- Volume 5, Issue 8, 2023

The microbiome profoundly influences many traits in medically relevant vectors such as mosquitoes, and a greater functional understanding of host–microbe interactions may be exploited for novel microbial-based approaches to control mosquito-borne disease. Here, we characterized two novel clustered regularly interspaced short palindromic repeats (CRISPR)/Cas systems in Serratia sp. Ag1, which was isolated from the gut of an Anopheles gambiae mosquito. Two distinct CRISPR/Cas systems were identified in Serratia Ag1, CRISPR1 and CRISPR2. Based on cas gene composition, CRISPR1 is classified as a type I-E CRISPR/Cas system and has a single array, CRISPR1. CRISPR2 is a type I-F system with two arrays, CRISPR2.1 and CRISPR2.2. RT-PCR analyses show that all cas genes from both systems are expressed during logarithmic growth in culture media. The direct repeat sequences of CRISPRs 2.1 and 2.2 are identical and found in the arrays of other Serratia spp., including S. marcescens and S. fonticola , whereas CRISPR1 is not. We searched for potential spacer targets and revealed an interesting difference between the two systems: only 9 % of CRISPR1 (type I-E) targets are in phage sequences and 91 % are in plasmid sequences. Conversely, ~66 % of CRISPR2 (type I-F) targets are found within phage genomes. Our results highlight the presence of CRISPR loci in gut-associated bacteria of mosquitoes and indicate interplay between symbionts and invasive mobile genetic elements over evolutionary time.

Background. Staphylococcus aureus and Streptococcus pneumoniae are common inhabitants of the nasopharynx of children. HIV-infected children have higher risk of invasive diseases caused by these pathogens. With widespread use of pneumococcal conjugate vaccines and the emergence of methicillin-resistant S. aureus , the interaction between S. aureus and S. pneumoniae is of a particular significance. We sought to determine the magnitude of colonization by methicillin-sensitive and -resistant S. aureus and colonization by S. pneumoniae ; associated risk factors and antimicrobial susceptibility pattern among HIV-infected children in Addis Ababa, Ethiopia.

Method. A prospective observational study was conducted among 183 HIV-infected children at ALERT hospital Addis Ababa, Ethiopia from September 2016 to August 2018. S. aureus and S. pneumoniae were identified using standard bacteriological techniques, antimicrobial susceptibility testing was performed on S. aureus and screening for methicillin resistance was carried out by amplifying the mecA gene. Risk factors were analysed by using binary logistic regression.

Results. The prevalence of nasopharyngeal S. aureus , MRSA and S. pneumoniae colonization were 27.3, 2.7 and 43.2 %, respectively. Multivariable analysis indicated an inverse association between S. aureus and S. pneumoniae nasopharyngeal colonization [aOR, 0.49; CI, (0.24, 0.99); P=0.046]. The highest level of resistance in both methicillin-sensitive S. aureus (MSSA) and MRSA was observed against tetracycline.

Conclusions. We found an inverse association between S. aureus and S. pneumoniae colonization among HIV-infected children. Continued assessment of the impact of pneumococcal conjugate vaccines and antiretroviral therapy on nasopharyngeal bacterial ecology is warranted.

Background. Since Anopheles mosquitoes which transmit and maintain the malaria parasite breed in the outdoor environment, there is an urgent need to manage these mosquito breeding sites. In order to elaborate more on the ecological landscape of mosquito breeding sites, the bacterial community structure and their interactions with physicochemical factors in mosquito larval habitats was characterised in Kwale County (Kenya), where malaria is endemic.

Methods. The physical characteristics and water physicochemical parameters of the habitats were determined and recorded. Water samples were also collected from the identified sites for total metagenomic DNA extraction in order to characterise the bacterial communities within the breeding sites.

