Screening Strategies in Different Resource Settings

Health care-associated infections/ Hospital-acquired infections (HAIs) have a significant impact on patients' morbidity and mortality. The risk of HAIs in resource-limited settings (RLS) has been reported 2-20 times higher than that in developed countries. Moreover, multi-drug- resistant organisms (MDROs) have emerged and spread throughout the world. In addition, increases in HAIs were observed during the COVID-19 pandemic throughout the world.Thus, screening strategies/surveillance of MDROs were recommended as a core component of infection prevention and control (IPC) measures for the effective HAIs prevention. We review and summarize current critical knowledge on screening strategies in different resource settings, especially on guidelines for the prevention and control of carbapenem- resistant Enterobacteriaceae (CRE), Acinetobacter baumannii (CRAB), and Pseudomonas aeruginosa (CRPsA) in health care facilities. The guidelines (especially WHO) were strongly recommended for surveillance of CRE-CRAB-CRPsA infections and surveillance cultures of asymptomatic CRE colonization. There were conditional recommended on surveillance cultures of the environment for CRE-CRAB-CRPsA colonization/contamination. The surveillance cultures (stool samples or rectal swabs) allowed the early introduction of IPC measures to prevent transmission to other patients and the hospital environment. Given the clinical importance of CRE-CRAB-CRPsA infections, regular ongoing active surveillance of infections were required in all microbiology laboratory settings. In addition, surveillance cultures for asymptomatic CRE colonization should also be performed, guided by local epidemiology and risk assessment. The surveillance cultures of asymptomatic CRE colonization should be considered for patients with previous CRE colonization and patients with a history of recent hospitalization in endemic CRE settings or contacted CRE colonized/ infected patients. In contrast, the evidence available on surveillance cultures for CRAB and CRPsA colonization in asymptomatic patients was not sufficiently relevant for the recommendation. Nowadays, the CRE surveillance strategies have been implemented in various methods from traditional culture- based methods to molecular assays. The limitation of microbiology laboratory capacity for MDROs in RLS was concerning. However, the surveillance data would help with appropriate IPC measure implementation and outbreak investigations. Thus, the proper screening strategies and strengthening microbiology laboratory capacity, especially in RLS are challenge for improving IPC measures and patient outcomes.Copyright © 2023

Long Term Circulation of Sars-Cov-2 Related Lineages in Bats in Cambodia

Intro: Recent evidence shows the Greater Mekong Subregion to be a hotspot for Sarbecoviruses in bats, especially insectivorous Horseshoe bats (genus Rhinolophus). However, prevalence, maintenance, and evolution of these viruses in Rhinolophids is still poorly understood. Sampling efforts are still limited and generally only cover cross-sectional surveillance at single points in time. Following the detection of Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2)-related viruses in Rhinolophus shameli from 2010 in Steung Treng, Cambodia, further active longitudinal surveillance in the same area between 2020-2021 continued the detection of these viruses. Method(s): Live bat capture and sampling has been implemented in several sites located in Stung Treng province. All rectal swabs of bats were tested for the detection of SARS-CoV-2 or Sarbecoviruses by real time RT-PCR. RNA samples from positive RT-PCR bats were then sequenced using a highly multiplexed PCR amplicon approach using new designed primers set guided by the ARTIC Network multiplex PCR primers set (https://artic.network/ncov-2019), on Oxford Nanopore technology. Finding(s): The sarbecoviruses were detected in four Rhinolophus shameli bats, a percentage of similarity ranging at the nucleotide level between 98.8% - 99.1% when compared to two other Cambodian bat sarbecoviruses from 2010 and between 92.4% - 94.5% when compared to human SARS-CoV-2 across the whole genome. Discussion(s): The bat SARS-CoV-2 related virus recently detected in four positive bats in 2020-2021 are genetically homologous with the virus detected in 2010, indicating a geographically/host limited population that is stable over time in the past ten years. Conclusion(s): Overall, our findings indicate further complexity in the diversity and evolution of sarbecoviruses and add intricacy to the search for the origins of the Coronavirus Disease 2019 (COVID-19) pandemic.Copyright © 2023

