Laboratory-acquired infections of Salmonella enterica serotype Typhi in South Africa: phenotypic and genotypic analysis of isolates

Typhoid fever due to laboratory-acquired Salmonella Typhi, confirmed by core genome multi-locus sequence typing

We present a case of laboratory-acquired Salmonella Typhi, resulting in hospitalization of a technician. Blood and stool cultures revealed a S. Typhi strain, identical to the strain with which the employee had recently worked, confirmed using core-genome multilocus sequence typing. The incident occurred despite working in a biosafety cabinet.

Enteric fever cluster identification in South Africa using genomic surveillance of Salmonella enterica serovar Typhi

The National Institute for Communicable Diseases in South Africa participates in national laboratory-based surveillance for human isolates of Salmonella species. Laboratory analysis includes whole-genome sequencing (WGS) of isolates. We report on WGS-based surveillance of Salmonella enterica serovar Typhi (Salmonella Typhi) in South Africa from 2020 through 2021. We describe how WGS analysis identified clusters of enteric fever in the Western Cape Province of South Africa and describe the epidemiological investigations associated with these clusters. A total of 206 Salmonella Typhi isolates were received for analysis. Genomic DNA was isolated from bacteria and WGS was performed using Illumina NextSeq technology. WGS data were investigated using multiple bioinformatics tools, including those available at the Centre for Genomic Epidemiology, EnteroBase and Pathogenwatch. Core-genome multilocus sequence typing was used to investigate the phylogeny of isolates and identify clusters. Three major clusters of enteric fever were identified in the Western Cape Province; cluster one (n=11 isolates), cluster two (n=13 isolates), and cluster three (n=14 isolates). To date, no likely source has been identified for any of the clusters. All isolates associated with the clusters, showed the same genotype (4.3.1.1.EA1) and resistome (antimicrobial resistance genes: bla _TEM-1B, catA1, sul1, sul2, dfrA7). The implementation of genomic surveillance of Salmonella Typhi in South Africa has enabled rapid detection of clusters indicative of possible outbreaks. Cluster identification allows for targeted epidemiological investigations and a timely, coordinated public health response.

Characterization of SARS-CoV-2 Distribution and Microbial Succession in a Clinical Microbiology Testing Facility during the SARS-CoV-2 Pandemic

The exchange of microbes between humans and the built environment is a dynamic process that has significant impact on health. Most studies exploring the microbiome of the built environment have been predicated on improving our understanding of pathogen emergence, persistence, and transmission. Previous studies have demonstrated that SARS-CoV-2 presence significantly correlates with the proportional abundance of specific bacteria on surfaces in the built environment. However, in these studies, SARS-CoV-2 originated from infected patients. Here, we perform a similar assessment for a clinical microbiology lab while staff were handling SARS-CoV-2 infected samples. The goal of this study was to understand the distribution and dynamics of microbial population on various surfaces within different sections of a clinical microbiology lab during a short period of 2020 Coronavirus disease (COVID-19) pandemic. We sampled floors, benches, and sinks in 3 sections (bacteriology, molecular microbiology, and COVID) of an active clinical microbiology lab over a 3-month period. Although floor samples harbored SARS-CoV-2, it was rarely identified on other surfaces, and bacterial diversity was significantly greater on floors than sinks and benches. The floors were primarily colonized by bacteria common to natural environments (e.g., soils), and benchtops harbored a greater proportion of human-associated microbes, including Staphylococcus and Streptococcus. Finally, we show that the microbial composition of these surfaces did not change over time and remained stable. Despite finding viruses on the floors, no lab-acquired infections were reported during the study period, which suggests that lab safety protocols and sanitation practices were sufficient to prevent pathogen exposures. IMPORTANCE For decades, diagnostic clinical laboratories have been an integral part of the health care systems that perform diagnostic tests on patient's specimens in bulk on a regular basis. Understanding their microbiota should assist in designing and implementing disinfection, and cleaning regime in more effective way. To our knowledge, there is a lack of information on the composition and dynamics of microbiota in the clinical laboratory environments, and, through this study, we have tried to fill that gap. This study has wider implications as understanding the makeup of microbes on various surfaces within clinical laboratories could help identify any pathogenic bacterial taxa that could have colonized these surfaces, and might act as a potential source of laboratory-acquired infections. Mapping the microbial community within these built environments may also be critical in assessing the reliability of laboratory safety and sanitation practices to lower any potential risk of exposures to health care workers.

