Burden, Antibiotic Resistance, and Clonality of Shigella spp. Implicated in Community-Acquired Acute Diarrhoea in Lilongwe, Malawi

Prevalence of antibiotic self-medication and knowledge of antimicrobial resistance among community members in Neno District rural Malawi: A cross-sectional study

Objectives

Despite global efforts to address antibiotic self-medication, it is still significantly prevalent. This study aimed to investigate the prevalence of antibiotic self-medication and assess knowledge of antibiotic resistance among community members in Neno District, rural Malawi.

Methods

A cross-sectional, community-based study was conducted from September to November 2023, using simple random sampling across 169 villages. Participants from two households per village were surveyed using a "drug bag" method, focusing on those who had taken antibiotics within the preceding 6 months. In addition, drug retailers were selected via snowball sampling for interviews.

Results

Of the 531 participants and 39 drug retailers, 71.1% reported antibiotic use, with 69.5% self-medicating in the past 6 months, with convenience (31.5%) and confidence (26.7%) being the reasons. Common symptoms prompting self-medication included cough (29.9%), sore throat (28.6%), and aches and pain (28.6%). Amoxicillin (61.1%) and cotrimoxazole (29.6%) were the most used antibiotics. More than half (53.1%) reused leftover antibiotics from health facilities, with employed participants significantly more likely to self-medicate. Awareness of antibiotic resistance was low (16.1%), mainly learned from hospitals. Unlawful antibiotic sales by drug retailers (46.2%) were noted.

Conclusions

The study highlights the urgent need for government-led efforts to regulate antibiotic use and increase public awareness to mitigate the impact on public health.

Prevalence of Shigella species and antimicrobial resistance patterns in Africa: systematic review and meta-analysis

BACKGROUND

Shigellosis continues to pose a significant public health problem in Africa; however, there is a lack of comprehensive knowledge regarding its prevalence, serogroup distribution, and antimicrobial resistance profiles. Therefore, the objective of this systematic review and meta-analysis was to determine the overall prevalence of Shigella, the distribution of species, and the patterns of antimicrobial resistance across Africa.

METHODS

Following PRISMA guidelines, a systematic search strategy was conducted using the PubMed, Web of Science and Scopus databases from January 31, 2024 to February 10, 2024. The study quality was assessed using the Joanna Briggs Institute checklist, and data were analyzed using the R statistical language and the R package 'meta'. The random effects model was employed to estimate the pooled prevalence, while heterogeneity was assessed using the I2 statistic and prediction interval.

RESULTS

A total of 116 studies from 29 African countries were included in this meta-analysis, involving the examination of 99,510 samples. The overall pooled estimate of Shigella prevalence was determined to be 5.9% (95% CI: 4.9 - 7.0%). Regional prevalence showed prevalences of Southern Africa (6.9 [95% CI: 3.0 - 12.2%]), Northern Africa (6.7% [95% CI: 4.1 - 9.8%]), Eastern Africa (6.2% [95% CI: 4.9 - 7.6%]), Central Africa (4.5% [95% CI: 2.6 - 6.8%]) and Western Africa (4.0% [95% CI: 2.5 - 5.9%]). Shigella prevalence was found to be higher in children (6.6%, 95% CI: 3.2 - 11.1%) than in adults (3.6%, 95% CI: 1.6 - 6.3%). The most prevalent species was S. flexneri (53.6%, 95% CI: 46.1%-61.0%), followed by S. sonnei (11.5%, 95% CI: 7.7%-15.7%), S. dysenteriae (10.1%, 95% CI: 6.2 - 14.5%) and S. boydii (7.7%, 95% CI: 4.7 - 11.1%). Among the currently recommended first-line antibiotics, ciprofloxacin and ceftriaxone showed resistance prevalences of 10.0% (95% CI: 4.5%-16.9%) and 8.5% (95% CI: 2.4-16.9%) respectively.

