- Volume 72, Issue 12, 2024
Volume 72, Issue 12, 2024
- Editorials
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- JMM Profiles
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JMM Profile: Rift Valley fever: a zoonotic viral haemorrhagic disease
More LessRift Valley fever (RVF) is caused by infection with Rift Valley fever virus (RVFV), a mosquito-borne RNA virus that affects both humans and livestock species. Humans can also acquire infection from contact with infected animals and contaminated bodily fluid. Veterinary vaccines are available for use in livestock, but no vaccines have been approved for humans to date. The virus is currently endemic in most sub-Saharan regions of Africa but numerous incursions into Middle Eastern countries and islands in the Indian Ocean, such as Mayotte (an overseas Department of France), have occurred in the past decade. The risk of further geographical expansion is high and therefore additional investigation is warranted to better understand disease transmission and pathogenic mechanisms to develop threat mitigation strategies.
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- Antimicrobial Resistance
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Preliminary view of the distribution and spread of the plasmid-mediated resistance genes in Glaesserella parasuis
Introduction. Various plasmid-mediated resistance genes have been reported in Glaesserella parasuis , but little is known about their global distribution features, evolution pattern and spread.
Gap Statement. The potential mobilization mechanisms of resistance plasmids in G. parasuis have been poorly explored.
Aim. The aim of the study was to investigate the prevalence and diversity of plasmid-mediated resistance genes among G. parasuis isolates, and focus on the analysis of the features of the resistance plasmids from G. parasuis .
Method. The plasmids tested were sequenced using the Illumina HiSeq platform in conjunction with PCR and inverted PCR. The susceptibility of the host strains was determined by broth microdilution. The transfer of plasmids tested was conducted by electroporation. The sequence data were compared using bioinformatics tools and the data from our laboratory and the National Center for Biotechnology Information (NCBI) database.
Results. Nineteen plasmids were identified from our laboratory and these resistance plasmids were functional and transferable. Moreover, we clustered five types of genetic backbones of plasmids from G. parasuis and revealed the global distribution features of the plasmid-mediated resistance genes.
Conclusions. This is the first report of the coexistence of tet(H)-bearing type I plasmid and lnu(C)-bearing type II plasmid in one G. parasuis clinical isolate. In addition, this study provides the first view of the global distribution of plasmid-mediated resistance genes and classifies the plasmids in G. parasuis according to their backbone regions.
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Multi-drug-resistant tuberculosis and its associated factors among pulmonary tuberculosis patients linked to first-line anti-tuberculosis drugs in north-west Ethiopia
More LessIntroduction. Multi-drug-resistant tuberculosis (MDR-TB) is an emerging global challenge. Ethiopia is one of the 20 top countries with the highest estimated numbers of incidents of MDR-TB. Recently, the World Health Organization warned that drug-resistant TB is escalating and called for concerted action to reduce the spread of drug resistance.
Hypothesis. The current study investigated MDR-TB in patients receiving first-line anti-TB drug treatment and associated factors.
Aim. The study aimed to determine the prevalence of MDR-TB and its associated factors among smear-positive pulmonary TB patients receiving first-line anti-TB drug treatment.
Methodology. An institution-based cross-sectional study was employed. All data were collected from laboratory result log books and information via a questionnaire. Samples from 205 smear-positive pulmonary TB patients were selected among first-line drug treatment by a systematic sampling method. Specimens were transported to Felege Hiwot referral hospital laboratory for GeneXpert testing. Factors associated with an outcome variable in binary multi-variable logistic regression analysis at P<0.05 were considered statistically significant variables. An ethical approval letter was taken to the respective health facility and written consent was obtained from each participant.
Results. The overall prevalence of MDR-TB was 9.3 % (95 % CI, 5.4 13.7 %). Sign and symptom experience of anti-TB drug side effects [adjusted odds ratio (AOR)=0.18, 95 % CI=0.03–0.99, P=0.049] and co-morbidity (AOR=0.03, 95 % CI=0.01–0.55, P=0.02) were statistically associated with the development of MDR-TB infection
Conclusion. The prevalence of MDR-TB was high (9.3 %) and contributed highly to new cases (8.3 %). Factors associated with MDR-TB were previous treatment, co-morbidity and laboratory diagnosis method prior to TB treatment. Therefore, this finding aims to maximize early detection and treatment, strengthening TB infection control, and proper implementation of directly observed therapy short course recommendations to reduce the burden of MDR-TB.