Metagenomics-enabled microbial surveillance

Lessons learnt from the COVID-19 pandemic include increased awareness of the potential for zoonoses and emerging infectious diseases that can adversely affect human health. Although emergent viruses are currently in the spotlight, we must not forget the ongoing toll of morbidity and mortality owing to antimicrobial resistance in bacterial pathogens and to vector-borne, foodborne and waterborne diseases. Population growth, planetary change, international travel and medical tourism all contribute to the increasing frequency of infectious disease outbreaks. Surveillance is therefore of crucial importance, but the diversity of microbial pathogens, coupled with resource-intensive methods, compromises our ability to scale-up such efforts. Innovative technologies that are both easy to use and able to simultaneously identify diverse microorganisms (viral, bacterial or fungal) with precision are necessary to enable informed public health decisions. Metagenomics-enabled surveillance methods offer the opportunity to improve detection of both known and yet-to-emerge pathogens.

Zika Virus Infection During Research Vaccine Development: Investigation of the Laboratory-Acquired Infection via Nanopore Whole-Genome Sequencing

Zika virus (ZIKV) emerged as a serious public health problem since the first major outbreak in 2007. Current ZIKV diagnostic methods can successfully identify known ZIKV but are impossible to track the origin of viruses and pathogens other than known ZIKV strains. We planned to determine the ability of Whole Genome Sequencing (WGS) in clinical epidemiology by evaluating whether it can successfully detect the origin of ZIKV in a suspected case of laboratory-acquired infection (LAI). ZIKV found in the patient sample was sequenced with nanopore sequencing technology, followed by the production of the phylogenetic tree, based on the alignment of 38 known ZIKV strains with the consensus sequence. The closest viral strain with the consensus sequence was the strain used in the laboratory, with a percent identity of 99.27%. We think WGS showed its time-effectiveness and ability to detect the difference between strains to the level of a single base. Additionally, to determine the global number of LAIs, a literature review of articles published in the last 10 years was performed, and 53 reports of 338 LAIs were found. The lack of a universal reporting system was worrisome, as in the majority of cases (81.1%), the exposure route was unknown.

Genomic Characterization of Endemic and Ecdemic Non-typhoidal Salmonella enterica Lineages Circulating Among Animals and Animal Products in South Africa

In Africa, the burden of illness caused by non-typhoidal Salmonella enterica is disproportionally high; however, whole-genome sequencing (WGS) efforts are overwhelmingly concentrated in world regions with lower burdens. While WGS is being increasingly employed in South Africa to characterize Salmonella enterica, the bulk of these efforts have centered on characterizing human clinical strains. Thus, very little is known about lineages circulating among animals in the country on a genomic scale. Here, we used WGS to characterize 63 Salmonella enterica strains isolated from livestock, companion animals, wildlife, and animal products in South Africa over a 60-year period. Genomes were assigned to serotypes Dublin, Hadar, Enteritidis, and Typhimurium (n = 18, 8, 13, and 24 strains, respectively) and sequence types (STs) ST10 (all S. Dublin), ST33 (all S. Hadar), ST11/ST366 (n = 12 and 1 S. Enteritidis, respectively), and ST19/ST34 (n = 23 and 1 S. Typhimurium, respectively; via seven-gene multi-locus sequence typing). Within-ST phylogenies were constructed using genomes sequenced in this study, plus publicly available genomes representative of each ST's (i) global (n = 2,802 and 1,569 S. Dublin and Hadar genomes, respectively) and (ii) African (n = 716 and 343 S. Enteritidis and Typhimurium genomes, respectively) population. For S. Dublin ST10, a largely antimicrobial-susceptible, endemic lineage circulating among humans, animals, and food in South Africa was identified, as well as a lineage that was likely recently introduced from the United States. For S. Hadar ST33, multiple South African lineages harboring streptomycin and tetracycline resistance-conferring genes were identified. African S. Enteritidis ST11 could be primarily partitioned into one largely antimicrobial-susceptible and one largely multidrug-resistant (MDR) clade, with South African isolates confined to the largely antimicrobial-susceptible clade. S. Typhimurium ST19/ST34 strains sequenced here were distributed across the African S. Typhimurium ST19/ST34 phylogeny, representing a diverse range of lineages, including numerous MDR lineages. Overall, this study provides critical insights into endemic and ecdemic non-typhoidal Salmonella enterica lineages circulating among animals, foods, and humans in South Africa and showcases the utility of WGS in characterizing animal-associated strains from a world region with a high salmonellosis burden.

