Detection and Phylogenetic Analysis of Extended-Spectrum ß-Lactamase (ESBL)-Genetic Determinants in Gram-Negative Fecal-Microbiota of Wild Birds and Chicken Originated at Trimmu Barrage.

Extended-spectrum ß-lactamases (ESBL) give rise to resistance against penicillin and cephalosporin antibiotics in multiple bacterial species. The present study was conducted to map genetic determinants and related attributes of ESBL-producing bacteria in three wild aquatic bird species and chickens at the "Trimmu Barrage" in district Jhang, Punjab province, Pakistan. To study the prevalence of ESBL-producing bacteria, a total of 280 representative samples were collected from wild bird species; cattle egrets (Bubulcus ibis), little egrets (Egretta garzetta) and common teals (Anas crecca) as well as from indigenous chickens (Gallus gallus domesticus) originating from a local wet market. The isolates were confirmed as ESBL producers using a double disc synergy test (DDST) and bacterial species were identified using API-20E and 20NE strips. A polymerase chain reaction (PCR) was used to detect ESBL genetic determinants and for genus identification via 16S rRNA gene amplification. A phenotypic antimicrobial susceptibility test was performed for ESBL-producing isolates against 12 clinically relevant antibiotics using the Kirby-Bauer disk diffusion susceptibility test. A phylogenetic tree was constructed for the sequence data obtained in this study and comparative sequence data obtained from GenBank. The overall prevalence of ESBL-producing bacteria was 34.64% (97/280). The highest percentage (44.28%; 31/70) of ESBL-producing bacteria was recovered from chickens (Gallus gallus domesticus), followed by little egrets (Egretta garzetta) (41.43%; 29/70), common teal (Anas crecca) (28.57%; 20/70) and cattle egrets (Bubulcus ibis) (24.28%; 17/70). Five different ESBL-producing bacteria were identified biochemically and confirmed via 16S rRNA gene sequencing, which included Escherichia coli (72; 74.23%), Enterobacter cloacae (11; 11.34%), Klebsiella pneumoniae (8; 8.25%), Salmonella enterica (4; 4.12%) and Pseudomonas aeruginosa (2; 2.06%). Based on PCR, the frequency of obtained ESBL genes in 97 isolates was blaCTX-M (51.55%), blaTEM (20.62%), blaOXA (6.18%) and blaSHV (2.06%). In addition, gene combinations blaCTX-M + blaTEM, blaTEM + blaOXA and blaCTX-M + blaSHV were also detected in 16.49%, 2.06% and 1.03% of isolates, respectively. The ESBL gene variation was significant (p = 0.02) in different bacterial species while non-significant in relation to different bird species (p = 0.85). Phylogenetic analysis of amino acid sequence data confirmed the existence of CTX-M-15 and TEM betalactamases. The average susceptibility of the antibiotics panel used was lowest for both Klebsiella pneumoniae (62.5% ± 24.42) and Salmonella enterica (62.5% ± 31.08) as compared to Enterobacter cloacae (65.90% ± 21.62), Pseudomonas aeruginosa (70.83% ± 33.42) and Escherichia coli (73.83% ± 26.19). This study provides insight into the role of aquatic wild birds as reservoirs of ESBL-producing bacteria at Trimmu Barrage, Punjab, Pakistan. Hence, active bio-surveillance and environment preservation actions are necessitated to curb antimicrobial resistance.

ICTV Virus Taxonomy Profile: Arenaviridae 2023.

Arenaviridae is a family for ambisense RNA viruses with genomes of about 10.5 kb that infect mammals, snakes, and fish. The arenavirid genome consists of two or three single-stranded RNA segments and encodes a nucleoprotein (NP), a glycoprotein (GP) and a large (L) protein containing RNA-directed RNA polymerase (RdRP) domains; some arenavirids encode a zinc-binding protein (Z). This is a summary of the International Committee on Taxonomy of Viruses (ICTV) report on the family Arenaviridae, which is available at www.ictv.global/report/arenaviridae.

Anthrax bio-surveillance of livestock in Arua District, Uganda, 2017-2018.

