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Pertussis, a highly infectious bacterial respiratory infection, is caused by the gram-negative bacterium Bordetella pertussis. In 2018, the World Health Organization (WHO) reported 151,074 cases of pertussis globally, with 89,000 estimated deaths and 86% estimated diphtheria-tetanus-pertussis (DTP3) immunization (Al Awaidy, 2018). The incidence of pertussis in Oman has been reported to be 21 cases per 100,000 population between the years, 2011 and 2015, with 90% under the age of 6 months (Al Hanshi et al., 2014).

Journal of Medical Virology, Accepted Article.

Journal of Medical Virology, Accepted Article.

Journal of Medical Virology, Accepted Article.

Journal of Medical Virology, Accepted Article.

Journal of Medical Virology, Accepted Article.

Journal of Medical Virology, Accepted Article.

Journal of Medical Virology, Accepted Article.

Journal of Medical Virology, Accepted Article.

Journal of Medical Virology, Accepted Article.

Journal of Medical Virology, Accepted Article.

Journal of Medical Virology, Accepted Article.

Journal of Medical Virology, Accepted Article.

Journal of Medical Virology, Accepted Article.

Abstract Background Increasingly complex models have been developed to characterize the transmission dynamics of malaria. The multiplicity of malaria transmission factors calls for a realistic modelling approach that incorporates various complex factors such as the effect of control measures, behavioural impacts of the parasites to the vector, or socio-economic variables. Indeed, the crucial impact of household size in eliminating malaria has been emphasized in previous studies. However, increasing complexity also increases the difficulty of calibrating model parameters. Moreover, despite the availability of much field data, a common pitfall in malaria transmission modelling is to obtain data that could be directly used for model calibration. Methods In this work, an approach that provides a way to combine in situ field data with the parameters of malaria transmission models is presented. This is achieved by agent-based stochastic simulations, initially calibrated with hut-level experimental data. The simulation results provide synthetic data for regression analysis that enable the calibration of key parameters of classical models, such as biting rates and vector mortality. In lieu of developing complex dynamical models, the approach is demonstrated using most classical malaria models, but with the model parameters calibrated to account for such complex factors. The performance of the approach is tested against a wide range of field data for Entomological Inoculation Rate (EIR) values. Results The overall transmission characteristics can be estimated by including various features that impact EIR and malaria incidence, for instance by reducing the mosquito–human contact rates and increasing the mortality through control measures or socio-economic factors. Conclusion Complex phenomena such as the impact of the coverage of the population with long-lasting insecticidal nets (LLINs), changes in behaviour of the infected vector and the impact of socio-economic factors can be included in continuous level modelling. Though the present work should be interpreted as a proof of concept, based on one set of field data only, certain interesting conclusions can already be drawn. While the present work focuses on malaria, the computational approach is generic, and can be applied to other cases where suitable in situ data is available.

New England Journal of Medicine, Volume 384, Issue 15, Page 1448-1456, April 2021.

New England Journal of Medicine, Volume 384, Issue 15, April 2021.

New England Journal of Medicine, Ahead of Print.

New England Journal of Medicine, Ahead of Print.

A. N. Alshukairi et al.

K. Lee et al.

A. Y. Rosinger et al.

Abstract Background Human Norovirus (HuNoV) has recently been identified as a major cause of diarrhea among kidney transplant recipients (KTR). Data regarding risk factors associated with the occurrence of HuNoV infection, and its long-term impact on kidney function are lacking. Methods We conducted a retrospective case-control study including all KTR with a diagnosis of HuNoV diarrhea. Each case was matched to a single control according to age and date of transplantation, randomly selected among our KTR cohort and who did not develop HuNoV infection. Risk factors associated with HuNoV infection were identified using conditional logistic regression, and survival was estimated using Kaplan-Meier estimator. Results From January 2012 to April 2018, 72 cases of NoV diarrhea were identified among 985 new KT, leading to a prevalence of HuNoV infection of 7.3%. Median time between kidney transplantation and diagnosis was 46.5 months (Inter Quartile Range [IQR]:17.8–81.5), and the median duration of symptoms 40 days (IQR: 15–66.2). Following diagnosis, 93% of the cases had a reduction of immunosuppression. During follow-up, de novo Donor Specific Antibody (DSA) were observed in 8 (9%) cases but none of the controls (p = 0.01). Acute rejection episodes were significantly more frequent among cases (13.8% versus 4.2% in controls; p = 0,03), but there was no difference in serum creatinine level at last follow-up between the two groups (p = 0.08). Pre-transplant diabetes and lymphopenia below 1000/mm3 were identified as risks factors for HuNoV infection in multivariate analysis. Conclusion HuNoV infection is a late-onset and prolonged infection among KTR. The current management, based on the reduction of immunosuppressive treatment, is responsible for the appearance of de novo DSA and an increase in acute rejection episodes.