PROLONGED SARS-CoV-2 VIRAL BURDEN IN SIV-SARS-CoV-2 COINFECTED MACAQUES

Background: Individuals living with HIV are at increased risk of morbidity and mortality from COVID-19. Furthermore, SARS-CoV-2 infection in immunocompromised HIV infected individuals poses a risk to prolonged infection and viral shedding and the emergence of new variants of concern (VOCs). Using the SIV macaque model for AIDS, we are investigating the hypothesis that immune dysfunction during HIV infection will prolong SARSCoV- 2 viral infection, promote enhanced COVID-19 disease, and accelerate viral evolution. Here, we report the impact of SIV-CoV-2 co-infection on immune responses and pathogenesis. Method(s): Eight female rhesus macaques (aged 7-15 years, 5.5-9.9kg) were infected with SIVmac251 via low dose intravaginal challenge and then inoculated with 6.5x105 TCID50/mL SARS-CoV-2 (WA-1) at 17-34 weeks post-SIV infection via combined intranasal and intratracheal routes. Blood, bronchoalveolar lavage (BAL), stool, and nasal, oral, and rectal swabs were collected pre-infection through 14 days post-infection (DPI) to measure immune responses and viremia. ELISAs, ELISPOT, qRT-PCR, lung pathology, cytokine multiplex, and virus neutralization assays were performed to measure viral loads, pathogenesis, and immune responses. Result(s): Three days post-SARS-CoV-2 infection, we observed a transient decrease in CD4 counts, but there were no changes in clinical symptoms or plasma SIV viral loads. However, SARS-CoV-2 replication persisted in the upper respiratory tract, but not the lower respiratory tract. In addition, SARS-CoV-2 IgG seroconversion was delayed and antigen-specific T-cell responses were dampened. Notably, viral RNA levels in nasal swabs were significantly higher 7-14 DPI in SIV+ compared to previously published results using the same SARS-CoV-2 challenge virus in SIV- rhesus (PMCID: PMC8462335, PMC8829873). In addition, SIV/CoV-2 co-infected animals exhibited elevated levels of myeloperoxidase (MPO), a marker of neutrophil activation and increased lung inflammation. Conclusion(s): Here we provide evidence for the utility of the rhesus macaque in modeling human HIV-SARS-CoV-2 co-infection. Our results suggest that immunosuppression during SIV infection impairs de novo generation of anti-SARS-CoV-2 immunity, that may contribute to prolonged SARS-CoV-2 viral shedding, increased transmission windows, altered disease pathogenesis, and lower protection against subsequent SARS-CoV-2 exposures. Studies in progress will determine if SARS-CoV-2 viral evolution is accelerated in SIV-infected macaques.

Assessment of Fecal Viral Shedding Among Children Who Have COVID-19 by Polymerase Chain Reaction

Objective: This study aimed to assess fecal viral shedding in children who have been confirmed COVID-19 by real time polymerase chain reaction (RT-PCR). Material(s) and Method(s): We enrolled fifty inpatient children who have been confirmed COVID-19 during first wave of outbreak in our region. All of the patients have been twice confirmed by RT-PCR within nasopharyngeal swabs. Each case was evaluated with clinical data, laboratory tests and rectal swabs. The rectal swabs were obtained five days after nasopharyngeal positivity. The clinical data was recorded within two basic categories, including common symptoms or digestive symptoms. Detection of SARS-CoV-2 in rectal swabs was performed by RT-PCR method. Result(s): Fifteen patients (30%) had digestive symptoms. On the 5th day, 50 rectal swabs were studied with PCR-RT. Only one of them was positive (2%). The only patient who was positive for SARS-CoV-2 on rectal swab was a symptomatic threeand-a-half-year-old girl. The patient, who became asymptomatic in the follow-up, was retested with a nasopharyngeal swab one week later, the result was negative and she was discharged on the 10th day. The second rectal smear of the patient was negative. Conclusion(s): We found very low rate (2%) fecal viral shedding with rectal swab PCR among children who have been confirmed COVID-19 by nasopharyngeal swab PCR. We thought that this result was due to the mild clinical course of the patients who has been diagnosed with COVID-19 we followed up. However, fecal oral transmission might still matter in children. Copyright © 2022 Ankara Pediatric Hematology Oncology Training and Research Hospital. All rights reserved.

The Entero-Mammary Pathway and Perinatal Transmission of Gut Microbiota and SARS-CoV-2.