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- Disease, Diagnosis and Diagnostics
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Mixture modelling of Bordetella pertussis serology samples to evaluate anti-pertussis toxin immunoglobulin G titre thresholds for positivity: England 2008–2022
Introduction. Antibody testing for evidence of a recent Bordetella pertussis infection by estimating anti-pertussis toxin immunoglobulin G (anti-PT-IgG) titres by enzyme-linked immunosorbent assays is often recommended for those with a cough lasting more than 14 days. Interpreting results varies, with studies recommending different anti-PT-IgG titre thresholds for assigning positivity. In England, early work looking at antibody titre distributions for samples submitted from April 2010 to July 2012 found an optimal threshold of greater than 70 IU ml−1 for good sensitivity, specificity and positive predictive value.
Aim. The aim of this study is to use the same mixture modelling technique to determine if the 70 IU ml−1 threshold remains appropriate when assessing data before, during and after the outbreak of pertussis in 2011–2012.
Methods. We reviewed titres for all serology-tested samples in England between 1 July 2008 to 30 June 2022. IgG titres were used to calculate the positivity based on the current threshold of 70 IU ml−1, the median duration of cough for individuals who tested positive and, through mixture modelling, the sensitivity, specificity, positive and negative predictive values (PPV and NPV) of assay thresholds.
Results. Positivity rates increased from 21.7 % prior to the outbreak to 30.3 % during the outbreak and dropped to 25.1 % post-outbreak; similar to estimates from the mixture model of 20.5, 33.3 and 28.7 %, respectively. Although the estimated sensitivity dropped during and after the outbreak when applying the 70 IU ml−1 threshold, the PPV remained high and therefore no change to this threshold is warranted.
Conclusion. Mixture modelling is a useful tool to establish thresholds, but reassessment should also be done when there have been changes to prevalence and/or testing regimes to determine whether there have been any changes in sensitivity, specificity, PPV, and NPV and whether the threshold should be revised.
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Engineering of the LAMP-CRISPR/Cas12b platform for Chlamydia psittaci detection
More LessIntroduction. Chlamydia psittaci ( C. psittaci ) is a zoonotic infection, that causes psittacosis (parrot fever) in humans, leading to severe clinical manifestations, including severe pneumonia, adult respiratory distress syndrome, and, in rare cases, death.
Gap Statement. Rapid, sensitive and specific detection of C. psittaci facilitates timely diagnosis and treatment of patients.
Aim. This study aimed to engineer the LAMP-CRISPR/Cas12b platform for C. psittaci detection.
Methodology. The loop-mediated isothermal amplification (LAMP) technique and clustered regularly interspaced short palindromic repeats-CRISPR associated protein 12b (CRISPR-Cas12b) assay were combined to establish two-step and one-tube LAMP-CRISPR/Cas12b reaction systems, respectively, for rapidly detecting C. psittaci .
Results. The two-step and one-tube LAMP-CRISPR/Cas12b assay could complete detection within 1 h. No cross-reactivity was observed from non- C. psittaci templates with specific LAMP amplification primers and single-guide RNA (sgRNA) targeting the highly conserved short fragment CPSIT_0429 gene of C. psittaci . The detection limits of the two-step and one-tube LAMP-CRISPR/Cas12b reaction were 102 aM and 103 aM, respectively. The results were consistent with qPCR for nucleic acid detection in 160 clinical samples, including 80 suspected C. psittaci samples, kept in the laboratory.
Conclusions. The LAMP-CRISPR/Cas12b assay developed in this study provides a sensitive and specific method for rapidly detecting C. psittaci and offers technical support for its rapid diagnosis.
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Evaluation of a novel chromogenic screening method for detection of carbapenem-resistant Escherichia coli
Introduction. Early detection of carbapenem-resistant Escherichia coli (CREco), categorized as a critical priority pathogen by the World Health Organization (WHO), is crucial in optimizing therapeutic options and to thwart outbreaks in clinical settings.
Gap statement. The need of the hour is a diagnostic method that can detect carbapenem resistance conferred by intrinsic or acquired carbapenem resistance mechanisms or both.
Aim. The study investigates the performance of a novel screening chromogenic method for detection of CREco.
Methodology. Carbapenem-susceptible (n=23) and non-susceptible (n=90) E. coli were used to investigate the efficiency of the blue chromogenic test. All of the isolates were received from a tertiary referral hospital in Silchar, India and subjected to the blue chromogenic test and observed for colour change. A colour change from colourless to blue is interpreted as a positive result. The test results were further compared with available methods for detection of carbapenem resistance conferred by carbapenemase production or other carbapenem resistance mechanisms.
Results. The blue chromogenic test generated 100 % (CI: 95.98–100 %) sensitive and 100 % (CI: 85.75–100 %) specific results for the detection of CREco with no false-positive or false-negative results. Within 3 h after incubation, the test detects all CREco with carbapenemase activity. Additionally, the blue chromogenic test also positively detected E. coli harbouring carbapenemase variants and with efflux and porin activity, compared to other phenotypic-based approaches.