Climate change and dengue risk in central region of Thailand

Dengue poses a huge public health threat. It places physical and financial burden on individuals affected, family, and national health systems. This descriptive study aimed for two specific objectives; to investigate the weather effects on dengue incidence and to estimate level of risk in the central region of Thailand. It utilized a 10-year population level dengue morbidity data and meteorological data from 2007 to 2016. Kriging method was used to interpolate a weighted risk factor upon a 5-point risk estimate was developed for estimating area risk on a 5-point scale. The findings showed that 2 out of 16 provinces (12.5%) are strong to very strong risk areas for dengue, including Bangkok and Nonthaburi provinces. The study revealed that the impact of La Niña and El Niño on increased dengue incidence and risk level in Bangkok. We recommend further studies to establish intersections of dengue disease and social determinants of health.

Incidence and Characterization of Salmonella Isolates From Raw Meat Products Sold at Small Markets in Hubei Province, China

Salmonella is a leading cause of foodborne disease and is often associated with the consumption of foods of animal origin. In this study, sixty-six Salmonella isolates were obtained from 631 raw meat samples purchased at small retail suppliers in Hubei Province, China. The most prevalent Salmonella serotypes were Thompson (18.2%) and Agona (13.6%). Frequent antimicrobial resistance was observed for the sulfonamides (43.9%), tetracycline (43.9%), and the β-lactams amoxicillin and ampicillin (36.4% for each). Interestingly, a high incidence of resistance to cephazolin was observed in strains of the most common serotype, S. Thompson. Class I integrons were found in 27.3% (18/66) of the isolates and five of these integrons contained different gene cassettes (aacA4C-arr-3-dfr2, dfrA12-aadA21, aadA2, dfrA12-aadA2, dfr17-aadA5). Additional antimicrobial resistance genes, including bla _TEM-1, bla _CTX-M-65, bla _CTX-M-15, qnrB, and qnrS, were also identified among these Salmonella isolates. Results of replicon typing and conjugation experiments revealed that an integron with qnrB and bla _CTX-M-15 genes was present on incH12 mobile plasmid in S. Thompson strain. Multilocus sequence typing (MLST) analysis revealed 32 sequence types, indicating that these isolates were phenotypically and genetically diverse, among which ST26 (18.2%) and ST541 (12.1%) were the predominant sequence types. The integrons, along with multiple antimicrobial resistance genes on mobile plasmids, are likely contributors to the dissemination of multidrug resistance in Salmonella.

Assessment of knowledge and attitude among postnatal mothers towards childhood vaccination in Malaysia