We thank Mattia Trunfio and colleagues for their interest in our Personal View regarding the impact of non-pharmaceutical interventions (NPIs) on the viral inoculum of SARS-CoV-2.1 We agree that increasing evidence supports that NPIs are expected to lower the viral inoculum, potentially contributing to lower transmission. We acknowledge Trunfio and colleagues' point that the evidence supporting the impact of reduced inoculum on COVID-19 severity is less strong than that on infection; we had, therefore, presented this idea as a hypothesis and suggested potential experimental approaches.

We read with interest the Personal View by Matthew A Spinelli and colleagues.1 We agree with the authors on the evident advantage provided by non-pharmaceutical interventions (facial masking, social distancing, and improved ventilation) in lowering SARS-CoV-2 inoculum, thereby reducing viral transmission. Nevertheless, we call for caution before asserting that such measures could make a substantial difference in reducing COVID-19 severity.

Earlier this century, Plasmodium falciparum malaria parasites developed the ability to evade the action of artemisinin antimalarials. This delayed clearance phenotype, referred to as artemisinin resistance, is widespread in the Greater Mekong Subregion of southeast Asia, where it is associated with treatment failures for some artemisinin-based combination therapies (ACTs), the drugs of choice to treat P falciparum malaria.1 However, there is little evidence of artemisinin resistance beyond southeast Asia.

We confirm evidence of emerging artemisinin partial resistance in Rwanda. Although artemether–lumefantrine remains efficacious, vigilance for decreasing efficacy, further characterisation of artemisinin partial resistance, and evaluation of additional antimalarials in Rwanda should be considered.

Interactions between microorganisms in multispecies communities are thought to have substantial consequences for the community. Identifying the molecules and genetic pathways that contribute to such interplay is thus crucial to understand as well as modulate community dynamics. Here I focus on recent studies that utilize experimental systems biology techniques to study these phenomena in simplified model microbial communities. These unbiased biochemical and genomic approaches have identified novel interactions and described the underlying genetic and molecular mechanisms.

Chlamydia trachomatis (CT) is frequently detected in the human gastrointestinal (GI) tract despite its leading role in sexually transmitted bacterial infections in the genital tract. Chlamydia muridarum (CM), a model pathogen for investigating CT pathogenesis in the genital tract, can also colonize the mouse GI tract for long periods. Genital-tract mutants of CM no longer colonize the GI tract. The mutants lacking plasmid functions are more defective in colonizing the upper GI tract while certain chromosomal gene-deficient mutants are more defective in the lower GI tract, suggesting that Chlamydia may use the plasmid for promoting its spread to the large intestine while using the chromosome-encoded factors for maintaining its colonization in the large intestine.

Lacticaseibacillus rhamnosus GR-1 (LGR-1) (previously classified as Lactobacillus rhamnosus GR-1) is the most researched probiotic strain for women’s health. Its various urogenital health effects, including a reduction in the recurrence of bacterial vaginosis and urinary-tract infection, are well documented. The strain has also been safely used by HIV-positive subjects, a portion of whom have reported reduced diarrhea and increased CD4 counts. Unlike most probiotic strains used for urogenital health, LGR-1 has been extensively studied for its properties, including its genomic and metabolic traits and its surface properties.

The bacterial flagellar motor, a remarkable rotary machine, can rapidly switch between counterclockwise (CCW) and clockwise (CW) rotational directions to control the migration behavior of the bacterial cell. The flagellar motor consists of a bidirectional spinning rotor surrounded by torque-generating stator units. Recent high-resolution in vitro and in situ structural studies have revealed stunning details of the individual components of the flagellar motor and their interactions in both the CCW and CW senses.

Cases of SARS-CoV-2 infection in Manaus, Brazil, resurged in late 2020, despite previously high levels of infection. Genome sequencing of viruses sampled in Manaus between November 2020 and January 2021 revealed the emergence and circulation of a novel SARS-CoV-2 variant of concern. Lineage P.1, acquired 17 mutations, including a trio in the spike protein (K417T, E484K and N501Y) associated with increased binding to the human ACE2 receptor. Molecular clock analysis shows that P.1 emergence occurred around mid-November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.7–2.4-fold more transmissible, and that previous (non-P.1) infection provides 54–79% of the protection against infection with P.1 that it provides against non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness.

