- Volume 5, Issue 7, 2023
Volume 5, Issue 7, 2023
- Research Articles
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Male-killer symbiont screening reveals novel associations in Adalia ladybirds
More LessWhile male-killing bacteria are known to infect across arthropods, ladybird beetles represent a hotspot for these symbioses. In some host species, there are multiple different symbionts that vary in presence and frequency between populations. To further our understanding of spatial and frequency variation, we tested for the presence of three male-killing bacteria: Wolbachia , Rickettsia and Spiroplasma , in two Adalia ladybird species from a previously unexplored UK population. The two-spot ladybird, A. bipunctata, is known to harbour all three male-killers, and we identified Spiroplasma infection in the Merseyside population for the first time. However, in contrast to previous studies on two-spot ladybirds from continental Europe, evidence from egg-hatch rates indicates the Spiroplasma strain present in the Merseyside population does not cause embryonic male-killing. In the related ten-spot ladybird, A. decempunctata, there is only one previous record of a male-killing symbiont, a Rickettsia , which we did not detect in the Merseyside sample. However, PCR assays indicated the presence of a Spiroplasma in a single A. decempunctata specimen. Marker sequence indicated that this Spiroplasma was divergent from that found in sympatric A. bipunctata. Genome sequencing of the Spiroplasma -infected A. decempunctata additionally revealed the presence of cobionts in the form of a Centistes parasitoid wasp and the parasitic fungi Beauveria. Further study of A. decempunctata from this population is needed to resolve whether it is the ladybird or wasp cobiont that harbours Spiroplasma , and to establish the phenotype of this strain. These data indicate first that microbial symbiont phenotype should not be assumed from past studies conducted in different locations, and second that cobiont presence may confound screening studies aimed to detect the frequency of a symbiont in field collected material from a focal host species.
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Are non-lactose-fermenting Escherichia coli important diarrhoeal pathogens in children and adults?
Introduction. Diarrhoeagenic Escherichia coli (DEC) remains one of the major causes of acute diarrhoea episodes in developing countries. The percentage of acute diarrhoea cases caused by DEC is 30–40 % in these countries. Approximately 10% of E. coli isolates obtained from stool specimens have been reported to be non-lactose-fermenting (NLF). The available literature is sparse regarding the pathogenicity of NLF E. coli causing infectious diarrhoea.
Aim. We aimed to elucidate the importance of NLF E. coli in causing diarrhoea in both adults and children by detecting various DEC pathotypes among NLF E. coli in stool samples taken from gastroenteritis cases.
Material and Methods. A total of 376 NLF E. coli isolates from 3110 stool samples from diarrhoea/gastroenteritis patients were included in the study. Up to three NLF colonies that were not confirmed as Vibrio cholerae , Aeromonas spp., Salmonella spp. or Shigella spp., but were identified as E. coli using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF), were carefully picked up from each MacConkey agar plate and then meticulously streaked onto freshly prepared, sterilized nutrient agar plates, and biochemical reactions were conducted. Multiplex PCR was conducted for the EAEC, EPEC, ETEC and EHEC pathotypes and PCR for the ipaH gene was conducted for EIEC. The disc diffusion method was used for antibiotic sensitivity testing.
Results. Using multiplex PCR and ipaH PCR, a total of 63 pathotypes of DEC were obtained, with EAEC being the most predominant (n=31) followed by EIEC (n=22), EPEC (n=8) and ETEC (n=2). To further differentiate EIEC from Shigella , additional biochemical tests were performed, including acetate utilization, mucate and salicin fermentation, and aesculin hydrolysis. Antimicrobial susceptibility testing (AST) showed that maximum resistance was seen against ciprofloxacin (82.5 %) followed by ampicillin (77.8 %) and cotrimoxazole (68.2 %), and minimum resistance was seen against ertapenem (4.8 %).
Conclusion. In our study two pathotypes (EAEC, EIEC) were predominant among NLF E. coli and these were not only important aetiological agents in children, but also in adults. Our study also sheds light on the epidemiology of EIEC, which is one of the most neglected DEC pathotypes, as hardly any microbiological laboratories process NLF E. coli for EIEC.