Aim: Mothers knowledge and attitude toward childhood vaccination influence uptake is the most adequate tool and preventive aspects to infectious disease epidemics. The present study assesses and measures knowledge and attitude of postnatal mothers toward vaccination.Methods and results: The present study adopted a cross-sectional study design, whereby 200 postnatal mothers were identified during their postnatal visit to clinics. The subjects were accessed using questionnaire to assess the level of knowledge and attitude of mothers regarding vaccination. The objectives were to study the level of knowledge, the attitude, and to find the association between knowledge and attitude of the study subjects. The data were analyzed using SPSS version 16. The results was analyzed through chi-square test. The association between age (p = .031), education (p = .021), occupation (p = .013), and knowledge score toward vaccination was found to be statistically significant. However, ethnicity (p = .127), employment (p = .197), and mode of delivery (p = .750) toward mothers vaccination knowledge were not significant for the study. Mothers education, age, and occupation were found to be associated with attitude toward childhood vaccination. No association was found between ethnicity, employment, and mode of delivery with attitude of childhood vaccination.Conclusion: More than half of the studied mothers had good knowledge scores on vaccination, more than two-thirds of the studied mothers had good attitude scores on vaccination. However, the religious misconception and fear of autism was the main cause of vaccine resistance in Malaysia.

Diagnostic Performance of MALDI-TOF MS Compared to Conventional Microbiological Cultures in Patients with Suspected Endophthalmitis

Purpose: To evaluate the performance and speed of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) when identifying the pathogenic microorganism of endophthalmitis compared to conventional microbiological culturing.Methods: Forty-four patients with suspected endophthalmitis who had undergone vitrectomy were enrolled. Vitreous specimen was analyzed using either conventional culturing or MALDI-TOF MS.Results: The identification rates of the conventional microbiological culture and MALDI-TOF MS were 45.5% (20/44) and 65.9% (29/44), respectively (Kappa value 0.787, P < 0.000). The mean detection times by the standard culturing method and MALDI-TOF MS were 5.39 ± 0.56d and 3.17 ± 0.40d (P < 0.001). The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of MALDI-TOF MS were 70.59%, 54.17%, 80.00%, and 86.67%, respectively. Polymicrobial endophthalmitis was identified in 6.82% of the patients (3/44) using conventional microbiological culturing. However, MALDI-TOF MS failed to identify any polymicrobial infection.Conclusions: With a higher sensitivity, acceptable specificity and a shorter detection time, MALDI-TOF MS was an efficient technique for the rapid identification of a pathogenic microorganism in endophthalmitis.

Outbreak of Listeria monocytogenes in South Africa, 2017-2018: Laboratory Activities and Experiences Associated with Whole-Genome Sequencing Analysis of Isolates

In South Africa, a progressive increase in listeriosis cases was noted from mid-June 2017, heralding what was to become the world's largest listeriosis outbreak. A total of 1060 cases were reported for the period January 1, 2017 to July 17, 2018. We describe laboratory activities, experiences, and results of whole-genome sequencing (WGS) analysis of Listeria monocytogenes isolates associated with this outbreak. Bacteria were identified using the VITEK-2 COMPACT 15 microbial identification system. WGS was performed using Illumina MiSeq technology. WGS data were analyzed using CLC Genomics Workbench Software and free-to-use on-line analysis tools/pipelines. Multilocus sequence typing (MLST) showed that 91% of clinical isolates were sequence type 6 (ST6), determining that the outbreak was largely associated with L. monocytogenes ST6. Epidemiological and laboratory findings led to investigation of a large ready-to-eat processed meat production facility in South Africa, named Enterprise Foods. L. monocytogenes ST6 was found in environmental sampling swabs of the production facility and in ready-to-eat processed meat products (including polony, a product similar to bologna sausage) manufactured at the facility. ST6 isolates, sourced at the Enterprise Foods production facility and from Enterprise food products, were shown by single nucleotide polymorphism (SNP) analysis to be highly related to clinical isolates; these nonclinical ST6 isolates showed <10 SNP differences when compared to clinical ST6 isolates. Core-genome MLST showed that clinical ST6 isolates and Enterprise-related ST6 isolates had no more than 4 allele differences between each other, suggestive of a high probability of epidemiological relatedness. WGS data interpreted together with epidemiological data concluded that the source of the listeriosis outbreak was ready-to-eat processed meat products manufactured by Enterprise Foods. Listeriosis has now been added to the South African list of mandatory notifiable medical conditions. Surveillance systems have been strengthened to facilitate prevention and early detection of listeriosis outbreaks.

