s localization in E. coli using immunolabelling; this method enables the detection of endogenous proteins. The midcell localization of Pal and TolB, as seen with fluorescent protein fusions, during cell division, was confirmed. The retention of Pal in newly formed cell poles seemed to persist longer than observed with fluorescent Pal fusions. The concentration of endogenous Pal during the cell division cycle fluctuated: it decreased initially (to half the fluorescence concentration (32.1 au µm−3) of the maximum (64.1 au µm−3) reached during the cell cycle) and then increased during the second half of the cell division cycle. We probed for possible regulators and proposed two new putative regulators of Pal. By deleting the periplasmic protease, Prc decreased the total Pal abundance (to ~65% of the fluorescence concentration in WT cells) and affected its concentration fluctuation during the cell cycle. This suggests that Prc controls a cell division stage-specific regulator of Pal. Immunolabelling also supported the prediction that the small RNA MicA suppresses Pal expression (the fluorescence concentration of Pal in cells without MicA is double that of Pal in WT cells). However, the regulation by MicA occurred in a cell cycle-independent manner. All these findings urge further research on the tight regulation of the dividing cell envelope stability.

Health authorities were notified of a suspected outbreak of foodborne disease in a hospital in South Africa, where staff and patients reported acute onset of abdominal cramps, diarrhoea, fever and rigours after eating a chicken pasta meal. The aim of this report is to discuss the use of whole genome sequencing (WGS) analysis of bacterial isolates to support an epidemiological investigation. An epidemiological investigation led by the Infection Control Manager of the hospital and supported by an outbreak response team was conducted. Standard microbiological procedures were used to process stool samples and culture/identify diarrhoeal pathogens. Bacterial cultures were investigated using WGS performed using Illumina NextSeq technology, and WGS data were analysed using multiple bioinformatics tools, including those available at the Center for Genomic Epidemiology and EnteroBase. Core genome multilocus sequence typing (cgMLST) was used to investigate the phylogeny of isolates. Forty-nine cases were identified, with stool samples collected from 21 cases, and nontyphoidal Salmonella isolated from 19 out of 21 (90%) of the samples. All isolates were identified as Salmonella enterica serovar Enteritidis and differed from each other by ≤2 allele differences on cgMLST, indicating that isolates are highly genetically related. Delays in testing of food retention samples rendered the negative test results of limited value. A case–control study was conducted; eating chicken pasta was strongly associated with developing gastroenteritis (odds ratio (OR) = 15.4, Chi-Square test with Yates correction p value = 0.02). The epidemiological evidence suggests that the chicken pasta was the likely vehicle of transmission in this outbreak, although the source of S. enterica serovar Enteritidis remains unknown.

Antimicrobial-resistant pathogens such as Pseudomonas aeruginosa and Acinetobacter baumannii can cause potentially fatal infections in susceptible individuals, with respiratory tract infections among the most common clinical presentations. The development of novel treatments or prophylactic interventions to combat these infections is urgently needed and requires robust, reliable animal models for their preclinical evaluation. In particular, the bacterial burden needs to be accurately determined before and after administration of the potential therapy under evaluation to quantify the effectiveness of the treatment. We provide two reliable, non-invasive murine acute lung challenge models with either P. aeruginosa or A. baumannii using an oropharyngeal aspiration technique, which has been widely overlooked in studies testing vaccines or treatments for these pathogens. Here, we show that this non-surgical technique to deliver suspensions into mouse lungs does not significantly impact animal welfare (based on welfare monitoring and weight) and allows uniform bilateral distribution of the bacterial dose, resulting in even bioburden in both lungs. The optimal timepoint for humane killing and organ harvest was 24 h after challenge for both pathogens, and at least 4×106 and 107 c.f.u. per mouse were needed to obtain a reproducible P. aeruginosa or A. baumannii bioburden, respectively. These mouse challenge models offer a valuable tool to assess therapeutic interventions against P. aeruginosa or A. baumannii infections.

The use of membrane-specific dyes for in vivo fluorescent microscopy is commonplace. However, most of these reagents are non-specific and cannot track specific lipid species movement, instead often acting as non-covalent lipid-associated probes or requiring the uptake of whole lipids and acyl tails into the membrane. This issue has been solved in eukaryotic cell biology by the use of click-chemistry-liable phospholipid headgroup pulse labels. Here, we describe a method for in vivo phospholipid labelling by fluorescent imaging in Pseudomonas aeruginosa using a phosphatidylcholine mimic, ‘propargyl-choline’ (PCho). This click-chemistry-liable headgroup mimic is visible by microscopy and allows the covalent labelling of lipids. Fluorescence of the cell membranes, visible in heterogeneous patches, is dependent on PCho concentration and is localized in the membrane fraction of cells, demonstrating that it is suitable for membrane labelling and cell imaging.