Anthrax, caused by Bacillus anthracis, is a widespread zoonotic disease with many human cases, especially in developing countries. Even with its global distribution, anthrax is a neglected disease with scarce information about its actual impact on the community level. Due to the ecological dynamics of anthrax transmission at the wildlife-livestock interface, the Sub-Saharan Africa region becomes a high-risk zone for maintaining and acquiring the disease. In this regard, some subregions of Uganda are endemic to anthrax with regular seasonal trends. However, there is scarce data about anthrax outbreaks in Uganda. Here, we confirmed the presence of B. anthracis in several livestock samples after a suspected anthrax outbreak among livestock and humans in Arua District. Additionally, we explored the potential risk factors of anthrax through a survey within the community kraals. We provide evidence that the most affected livestock species during the Arua outbreak were cattle (86%) compared to the rest of the livestock species present in the area. Moreover, the farmers' education level and the presence of people's anthrax cases were the most critical factors determining the disease's knowledge and awareness. Consequently, the lack of understanding of the ecology of anthrax may contribute to the spread of the infection between livestock and humans, and it is critical to reducing the presence and persistence of the B. anthracis spores in the environment. Finally, we discuss the increasingly recognized necessity to strengthen global capacity using a One Health approach to prevent, detect, control, and respond to public threats in Uganda.

Hospital-based autonomous pre-clinical screening of COVID-19: An emergency triage using a vital signs recording system, Paris-Ile de France region.

Background: The COVID-19 pandemic has had a dramatic toll worldwide on the populations but also has been essentially supported by the existing public health system, particularly hospital-based emergency wards and intensive care units. In France, the first cases were identified on the 24th of January 2020. The first epidemic sprout emerged in the Eastern part of the country and spread in two weeks towards the center to the Paris-region where it peaked on the 14th of April 2020. In Paris and the region around it, the intensity of the epidemic has increased significantly to have a strong impact on all public and private hospital systems in a few weeks. During France's 2020 COVID-19 epidemic, a private hospital went into a major organizational change of its Emergency Department which mainly included the use of a Telemedicine Booth for vitals automatic recording during triage procedures.Purpose: The purpose of this study is to share a unique exerience centered on the use of a Telemedicine Booth as a screening process during an epidemic. Researche design: The present study is a case report describing the organizational scheme adopted by the hospital and discusses the data of 1844 patients that attended the facility over a month and the results of a questionaire survey adressed to the Emergency Department personnel.Study sample: The study population is the population that Data where collecte.Data collection and analysis: Quantitative activity indicators' data were collected with a specific triage register, patient management software and the Telemedicine Booth activity software and were analysed with basic statistics. Results and Conclusions: Among the 1844 patients, 766 were engaged in an automated triage process supported by a Telemedicine Booth. Patients' clinical characteristics are comparable to those found in international literature during the COVID-19 pandemic. The use of the Telemedicine Booth as a screening process facilitated patients' flow. It usefully participated in the patient rapid orientation, relieving the hospital emergency department, actively contributes in a safe and secure environment highly trusted by the hospital staff and health workers. To our knowledge, the Telemedicine Booth use as a screening process during an epidemic constitutes the first contribution to such an innovative approach.

Pre-Pandemic Cross-Reactive Immunity against SARS-CoV-2 among Central and West African Populations.

For more than two years after the emergence of COVID-19 (Coronavirus Disease-2019), significant regional differences in morbidity persist. These differences clearly show lower incidence rates in several regions of the African and Asian continents. The work reported here aimed to test the hypothesis of a pre-pandemic natural immunity acquired by some human populations in central and western Africa, which would, therefore, pose the hypothesis of an original antigenic sin with a virus antigenically close to the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). To identify such pre-existing immunity, sera samples collected before the emergence of COVID-19 were tested to detect the presence of IgG reacting antibodies against SARS-CoV-2 proteins of major significance. Sera samples from French blood donors collected before the pandemic served as a control. The results showed a statistically significant difference of antibodies prevalence between the collected samples in Africa and the control samples collected in France. Given the novelty of our results, our next step consists in highlighting neutralizing antibodies to evaluate their potential for pre-pandemic protective acquired immunity against SARS-CoV-2. In conclusion, our results suggest that, in the investigated African sub-regions, the tested populations could have been potentially and partially pre-exposed, before the COVID-19 pandemic, to the antigens of a yet non-identified Coronaviruses.