CONCLUSION

This review highlights the burden of shigellosis in Africa. S. flexneri remains the most prevalent species associated with shigellosis cases with S. sonnei being the second most dominant. The antimicrobial resistance patterns observed in the study suggest local antimicrobial patterns in choosing antibiotics for the treatment of Shigellosis.

RECOMMENDATION

There is the need to explore alternative treatments for shigellosis with particular focus on vaccine development. There is also the need for more genomic epidemiology studies exploring the dissemination and risk of drug-resistant S. sonnei clones in Africa.

High-Throughput Luminescence-Based Serum Bactericidal Assay Optimization and Characterization to Assess Human Sera Functionality Against Multiple Shigella flexneri Serotypes

Shigellosis represents a significant global health concern particularly affecting children under 5 years in low- and middle-income countries (LMICs) and is associated with stunting and antimicrobial resistance. There is a critical need for an effective vaccine offering broad protection against the different Shigella serotypes. A correlate of protection has not yet been established but there is a general consensus about the relevant role of anti-O-Antigen-specific IgG and its functionality evaluated by the Serum Bactericidal Assay (SBA). This study aims to characterize a high-throughput luminescence-based SBA (L-SBA) against seven widespread Shigella serotypes. The assay was previously developed and characterized for S. sonnei and S. flexneri 1b, 2a, and 3a and has now been refined and extended to an additional five serotypes (S. flexneri 4a, 5b, 6, X, and Y). The characterization of the assay with human sera confirmed the repeatability, intermediate precision, and linearity of the assays; both homologous and heterologous specificity were verified as well; finally, limit of detection and quantification were established for all assays. Moreover, different sources of baby rabbit complement showed to have no impact on L-SBA output. The results obtained confirm the possibility of extending the L-SBA to multiple Shigella serotypes, thus enabling analysis of the functional response induced by natural exposure to Shigella in epidemiological studies and the ability of candidate vaccines to elicit cross-functional antibodies able to kill a broad panel of prevalent Shigella serotypes in a complement-mediated fashion.

Prevalence of plasmid-mediated quinolone resistance genes and biofilm formation in different species of quinolone-resistant clinical Shigella isolates: a cross-sectional study

BACKGROUND

The purpose of this study was to look into the presence of plasmid-mediated quinolone resistance (PMQR) genes and biofilm formation in several species of clinical Shigella isolates that were resistant to quinolones.

METHODS

The stool samples of 150 patients (younger than 10 years) with diarrhea were collected in this cross-sectional study (November 2020 to December 2021). After cultivation of samples on Hektoen Enteric agar and xylose lysine deoxycholate agar, standard microbiology tests, VITEK 2 system, and polymerase chain reaction (PCR) were utilized to identify Shigella isolates. The broth microdilution method was used to determine antibiotic susceptibility. PMQR genes including qnrA, qnrB, qnrC, qnrD, qnrE, qnrS, qnrVC, qepA, oqxAB, aac(6')-Ib-cr, and crpP and biofilm formation were investigated in quinolone-resistant isolates by PCR and microtiter plate method, respectively. An enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR) technique was used to determine the clonal relatedness of quinolone-resistant isolates.

RESULTS

A total of 95 Shigella isolates including S. sonnei (53, 55.8%), S. flexneri (39, 41.1%), and S. boydii (3, 3.2%) were identified. The highest resistance rates of the isolates were against ampicillin (92.6%, n = 88/95). Overall, 42 of 95 (44.2%) isolates were simultaneously resistant against two or more quinolones including 26 (61.9%) S. sonnei and 16 (38.1%) S. flexneri. All isolates were multidrug-resistant (resistance to more than 3 antibiotics). The occurrence of PMQR genes was as follows: qnrS (52.4%), qnrA and aac(6')-Ib-cr (33.3%), and qnrB (19.0%). The prevalence in species was as follows: 61.5% and 37.5% (qnrS), 19.2% and 56.3% (qnrA), 38.5% and 25.0 (aac(6')-Ib-cr), and 19.2% and 18.8% (qnrB) for S. sonnei and S. flexneri, respectively. The other PMQR genes were not detected. In total, 52.8% (28/53) of quinolone-susceptible and 64.3% (27/42) of quinolone-resistant isolates were biofilm producers. Biofilm formation was not significantly different between quinolone-resistant and quinolone-susceptible isolates (P-value = 0.299). Quinolone-resistant isolates showed a high genetic diversity according to the ERIC-PCR.