COVID-19 is a severe respiratory disease threatening pregnant women, which increases the possibility of adverse pregnancy outcomes. Several recent studies have demonstrated the ability of SARS-CoV-2 to infect the mother enterocytes, disturbing the gut microbiota diversity. The aim of this study was to characterize the entero-mammary microbiota of women in the presence of the virus during delivery. Fifty mother-neonate pairs were included in a transversal descriptive work. The presence of SARS-CoV-2 RNA was detected in nasopharyngeal, mother rectal swabs (MRS) and neonate rectal swabs (NRS) collected from the pairs, and human colostrum (HC) samples collected from mothers. The microbiota diversity was characterized by high-throughput DNA sequencing of V3-16S rRNA gene libraries prepared from HC, MRS, and NRS. Data were analyzed with QIIME2 and R. Our results indicate that several bacterial taxa are highly abundant in MRS positive for SARS-CoV-2 RNA. These bacteria mostly belong to the Firmicutes phylum; for instance, the families Bifidobacteriaceae, Oscillospiraceae, and Microbacteriaceae have been previously associated with anti-inflammatory effects, which could explain the capability of women to overcome the infection. All samples, both positive and negative for SARS-CoV-2, featured a high abundance of the Firmicutes phylum. Further data analysis showed that nearly 20% of the bacterial diversity found in HC was also identified in MRS. Spearman correlation analysis highlighted that some genera of the Proteobacteria and Actinobacteria phyla were negatively correlated with MRS and NRS (p < 0.005). This study provides new insights into the gut microbiota of pregnant women and their potential association with a better outcome during SARS-CoV-2 infection.

Molecular Detection of Middle East Respiratory Syndrome Coronavirus from Dromedary Camels Illegally Transferred to Iran

After the identification of Middle East respiratory syndrome coronavirus from camels in Saudi Arabia by 2012, it has been believed that camel is a primary reservoir of Middle East respiratory syndrome coronavirus, and viral transmission from camel to human could occur. The current study is the initial announcement on Middle East respiratory syndrome coronavirus detection from camels in Iran. Middle East respiratory syndrome genome was analyzed by real-time reverse transcription polymerase chain reaction in samples taken from camels that illegally entered Iran. The presence of Middle East respiratory syndrome coronavirus was investigated in nasal and rectal swab samples by real-time reverse transcription polymerase chain reaction using primers specific for upE and ORF 1a genes. Positive samples were then subjected to ORF 1a and N gene-distinct polymerase chain reaction and sequencing. The acquired sequences were applied for phylogenetic analysis in comparison with sequences of related regional human cases and non-regional camel isolates. Nasal swabs from 3 out of 18 camels showed positive results in both real-time reverse transcription polymerase chain reactions. The nucleotide sequencing revealed that N and ORF 1a fragments of the studied viruses had a high level of similarity to the Middle East respiratory syndrome coronaviruses isolated from camels in African countries, Arabian Peninsula, Pakistan, and to those isolated from a person in Iran. The current study is the primary report on the characterization of Middle East respiratory syndrome coronavirus from Iranian camels.

PROTECTIVE EFFICACY of A GASTROINTESTINAL SARS-CoV-2 VACCINE

Background: SARS-CoV-2 remains a global threat, despite the rapid deployment but limited coverage of multiple vaccines. Alternative vaccine strategies that have favorable manufacturing timelines, greater ease of distribution and improved coverage may offer significant public health benefits, especially in resource-limited settings. Live oral vaccines have the potential to address some of these limitations;however no studies have yet been conducted to assess the immunogenicity and protective efficacy of a live oral vaccine against SARS-CoV-2. Thus far, we assessed whether oral administration of live SARS-CoV-2 in non-human primates might offer prophylactic benefits. Methods: In this study, we assessed the immunogenicity of gastrointestinal (GI) delivery of SARS-CoV-2 and the protective efficacy against intranasal and intratracheal SARS-CoV-2 challenge in rhesus macaques. Esophagogastroduodenoscopy (EGD) administration of 106 50% Tissue Culture Infectious Dose (TCID50) of SARS-CoV-2 elicited low levels of serum neutralizing antibodies (NAb), which correlated with modestly diminished viral loads in nasal swabs (NS) and Bronchoalveolar Lavage (BAL) post-challenge. In addition, mucosal NAb titers from the rectal swabs (RS), NS, and BAL and Spike-specific T-cell responses appear to be below the limit of detection post-vaccination. Replicating virus was only observed in 44% of macaques and on limited number of dates post vaccination, suggesting limited, if any, productive infection in the GI tract. Results: We demonstrate that GI delivery of live 1x106 TCID50 SARS-CoV-2 elicited modest immune responses and provided partial protection against intranasal and intratracheal challenge with SARS-CoV-2. Moreover, serum neutralizing antibody titers correlated with protective efficacy. Conclusion: These data provide proof-of-concept that an orally administered vaccine can protect against respiratory SARS-CoV-2 challenge, but the limited immunogenicity and protective efficacy observed here suggests that the oral vaccine approach will require optimization.