Environmental Drivers of Monkeypox Transmission in the Democratic Republic of the Congo.

Monkeypox (MPX) is an emergent severe zoonotic disease resembling that of smallpox. To date, most cases of human MPX have been reported in the Democratic Republic of the Congo (DRC). While the number of cases has increased steadily in the DRC over the last 30 years, the environmental risk factors that drive the spatiotemporal dynamics of MPX transmission remain poorly understood. This study aimed to investigate the spatiotemporal associations between environmental risk factors and annual MPX incidence in the DRC. All MPX cases reported weekly at the health zone level over a 16-year period (2000-2015) were analyzed. A Bayesian hierarchical generalized linear mixed model was conducted to identify the spatiotemporal associations between annual MPX incidence and three types of environmental risk factors illustrating environment as a system resulting from physical, social and cultural interactions Primary forest (IRR 1.034 [1.029-1.040]), economic well-being (IRR 1.038 [1.031-1.047]), and temperature (IRR 1.143 [1.028-1.261]) were positively associated with annual MPX incidence. Our study shows that physical environmental risk factors alone cannot explain the emergence of MPX outbreaks in the DRC. Economic level and cultural practices participate from environment as a whole and thus, must be considered to understand exposure to MPX risk Future studies should examine the impact of these factors in greater detail.

Serological evidence of Rift Valley fever virus infection among domestic ruminant herds in Uganda.

BACKGROUND: Prior to the first recorded outbreak of Rift Valley fever (RVF) in Uganda, in March 2016, earlier studies done until the 1970's indicated the presence of the RVF virus (RVFV) in the country, without any recorded outbreaks in either man or animals. While severe outbreaks of RVF occurred in the neighboring countries, none were reported in Uganda despite forecasts that placed some parts of Uganda at similar risk. The Ministry of Agriculture, Animal Industry and Fisheries (MAAIF) undertook studies to determine the RVF sero-prevalence in risk prone areas. Three datasets from cattle sheep and goats were obtained; one from retrospective samples collected in 2010-2011 from the northern region; the second from the western region in 2013 while the third was from a cross-sectional survey done in 2016 in the south-western region. Laboratory analysis involved the use of the Enzyme Linked Immunosorbent Assays (ELISA). Data were subjected to descriptive statistical analyses, including non-parametric chi-square tests for comparisons between districts and species in the regions. RESULTS: During the Yellow Fever outbreak investigation of 2010-2011 in the northern region, a total sero-prevalence of 6.7% was obtained for anti RVFV reacting antibodies (IgG and IgM) among the domestic ruminant population. The 2013 sero-survey in the western region showed a prevalence of 18.6% in cattle and 2.3% in small ruminants. The 2016 sero-survey in the districts of Kabale, Kanungu, Kasese, Kisoro and Rubirizi, in the south-western region, had the respective district RVF sero-prevalence of 16.0, 2.1, 0.8, 15.1and 2.7% among the domestic ruminants combined for this region; bovines exhibited the highest cumulative sero-prevalence of 15.2%, compared to 5.3 and 4.0% respectively for sheep and goats per species for the region. CONCLUSIONS: The absence of apparent outbreaks in Uganda, despite neighboring enzootic areas, having minimal restrictions to the exchange of livestock and their products across borders, suggest an unexpected RVF activity in the study areas that needs to be unraveled. Therefore, more in-depth studies are planned to mitigate the risk of an overt RVF outbreak in humans and animals as has occurred in neighboring countries.

COVID-19: Spatial analysis of hospital case-fatality rate in France.

