Marginal effects of public health measures and COVID-19 disease burden in China: A large-scale modelling study.

China had conducted some of the most stringent public health measures to control the spread of successive SARS-CoV-2 variants. However, the effectiveness of these measures and their impacts on the associated disease burden have rarely been quantitatively assessed at the national level. To address this gap, we developed a stochastic age-stratified metapopulation model that incorporates testing, contact tracing and isolation, based on 419 million travel movements among 366 Chinese cities. The study period for this model began from September 2022. The COVID-19 disease burden was evaluated, considering 8 types of underlying health conditions in the Chinese population. We identified the marginal effects between the testing speed and reduction in the epidemic duration. The findings suggest that assuming a vaccine coverage of 89%, the Omicron-like wave could be suppressed by 3-day interval population-level testing (PLT), while it would become endemic with 4-day interval PLT, and without testing, it would result in an epidemic. PLT conducted every 3 days would not only eliminate infections but also keep hospital bed occupancy at less than 29.46% (95% CI, 22.73-38.68%) of capacity for respiratory illness and ICU bed occupancy at less than 58.94% (95% CI, 45.70-76.90%) during an outbreak. Furthermore, the underlying health conditions would lead to an extra 2.35 (95% CI, 1.89-2.92) million hospital admissions and 0.16 (95% CI, 0.13-0.2) million ICU admissions. Our study provides insights into health preparedness to balance the disease burden and sustainability for a country with a population of billions.

A novel humanized tri-receptor transgenic mouse model of HAdV infection and pathogenesis.

Human adenovirus (HAdV) is a highly virulent respiratory pathogen that poses clinical challenges in terms of diagnostics and treatment. Currently, no effective therapeutic drugs or prophylactic vaccines are available for HAdV infections. One factor contributing to this deficiency is that existing animal models, including wild-type and single-receptor transgenic mice, are unsuitable for HAdV proliferation and pathology testing. In this study, a tri-receptor transgenic mouse model expressing the three best-characterized human cellular receptors for HAdV (hCAR, hCD46, and hDSG2) was generated and validated via analysis of transgene insertion, receptor mRNA expression, and protein abundance distribution. Following HAdV-7 infection, the tri-receptor mice exhibited high transcription levels at the early and late stages of the HAdV gene, as well as viral protein expression. Furthermore, the tri-receptor mice infected with HAdV exhibited dysregulated cytokine responses and multiple tissue lesions. This transgenic mouse model represents human HAdV infection and pathogenesis with more accuracy than any other reported animal model. As such, this model facilitates the comprehensive investigation of HAdV pathogenesis as well as the evaluation of potential vaccines and therapeutic modalities for HAdV.

HIV viral suppression at different thresholds and duration of treatment in the dolutegravir treatment era in Sierra Leone: a nationwide survey.