ALTERED GUT MICROBIOTA and RESPIRATORY DYSFUNCTION 3 MONTHS after SEVERE COVID-19

Background: Although COVID-19 is primarily a respiratory infection, mounting evidence suggests that the GI tract is involved in the disease, with gut barrier dysfunction and gut microbiota alterations being related to disease severity. Whether these alterations persist and associate with long-term respiratory dysfunction is unknown. Methods: From the NOR-Solidarity trial (n=181), plasma was collected during hospital admission and after three months, and analyzed for markers of gut barrier dysfunction and inflammation. At the three-month follow-up, pulmonary function was assessed by measuring diffusing capacity of the lungs for carbon monoxide (DLCO), and rectal swabs for gut microbiota analyses were collected (n= 97) and analysed by sequencing of the 16S rRNA gene. Results: Gut microbiota diversity was reduced in COVID-19 patients with respiratory dysfunction, defined as DLCO below lower limit of normal three months after hospitalization. These patients also had an altered global gut microbiota composition (Fig. 1), with reduced abundance of Erysipelotrichaceae UCG-003 and increased abundance of Flavonifractor and Veillonella, the latter potentially being linked to fibrosis. During hospitalization, increased plasma levels of lipopolysaccharide-binding protein (LBP) were strongly associated with respiratory failure, defined as pO2/fiO2-(P/F-ratio)<26.6 kPa. LBP levels remained elevated during and after hospitalization, and were associated with low-grade inflammation and respiratory dysfunction after three months. Figure 1 legend: Gut microbial composition in patients with respiratory dysfunction at the three-month follow-up (DLCO<="" div=""> Conclusion: Respiratory dysfunction after COVID-19 is associated with reduced biodiversity and gut microbiota alterations, along with persistently elevated LBP levels. Our results point to a potential gut-lung axis that should be further investigated in relation to long-term pulmonary dysfunction and long COVID.

COVID-19 infection in the elderly in French-speaking Switzerland: an inventory of beliefs, convictions and certainties

Most patients hospitalized for COVID-19 are aged over 70 years old, and half of those who die are over 83 years old. Older patients do not always present with typical symptoms (fever, cough and dyspnoea) but sometimes are and remain asymptomatic (contact screening), or have aspecific presentations (altered general condition, falls, delirium, unusual fatigue). Rectal swab, which minimizes exposition risk, appears useful in long-term care patients with diarrhea. Older age is associated with worse prognosis, but the analysis should be refined by means of prognostic indexes that account for the heterogeneous health, functional, and cognitive status of the elderly population. Gathering elderly patients’ wishes and assessing their remaining life expectancy allows to anticipate care decisions according to the level of tension in the health system.

Carbapenem-Resistant Enterobacterales (CRE) Colonization Prevalence in Botswana: An Antibiotic Resistance in Communities and Hospitals (ARCH) Study