When the population risk factors and reporting systems are similar, the assessment of the case-fatality (or lethality) rate (ratio of cases to deaths) represents a perfect tool for analyzing, understanding and improving the overall efficiency of the health system. The objective of this article is to estimate the influence of the hospital care system on lethality in metropolitan France during the inception of the COVID-19 epidemic, by analyzing the spatial variability of the hospital case-fatality rate (CFR) between French districts. In theory, the hospital age-standardized CFR should not display significant differences between districts, since hospital lethality depends on the virulence of the pathogen (the SARS-CoV-2 virus), the vulnerability of the population (mainly age-related), the healthcare system quality, and cases and deaths definition and the recording accuracy. We analyzed hospital data on COVID-19 hospitalizations, severity (admission to intensive care units for reanimation or endotracheal intubation) and mortality, from March 19 to May 8 corresponding to the first French lockdown. All rates were age-standardized to eliminate differences in districts age structure. The results show that the higher case-fatality rates observed by districts are mostly related to the level of morbidity. Time analysis shows that the case-fatality rate has decreased over time, globally and in almost all districts, showing an improvement in the management of severe patients during the epidemic. In conclusion, it appears that during the first critical phase of COVID-19 ramping epidemic in metropolitan France, the higher case-fatality rates were generally related to the higher level of hospitalization, then potentially related to the overload of healthcare system. Also, low hospitalization with high case-fatality rates were mostly found in districts with low population density, and could due to some limitation of the local healthcare access. However, the magnitude of this increase of case-fatality rate represents less than 10 per cent of the average case-fatality rate, and this variation is small compared to much greater variation across countries reported in the literature.

Rabies in Uganda: rabies knowledge, attitude and practice and molecular characterization of circulating virus strains.

BACKGROUND: Rabies is a deadly preventable viral disease that affects all warm-blooded animals and widespread in many regions including Africa. The disease remains of major public health importance in Uganda. The purpose of this study was to establish Knowledge, Attitude, Practice (KAP) of Rabies in Moyo and Ntoroko districts and to characterize Rabies virus (RABV) strains from seven districts of Uganda with consistent prevalence of rabies. METHODS: KAP survey data were collected based on animal biting history by interviewing the head of the veterinary departments, the medical centers and selected households from the study sites. Data were obtained from 84 households in Ntoroko and Moyo districts. Thirty-five (35) brain samples were collected from bovine, dogs, goats, foxes, jackals ad sheep between 2011 and 2013. Samples were tested using fluorescent antibody test (FAT), One step RT-PCR (following RNA extraction) and partial RABV N gene was sequenced by Sanger method before phylogenetic and phylogeographic analyses of sequences. RESULTS: Scarcity of post-exposure prophylaxis services in the health centers was noted. Poor attitude of wound washing and deficiency of knowledge on how to handle wounds related to dog bites and the significance among household participants lacked. There is a high risk of rabies infection due to a limited dog's vaccination. Dog biting episodes in humans were of 75.00 and 62.50% in Moyo and Ntoroko districts respectively. Twenty-seven (27) samples tested positive for rabies by FAT and PCR. Ugandan sequences were closely related (97% nucleotide id) to the rabies virus sequences from Tanzania, Rwanda, Burundi, Nigeria, Central African Republic and Sudan with both the "Africa 1A" and "Africa 1B" RABV clades represented. A putative new clade 1D was also detected. CONCLUSIONS: Rabies remains a public health hazard in Uganda. There is urgent need to establish advocacy programs in both schools and communities to curtail the spread of rabies. Increasing the knowledge regarding wound washing, post-exposure prophylaxis and dogs vaccination would enhance prevention of rabies. A strong collaboration between medical and veterinary sectors under a one health platform is required to ensure sufficient preventative services to the communities.

Temporal and Spatial Dynamics of Monkeypox in Democratic Republic of Congo, 2000-2015.