Brazil has been severely hit by COVID-19, with rapid spatial spread of both cases and deaths. We use daily data on reported cases and deaths to understand, measure, and compare the spatiotemporal pattern of the spread across municipalities. Indicators of clustering, trajectories, speed, and intensity of the movement of COVID-19 to interior areas, combined with indices of policy measures show that while no single narrative explains the diversity in the spread, an overall failure of implementing prompt, coordinated, and equitable responses in a context of stark local inequalities fueled disease spread. This resulted in high and unequal infection and mortality burdens. With a current surge in cases and deaths and several variants of concern in circulation, failure to mitigate the spread could further aggravate the burden.

Anopheles stephensi originated in Southeast Asia and the Arabian Peninsula. It has recently emerged as an efficient and invasive urban malaria vector. There are three known forms, 'type', 'intermediate', and 'mysorensis', of which the type and intermediate forms are efficient vectors in both rural and urban environments. Typical breeding sites are artificial containers, such as domestic wells, cisterns, overhead water tanks, and roof gutters, with clean and unpolluted water allowing rapid expansion to urban environments.

Abstract Background The SARS-CoV-2 infection has emerged as a rapidly spreading infection. Today it is relatively easy to isolate Covid-19 symptomatic cases, while remains problematic to control the disease spread by infected but symptom-free individuals. The control of this possible path of contagion requires drastic measures of social distancing, which imply the suspension of most activities and generate economic and social issues. This study is aimed at estimating the percentage of asymptomatic SARS-CoV-2 infection in a geographic area with relatively low incidence of Covid-19. Methods Blood serum samples from 388 healthy volunteers were analyzed for the presence of anti-SARS-CoV-2 IgG by using an ELISA assay based on recombinant viral nucleocapsid protein. Results We found that 7 out of 388 healthy volunteers, who declared no symptoms of Covid-19, like fever, cough, fatigue etc., in the preceding 5 months, have bona fide serum anti-SARS-CoV-2 IgG, that is 1.8% of the asymptomatic population (95% confidence interval: 0.69–2.91%). Conclusions The estimated range of asymptomatic individuals with anti-SARS-CoV-2 IgG should be between 26,565 and 112, 350. In the same geographic area, there are 4665 symptomatic diagnosed cases.

by Jennifer L. Essler, Sarah A. Kane, Pat Nolan, Elikplim H. Akaho, Amalia Z. Berna, Annemarie DeAngelo, Richard A. Berk, Patricia Kaynaroglu, Victoria L. Plymouth, Ian D. Frank, Susan R. Weiss, Audrey R. Odom John, Cynthia M. Otto While the world awaits a widely available COVID-19 vaccine, availability of testing is limited in many regions and can be further compounded by shortages of reagents, prolonged processing time and delayed results. One approach to rapid testing is to leverage the volatile organic compound (VOC) signature of SARS-CoV-2 infection. Detection dogs, a biological sensor of VOCs, were utilized to investigate whether SARS-CoV-2 positive urine and saliva patient samples had a unique odor signature. The virus was inactivated in all training samples with either detergent or heat treatment. Using detergent-inactivated urine samples, dogs were initially trained to find samples collected from hospitalized patients confirmed with SARS-CoV-2 infection, while ignoring samples collected from controls. Dogs were then tested on their ability to spontaneously recognize heat-treated urine samples as well as heat-treated saliva from hospitalized SARS-CoV-2 positive patients. Dogs successfully discriminated between infected and uninfected urine samples, regardless of the inactivation protocol, as well as heat-treated saliva samples. Generalization to novel samples was limited, particularly after intensive training with a restricted sample set. A unique odor associated with SARS-CoV-2 infection present in human urine as well as saliva, provides impetus for the development of odor-based screening, either by electronic, chemical, or biological sensing methods. The use of dogs for screening in an operational setting will require training with a large number of novel SARS-CoV-2 positive and confirmed negative samples.