Results and Discussion. Sites where mosquito larvae were found were described as positive and those without mosquito larvae as negative. Electrical conductivity, total dissolved solids, salinity and ammonia were lower in the rainy season than in the dry season, which also coincided with a high proportion of positive sites. Pseudomonadota was the most common phyla recovered in all samples followed by Bacteroidota and then Actinomycetota. The presence or absence of mosquito larvae in a potential proliferation site was not related to the bacterial community structure in the sampled sites, but was positively correlated with bacterial richness and evenness.

Conclusion. Generally, the presence of Anopheles mosquito larvae was found to be positively correlated with rainy season, bacterial richness and evenness, and negatively correlated with electrical conductivity, total dissolved solids, salinity and ammonia. The findings of this study have implications for predicting the potential of environmental water samples to become mosquito proliferation sites.

Background. Escherichia coli is a common cause of urinary tract infections. Due to the increase in antimicrobial resistance (AMR) and global differences in antimicrobial susceptibility data, routine assessment of local antimicrobial susceptibility patterns is necessary to guide the selection of appropriate empirical therapy. The aim of this study was to evaluate the antimicrobial susceptibility patterns of community-acquired uropathogenic Escherichia coli within a catchment area in Dublin over a 13 year period, 2010–2022.

Methods. All mid-stream urine samples received from local general practitioners in which there was significant E. coli bacteriuria during the study period, 2010–2022, were included in the analysis. Antimicrobial susceptibility testing was performed by disc diffusion as per the European Committee on Antimicrobial Susceptibility Testing recommendations.

Results. An average of 11 407 urine samples per month had significant bacteriuria, with E. coli accounting for an average of 67 % of those. Overall AMR rates were highest for ampicillin (53.9 %), followed by trimethoprim (32.4 %), gentamicin (18.6 %), co-amoxiclav (16.5 %), ciprofloxacin (12.3 %), cephalexin (8.3 %), cefpodoxime (6.8 %) and nitrofurantoin (2 %). While rates appeared grossly static, statistically significant reduced resistance rates were noted for co-amoxiclav (rs=−0.95; P=<0.001), cephalexin prior to 2019 (rs=−0.783; P=0.013) and trimethoprim (rs=−0.639; P=0.019), with a statistically significant increase in non-susceptibility to cefpodoxime (rs=0.802; P=0.001).

Conclusions. In order to generate efficient empirical antimicrobial prescribing guidelines, knowledge of region-specific contemporaneous antimicrobial susceptibility patterns is pivotal. Our findings support the use of nitrofurantoin or cephalexin as empirical antimicrobial therapy within our setting.

Introduction. Acinetobacter species are non-fermenting and ubiquitous Gram-negative coccobacilli, which in recent years have become the leading cause of healthcare-associated infections worldwide. Our objective here was to study the epidemiology and risk factors associated with Acinetobacter baumannii infections in the intensive care unit (ICU).

Methods. This retrospective case-control study was conducted collaboratively between the Medical Bacteriology Department and the two ICUs of the Military Hospital of Instruction Mohammed V-Rabat over a 3 month period.

Results. We included 180 patients, of whom 60 had A. baumannii infection. We observed a male predominance in both matched groups, with a sex ratio of 1.6. The median age was 67 years [interquartile range (IQR) 59.5–77]. The median length of stay in the ICU before infection was 8.5 days (IQR 5–14). Multivariate logistic regression analysis identified the risk factors statistically associated with A. baumannii infection at the ICU level as follows: duration of invasive procedures >7 days [odds ratio (OR)=1.02], parenteral nutrition (OR=3.514), mechanical ventilation (OR=3.024), imipenem (OR=18.72), colistin (OR=5.645), probabilistic antibiotic therapy >4 days (OR=9.063) and neoplastic pathology (OR=5.727).

Conclusion. Based on our results, it can be inferred that shortening the duration of stay in the resuscitation setting, implementing rational use of medical devices and optimizing antibiotic therapy could decrease the incidence of these infections.