Monkeypox is a viral disease with a clinical presentation resembling that of smallpox. Although monkeypox is considered to be an important zoonotic viral disease, its epidemiology remains poorly understood, especially the spatial and temporal distribution of the disease. The present study examined weekly reports of monkeypox cases collected from 2000 to 2015 at the health zone scale in the Democratic Republic of Congo. SaTScan® was performed to identify spatial and temporal clusters of monkeypox cases. Significant primary spatial clusters were detected in the districts of Sankuru and Tshuapa. A centrifugal pattern was found, with significant primary spatial clusters extending over time from Sankuru and Tshuapa to several neighboring districts. Peaks of cases occurred from July to September for the 2000-2002 and 2003-2009 sub-periods and from January to March for the 2010-2015 sub-period. Despite the lack of additional data for confirmation, the increasing of monkeypox reported incidence was observed in the Democratic Republic of Congo during 2000-2015 period and this increase cannot be explain only by the improvements of surveillance systems. The detected spatial clusters were located in the dense rainforest of the Congo basin. The reasons for the excess incidence of monkeypox cases in the central region of the country are unknown, and the relative influence of ecological, environmental, and human factors on the mechanism of emergence of monkeypox has yet to be identified.

ICTV Virus Taxonomy Profile: Arenaviridae.

Members of the family Arenaviridae produce enveloped virions containing genomes consisting of two or three single-stranded RNA segments totalling about 10.5 kb. Arenaviruses can infect mammals, including humans and other primates, snakes, and fish. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Arenaviridae, which is available at www.ictv.global/report/arenaviridae.

Taxonomy of the order Bunyavirales: update 2019.

In February 2019, following the annual taxon ratification vote, the order Bunyavirales was amended by creation of two new families, four new subfamilies, 11 new genera and 77 new species, merging of two species, and deletion of one species. This article presents the updated taxonomy of the order Bunyavirales now accepted by the International Committee on Taxonomy of Viruses (ICTV).

The score of integrated disease surveillance and response adequacy (SIA): a pragmatic score for comparing weekly reported diseases based on a systematic review.

BACKGROUND: The Integrated Disease Surveillance and Response (IDSR) strategy implemented by the World Health Organization (WHO) in Africa has produced a large amount of data on participating countries, and in particular on the Democratic Republic of Congo (DRC). These data are increasingly considered as unevaluable and, therefore, as requiring a rigorous process of validation before they can be used for research or public health purposes. The aim of this study was to propose a method to assess the level of adequacy of IDSR morbidity data in reflecting actual morbidity. METHODS: A systematic search of English- and French-language articles was performed in Scopus, Medline, Science Direct, Springer Link, Cochrane, Cairn, Persée, and Erudit databases. Other types of documents were identified through manual searches. Selected articles focused on the determinants of the discrepancies (differences) between reported morbidity and actual morbidity. An adequacy score was constructed using some of the identified determinants. This score was applied to the 15 weekly reported diseases monitored by IDSR surveillance in the DRC. A classification was established using the Jenks method and a sensitivity analysis was performed. Twenty-three classes of determinants were identified in 35 IDSR technical guides and reports of outbreak investigations and in 71 out of 2254 researched articles. For each of the 15 weekly reported diseases, the SIA was composed of 12 items grouped in 6 dimensions. RESULTS: The SIA classified the 15 weekly reported diseases into 3 categories or types: high score or good adequacy (value > = 14), moderate score or fair adequacy (value > = 8 and < 14), and low score or low or non-adequacy (value < 8). Regardless of the criteria used in the sensitivity analysis, there was no notable variation in SIA values or categories for any of the 15 weekly reported diseases. CONCLUSION: In a context of sparse health information in low- and middle-income countries, this study developed a score to help classify IDSR morbidity data as usable, usable after adjustment, or unusable. This score can serve to prioritize, optimize, and interpret data analyses for epidemiological research or public health purposes.

Exploiting the Legacy of the Arbovirus Hunters.

In recent years, it has become evident that a generational gap has developed in the community of arbovirus research. This apparent gap is due to the dis-investment of training for the next generation of arbovirologists, which threatens to derail the rich history of virus discovery, field epidemiology, and understanding of the richness of diversity that surrounds us. On the other hand, new technologies have resulted in an explosion of virus discovery that is constantly redefining the virosphere and the evolutionary relationships between viruses. This paradox presents new challenges that may have immediate and disastrous consequences for public health when yet to be discovered arboviruses emerge. In this review we endeavor to bridge this gap by providing a historical context for the work being conducted today and provide continuity between the generations. To this end, we will provide a narrative of the thrill of scientific discovery and excitement and the challenges lying ahead.