by Ashraf Mohabati Mobarez, Mohammad Khalili, Ehsan Mostafavi, Saber Esmaeili Background Coxiella burnetii is the causative agent of Q fever which is a highly infectious zoonotic disease. C. burnetii has become one of the most important causes of abortion in livestock, which can lead to widespread abortions in these animals. There are very limited studies on the prevalence of C. burnetii infection in cases of animal abortion in Iran. The aim of this study was to investigate the occurrence of C. burnetii in ruminant abortion samples in Iran. Methods Abortion samples from cattle, sheep and goats were collected from different parts of Iran and were tested using Real-time PCR targeting the IS1111 element of C. burnetii. Results In this study, 36 samples (24.7%) of the 146 collected samples were positive for C. burnetii. The prevalence of C. burnetii was 21.3% (20 of 94 samples) in sheep samples. Also, 10 of 46 cattle samples (21.7%) were positive. All six goat abortion samples were positive for C. burnetii. Conclusions The findings of the study demonstrate that C. burnetii plays an important role in domestic ruminant abortions in Iran, suggesting that more attention should be paid to the role of C. burnetii in domestic animal abortions by veterinary organizations. The risk of transmitting the infection to humans due to abortion of animals should also be considered.

by Hongwei Zhao, Naveed N. Merchant, Alyssa McNulty, Tiffany A. Radcliff, Murray J. Cote, Rebecca S. B. Fischer, Huiyan Sang, Marcia G. Ory Background Prediction of the dynamics of new SARS-CoV-2 infections during the current COVID-19 pandemic is critical for public health planning of efficient health care allocation and monitoring the effects of policy interventions. We describe a new approach that forecasts the number of incident cases in the near future given past occurrences using only a small number of assumptions. Methods Our approach to forecasting future COVID-19 cases involves 1) modeling the observed incidence cases using a Poisson distribution for the daily incidence number, and a gamma distribution for the series interval; 2) estimating the effective reproduction number assuming its value stays constant during a short time interval; and 3) drawing future incidence cases from their posterior distributions, assuming that the current transmission rate will stay the same, or change by a certain degree. Results We apply our method to predicting the number of new COVID-19 cases in a single state in the U.S. and for a subset of counties within the state to demonstrate the utility of this method at varying scales of prediction. Our method produces reasonably accurate results when the effective reproduction number is distributed similarly in the future as in the past. Large deviations from the predicted results can imply that a change in policy or some other factors have occurred that have dramatically altered the disease transmission over time. Conclusion We presented a modelling approach that we believe can be easily adopted by others, and immediately useful for local or state planning.

by Gayatri Shankar Chilambi, Hayley R. Nordstrom, Daniel R. Evans, Regis P. Kowalski, Deepinder K. Dhaliwal, Vishal Jhanji, Robert M. Q. Shanks, Daria Van Tyne Enterococcus faecalis are hospital-associated opportunistic pathogens and also causative agents of post-operative endophthalmitis. Patients with enterococcal endophthalmitis often have poor visual outcomes, despite appropriate antibiotic therapy. Here we investigated the genomic and phenotypic characteristics of E. faecalis isolates collected from 13 patients treated at the University of Pittsburgh Medical Center Eye Center over 19 years. Comparative genomic analysis indicated that patients were infected with E. faecalis belonging to diverse multi-locus sequence types (STs) and resembled E. faecalis sampled from clinical, commensal, and environmental sources. We identified known E. faecalis virulence factors and antibiotic resistance genes in each genome, including genes conferring resistance to aminoglycosides, erythromycin, and tetracyclines. We assessed all isolates for their cytolysin production, biofilm formation, and antibiotic susceptibility, and observed phenotypic differences between isolates. Fluoroquinolone and cephalosporin susceptibilities were particularly variable between isolates, as were biofilm formation and cytolysin production. In addition, we found evidence of E. faecalis adaptation during recurrent endophthalmitis by identifying genetic variants that arose in sequential isolates sampled over eight months from the same patient. We identified a mutation in the DNA mismatch repair gene mutS that was associated with an increased rate of spontaneous mutation in the final isolate from the patient. Overall this study documents the genomic and phenotypic variability among E. faecalis causing endophthalmitis, as well as possible adaptive mechanisms underlying bacterial persistence during recurrent ocular infection.