Using ion torrent sequencing of the V4 region of the 16S rRNA gene, we investigated the sediment from four anchialine caves on Eleuthera (Bahamas). Anchialine caves are secluded, landlocked marine ecosystems, with high degrees of endemism. In the cave sediments, the bacterial and archaeal communities differ from marine communities and between caves, while often resembling those from low oxygen or anaerobic marine sediments. The waters of all caves investigated here were mostly saline and oxygenated, with Windermere Abyss differing from the other caves. This was mirrored by the bacterial and archaeal communities, with members of the wb1-A12 clade, Nitrosopumilaceae , members of the NB1-j phylum, and Actinomarinales being dominant in Preacher’s Blue Hole, Valentine’s Cave, and Bung Hole while Desulfatiglans , Bathyarchaeia, and members of the GIF3 and Sva0485 clades were dominant in Windermere Abyss. All communities showed taxa found in oxygenated and anoxic sediments, thus indicating a variety of chemoautotrophic lifestyles, including methane-, nitrogen- and sulphur cycling. The communities were different from other caves and included understudied or otherwise rare taxa, partially from deep sea sediments, implying that the isolation might be an evolutionary factor, and indicating that anchialine caves could be a window into the deep sea.

Alternative methods for arbuscular mycorrhizal (AM) fungal colonized root staining have recently gained more attention for the reduction of hazard exposure to the user. Sheaffer blue ink has been employed for such an identification and quantification, having shown an increased degree of image clarity. However, sourcing Sheaffer blue ink is becoming problematic, leading to the need to find alternative inks that are readily available. Parker ink is a well-known brand, providing comparable colour options to Sheaffer. Two Parker inks, blue and washable blue, were employed alongside Sheaffer blue for comparative AM fungal colonized root staining. From quantified AM fungal vesicles and arbuscles, along with the degree of stained image clarity under microscopy, none of the inks utilized for this comparison produce a significantly (P=0.97) different AM fungal quantification or change in image clarity. Therefore, the results of the present communication suggest that Parker blue and washable blue inks are alternative ink stains for the viewing and quantification of AM fungi in host cortical root tissues.

Introduction. Kingella kingae is a Gram-negative micro-organism that is rarely isolated as a pathogen in the adult population. Although widely reported to affect prosthetic heart valves, there have been no previously reported cases of K. kingae infecting prosthetic joints in adults.

Case Presentation. A 61-year-old patient with a history of rheumatoid arthritis presented with insidious onset of pain and swelling in her right shoulder, which had progressed to a discharging sinus. The patient had undergone a total shoulder replacement 11 years previously and had not developed any prior post-operative infections. She had been taking anti-TNF medication for 5 years prior to review for her rheumatoid disease. The patient underwent a two-stage revision replacement procedure, including implant removal, sinus excision and debridement. Deep tissue samples grew K. kingae post-operatively. The patient was commenced on intravenous ceftriaxone for 14 days, followed by a further 28 days of oral ciprofloxacin. A second-stage custom shoulder replacement was undertaken 10 months following the first stage and the patient made a good functional recovery.

Conclusion. The authors suggest that clinicians should be attuned to K. kingae as a potential pathogen for prosthetic joint infection, particularly in patients who are immunosuppressed. Two-stage revision procedures can ensure a favourable outcome and eradication of this pathogen from the joint. Beta lactams remain the principal antibiotic of choice.

Introduction. The human oral cavity comprises various niches such as teeth, gingiva, tongue, soft and hard palate, and various dental prostheses, all inhabited by different bacterial species. Although more than 600 taxa belong to the oral cavity, identifying Staphylococcus arlettae , an incompletely understood bacterium, has been rare.

Methods. Three patients who underwent periodontal flap surgeries were reported with the incidental finding of S. arlettae associated with the intra-oral sutures placed. Environmental sampling was performed, to establish the exact source of this bacterium.

Results. Staphylococcus arlettae was isolated in three patients’ intra-oral sutures. All environmental samples were negative for the presence of the bacterium.

Conclusion. To this date, no studies have identified such an occurrence of Staphylococcus arlettae with intra-oral sutures. Its identification in association with foreign materials, such as sutures, can be considered a potential for surgical site infections and requires further investigation.