INTRODUCTION: Viral load assessment for people living with HIV is key for monitoring treatment and achieving the 95-95-95. In this study, we aimed to assess the degree of viral suppression at different thresholds and treatment duration after the introduction of dolutegravir-based therapy in ten public hospitals in Sierra Leone. METHODS: We used a cross-sectional study design to recruits patients aged 18 years or older between August 2022 and January 2023. Statistical analyses were performed using R-software. Logistic regression was used to assess factors independently associated with viral suppression. The level of significance was set at P < 0.05. RESULTS: Of the 2,253 patients recruited, 1,720 (76%) were women and 1,705 (76%) were receiving a fixed dose combination of tenofovir, lamivudine and dolutegravir. The median age and duration of anti-retroviral therapy (ART) was 36.0 (IQR, 28.0-45.0) years and 40.9 (IQR, 14.4-79.6) months, respectively. Using a threshold of HIV RNA < 1000 copies/mL, 1,715 (88.4%) patients on ART for more than 6 months were virally suppressed. Viral suppression rates were higher with dolutegravir-based (1,277, 89.5%) than efavirenz-based (418, 86.2%) ART. HIV RNA was < 200 copies/mL in 1,643 (84.6%) patients or < 50 copies/mL in 1,487 (76.6%) patients or between 50 and 999 copies/mL in 228 (11.7%) patients. Viral suppression rates at different ART durations (months) were as follows: 84.2% (≤ 3), 88.8% (4-6), 90.9% (6-12), and 88.1% (> 12). Viral suppression rates were higher for patients aged 40 or older (40-50 years: aOR 2.05, 95%CI 1.41-3.04, P < 0.01; 50-60 years: aOR 2.51, 95%CI 1.53-4.35, P < 0.01; >60 years: aOR 2.69, 95%CI 1.28-6.63, P = 0.02). Men had 49% lower odds of viral suppression than women (aOR 0.50, 95% CI 0.38-0.67, P < 0.01). CONCLUSION: We report a viral suppression rate of 88.4% among patients on treatment for at least 6 months, with higher rate of suppression with dolutegravir than efavirenz. Factors associated with virological suppression were age and gender, emphasizing the need for innovative differentiated ART delivery models to optimize viral suppression and achieve the 95% target.

An outbreak of acute respiratory disease caused by HAdV-55 in Beijing, China, 2020.

Human adenoviruses (HAdVs) can cause acute respiratory diseases (ARDs) worldwide, and HAdV-55 is a reemergent pathogen in recent years. In the study, we investigated an outbreak of ARD at a school due to HAdV-55 in Beijing, China, during the early outbreak of coronavirus disease 2019 (COVID-19). The epidemic prevention team was dispatched to the school to collect epidemiologic data and nasopharyngeal samples. Then, real-time reverse transcription polymerase chain reaction (PCR) and multiplex PCR assays were used to detect severe acute respiratory syndrome coronavirus 2 and other respiratory pathogens, respectively. One representative HAdV-55 isolate was selected and submitted for whole-genome sequencing using a MiSeq system and the whole-genome phylogenetic tree was conducted based on the maximum likelihood method. The outbreak lasted from January 27 to February 6, 2020, and 108 students developed fever, among whom 60 (55.56%) cases were diagnosed with HAdV-55 infection in the laboratory using real-time PCR and 56 cases were hospitalized. All the confirmed cases had a fever and 11 cases (18.33%) presented with a fever above 39°C. Other main clinical symptoms included sore throat (43.33%) and headache (43.33%). We obtained and assembled the full genome of one isolate, BJ-446, with 34 761 nucleotides in length. HAdV-55 isolate BJ-446 was 99.85% identical to strain QS-DLL, which was the first HAdV-55 strain in China isolated from an ARD outbreak in Shanxi in 2006. One and four amino acid mutations were observed in the hexon gene and the coding region of L2 pV 40.1 kDa protein, respectively. We identified the first HAdV-55 infection associated with the ARD outbreak in Beijing since the emergence of COVID-19. The study suggests that improved surveillance of HAdV is needed, although COVID-19 is still prevalent in the world.

Using a grey relational analysis in an improved Grunow-Finke assessment tool to detect unnatural epidemics.

The Grunow-Finke epidemiological assessment tool (GFT) has several limitations in its ability to differentiate between natural and man-made epidemics. Our study aimed to improve the GFT and analyze historical epidemics to validate the model. Using a gray relational analysis (GRA), we improved the GFT by revising the existing standards and adding five new standards. We then removed the artificial weights and final decision threshold. Finally, by using typically unnatural epidemic events as references, we used the GRA to calculate the unnatural probability and obtain assessment results. Using the advanced tool, we conducted retrospective and case analyses to test its performance. In the validation set of 13 historical epidemics, unnatural and natural epidemics were divided into two categories near the unnatural probability of 45%, showing evident differences (p < 0.01) and an assessment accuracy close to 100%. The unnatural probabilities of the Ebola virus disease of 2013 and Middle East Respiratory Syndrome of 2012 were 30.6% and 36.1%, respectively. Our advanced epidemic assessment tool improved the accuracy of the original GFT from approximately 55% to approximately 100% and reduced the impact of human factors on these outcomes effectively.