State of knowledge of human papillomavirus (HPV), HPV vaccine and testing: a cross-sectional study among female university students in Cyprus

This study aimed to evaluate human papillomavirus (HPV)-related knowledge of women aged 18-25 years and estimate the reported uptake of HPV vaccine and testing. A cross-sectional study was conducted among female students of the University of Cyprus between March and April 2017. The participants self-completed a questionnaire, which consisted of 37 items on demographics, general HPV-related knowledge, and HPV vaccination and testing. In total, 283 young females (mean age: 19.7 ± 1.5 years) took part in the study. Of these, about half (53.7%) reported that they were aware of HPV; one-third (30.7%) reported having been vaccinated; 38.8% had been informed of the recent introduction of the HPV vaccine in the National Immunization Schedule in Cyprus, while 14.3% reported a previous Pap-test and 3.4% a previous HPV DNA test. The mean Overall Knowledge Index (max: 25 correct answers) was 6.1 (±3.8) and was positively associated with the reported uptake of the HPV vaccine (adjusted Odds ratio: 1.14, 95% Confidence Interval (CI): 1.04-1.24). Knowledge about HPV has to be improved as it is associated with increased reported rates of HPV vaccination.

An intervention to improve pneumococcal vaccination uptake in high risk 50-64 year olds vs. expanded age-based recommendations: an exploratory cost-effectiveness analysis

In the U.S., pneumococcal polysaccharide vaccine (PPSV23) uptake among high-risk adults aged <65 years is consistently low and improvement is needed. One barrier to improved vaccine coverage is the complexity of the adult vaccination schedule. This exploratory analysis compared the cost-effectiveness of strategies to increase pneumococcal vaccine uptake in high-risk adults aged 50-64 years. We used a Markov model to compare strategies for non-immunocompromised 50-64 year olds: 1) current pneumococcal polysaccharide vaccine (PPSV23) recommendations; 2) current recommendations enhanced by an intervention; 3) PPSV23 plus pneumococcal conjugate vaccine (PCV13) for high-risk patients with no intervention; or 4) both vaccines for all 50-year-olds with no intervention. Parameters included CDC data and other US data, varied extensively in sensitivity analyses. In the analysis, vaccinating high-risk individuals with PPSV23/PCV13 was the least costly strategy, with total costs of $424/person. Vaccinating all 50 year olds with PPSV23/PCV13 cost $40 more and gained 0.00068 quality-adjusted life years (QALY), or $57,786/QALY gained. Current recommendations with or without an intervention program were more expensive and less effective than other strategies. In multi-way sensitivity analyses, the current recommendations/intervention program strategy was favored at a $100,000/QALY threshold only if non-bacteremic pneumococcal pneumonia rate or PCV13 serotype coverage were substantially lower than base case values. Thus, an intervention program to improve pneumococcal vaccine uptake among high-risk 50-64 year-olds was not cost-effective in most scenarios. High-risk individuals receiving both PCV13 and PPSV23 could be economically favorable, and vaccinating all 50-year-olds with both vaccines could be considered.

Varicella healthcare resource utilization in middle income countries: a pooled analysis of the multi-country MARVEL study in Latin America & Europe

Varicella is a mild and self-limited illness in children, but can result in significant healthcare resource utilization (HCRU). To quantify/contrast varicella-associated HCRU in five middle-income countries (Hungary, Poland, Argentina, Mexico, and Peru) where universal varicella vaccination was unimplemented, charts were retrospectively reviewed among 1-14 year-olds. Data were obtained on management of primary varicella between 2009-2016, including outpatient/inpatient visits, allied healthcare contacts, tests/procedures, and medications. These results are contrasted across countries, and a regression model is fit to extrapolated country-level costs as a function of gross domestic product (GDP). A total of 401 outpatients and 386 inpatients were included. Significant differences between countries were observed in the number of skin lesions among outpatients, ranging from 5.3% to 25.4% of patients with ≥250 lesions. Among inpatients, results were less variable. Average ambulatory medical visits ranged from 1.1 to 2.2. Average hospital stay ranged from 3.6 to 6.8 days. Use of tests/procedures was infrequent in outpatients, except in Argentina (13.3%); among inpatients, a test/procedure was ordered for 81.3% of patients, without regional variation. Prescription medications were administered in 44.4% of outpatients (range 9.3%-80.0%), and in 86% of inpatients (range 70.4%-94.9%). Total estimated spending on varicella treatment in the absence of vaccination was predicted from income levels (GDP) with an exponential function (R² = 0.89). This study demonstrates that substantial HCRU is associated with varicella resulting in significant public health burden that could be alleviated through the use of varicella vaccination. Differences observed between countries possibly reflect treatment guidelines, healthcare resource availabilities and physician practices.