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Occurrence and prevalence of bacteria on door handles at the University of Port Harcourt Teaching Hospital and the multidrug resistance implications
More LessBackground. The coronavirus disease 2019 (COVID-19) pandemic has heightened concerns regarding transmitting hospital-acquired infections through high-contact points in healthcare facilities, such as door handles, which can serve as reservoirs for pathogenic micro-organisms. With the increased infectivity of the serious acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, there is greater awareness of the risk of multidrug-resistant bacteria on these surfaces, necessitating strict surveillance prevention protocols.
Objective. This study assesses the occurrence and prevalence of bacteria on toilet door handles at the University of Port Harcourt Teaching Hospital in Nigeria and the multidrug resistance implications. We examined the hospital infection level and overall sanitary conditions.
Method. Experimental data from our study on hospital door handles in different locations were assessed. Eighty-six samples were collected from toilet door handles at the University of Port Harcourt Teaching Hospital. Ethical approval was obtained from the hospital departments and the university research ethics committee. Samples from private offices and doors without handles were excluded. Bacteria were isolated from the samples, and antibiotic sensitivity testing was performed.
Result. Of the 329 bacteria isolated, 55.5 % were Gram-positive and 44.4 % Gram-negative. The most prevalent bacteria were Staphylococcus epidermidis , followed by Bacillus sp. The prevalence of multidrug-resistant bacteria was also low, with Enterococcus sp. having the highest prevalence of 28.57%, followed by Micrococcus sp. at 3.45 % and S. epidermidis at 1.96 %.
Conclusion. The results show that, despite the occurrence of pathogenic micro-organisms, there has been a reduction in the prevalence of multidrug-resistant bacteria strains. This study can be used as an example for environmental microbiological surveillance in suspected outbreak investigations and assessment of sanitary conditions and the prevalence of multidrug-resistant bacteria in healthcare facilities.
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Genetic characterization of Escherichia coli and Klebsiella spp. from humans and poultry in Nigeria
The emergence of antibiotic resistance in livestock, especially food-producing animals, is of major public health importance as a result of the possibility of these bacteria entering the food chain. In this study, the genetic characteristics of antibiotic-resistant Escherichia coli and Klebsiella spp. isolates from humans and poultry in Edo state, Nigeria, were investigated. In April 2017, 45 Klebsiella spp. and 46 E. coli isolates were obtained from urine, clinical wounds, nasal and chicken faecal samples. Isolates were recovered and identified as previously described. Species identification was achieved by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry and ribosomal multilocus sequence typing. Antimicrobial susceptibility testing was carried out using the Kirby–Bauer method for 12 antibiotics. A double disc synergy test was used to screen for extended-spectrum beta-lactamse (ESBL) production. Whole genome sequencing was performed for strain characterization of the isolates. Thirteen Klebsiella spp. isolates yielded positive results by the ESBL phenotypic test and harboured ESBL genes. Of the 46 E. coli isolates, 21 human and 13 poultry isolates were resistant to at least one of the tested antibiotics. Four human E. coli isolates harboured ESBL genes and revealed positive results when applying ESBL double disc synergy tests. ESBL genes in the Klebsiella spp. and E. coli isolates include bla CTX-M-15 and bla SHV-28. Whole genome-based core gene multilocus sequence typing of the Klebsiella spp. and E. coli isolates revealed a close relatedness among the isolates. An integrated ‘One Health’ surveillance system is required to monitor transmission of antimicrobial resistance in Nigeria.
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The Vibrio vulnificus stressosome is dispensable in nutrient-rich media
More LessThe stressosome is a protein complex that senses environmental stresses and mediates the stress response in several Gram-positive bacteria through the activation of the alternative sigma factor SigB. The stressosome locus is found in 44 % of Gram-negative Vibrio vulnificus isolates. However, V. vulnificus does not possess SigB. Nonetheless, in nutrient-limited media, the stressosome modulates gene transcription and bacterial behaviour. In this work, the expression of the stressosome genes was proven during stationary phase in nutrient-rich media and co-transcription as one operonic unit of the stressosome locus and its putative downstream regulatory locus was demonstrated. The construction of a stressosome mutant lacking the genes encoding the four proteins constituting the stressosome complex (VvRsbR, VvRsbS, VvRsbT, VvRsbX) allowed us to examine the role of this complex in vivo. Extensive phenotypic characterization of the ΔRSTX mutant in nutrient-rich media showed that the stressosome does not contribute to growth of V. vulnificus . Moreover, the stressosome did not modulate the tolerance or survival response of V. vulnificus to the range of stresses tested, which included ethanol, hyperosmolarity, hypoxia, high temperature, acidity and oxidative stress. Furthermore, the stressosome was dispensable for motility and exoenzyme production of V. vulnificus in nutrient-rich media. Therefore, in conclusion, although stressosome gene transcription occurs in nutrient-rich media, the stressosome neither has an essential role in stress responses of V. vulnificus nor does it seem to modulate these activities in these conditions. We hypothesise that the stressosome is expressed in nutrient-rich conditions as a sensor complex, but that activation of the complex does not occur in this environment.