by Rohit Kapila, Mayank Kashyap, Soumyadip Poddar, Shreya Gangwal, N. G. G. Prasad The environment experienced by individuals during their juvenile stages has an impact on their adult stages. In holometabolous insects like Drosophila melanogaster, most of the resource acquisition for adult stages happens during the larval stages. Larval-crowding is a stressful environment, which exposes the larvae to scarcity of food and accumulation of toxic waste. Since adult traits are contingent upon larval stages, in larval-crowding like conditions, adult traits are prone to get affected. While the effect of resource limited, poor-developmental environment on adult immune response has been widely studied, the effect of adaptation to resource-limited developmental environment has not been studied, therefore in this study we assayed the evolution of ability to survive infection in adult stages as a correlated response to adaptation to larval crowding environments. Using four populations of Drosophila melanogaster adapted to larval crowding for 240 generations and their respective control populations, we show that populations adapted to larval crowding show an improved and evolved post-infection survivorship against a gram-negative bacteria Pseudomonas entomophila. Whereas, against a gram-positive bacteria Enterococcus faecalis, no difference in post-infection survivorship was observed across control and selected populations. In this study, we report the co-related evolution of pathogen-specific increased survivorship post-infection in populations of Drosophila melanogaster as a result of adaptation to larval crowding environment.

by Abdulelah A. Alghamdi The COVID-19 pandemic led to surprising and unexpected experiences for Saudi university students. Precautionary and preventive measures taken to contain this pandemic impacted the social and educational aspects of these students’ lives. All Umm Al-Qura University (UQU) students were invited to participate in an online survey on 30 impacts, both positive and negative, of the COVID-19 pandemic on their lives. Social impact theory (SIT) was applied to illustrate these impacts. The survey yielded 1,360 responses. The results showed high to moderate levels of agreement regarding students’ perceptions of the positive and negative impact of the COVID-19 pandemic on their lives, with social aspects impacted more than educational ones; and no statistically significant gender differences. Weak correlations were found between the social aspects and the educational aspects of students’ lives in relation to the impact of the pandemic, although all aspects were correlated positively. The SIT framework provided insights into how the COVID-19 pandemic impacted students’ lives.

by Selamawit Woldesenbet, Tendesayi Kufa-Chakezha, Carl Lombard, Samuel Manda, Mireille Cheyip, Kassahun Ayalew, Brian Chirombo, Peter Barron, Karidia Diallo, Bharat Parekh, Adrian Puren Introduction New HIV infection during pre-conception and pregnancy is a significant contributor of mother–to–child transmission of HIV in South Africa. This study estimated HIV incidence (defined as new infection within the last one year from the time of the survey which included both new infections occurred during pregnancy or just before pregnancy) among pregnant women and described the characteristics of recently infected pregnant women at national level. Methods Between 1 October and 15 November 2017, we conducted a national cross–sectional survey among pregnant women aged 15–49 years old attending antenatal care at 1,595 public facilities. Blood specimens were collected from pregnant women and tested for HIV in a centralised laboratory. Plasma viral load and Limiting Antigen Avidity Enzyme Immunosorbent Assay (LAg) tests were further performed on HIV positive specimens to differentiate between recent and long–term infections. Recent infection was defined as infection that occurred within one year from the date of collection of blood specimen for the survey. Data on age, age of partner, and marital status were collected through interviews. Women whose specimens were classified as recent by LAg assay and with viral loads >1,000 copies/mL were considered as recently infected. The calculated proportion of HIV positive women with recent infection was adjusted for assay–specific parameters to estimate annual incidence. Survey multinomial logistic regression was used to examine factors associated with being recently infected using HIV negative women as a reference group. Age–disparate relationship was defined as having a partner 5 or more years older. Results Of 10,049 HIV positive participants with LAg and viral load data, 1.4% (136) were identified as recently infected. The annual HIV incidence was 1.5% (95% confidence interval (CI): 1.2–1.7). In multivariable analyses, being single (adjusted odds ratio, aOR: 3.4, 95% CI: 1.8–6.2) or cohabiting (aOR: 3.8, 95% CI: 1.8–7.7), compared to being married as well as being in an age–disparate relationship among young women (aOR: 3.1, 95% CI: 2.0–4.7; reference group: young women (15–24years) whose partners were not 5 years or more older) were associated with higher odds of recent infection. Conclusions Compared to previous studies among pregnant women, the incidence estimated in this study was substantially lower. However, the UNAIDS target to reduce incidence by 75% by 2020 (which is equivalent to reducing incidence to…