Human Monkeypox in Sierra Leone after 44-Year Absence of Reported Cases.

We note the reemergence of human monkeypox in Sierra Leone following a 44-year absence of reported disease. The persons affected were an 11-month-old boy and, several years later, a 35-year-old man. The reappearance of monkeypox in this country suggests a need for renewed vigilance and awareness of the disease and its manifestations.

Taxonomy of the order Bunyavirales: second update 2018.

In October 2018, the order Bunyavirales was amended by inclusion of the family Arenaviridae, abolishment of three families, creation of three new families, 19 new genera, and 14 new species, and renaming of three genera and 22 species. This article presents the updated taxonomy of the order Bunyavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).

Rift Valley fever seroprevalence and abortion frequency among livestock of Kisoro district, South Western Uganda (2016): a prerequisite for zoonotic infection.

BACKGROUND: Rift Valley fever (RVF) is classified as viral hemorrhagic fever and is endemic in East and West Africa. RVF is caused by an arthropod borne virus (RVFV); the disease is zoonotic and affects human, animal health as well as international trade. In livestock it causes abortions, while human infection occurs through close contact with infected animals or animal products. METHODS: A quantitative observational study using stratified sampling was conducted in the western region of Uganda. Blood samples and abortion events from 1000 livestock (goats, sheep and cattle) was collected and recorded. Serum was analyzed for RVFV IgG reacting antibodies using competitive ELISA test. RESULTS: The overall RVFV seroprevalence was of 10.4% (104/1000). Cattle had the highest seroprevalence (7%) followed by Sheep (2.2%) then goats (1.2%). Species specific RVFV seroprevalence was highest in cattle (20.5%) followed by sheep (6.8%) then goats (3.6%). RVFV seroprevalence in northern highlands (21.8%) was significantly higher (p < 0.001) than in the southern lowlands (3.7%). Overall prevalence of abortion was (17.4%), sheep had the highest prevalence of abortion (7.8%) followed by goats (6.3%) and then cattle (3.3%). Species specific abortion prevalence was highest in Sheep (24.1%) followed by goats (18.8%) and then 9.7% in cattle. CONCLUSION: RVFV is endemic in Kisoro district and livestock in the highland areas are more likely to be exposed to RVFV infection compared to those in the southern lowlands. Out breaks in livestock most likely will lead to zoonotic infection in Kisoro district.

Taxonomy of the family Arenaviridae and the order Bunyavirales: update 2018.

In 2018, the family Arenaviridae was expanded by inclusion of 1 new genus and 5 novel species. At the same time, the recently established order Bunyavirales was expanded by 3 species. This article presents the updated taxonomy of the family Arenaviridae and the order Bunyavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV) and summarizes additional taxonomic proposals that may affect the order in the near future.

Virus-encoded miRNAs in Ebola virus disease.

Ebola virus (EBOV) is a negative-strand RNA virus that replicates in the cytoplasm and causes an often-fatal hemorrhagic fever. EBOV, like other viruses, can reportedly encode its own microRNAs (miRNAs) to subvert host immune defenses. miRNAs are short noncoding RNAs that can regulate gene expression by hybridizing to multiple mRNAs, and viral miRNAs can enhance viral replication and infectivity by regulating host or viral genes. To date, only one EBOV miRNA has been examined in human infection. Here, we assayed mouse, rhesus macaque, cynomolgus macaque, and human samples infected with three EBOV variants for twelve computationally predicted viral miRNAs using RT-qPCR. Ten miRNAs aligned to EBOV variants and were detectable in the four species during disease with several viral miRNAs showing presymptomatic amplification in animal models. miRNA abundances in both the mouse and nonhuman primate models mirrored the human cohort, with miR-1-5p, miR-1-3p, and miR-T3-3p consistently at the highest levels. These striking similarities in the most abundant miRNAs during infection with different EBOV variants and hosts indicate that these miRNAs are potential valuable diagnostic markers and key effectors of EBOV pathogenesis.