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Comparative analysis of clinical breakpoints, normalized resistance interpretation and epidemiological cut-offs in interpreting antimicrobial resistance of Escherichia coli isolates originating from poultry in different farm types in Tanzania
More LessIntroduction. Existing breakpoint guidelines are not optimal for interpreting antimicrobial resistance (AMR) data from animal studies and low-income countries, and therefore their utility for analysing such data is limited. There is a need to integrate diverse data sets, such as those from low-income populations and animals, to improve data interpretation.
Gap statement. There is very limited research on the relative merits of clinical breakpoints, epidemiological cut-offs (ECOFFs) and normalized resistance interpretation (NRI) breakpoints in interpreting microbiological data, particularly in animal studies and studies from low-income countries.
Aim. The aim of this study was to compare antimicrobial resistance in Escherichia coli isolates using ECOFFs, CLSI and NRI breakpoints.
Methodology. A total of 59 non-repetitive poultry isolates were selected for investigation based on lactose fermentation on MacConkey agar and subsequent identification and confirmation as E. coli using chromogenic agar and uidA PCR. Kirby Bauer disc diffusion was used for susceptibility testing. For each antimicrobial agent, inhibition zone diameters were measured, and ECOFFs, CLSI and NRI bespoke breakpoints were used for resistance interpretation.
Results. According to the interpretation of all breakpoints except ECOFFs, tetracycline resistance was significantly higher (TET) (67.8 –69.5 %), than those for ciprofloxacin (CIPRO) (18.6 –32.2 %), imipenem (IMI) (3.4 –35 %) and ceftazidime (CEF) (1.7 –45.8 %). Prevalence estimates of AMR using CLSI and NRI bespoke breakpoints did not differ for CEF (1.7 % CB and 1.7 % COWT), IMI (3.4 % CB and 4.0 % COWT) and TET (67.8 % CB and 69.5 % COWT). However, with ECOFFs, AMR estimates for CEF, IMI and CIP were significantly higher (45.8, 35.6 and 64.4 %, respectively; P<0.05). Across all the three breakpoints, resistance to ciprofloxacin varied significantly (32.2 % CB, 64.4 % ECOFFs and 18.6 % COWT, P<0.05).
Conclusion. AMR interpretation is influenced by the breakpoint used, necessitating further standardization, especially for microbiological breakpoints, in order to harmonize outputs. The AMR ECOFF estimates in the present study were significantly higher compared to CLSI and NRI.
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Assessing the evolution of SARS-CoV-2 lineages and the dynamic associations between nucleotide variations
More LessDespite seminal advances towards understanding the infection mechanism of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), it continues to cause significant morbidity and mortality worldwide. Though mass immunization programmes have been implemented in several countries, the viral transmission cycle has shown a continuous progression in the form of multiple waves. A constant change in the frequencies of dominant viral lineages, arising from the accumulation of nucleotide variations (NVs) through favourable selection, is understandably expected to be a major determinant of disease severity and possible vaccine escape. Indeed, worldwide efforts have been initiated to identify specific virus lineage(s) and/or NVs that may cause a severe clinical presentation or facilitate vaccination breakthrough. Since host genetics is expected to play a major role in shaping virus evolution, it is imperative to study the role of genome-wide SARS-CoV-2 NVs across various populations. In the current study, we analysed the whole genome sequence of 3543 SARS-CoV-2-infected samples obtained from the state of Telangana, India (including 210 from our previous study), collected over an extended period from April 2020 to October 2021. We present a unique perspective on the evolution of prevalent virus lineages and NVs during this period. We also highlight the presence of specific NVs likely to be associated favourably with samples classified as vaccination breakthroughs. Finally, we report genome-wide intra-host variations at novel genomic positions. The results presented here provide critical insights into virus evolution over an extended period and pave the way to rigorously investigate the role of specific NVs in vaccination breakthroughs.