Background. Although CRE are a global threat, data in low- and middle-income countries are scarce. Colonization data are vital for informing antibiotic resistance strategies. We characterized the colonization prevalence of CRE in various settings in Botswana. Methods. This study was conducted in 3 districts in Botswana (1 hospital and 2 clinics per district). Adult inpatients and clinic patients were randomly selected for enrollment. Community subjects were enrolled by inviting each enrolled clinic subject to refer up to 3 adults. Each adult clinic or community subject was also asked to refer their children. All subjects had rectal swabs obtained and inoculated on selective chromogenic media for preliminary identification of CRE. Final identification and susceptibility testing were performed using MALDI-TOF MS and VITEK-2, respectively. CRE underwent genotyping for carbapenemase genes. Results. Subjects were enrolled from 1/15/20-9/4/20 with a pause from 4/2/20-5/21/20 due to a countrywide COVID lockdown. Of 5,088 subjects approached, 2,469 (49%) participated. Enrollment by subject type was: hospital - 469 (19%);clinic - 959 (39%);community adult - 477 (19%);and community child - 564 (23%). Of 2,469 subjects, the median (interquartile range) age was 32 years (19-44) and 1,783 (72%) were female. 42 (1.7%) subjects were colonized with at least one CRE;10 subjects were colonized with multiple strains. E. coli (n=17), K. pneumoniae (n=20), and E. cloacae complex (n=11) were most common. CRE colonization prevalence was 6.8% for hospital subjects, 0.7% for clinic subjects, 0.2% for adult community subjects, and 0.5% for child community subjects (p< 0.001)). CRE prevalence varied across regions (Figure 1) and was significantly higher pre- vs post-lockdown (Figure 2). VIM and NDM were the most common carbapenemase genes (Figure 3). Conclusion. CRE colonization was significantly higher in hospital vs community settings in Botswana. CRE prevalence varied by region and decreased significantly following a countrywide lockdown. With CRE prevalence still modest, elucidating risk factors for CRE colonization holds promise in developing strategies to curb further emergence of CRE. Additional investigation of the CRE isolates without identified resistance genes is warranted.

Colonization with Extended-Spectrum Cephalosporin-Resistant Enterobacterales (ESCrE) in Healthcare and Community Settings in Botswana: An Antibiotic Resistance in Communities and Hospitals (ARCH) Study

Background. Although ESCrE are a global challenge, data on ESCrE in low- and middle-income countries are limited. In particular, colonization data are critical for larger antibiotic resistance efforts. We characterized the colonization prevalence of ESCrE in various settings in Botswana. Methods. This study was conducted in 3 hospitals and 6 clinics located in 3 districts in Botswana. In each hospital, we conducted surveillance of adult patients. Adult clinic patients were also randomly selected for participation. Finally, we enrolled community subjects by inviting each enrolled clinic subject to refer up to 3 adults. Each adult clinic or community subject was also allowed to refer their children. All subjects had rectal swabs obtained which were inoculated onto chromogenic media for preliminary identification of ESCrE. Final identification and susceptibility testing were performed using MALDI-TOF MS and VITEK-2, respectively. Genotyping was done for identification of extended-spectrum beta-lactamase (ESBL) genes. Results. Enrollment occurred from 1/15/20-9/4/20 but paused from 4/2/20-5/21/20 due to a countrywide COVID lockdown. Of 5,088 subjects approached, 2,469 (49%) participated. Enrollment by subject type was: hospital - 469 (19%);clinic - 959 (39%);community adult - 477 (19%);and community child - 564 (23%). Of 2,469 subjects, the median (interquartile range) age was 32 years (19-44) and 1,783 (72%) were female. 759 (31%) subjects were colonized with at least one ESCrE;130 subjects were colonized with multiple strains. E. coli (n=663) and K. pneumoniae (n=121) were most common. ESCrE colonization prevalence was 43% for hospital subjects, 31% for clinic subjects, 24% for adult community subjects, and 26% for child community subjects (p< 0.001)). ESCrE prevalence varied significantly across regions (Figure 1) and was significantly higher pre-lockdown vs post-lockdown (Figure 2). CTX-M was the most common ESBL gene (Figure 3). Conclusion. ESCrE colonization was common in both healthcare and community settings in Botswana. Colonization prevalence varies by region and clinical setting and decreased following a countrywide lockdown. These findings provide important clues regarding potential drivers of ESCrE that might serve as targets for intervention.