CONCLUSION

It seems that qnrS, qnrA, and aac(6')-Ib-cr play a significant role in the quinolone resistance among Shigella isolates in our region. Also the quinolone-resistant S. flexneri and S. sonnei isolates had a high genetic diversity. Hence, antibiotic therapy needs to be routinely revised based on the surveillance findings.

The Enterics for Global Health (EFGH) Shigella Surveillance Study in Malawi

Background

Malawi is among 7 countries participating in the Enterics for Global Health (EFGH) Shigella surveillance study, which aims to determine the incidence of medically attended diarrhea attributed to Shigella, a leading bacterial cause of diarrhea in children in low-resource settings.

Methods

We describe the EFGH study site in the densely populated informal settlement of Ndirande Township, Blantyre, Malawi. We explore the site's geographical location, demographic characteristics, and the healthcare-seeking behavior of its population, particularly for childhood diarrhea. We also describe the management of childhood diarrhea at the health facility, and the associated challenges to attaining optimum adherence to local and national guidelines at the site.

Conclusions

Our overarching aim is to improve global health through understanding and mitigating the impact of diarrhea attributed to Shigella.

Prevalence and changing antimicrobial resistance profiles of Shigella spp. isolated from diarrheal patients in Kolkata during 2011-2019

BACKGROUND

The primary aim of this study was to investigate the occurrence, characteristics, and antimicrobial resistance patterns of various Shigella serogroups isolated from patients with acute diarrhea of the Infectious Diseases Hospital in Kolkata from 2011-2019.

PRINCIPAL FINDINGS

During the study period, Shigella isolates were tested for their serogroups, antibiotic resistance pattern and virulence gene profiles. A total of 5.8% of Shigella spp. were isolated, among which S. flexneri (76.1%) was the highest, followed by S. sonnei (18.7%), S. boydii (3.4%), and S. dysenteriae (1.8%). Antimicrobial resistance against nalidixic acid was higher in almost all the Shigella isolates, while the resistance to β-lactamases, fluoroquinolones, tetracycline, and chloramphenicol diverged. The occurrence of multidrug resistance was found to be linked with various genes encoding drug-resistance, multiple mutations in the topoisomerase genes, and mobile genetic elements. All the isolates were positive for the invasion plasmid antigen H gene (ipaH). Dendrogram analysis of the plasmid and pulsed-field electrophoresis (PFGE) profiles revealed 70-80% clonal similarity among each Shigella serotype.

CONCLUSION

This comprehensive long-term surveillance report highlights the clonal diversity of clinical Shigella strains circulating in Kolkata, India, and shows alarming resistance trends towards recommended antibiotics. The elucidation of this study's outcome is helpful not only in identifying emerging antimicrobial resistance patterns of Shigella spp. but also in developing treatment guidelines appropriate for this region.

The genomic epidemiology of shigellosis in South Africa

Shigellosis, a leading cause of diarrhoeal mortality and morbidity globally, predominantly affects children under five years of age living in low- and middle-income countries. While whole genome sequence analysis (WGSA) has been effectively used to further our understanding of shigellosis epidemiology, antimicrobial resistance, and transmission, it has been under-utilised in sub-Saharan Africa. In this study, we applied WGSA to large sub-sample of surveillance isolates from South Africa, collected from 2011 to 2015, focussing on Shigella flexneri 2a and Shigella sonnei. We find each serotype is epidemiologically distinct. The four identified S. flexneri 2a clusters having distinct geographical distributions, and antimicrobial resistance (AMR) and virulence profiles, while the four sub-Clades of S. sonnei varied in virulence plasmid retention. Our results support serotype specific lifestyles as a driver for epidemiological differences, show AMR is not required for epidemiological success in S. flexneri, and that the HIV epidemic may have promoted Shigella population expansion.