Bearing Fault Diagnosis Using Piecewise Aggregate Approximation and Complete Ensemble Empirical Mode Decomposition with Adaptive Noise.

Complete ensemble empirical mode decomposition with adaptive noise (CEEMDAN) effectively separates the fault vibration signals of rolling bearings and improves the diagnosis of rolling bearing faults. However, CEEMDAN has high memory requirements and low computational efficiency. In each iteration of CEEMDAN, fault vibration signals are added with noises, both the vibration signals added with noises and the added noises are decomposed with classical empirical mode decomposition (EMD). This paper proposes a rolling bearing fault diagnosis method that combines piecewise aggregate approximation (PAA) with CEEMDAN. PAA enables CEEMDAN to decompose long signals and to achieve enhanced diagnosis. In particular, the method first yields the vibration envelope using bandpass filtering and demodulation, then compresses the envelope using PAA, and finally decomposes the compressed signal with CEEMDAN. Test data verification results show that the proposed method is more effective and more efficient than CEEMDAN.

Source-tracking of the Chinese Chikungunya viruses suggests that Indian subcontinent and Southeast Asia act as major hubs for the recent global spread of Chikungunya virus.

BACKGROUND: Chikungunya fever, caused by the Chikungunya virus (CHIKV), has become a major global health concern, causing unexpected large outbreaks in Africa, Asia, Europe, and the Americas. CHIKV is not indigenous to China, and its origin in the country is poorly understood. In particular, there is limited understanding of the recent global spread of CHIKV in the context of the CHIKV epidemic. METHODS: Here we investigated a novel Chikungunya patient who came from Myanmar to China in August, 2019. Direct genome sequencing was performed via combined MinION sequencing and BGISEQ-500 sequencing. A complete CHIKV genome dataset, including 727 CHIKV genomes retrieved from GenBank and the genome sequenced in this study, was constructed. An updated and comprehensive phylogenetic analysis was conducted to understand the virus's origin, evolution, transmission routes and genetic adaptation. RESULTS: All globally distributed CHIKV genomes were divided into West Africa, East/Central/South African and Asian genotypes. The genome sequenced in this study was located in the Indian Ocean lineage, and was closely related to a strain isolated from an Australian patient who returned from Bangladesh in 2017. A comprehensive phylogenetic analysis showed that the Chinese strains mainly originated from the Indian subcontinent and Southeast Asia. Further analyses indicated that the Indian subcontinent and Southeast Asia may act as major hubs for the recent global spread of CHIKV, leading to multiple outbreaks and epidemics. Moreover, we identified 179 distinct sites, including some undescribed sites in the structural and non-structural proteins, which exhibited apparent genetic variations associated with different CHIKV lineages. CONCLUSIONS: Here we report a novel CHIKV isolate from a chikungunya patient who came from Myanmar to China in 2019, and summarize the source and evolution of Chinese CHIKV strains. Our present findings provide a better understanding of the recent global evolution of CHIKV, highlighting the urgent need for strengthened surveillance against viral diversity.

Antibiotic resistance and molecular characterization of the hydrogen sulfide-negative phenotype among diverse Salmonella serovars in China.