Salmonella enterica serotype Enteritidis is a generalist serotype that adapts to different hosts and transmission niches. It has significant epidemiological relevance and is among the most prevalent serotypes distributed in several countries. Salmonella Enteritidis causes self-limited gastroenteritis in humans, which can progress to systemic infection in immunocompromised individuals. The Salmonella pathogenicity mechanism is multifactorial and complex, including the presence of virulence factors that are encoded by virulence genes. Poultry products are considered significant reservoirs of many Salmonella serotypes, and Salmonella Enteritidis infections are often related to the consumption of chicken meat and eggs. This study reports the whole-genome sequence of Salmonella Enteritidis PT4 strain 578. A total of 165 genes (3.66%) of the 4506 coding sequences (CDS) predicted in its genome are virulence factors associated with cell invasion, intestinal colonization, and intracellular survival. The genome harbours twelve Salmonella pathogenicity islands (SPIs), with the SPI-1 and SPI-2 genes encoding type III secretion systems (T3SS) showing high conservation. Six prophage-related sequences were found, with regions of intact prophages corresponding to Salmon_118970_sal3 and Gifsy-2. The genome also contains two CRISPR systems. Comparative genome analysis with Salmonella Enteritidis ATCC 13076, Salmonella Typhimurium ATCC 13311, and Salmonella Typhimurium ATCC 14028 demonstrates that most unshared genes are related to metabolism, membrane, and hypothetical proteins. Finally, the phenotypic characterization evidenced differences among Salmonella Enteritidis PT4 578 and the other three serotypes regarding the expression of the red, dry, and rough (rdar) morphotype and biofilm formation. Overall, the genomic characterization and phenotypic properties expand knowledge of the mechanisms of pathogenicity in Salmonella Enteritidis PT4 578.

Our study aimed to identify the bacterial source of a previously detected mobile antibiotic-resistant gene, mecA, found in a lake that serves as a source to a water treatment plant operated by a First Nation reserve. Three methicillin-resistant presumptive Staphylococcus spp. isolated from the sample using selective media were verified as mecA positive by PCR. MALDI-TOF and whole-genome sequencing of each isolate confirmed that all three were Mammaliicoccus fleurettii. Antibiotic-resistant gene analysis of the assembled genomes predicted mecA with 99.7% sequence identity, and phylogenetic analysis grouped our three mecA genes with the mecA allele from a methicillin-resistant strain of Staphylococcus aureus. Identifying microbial species known to harbour mobile antibiotic-resistant elements can provide greater depth of information about drinking water, an especially essential need in First Nation reserves where water quality too frequently is poor.

We announce the deposition of the first two enterotoxigenic Escherichia coli (ETEC) genomes from Malawi. They were isolated from the faeces of asymptomatically infected children obtained in 2014. Both genomes encode the porcine variant of the heat-labile toxin and no known ETEC colonization factors.

Salmonella enterica serovar Typhi primarily persists in chronic carriers by forming biofilms on gallstones in the gallbladder. We have developed a gallstone mouse model to study chronic carriage. To better understand the infection timeline and differentiate between mice that have maintained long-term gallbladder carriage from those that have cleared infection, we utilized bioluminescent S. Typhimurium and in vivo imaging to detect and track the organ-specific presence of bacteria in living mice. The mice infected with our bioluminescent S. Typhimurium showed luminescence in the abdomen as early as 3 days in comparison to the mice infected with non-luminescent WT S. Typhimurium. With our methods, we achieve image resolution such that we can confidently identify the presence of S. Typhimurium in the gallbladder at >60 days post-infection. Using these methods, we have determined that the minimum number of bacteria necessary to detect luminescence in the mice is 103 c.f.u. and that one out of six initially infected mice will remain persistently infected for greater than 60 days, with gallbladder bacterial loads reaching upwards of 103 per milligram of tissue. Given that our limit of detection of luminescence is 103 c.f.u., our sensitivity is robust enough to identify the bacterial loads present in the average chronically infected mouse. The quantification of individual organs’ bacterial c.f.u. and comparison of luminescence between WT and luminescent S. Typhimurium validate that our technique is specific and sensitive enough to detect organ-specific infection in our model of typhoidal chronic carriage.

In the European region, diphtheria is now rarely suspected in patients presenting with upper respiratory tract symptoms. Corynebacterium ulcerans is the underestimated zoonosis that is replacing C. diphtheria infections in industrialized countries, but extensive human and animal prevalence studies are lacking. The range of hosts that can act as reservoirs for C. ulcerans is very broad, companion pets currently being the main source of human infection. We report a case of macrolide-resistant C. ulcerans infection with no apparent zoonotic transmission and outline the efforts required for the public and zooprophylactic management of these cases. We describe the main critical issues to be addressed to comprehensively tackle this zoonosis in the future.