Use of Mail-Out Sexually Transmitted Infection Test Kits in a Telehealth Pre-exposure Prophylaxis Clinic

Background. Standard of care for patients receiving pre-exposure prophylaxis (PrEP) for human immunodeficiency virus (HIV) includes HIV screening and testing for sexually transmitted infections (STIs) at all sites of potential exposure every three months. We implemented a provider and pharmacist telehealth based PrEP program as part of the HIV, Hepatitis Specialty Telehealth Access Resource (H-START) Collaborative. Due to the COVID-19 pandemic and care via telehealth, we had limited ability to collect pharyngeal or rectal swabs in clinic. We created mail-out kits including swabs and instructions for self-collection to test for rectal and pharyngeal Neisseria gonorrhea and Chlamydia trachomatis. Methods. Kits were mailed out to patients between June 2020 and May 2021. Providers first confirmed patient comfort with self-swab collection during telehealth appointments. Kits included: an instruction sheet with visual diagrams for collection, swabs with appropriate labels;and a pre-paid envelope for patients to mail swabs back to our facility for laboratory testing. Prospective data collection included the date kits were mailed out to patients, the date of kit receipt at our facility and the test result. Charts were retrospectively reviewed to determine treatment completion. Results. 54 self-swab kits were mailed to patients. 53 of the patients were male and the average age was 41.3 years old. 38 (70.3%) swabs were returned. The median time for return of swabs was 21 days (Range 2-289). Of those returned, 5 (13.1%) were positive and all 5 patients were treated for their infection. Conclusion. Mail-out STI testing was effective in identifying STIs for a telehealth PrEP program and for maintaining standard of care practice during the COVID-19 pandemic. This model may increase rates of testing compliance for care provided via telehealth and decrease rates of STI transmission and complications. Better communication around returning kits in a timely-manner and understanding reasons for non-return warrant further investigation.

DETECTION OF SARS-COV-2 IN THE GASTROINTESTINAL TRACT AMONG PATIENTS WITH NEGATIVE NASOPHARYNGEAL COVID-19 TESTING PRIOR TO ENDOSCOPY: A PROSPECTIVE STUDY

BACKGROUND: COVID-19 patients can have persistent viral stool positivity despite negative respiratory samples, irrespective of symptoms. These patients could potentially go undetected under the current pre-endoscopy COVID-19 testing guidance recommendations. However, the clinical significance of viral RNA in the stool remains unclear. AIMS: We aimed to prospectively determine whether SARS-CoV-2 is detected via real-time reversetranscriptase polymerase chain reaction (rRT-PCR) in the GI tract of patients scheduled for endoscopy and if the virus obtained from these clinical specimens could be isolated in culture. METHODS: All patients underwent symptom screening and had negative nasopharyngeal testing for SARS-CoV-2 within 72 hours of their scheduled procedure. Study samples were collected via repeat nasopharyngeal swab, rectal swab, and fluid from the upper GI tract and/or colon based on their endoscopic procedure(s). Samples were tested for SARSCoV-2 via rRT-PCR. Clinical specimens confirmed to be positive for SARS-CoV-2 RNA were then isolated and cultured in Vero-E6 cells. RESULTS: 243 patients (mean age 63.1 years;54.3% men) were enrolled from July 15th, 2020 to September 2nd, 2020 (Table 1). Most patients (177;72.8%) were asymptomatic, with nausea/vomiting (23;9.5%) being the most commonly reported COVID-19 related symptom. SARS-CoV-2 testing was performed from 242(99.6%) nasopharyngeal, 243(100%) rectal, 183(75.3%) upper GI tract and 73(30%) colon samples. Only 1 patient (0.4%), with a history of COVID-19 infection 45 days prior to endoscopy, tested positive for SARS-CoV-2 on all the GI clinical specimens (fluid from upper GI tract, colon, and rectal swab), despite being asymptomatic and having 3 negative nasopharyngeal swabs 40, 37 and 3 days before her procedure (Figure 1). After 14-day incubation period, there was no evidence of virus growth in cells incubated with any of these specimens. CONCLUSIONS: SARS-CoV-2 is rarely detected in the GI tract of patients with negative screening nasopharyngeal COVID-19 testing prior to endoscopy. Infectious virus was not detected by culture from any of the GI specimens positive for SARS-CoV-2 RNA by rRT-PCR. Our results further highlight that presence of viral genome on its own is not sufficient proof of infectivity. Additional studies are needed to evaluate the temporal association between COVID-19 symptom onset and potential infectivity duration in the GI tract. (Table Presented)(Figure Presented)