BACKGROUND: Among 2179 Salmonella isolates obtained during national surveillance for salmonellosis in China from 2005 to 2013, we identified 46 non-H2S-producing strains originating from different sources. METHODS: The isolates were characterized in terms of antibiotic resistance and genetic variability by pulsed-field gel electrophoresis and multilocus sequence typing. Mutation in the phs operon, which may account for the non-H2S-producing phenotype of the isolated Salmonella strains, was performed in this study. RESULTS: Among isolated non-H2S-producing Salmonella strains, more than 50% were recovered from diarrhea patients, of which H2S-negative S. Gallinarum, S. Typhimurium, S. Choleraesuis and S. Paratyphi A isolates constituted 76%. H2S-negative isolates exhibited a high rate of resistance to ticarcillin, ampicillin, and tetracycline, and eight of them had the multidrug resistance phenotype. Most H2S-negative Salmonella isolates had similar pulsed-field gel electrophoresis profiles and the same sequence type as H2S-positive strains, indicating a close origin, but carried mutations in the phsA gene, which may account for the non-H2S-producing phenotype. CONCLUSIONS: Our data indicate that multiple H2S-negative strains have emerged and persist in China, emphasizing the necessity to implement efficient surveillance measures for controlling dissemination of these atypical Salmonella strains.

A Waterborne Outbreak of Shigella sonnei with Resistance to Azithromycin and Third-Generation Cephalosporins in China in 2015.

Here, we report for the first time a waterborne outbreak of Shigella sonnei in China in 2015. Eleven multidrug-resistant (MDR) S. sonnei isolates were recovered, showing high resistance to azithromycin and third-generation cephalosporins in particular, due to an mph(A)- and blaCTX-M-14-harboring IncB/O/K/Z group transmissible plasmid of 104,285 kb in size. Our study highlights the potential prevalence of the MDR outbreak of S. sonnei in China and its further dissemination worldwide with the development of globalization.

Comorbidity Analysis According to Sex and Age in Hypertension Patients in China.

BACKGROUND: Hypertension, an important risk factor for the health of human being, is often accompanied by various comorbidities. However, the incidence patterns of those comorbidities have not been widely studied. AIM: Applying big-data techniques on a large collection of electronic medical records, we investigated sex-specific and age-specific detection rates of some important comorbidities of hypertension, and sketched their relationships to reveal the risk for hypertension patients. METHODS: We collected a total of 6,371,963 hypertension-related medical records from 106 hospitals in 72 cities throughout China. Those records were reported to a National Center for Disease Control in China between 2011 and 2013. Based on the comprehensive and geographically distributed data set, we identified the top 20 comorbidities of hypertension, and disclosed the sex-specific and age-specific patterns of those comorbidities. A comorbidities network was constructed based on the frequency of co-occurrence relationships among those comorbidities. RESULTS: The top four comorbidities of hypertension were coronary heart disease, diabetes, hyperlipemia, and arteriosclerosis, whose detection rates were 21.71% (21.49% for men vs 21.95% for women), 16.00% (16.24% vs 15.74%), 13.81% (13.86% vs 13.76%), and 12.66% (12.25% vs 13.08%), respectively. The age-specific detection rates of comorbidities showed five unique patterns and also indicated that nephropathy, uremia, and anemia were significant risks for patients under 39 years of age. On the other hand, coronary heart disease, diabetes, arteriosclerosis, hyperlipemia, and cerebral infarction were more likely to occur in older patients. The comorbidity network that we constructed indicated that the top 20 comorbidities of hypertension had strong co-occurrence correlations. CONCLUSIONS: Hypertension patients can be aware of their risks of comorbidities based on our sex-specific results, age-specific patterns, and the comorbidity network. Our findings provide useful insights into the comorbidity prevention, risk assessment, and early warning for hypertension patients.

Human adenovirus type 7 infection associated with severe and fatal acute lower respiratory illness and nosocomial transmission.

A 23-year-old male died of severe pneumonia and respiratory failure in a tertiary hospital in Beijing, and 4 out of 55 close contacts developed fever. Molecular analysis confirmed human adenovirus type 7 (HAdV7) as the causative agent. We highlight the importance of early diagnosis and treatment and proper transmission control of HAdV7.

Polymorphism of CRISPR shows separated natural groupings of Shigella subtypes and evidence of horizontal transfer of CRISPR.