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Characterization and in vitro antibacterial activity of sulfated polysaccharides from freshwater alga Cladophora crispata
More LessBarada River is characterized by an abundant growth of freshwater algae. Cladophora sp. algae have emerged as a new source of bioactive compounds. In this research Cladophora crispata was cultivated with the outdoor method, and algal sulfated polysaccharides (SPs) were extracted by an ultrasonic-assisted extraction method. After extraction, gel filtration was used to purify the crude SPs, SP compounds were determined and selected, and the effect of purified SPs as antibacterial agents was investigated. The purified extract gave two fractions (F1 and F2). The chemical components of both crude and purified SPs were then determined. The highest carbohydrate content (74.12%) and protein content (4.02%) was found in the crude extract, while the highest sulfate content (12.17%) was found in purified fraction F2, and the highest uronic acid content (18.46%) was found in purified fraction F1. Fourier transform infrared spectroscopy (FT-IR) was used to confirm that the crude extract and fractions consist of sugar, uronic acids, protein and sulfate groups. Both F1 and F2 consisted of rhamnose, galactose, xylose and ribose based on high performance liquid chromatography (HPLC) separation. Each fraction showed an inhibitory effect on Gram-positive and Gram-negative bacteria. F2 has the lowest minimum inhibitory concentration (MIC) value against Staphylococcus aureus , Bacillus anthracis , Enterobacter aerogenes and Pseudomonas aeruginosa , where its MIC values were 6, 13, 25 and 30 mg ml−1, respectively. Algae polysaccharides are of key interest due to their antibacterial properties, which has led to them being included in pharmaceutics and food applications.
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- Short Communications
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Draft genome sequence of Enterobacter cloacae ST473 harbouring blaCMH-3 isolated from a human patient diagnosed with recurrent bacteriuria in Nigeria
Enterobacter cloacae is among the most frequently isolated species described in clinical infections and is commonly associated with a multidrug resistance (MDR) phenotype. We present the draft genome sequence of a MDR E. cloacae isolated in Nigeria from the urine sample of an adult male outpatient diagnosed with symptomatic recurrent bacteriuria. The isolate was found to be resistant to ceftriaxone, cefotaxime, cefepime and levofloxacin. Genome analysis revealed the presence of the beta-lactamase chromosomal gene blaCMH-3, which may be responsible for the antibiotic resistance observed in the recurrent E. cloacae urinary tract infection.
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Binding of respiratory syncytial virus particles to platelets does not result in their degranulation in vitro
More LessRespiratory syncytial virus (RSV) is a major cause of severe respiratory infection in infants and the elderly. The mechanisms behind severe RSV disease are incompletely understood, but a dysregulated immune response probably plays an important role. Platelets are increasingly being recognized as immune cells and are involved in the pathology of several viruses. The release of chemokines from platelets upon activation may attract, for example, neutrophils to the site of infection, which is a hallmark of RSV pathology. In addition, since RSV infections are sometimes associated with cardiovascular events and platelets express several known RSV receptors, we investigated the effect of RSV exposure on platelet degranulation. Washed human platelets were incubated with sucrose-purified RSV particles. P-selectin and CD63 surface expression and CCL5 secretion were measured to assess platelet degranulation. We found that platelets bind and internalize RSV particles, but this does not result in degranulation. Our results suggest that platelets do not play a direct role in RSV pathology by releasing chemokines to attract inflammatory cells.