Evaluation of reliability and performance of hepatitis B virus-e-antigen assays in tertiary care setting

Hepatitis B virus-e-antigen (HBeAg) is a viral marker to assess hepatitis B virus (HBV) replication. We have evaluated the reliability of three commonly available HBeAg immunoassays using World Health Organization-International Standard and clinical samples. In addition the performance of enzyme immunoassays (EIAs) was assessed by kinetic binding and reagent exchange experiments. Analytical and diagnostic sensitivity were significantly different among HBeAg assays (P < 0.01). The affinity of capture/detector antibodies varied significantly between EIAs (P < 0.01). Our findings suggest that significant difference in the affinity of capture/detector antibodies to HBeAg may impact the overall performance and the reliability of currently available HBeAg assays in HBV diagnosis and management.

The dawn of precision medicine in HIV: state of the art of pharmacotherapy

INTRODUCTION

Combination antiretroviral therapy (ART) reduces viral load to under the limit of detection, successfully decreasing HIV-related morbidity and mortality. Due to viral mutations, complex drug combinations and different patient response, there is an increasing demand for individualized treatment options for patients.

AREAS COVERED

This review first summarizes the pharmacokinetic and pharmacodynamic profile of clinical first-line drugs, which serves as guidance for antiretroviral precision medicine. Factors which have influential effects on drug efficacy and thus precision medicine are discussed: patients' pharmacogenetic information, virus mutations, comorbidities, and immune recovery. Furthermore, strategies to improve the application of precision medicine are discussed.

EXPERT OPINION

Precision medicine for ART requires comprehensive information on the drug, virus, and clinical data from the patients. The clinically available genetic tests are a good starting point. To better apply precision medicine, deeper knowledge of drug concentrations, HIV reservoirs, and efficacy associated genes, such as polymorphisms of drug transporters and metabolizing enzymes, are required. With advanced computer-based prediction systems which integrate more comprehensive information on pharmacokinetics, pharmacodynamics, pharmacogenomics, and the clinically relevant information of the patients, precision medicine will lead to better treatment choices and improved disease outcomes.

Non-uptake of childhood vaccination among the children of HIV-infected mothers in sub-Saharan Africa: A multilevel analysis

The aim of this study was to develop and test models for non–uptake of three doses of diphtheria-tetanus-pertussis containing vaccines (DTP3) among children of women living with HIV in sub-Saharan Africa. The study used demographic and health survey data from 27 sub-Saharan African countries that have the required HIV and immunization data sets. Multivariable logistic regression models were used to assess the relationship between individual and contextual factors associated with non-uptake of DTP3 among the children. At the individual level, the odds of non-uptake of DTP3 decreased with formal education, increasing age and access to media. The full model shows that the odds of non-uptake of DTP3 is increased among unemployed women, those living in communities with high illiteracy rate and in countries with low adult literacy level. For a child who moved to another country or community with a higher probability of DTP3 non-uptake, the median increase for the odds of DTP3 non-uptake would be 2.24% and 1.22% respectively for country and community. This study shows that individual and contextual factors contributed significantly to non-uptake of DTP3 among the children of women living with HIV. Interventions should be focused on women living with HIV who are young mothers, unemployed women, those without formal education, individuals living in communities with high illiteracy rate and in countries with low adult literacy rate. The use of mass media tools and creation of more employment opportunities for HIV-infected women could improve vaccination coverage among their children.