Clustered, regularly interspaced, short palindromic repeats (CRISPR) act as an adaptive RNA-mediated immune mechanism in bacteria. They can also be used for identification and evolutionary studies based on polymorphisms within the CRISPR locus. We amplified and analyzed 6 CRISPR loci from 237 Shigella strains belonging to the 4 species groups, as well as 13 Escherichia coli strains. The CRISPR-associated (cas) gene sequence arrays of these strains were screened and compared. The CRISPR sequences from Shigella were conserved among subtypes, suggesting that CRISPR may represent a new identification tool for the detection and discrimination of Shigella species. Secondary structure analysis showed a different stem-loop structure at the terminal repeat, suggesting a distinct recognition mechanism in the formation of crRNA. In addition, the presence of "self-target" spacers and polymorphisms within CRISPR in Shigella indicated a selective pressure for inhibition of this system, which has the potential to damage "self DNA." Homology analysis of spacers showed that CRISPR might be involved in the regulation of virulence transmission. Phylogenetic analysis based on CRISPR sequences from Shigella and E. coli indicated that although phenotypic properties maintain convergent evolution, the 4 Shigella species do not represent natural groupings. Surprisingly, comparative analysis of Shigella repeats with other species provided new evidence for CRISPR horizontal transfer. Our results suggested that CRISPR analysis is applicable for the detection of Shigella species and for investigation of evolutionary relationships.

New clustered regularly interspaced short palindromic repeat locus spacer pair typing method based on the newly incorporated spacer for Salmonella enterica.

A clustered regularly interspaced short palindromic repeat (CRISPR) typing method has recently been developed and used for typing and subtyping of Salmonella spp., but it is complicated and labor intensive because it has to analyze all spacers in two CRISPR loci. Here, we developed a more convenient and efficient method, namely, CRISPR locus spacer pair typing (CLSPT), which only needs to analyze the two newly incorporated spacers adjoining the leader array in the two CRISPR loci. We analyzed a CRISPR array of 82 strains belonging to 21 Salmonella serovars isolated from humans in different areas of China by using this new method. We also retrieved the newly incorporated spacers in each CRISPR locus of 537 Salmonella isolates which have definite serotypes in the Pasteur Institute's CRISPR Database to evaluate this method. Our findings showed that this new CLSPT method presents a high level of consistency (kappa = 0.9872, Matthew's correlation coefficient = 0.9712) with the results of traditional serotyping, and thus, it can also be used to predict serotypes of Salmonella spp. Moreover, this new method has a considerable discriminatory power (discriminatory index [DI] = 0.8145), comparable to those of multilocus sequence typing (DI = 0.8088) and conventional CRISPR typing (DI = 0.8684). Because CLSPT only costs about $5 to $10 per isolate, it is a much cheaper and more attractive method for subtyping of Salmonella isolates. In conclusion, this new method will provide considerable advantages over other molecular subtyping methods, and it may become a valuable epidemiologic tool for the surveillance of Salmonella infections.

Emergence and prevalence of non-H2S-producing Salmonella enterica serovar Senftenberg isolates belonging to novel sequence type 1751 in China.

Salmonella enterica serovar Senftenberg is a common nontyphoidal Salmonella serotype which causes human Salmonella infections worldwide. In this study, 182 S. Senftenberg isolates, including 17 atypical non-hydrogen sulfide (H2S)-producing isolates, were detected in China from 2005 to 2011. The microbiological and genetic characteristics of the non-H2S-producing and selected H2S-producing isolates were determined by using pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and clustered regularly interspaced short palindromic repeat (CRISPR) analysis. The phs operons were amplified and sequenced. The 17 non-H2S-producing and 36 H2S-producing isolates belonged to 7 sequence types (STs), including 3 new STs, ST1751, ST1757, and ST1758. Fourteen of the 17 non-H2S-producing isolates belonged to ST1751 and had very similar PFGE patterns. All 17 non-H2S-producing isolates had a nonsense mutation at position 1621 of phsA. H2S-producing and non-H2S-producing S. Senftenberg isolates were isolated from the same stool sample from three patients; isolates from the same patients displayed the same antimicrobial susceptibility, ST, and PFGE pattern but could be discriminated based on CRISPR spacers. Non-H2S-producing S. Senftenberg isolates belonging to ST1751 have been prevalent in Shanghai, China. It is possible that these emerging organisms will disseminate further, because they are difficult to detect. Thus, we should strengthen the surveillance for the spread of this atypical S. Senftenberg variant.