by Olga Spekker, Luca Kis, Andrea Deák, Eszter Makai, György Pálfi, Orsolya Anna Váradi, Erika Molnár Ancient human remains exhibiting bony changes consistent with osteoarticular tuberculosis (OATB) indicate that the disease has afflicted mankind for millennia. Nonetheless, not many pediatric OATB cases have been published in the paleopathological literature–from Hungary, only three cases have been described up to now. In our paper, we demonstrate a child (S0603) from the Árpádian Age cemetery of Győrszentiván-Révhegyi tag (northwestern Hungary), who represents a unique case of OATB regarding both the pattern and severity of the observed bony changes. During the macromorphological and radiological investigations, the most serious alterations were discovered in the upper thoracic spine–the development of osteolytic lesions led to severe bone loss and consequent collapse and fusion of several adjacent vertebrae. The pathological process terminated in a sharp, rigid angular kyphosis. Disruption of the normal spine curvature resulted in consequent deformation of the whole thoracic wall–it became “rugby-ball-shaped”. The overall nature and pattern of the detected alterations, as well as their resemblance to those of described in previously published archaeological and modern cases from the pre-antibiotic era indicate that they are most consistent with OATB. Based on the severity and extent of the lesions, as well as on the evidence of secondary healing, S0603 suffered from TB for a long time prior to death. Besides body deformation, OATB resulted in consequent disability in daily activities, which would have required regular and significant care from others to survive. It implies that in the Árpádian Age community of Győrszentiván-Révhegyi tag, there was a willingness to care for people in need. Detailed archaeological case studies can give us a unique insight into the natural history and different presentations of OATB. Furthermore, they can provide paleopathologists with a stronger basis for diagnosing TB and consequently, with a more sensitive means of assessing TB frequency in past populations.

by Charlie B. Fischer, Nedghie Adrien, Jeremiah J. Silguero, Julianne J. Hopper, Abir I. Chowdhury, Martha M. Werler Mask wearing has been advocated by public health officials as a way to reduce the spread of COVID-19. In the United States, policies on mask wearing have varied from state to state over the course of the pandemic. Even as more and more states encourage or even mandate mask wearing, many citizens still resist the notion. Our research examines mask wearing policy and adherence in association with COVID-19 case rates. We used state-level data on mask wearing policy for the general public and on proportion of residents who stated they always wear masks in public. For all 50 states and the District of Columbia (DC), these data were abstracted by month for April ─ September 2020 to measure their impact on COVID-19 rates in the subsequent month (May ─ October 2020). Monthly COVID-19 case rates (number of cases per capita over two weeks) >200 per 100,000 residents were considered high. Fourteen of the 15 states with no mask wearing policy for the general public through September reported a high COVID-19 rate. Of the 8 states with at least 75% mask adherence, none reported a high COVID-19 rate. States with the lowest levels of mask adherence were most likely to have high COVID-19 rates in the subsequent month, independent of mask policy or demographic factors. Mean COVID-19 rates for states with at least 75% mask adherence in the preceding month was 109.26 per 100,000 compared to 249.99 per 100,000 for those with less adherence. Our analysis suggests high adherence to mask wearing could be a key factor in reducing the spread of COVID-19. This association between high mask adherence and reduced COVID-19 rates should influence policy makers and public health officials to focus on ways to improve mask adherence across the population in order to mitigate the spread of COVID-19.

by Emma Peel, Yuanyuan Cheng, Julianne T. Djordjevic, Denis O’Meally, Mark Thomas, Michael Kuhn, Tania C. Sorrell, Wilhelmina M. Huston, Katherine Belov Devastating fires in Australia over 2019–20 decimated native fauna and flora, including koalas. The resulting population bottleneck, combined with significant loss of habitat, increases the vulnerability of remaining koala populations to threats which include disease. Chlamydia is one disease which causes significant morbidity and mortality in koalas. The predominant pathogenic species, Chlamydia pecorum, causes severe ocular, urogenital and reproductive tract disease. In marsupials, including the koala, gene expansions of an antimicrobial peptide family known as cathelicidins have enabled protection of immunologically naïve pouch young during early development. We propose that koala cathelicidins are active against Chlamydia and other bacteria and fungi. Here we describe ten koala cathelicidins, five of which contained full length coding sequences that were widely expressed in tissues throughout the body. Focusing on these five, we investigate their antimicrobial activity against two koala C. pecorum isolates from distinct serovars; MarsBar and IPTaLE, as well as other bacteria and fungi. One cathelicidin, PhciCath5, inactivated C. pecorum IPTaLE and MarsBar elementary bodies and significantly reduced the number of inclusions compared to the control (p<0.0001). Despite evidence of cathelicidin expression within tissues known to be infected by Chlamydia, natural PhciCath5 concentrations may be inadequate in vivo to prevent or control C. pecorum infections in koalas. PhciCath5 also displayed antimicrobial activity against fungi and Gram negative and positive bacteria, including methicillin-resistant Staphylococcus aureus (MRSA). Electrostatic interactions likely drive PhciCath5 adherence to the pathogen cell membrane, followed by membrane permeabilisation leading to cell death. Activity against E. coli was reduced in the presence of 10% serum and 20% whole blood. Future modification of the PhciCath5 peptide to enhance activity, including in the presence of serum/blood, may provide a novel solution to Chlamydia infection in koalas and other species.