Recent Advances in Electrochemical Biosensors for the Detection of Foodborne Pathogens: Current Perspective and Challenges

Foodborne pathogens cause many diseases and significantly impact human health and the economy. Foodborne pathogens mainly include Salmonella spp., Escherichia coli, Staphylococcus aureus, Shigella spp., Campylobacter spp. and Listeria monocytogenes, which are present in agricultural products, dairy products, animal-derived foods and the environment. Various pathogens in many different types of food and water can cause potentially life-threatening diseases and develop resistance to various types of antibiotics. The harm of foodborne pathogens is increasing, necessitating effective and efficient methods for early monitoring and detection. Traditional methods, such as real-time polymerase chain reaction (RT-PCR), enzyme-linked immunosorbent assay (ELISA) and culture plate, are time-consuming, labour-intensive and expensive and cannot satisfy the demands of rapid food testing. Therefore, new fast detection methods are urgently needed. Electrochemical biosensors provide consumer-friendly methods to quickly detect foodborne pathogens in food and the environment and achieve extensive accuracy and reproducible results. In this paper, by focusing on various mechanisms of electrochemical transducers, we present a comprehensive overview of electrochemical biosensors for the detection of foodborne pathogens. Furthermore, the review introduces the hazards of foodborne pathogens, risk analysis methods and measures of control. Finally, the review also emphasizes the recent research progress and solutions regarding the use of electrochemical biosensors to detect foodborne pathogens in food and the environment, evaluates limitations and challenges experienced during the development of biosensors to detect foodborne pathogens and discusses future possibilities.

"I don't hesitate to use the left-over antibiotics for my child" practices and experiences with antibiotic use among caregivers of paediatric patients at Zomba central hospital in Malawi

Background

Inappropriate use of antibiotics is among the major causes of the global emergency of antibiotic resistance among children. The problem of inappropriate use of antibiotics among children is of special concern because they are still developing immunological systems, hence they are susceptible to many infectious diseases. As such, they receive a considerable disproportional amount of antibiotics which exposes them to antibiotic resistance. This study explored the lived experiences of caregivers of children under the age of five years on the use of antibiotics at Zomba central hospital.

Objective

The main aim of this study was to explore the lived experiences of caregivers of children under the age of five years on antibiotic usage at Zomba Central Hospital, Zomba-Malawi.

Methodology

This was a descriptive qualitative study with a phenomenological approach to explore the lived experience of caregivers of paediatric patients on antibiotic usage from May 2019 to July 2020. The study used interview guides to conduct in-depth interviews with 16 caregivers and purposive sampling was used to select the participants from the children’s ward. All interviews were audio-recorded and qualitative data was transcribed verbatim and thematically analysed manually to extract major themes and concepts on the subject matter.

Results

Caregivers had little knowledge about antibiotic use and its resistance. most caregivers use the antibiotics inappropriately through self-medication, use of left-over antibiotics, buying antibiotics without prescription, and sharing of antibiotics.

Conclusion

Based on the findings of this study, investment in public awareness and organising community-led interventions in antibiotic use related information is key to improve the quality use of antibiotics. The Government should focus on promoting interventions that lessen the indiscriminate use of antibiotics among the caregivers. Stringent laws need to be enforced by the government to restrict the access of antibiotics to parents without a prescription.

Phylogenetic analysis and antibiotic resistance of Shigella sonnei isolates

Shigellosis is one of the most important gastric infections caused by different species of Shigella and has been regarded as a serious threat to public health. Lineage/sublineage profile of S. sonnei is strongly associated with the antibiotic resistance and population structure of this pathogen. In this study, we determined the phylogeny and antibiotic resistance profiles of S. sonnei strains, isolated from 1246 stool and 580 food samples, using multiplex PCR-HRMA genotyping and Kirby-Bauer disk diffusion methods, respectively. A total of 64 S. sonnei strains were isolated (13 food and 51 clinical isolates). Multiplex PCR-HMR assay was able to differentiate the lineages II and III, and sublineages IIIb and IIIc strains successfully considering the definite melting curves and temperatures. Lineage I and sublineage IIIa strain were not isolated in this study. We also demonstrated that most of the S. sonnei strains isolated from both food and clinical samples clustered within the lineage III and sublineage IIIc. Resistance against trimethoprim-sulfamethoxazole, tetracycline, chloramphenicol and streptomycin antibiotics were the most prevalent phenotypes among the S. sonnei lineage III and sublineage IIIc strains.