An atypical winter outbreak of hand, foot, and mouth disease associated with human enterovirus 71, 2010.

BACKGROUND: To analyze the epidemiological characteristics and pathogenic molecular characteristics of an hand, foot, and mouth disease (HFMD) outbreak caused by enterovirus 71 in Linyi City, Shandong Province, China during November 30 to December 28, 2010. METHODS: One hundred and seventy three stool specimens and 40 throat samples were collected from 173 hospitalized cases. Epidemiologic and clinical investigations, laboratory testing, and genetic analyses were performed to identify the causal pathogen of the outbreak. RESULTS: Among the 173 cases reported in December 2010, the male-female ratio was 1.88: 1; 23 cases (13.3%) were severe. The majority of patients were children aged < 5 years (95.4%). Some patients developed respiratory symptoms including runny nose (38.2%), cough (20.2%), and sore throat (14.5%). One hundred and thirty eight EV71 positive cases were identified based on real time reverse-transcription PCR detection and 107 isolates were sequenced with the VP1 region. Phylogenetic analysis of full-length VP1 sequences of 107 Linyi EV71 isolates showed that they belonged to the C4a cluster of the C4 subgenotype and were divided into 3 lineages (Lineage I, II and III). The two amino acid substitutions (Gly and Gln for Glu) at position 145 within the VP1 region are more likely to appear in EV71 isolates from severe cases (52.2%) than those recovered from mild cases (8.3%). CONCLUSION: This outbreak of HMFD was caused by EV71 in an atypical winter. EV71 strains associated with this outbreak represented three separate chains of transmission. Substitution at amino acid position 145 of the VP1 region of EV71 might be an important virulence marker for severe cases. These findings suggest that continued surveillance for EV71 variants has the potential to greatly impact HFMD prevention and control.

Analysing monkeypox epidemic drivers: Policy simulation and multi-index modelling across 39 nations.

Background: This study aimed to analyse the drivers of the monkeypox (Mpox) epidemic and policy simulation to support health care policies against the Mpox epidemic. Methods: We established a three-round selection mechanism for 164 factors using Lasso and negative binomial regression to investigate the correlation between significant drivers and the cumulative confirmed cases of Mpox. Policy simulation for each driver was evaluated, and the varying effects of implementation at different times were examined. Results: HIV/AIDS prevalence and air transport passengers carried were significant determinants of the risk of the Mpox epidemic across various countries, with regression coefficients of 1.417 and 0.766, respectively. A decrease in HIV/AIDS prevalence by 10, 20, 30, and 40% corresponded to reductions in the number of Mpox cases by 6.28, 6.55, 6.87, and 7.26%, respectively. Similarly, 20, 40, 60, and 80% travel restrictions led to reductions in Mpox cases by 7.16, 15.63, 26.28%, and 41.46%, respectively. Controlling air transport passengers carried in the first month could postpone outbreak onset by 0.5-2.0 months. Conclusions: Mpox prevention and control policies should primarily focus on travel restrictions during high disease-risk periods and flight suspensions from high-risk nations in combination with regular HIV/AIDS prevention and treatment strategies.

Indian Ocean temperature anomalies predict long-term global dengue trends.