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Draft genome sequences for ten strains of Xanthomonas species that have phylogenomic importance
Here we report draft-quality genome sequences for pathotype strains of eight plant-pathogenic bacterial pathovars: Xanthomonas campestris pv. asclepiadis, X. campestris pv. cannae, X. campestris pv. esculenti, X. campestris pv. nigromaculans, X. campestris pv. parthenii, X. campestris pv. phormiicola, X. campestris pv. zinniae and X. dyei pv. eucalypti (= X. campestris pv. eucalypti). We also sequenced the type strain of species X. melonis and the unclassified Xanthomonas strain NCPPB 1067. These data will be useful for phylogenomic and taxonomic studies, filling some important gaps in sequence coverage of Xanthomonas phylogenetic diversity. We include representatives of previously under-sequenced pathovars and species-level clades. Furthermore, these genome sequences may be useful in elucidating the molecular basis for important phenotypes, such as biosynthesis of coronatine-related toxins and degradation of fungal toxin cercosporin.
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Complete genome sequence of Staphylococcus casei strain DSM 15096
More LessWe present the first complete genome sequence of the species Staphylococcus casei . Strain DSM 15096 was sequenced with a hybrid approach using Oxford Nanopore Technologies long-read sequencing and Illumina short-read sequencing. The assembled sequences produced a 2 808 898 bp chromosomal molecule containing 2705 predicted genes, plus eight plasmids.
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- Case Reports
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Bordetella trematum bacteraemia secondary to an empyema in an immunocompromised host: A case report and review of the literature
More LessIntroduction. Bordetella trematum infection remains uncommon. More cases of bacteraemia are reported in recent years with the primary infection largely originating from skin and soft tissue sites. Yet, our understanding of its virulence, antibiotic susceptibility profile and treatment is still limited.
Case presentation. We report the first case of B. trematum bacteraemia from a left-sided empyema. An 87-year-old female patient with a past medical history of ischaemic heart disease, diabetes mellitus complicated by nephropathy and locally advanced left breast adenocarcinoma presented with fever, productive cough and shortness of breath. The B. trematum isolates from blood and pleural fluid were identified by MALDI-TOF and 16S rRNA sequencing. Ceftriaxone and azithromycin commenced empirically on admission were switched to piperacillin-tazobactam after 2 days due to lack of clinical improvement. Despite a pleurocentesis and 1 week of piperacillin-tazobactam with microbiological clearance in blood, the patient continued to deteriorate. Decision to withdraw treatment was made in view of the patient’s prognosis, and the patient succumbed on the fourteenth day of admission. The isolate was susceptible to piperacillin-tazobactam, imipenem and meropenem but had reduced susceptibility or was non-susceptible to cefuroxime, cefotaxime, ceftazidime, cefepime, the aminoglycosides and fluoroquinolones.
Conclusion. Invasive B. trematum infection is associated with significant mortality. Consensus for antibiotic treatment remains unclear, with limited susceptibility data to support specific antibiotic use. We expect more clinical cases will surface with improved microbial identification systems, as well as enhanced clinical awareness. Standardized and more robust susceptibility work are needed to provide clear recommendations and establish consensus in treating invasive infections.
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A case report of disseminated Streptococcus pneumoniae infection complicated by infective endocarditis, septic arthritis and epidural abscess in an immunocompetent patient
More LessStreptococcus pneumoniae is a highly virulent, vaccine-preventable pathogen which can cause disease on a spectrum from benign to fatal. Apart from pneumonia, it commonly causes septicaemia and meningitis. This case report describes an unusual range of complications in a 53-year-old Caucasian female presenting to a regional hospital, without any risk known factors for severe disease (such as extremes of age, immunodeficiency or co-morbidities). Progressing from an episode of otitis media, her condition rapidly progressed to mastoid sinusitis, septic arthritis, infective endocarditis, epidural abscesses and multiple subcutaneous abscesses. Following quick identification of S. pneumoniae from a positive blood culture, the patient was treated with high-dose benzylpenicillin and ceftriaxone and aggressive source control by surgery, enabling a good clinical recovery.
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Prevalence and resistance pattern of uropathogens from community settings of different regions: an experience from India
Sarita Mohapatra, Rajashree Panigrahy, Vibhor Tak, Shwetha J. V., Sneha K. C., Susmita Chaudhuri, Swati Pundir, Deepak Kocher, Hitender Gautam, Seema Sood, Bimal Kumar Das, Arti Kapil, Pankaj Hari, Arvind Kumar, Rajesh Kumari, Mani Kalaivani, Ambica R., Harshal Ramesh Salve, Sumit Malhotra and Shashi Kant
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