FTIR differentiation based on genomic DNA for species identification of Shigella isolates from stool samples

Shigellosis is one of the major public health concerns in developing and low-income countries caused by four species of Shigella. There is an apparent need to develop rapid, cost-effective, sensitive and specific methods for differentiation of Shigella species to be used in outbreaks and health surveillance systems. We developed a sensitive and specific Fourier-transform infrared spectroscopy (FTIR) based method followed by principal component analysis (PCA) and hierarchical clustering analysis (HCA) assays to differentiate four species of Shigella isolates from stool samples. The FTIR based method was evaluated by differentiation of 91 Shigella species from each other in clinical samples using both gold standards (culture-based and agglutination methods) and developed FTIR assay; eventually, the sensitivity and specificity of the developed method were calculated. In summary, four distinct FTIR spectra associated with four species of Shigella were obtained with wide variations in three definite regions, including 1800–1550 cm⁻¹, 1550–1100 cm⁻¹, and 1100–800 cm⁻¹ distinguish these species from each other. In this study, we found the FTIR method followed by PCA analysis with specificity, sensitivity, differentiation error and correct differentiation rate values of 100, 100, 0 and 100%, respectively, for identification and differentiation of all species of the Shigella in stool samples.

Non-Canonical Host Intracellular Niche Links to New Antimicrobial Resistance Mechanism

Globally, infectious diseases are one of the leading causes of death among people of all ages. The development of antimicrobials to treat infectious diseases has been one of the most significant advances in medical history. Alarmingly, antimicrobial resistance is a widespread phenomenon that will, without intervention, make currently treatable infections once again deadly. In an era of widespread antimicrobial resistance, there is a constant and pressing need to develop new antibacterial drugs. Unraveling the underlying resistance mechanisms is critical to fight this crisis. In this review, we summarize some emerging evidence of the non-canonical intracellular life cycle of two priority antimicrobial-resistant bacterial pathogens: Pseudomonas aeruginosa and Staphylococcus aureus. The bacterial factors that modulate this unique intracellular niche and its implications in contributing to resistance are discussed. We then briefly discuss some recent research that focused on the promises of boosting host immunity as a combination therapy with antimicrobials to eradicate these two particular pathogens. Finally, we summarize the importance of various strategies, including surveillance and vaccines, in mitigating the impacts of antimicrobial resistance in general.

Development of high-resolution melting (HRM) assay to differentiate the species of Shigella isolates from stool and food samples

Shigella species, a group of intracellular foodborne pathogens, are the main causes of bacillary dysentery and shigellosis in humans worldwide. It is essential to determine the species of Shigella in outbreaks and food safety surveillance systems. The available immunological and molecular methods for identifying Shigella species are relatively complicated, expensive and time-consuming. High resolution melting (HRM) assay is a rapid, cost-effective, and easy to perform PCR-based method that has recently been used for the differentiation of bacterial species. In this study, we designed and developed a PCR-HRM assay targeting rrsA gene to distinguish four species of 49 Shigella isolates from clinical and food samples and evaluated the sensitivity and specificity of the assay. The assay demonstrated a good analytical sensitivity with 0.01–0.1 ng of input DNA template and an analytical specificity of 100% to differentiate the Shigella species. The PCR-HRM assay also was able to identify the species of all 49 Shigella isolates from clinical and food samples correctly. Consequently, this rapid and user-friendly method demonstrated good sensitivity and specificity to differentiate species of the Shigella isolates from naturally contaminated samples and has the potential to be implemented in public health and food safety surveillance systems.