by Ninfa Marlen Chaves-Torres, Santiago Fadul, Jesus Patiño, Eduardo Netto Background Multidrug- and rifampicin (RMP)-resistant tuberculosis (MDR/RR-TB) requires prolonged and expensive treatment, which is difficult to sustain in the Colombian health system. This requires the joint action of different providers to provide timely health services to people with TB. Identifying factors associated with unfavorable treatment outcomes in patients with MDR/RR-TB who received drug therapy between 2013 and 2015 in Colombia can help guide the strengthening of the national TB control program. Method A retrospective cohort study was conducted with all patients who received treatment for MDR/RR-TB between January 2013 and December 2015 in Colombia who were registered and followed up by the national TB control program. A multivariate logistic regression model was used to estimate the associations between the exposure variables with the response variable (treatment outcome). Results A total of 511 patients with MDR/RR-TB were registered and followed up by the national TB control program in Colombia, of whom 16 (3.1%) had extensive drug resistance, 364 (71.2%) had multidrug resistance, and 131 (25.6%) had RMP monoresistance. The mean age was 39.9 years (95% confidence interval (CI): 38.5–41.3), most patients were male 285 (64.6%), and 299 (67.8%) were eligible for subsidized health services. The rate of unfavorable treatment outcomes in the RR-TB cohort was 50.1%, with rates of 85.7% for patients with extensive drug resistance, 47.6% for patients with multidrug resistance, and 52.6% for patients with RMP monoresistance. The 511 MDR/RR-TB patients were included in bivariate and multivariate analyses, patients age ≥ 60 years (crude odds ratio (ORc) = 2.4, 95% CI 1.1–5.8; adjusted odds ratio (ORa) = 2.7, 95% CI 1.1–6.8) and subsidized health regime affiliation (ORc = 3.6, 95% CI 2.3–5.6; ORa = 3.4, 95% CI 2.0–6.0) were associated with unfavorable treatment outcomes. Conclusion More than 50% of the patients with MDR/RR-TB in Colombia experienced unfavorable treatment outcomes. The patients who were eligible for subsidized care were more likely to experience unfavorable treatment outcomes. Those who were older than 60 years were also more likely to experience unfavorable treatment outcomes.

by Brydon Eastman, Cameron Meaney, Michelle Przedborski, Mohammad Kohandel The outbreak of SARS-CoV-2 is thought to have originated in Wuhan, China in late 2019 and has since spread quickly around the world. To date, the virus has infected tens of millions of people worldwide, compelling governments to implement strict policies to counteract community spread. Federal, provincial, and municipal governments have employed various public health policies, including social distancing, mandatory mask wearing, and the closure of schools and businesses. However, the implementation of these policies can be difficult and costly, making it imperative that both policy makers and the citizenry understand their potential benefits and the risks of non-compliance. In this work, a mathematical model is developed to study the impact of social behaviour on the course of the pandemic in the province of Ontario. The approach is based upon a standard SEIRD model with a variable transmission rate that depends on the behaviour of the population. The model parameters, which characterize the disease dynamics, are estimated from Ontario COVID-19 epidemiological data using machine learning techniques. A key result of the model, following from the variable transmission rate, is the prediction of the occurrence of a second wave using the most current infection data and disease-specific traits. The qualitative behaviour of different future transmission-reduction strategies is examined, and the time-varying reproduction number is analyzed using existing epidemiological data and future projections. Importantly, the effective reproduction number, and thus the course of the pandemic, is found to be sensitive to the adherence to public health policies, illustrating the need for vigilance as the economy continues to reopen.