Conclusion. The study highlights a novel method that is highly sensitive and specific, inexpensive, rapid and user-friendly for the detection of CREco. With the surge and expansion of CREco, this sensitive, specific, user-friendly and inexpensive method can be used in laboratories with limited facilities for early detection of CREco, thereby improving infection control along with averting future outbreaks.
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- Microbiome and Microbial Ecology in Health
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Meta-analysis of sputum microbiome studies identifies airway disease-specific taxonomic and functional signatures
More LessIntroduction. Studying taxonomic and functional signatures of respiratory microbiomes provide a better understanding of airway diseases.
Gap Statement. Several human airway metagenomics studies have identified taxonomic and functional features restricted to a single disease condition and the findings are not comparable across airway diseases due to use of different samples, NGS platforms, and bioinformatics databases and tools.
Aim. To study the microbial taxonomic and functional components of sputum microbiome across airway diseases and healthy smokers.
Methodology. Here, 57 whole metagenome shotgun sequencing (WMSS) runs coming from the sputum of five airway diseases: asthma, bronchiectasis, chronic obstructive pulmonary diseases (COPD), cystic fibrosis (CF), tuberculosis (TB), and healthy smokers as the control were reanalysed using a common WMSS analysis pipeline.
Results. Shannon’s index (alpha diversity) of the healthy smoker group was the highest among all. The beta diversity showed that the sputum microbiome is distinct in major airway diseases such as asthma, COPD and cystic fibrosis. The microbial composition based on differential analysis showed that there are specific markers for each airway disease like Acinetobacter bereziniae as a marker for COPD and Achromobacter xylosoxidans as a marker of cystic fibrosis. Pathways and metabolites identified from the sputum microbiome of these five diseases and healthy smokers also show specific markers. ‘ppGpp biosynthesis’ and ‘purine ribonucleosides degradation’ pathways were identified as differential markers for bronchiectasis and COPD. In this meta-analysis, besides bacteria kingdom, Aspergillus fumigatus was detected in asthma and COPD, and Roseolovirus human betaherpesvirus 7 was detected in COPD. Our analysis showed that the majority of the gene families specific to the drug-resistant associated genes were detected from opportunistic pathogens across all the groups.
Conclusion. In summary, the specific species in the sputum of airway diseases along with the microbial features like specific gene families, pathways, and metabolites were identified which can be explored for better diagnosis and therapy.
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Volumes and issues
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Volume 73 (2024)
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Volume 72 (2023 - 2024)
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Volume 71 (2022)
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Volume 70 (2021)
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Volume 69 (2020)
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Volume 68 (2019)
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Volume 67 (2018)
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Volume 66 (2017)
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Volume 65 (2016)
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Volume 64 (2015)
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Volume 63 (2014)
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Volume 62 (2013)
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Volume 61 (2012)
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Volume 60 (2011)
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Volume 59 (2010)
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Volume 58 (2009)
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Volume 57 (2008)
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Volume 56 (2007)
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Volume 55 (2006)
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Volume 54 (2005)
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Volume 53 (2004)
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Volume 52 (2003)
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Volume 51 (2002)
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Volume 50 (2001)
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Volume 49 (2000)
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Volume 48 (1999)
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Volume 47 (1998)
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Volume 46 (1997)
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Volume 45 (1996)
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Volume 44 (1996)
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Volume 43 (1995)
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Volume 42 (1995)
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Volume 41 (1994)
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Volume 40 (1994)
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Volume 39 (1993)
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Volume 38 (1993)
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Volume 37 (1992)
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Volume 36 (1992)
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Volume 35 (1991)
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Volume 34 (1991)
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Volume 33 (1990)
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Volume 32 (1990)
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Volume 31 (1990)
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Volume 30 (1989)
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Volume 29 (1989)
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Volume 28 (1989)
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Volume 27 (1988)
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Volume 26 (1988)
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Volume 25 (1988)
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Volume 24 (1987)
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Volume 23 (1987)
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Volume 22 (1986)
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Volume 21 (1986)
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Volume 20 (1985)
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Volume 19 (1985)
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Volume 18 (1984)
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Volume 17 (1984)
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Volume 16 (1983)
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Volume 15 (1982)
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Volume 14 (1981)
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Volume 13 (1980)
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Volume 12 (1979)
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Volume 11 (1978)
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Volume 10 (1977)
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Volume 9 (1976)
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Volume 8 (1975)
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Volume 7 (1974)
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Volume 6 (1973)
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Volume 5 (1972)
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Volume 4 (1971)
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Volume 3 (1970)
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Volume 2 (1969)
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Volume 1 (1968)