by Kim Sui Wan, Peter Seah Keng Tok, Kishwen Kanna Yoga Ratnam, Nuraini Aziz, Marzuki Isahak, Rafdzah Ahmad Zaki, Nik Daliana Nik Farid, Noran Naqiah Hairi, Sanjay Rampal, Chiu-Wan Ng, Mohd Fauzy Samsudin, Vinura Venugopal, Mohammad Asyraf, Narisa Hatun Damanhuri, Sanpagavalli Doraimuthu, Catherine Thamarai Arumugam, Thaneswaran Marthammuthu, Fathhullah Azmie Nawawi, Faiz Baharudin, Diane Woei Quan Chong, Vivek Jason Jayaraj, Venna Magarita, Sasheela Ponnampalavanar, Nazirah Hasnan, Adeeba Kamarulzaman, Mas Ayu Said Introduction The reporting of Coronavirus Disease 19 (COVID-19) mortality among healthcare workers highlights their vulnerability in managing the COVID-19 pandemic. Some low- and middle-income countries have highlighted the challenges with COVID-19 testing, such as inadequate capacity, untrained laboratory personnel, and inadequate funding. This article describes the components and implementation of a healthcare worker surveillance programme in a designated COVID-19 teaching hospital in Malaysia. In addition, the distribution and characteristics of healthcare workers placed under surveillance are described. Material and methods A COVID-19 healthcare worker surveillance programme was implemented in University Malaya Medical Centre. The programme involved four teams: contact tracing, risk assessment, surveillance and outbreak investigation. Daily symptom surveillance was conducted over fourteen days for healthcare workers who were assessed to have low-, moderate- and high-risk of contracting COVID-19. A cross-sectional analysis was conducted for data collected over 24 weeks, from the 6th of March 2020 to the 20th of August 2020. Results A total of 1,174 healthcare workers were placed under surveillance. The majority were females (71.6%), aged between 25 and 34 years old (64.7%), were nursing staff (46.9%) and had no comorbidities (88.8%). A total of 70.9% were categorised as low-risk, 25.7% were moderate-risk, and 3.4% were at high risk of contracting COVID-19. One-third (35.2%) were symptomatic, with the sore throat (23.6%), cough (19.8%) and fever (5.0%) being the most commonly reported symptoms. A total of 17 healthcare workers tested positive for COVID-19, with a prevalence of 0.3% among all the healthcare workers. Risk category and presence of symptoms were associated with a positive COVID-19 test (p<0.001). Fever (p<0.001), cough (p = 0.003), shortness of breath (p = 0.015) and sore throat (p = 0.002) were associated with case positivity. Conclusion COVID-19 symptom surveillance and risk-based assessment have merits to be included in a healthcare worker surveillance programme to safeguard the health of the workforce.

by Gordana Kovacevic, Vesna Milosevic, Natasa Nikolic, Aleksandra Patic, Nela Dopudj, Jelena Radovanov, Ivana Hrnjakovic Cvjetkovic, Vladimir Petrovic, Milena Petrovic This study evaluates the pre-vaccination prevalence of HPV infection in women from Vojvodina, Serbia, according to age and cytological status. A total of 1,495 women, ranging from 18 to 65 years of age, with different cytological results were enrolled. The HPV genotyping assay was performed using the EUROArray HPV test in order to detect thirty genitally relevant HPV subtypes. In our study, the most prevalent genotypeswere HPV 16, 31, 51, and 53. Among these, HPV 16 was consistently present in all cytological subgroups. Twelve HPV genotypes classified as carcinogenic to humans (Group 1) were detected in 77.8.0% of HSIL/ASCH and 55.0% of NILM with abnormal colposcopy findings. Six possible carcinogens—HRs (group 2B) were often found in women with normal cytology (14.8%) and mild abnormalities (ASCUS and LSIL), but with lower frequence in HSIL/ASCH lesions (7.1%). HPVs 6 and 11(Group 3) were not found in the cases of HSIL/ASCH. Unclassified HPV types were equally distributed in all cytology groups: 20.7%, 19.1%, 16.3% and 13% of NILM, ASCUS, LSIL and HSIL/ASCH, respectively. Our findings highlight that majority of abnormal Pap test results are caused by Group 1 HPVs among women from our region. Low frequency HPVs of group 2A/2B, especially HSIL/ASCH, supports the conclusion that individual genotypes require consideration of each type as an individual agent. We expect a positive impact of HPV vaccine in reducing HPV-associated cervical lesions among women from Vojvodina province, after establishing vaccination programs in our country.