Despite identifying El Niño events as a factor in dengue dynamics, predicting the oscillation of global dengue epidemics remains challenging. Here, we investigate climate indicators and worldwide dengue incidence from 1990 to 2019 using climate-driven mechanistic models. We identify a distinct indicator, the Indian Ocean basin-wide (IOBW) index, as representing the regional average of sea surface temperature anomalies in the tropical Indian Ocean. IOBW is closely associated with dengue epidemics for both the Northern and Southern hemispheres. The ability of IOBW to predict dengue incidence likely arises as a result of its effect on local temperature anomalies through teleconnections. These findings indicate that the IOBW index can potentially enhance the lead time for dengue forecasts, leading to better-planned and more impactful outbreak responses.

SARS-CoV-2 seroprevalence and associated factors among people living with HIV in Sierra Leone.

BACKGROUND: Human immunodeficiency virus (HIV) infection is an important risk factor for Coronavirus Disease 2019 (COVID-19), but data on the prevalence of COVID-19 among people living with HIV (PLWH) is limited in low-income countries. Our aim was to assess the seroprevalence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) specific antibodies and associated factors among PLWH in Sierra Leone. METHODS: We conducted a cross-sectional survey of PLWH aged 18 years or older in Sierra Leone between August 2022 and January 2023. Participants were tested for SARS-CoV-2 antibodies using a rapid SARS-CoV-2 antibody (immunoglobulin M/immunoglobulin G [IgG]) kits. Stepwise logistic regression was used to explore factors associated with SARS-CoV-2 antibody seroprevalence with a significance level of p < .05. RESULTS: In our study, 33.4% (1031/3085) participants had received a COVID-19 vaccine, and 75.7% were SARS-CoV-2 IgG positive. Higher IgG seroprevalence was observed in females (77.2% vs. 71.4%, p = .001), adults over 60 years (88.2%), those with suppressed HIV RNA (80.7% vs. 51.7%, p < .001), antiretroviral therapy (ART)-experienced individuals (77.9% vs. 44.6%, p < .001), and vaccinated participants (80.7% vs. 73.2%, p < .001). Patients 60 years or older had the highest odds of IgG seroprevalence (adjusted odds ratio [aOR] = 2.73, 95% CI = 1.68-4.65). Female sex (aOR = 1.28, 95%CI = 1.05-1.56), COVID-19 vaccination (aOR = 1.54, 95% CI = 1.27-1.86), and ART (aOR = 2.20, 95% CI = 1.56-3.11) increased the odds, whereas HIV RNA ≥ 1000 copies/mL (aOR = 0.32, 95% CI = 0.26-0.40) reduced the odds of IgG seroprevalence. CONCLUSIONS: We observed a high seroprevalence of SARS-CoV-2 antibody among PLWH in Sierra Leone. We recommend the introduction of targeted vaccination for PLWH with a high risk of severe COVID-19, especially those with an unsuppressed HIV viral load.

Characterization of a Salmonella enterica serovar Typhimurium lineage with rough colony morphology and multidrug resistance.

Salmonella enterica serovar Typhimurium (S. Typhimurium) is a major cause of salmonellosis, and the emergence of multidrug-resistant pathovariants has become a growing concern. Here, we investigate a distinct rough colony variant exhibiting a strong biofilm-forming ability isolated in China. Whole-genome sequencing on 2,212 Chinese isolates and 1,739 publicly available genomes reveals the population structure and evolutionary history of the rough colony variants. Characterized by macro, red, dry, and rough (mrdar) colonies, these variants demonstrate enhanced biofilm formation at 28 °C and 37 °C compared to typical rdar colonies. The mrdar variants exhibit extensive multidrug resistance, with significantly higher resistance to at least five classes of antimicrobial agents compared to non-mrdar variants. This resistance is primarily conferred by an IncHI2 plasmid harboring 19 antimicrobial resistance genes. Phylogenomic analysis divides the global collections into six lineages. The majority of mrdar variants belong to sublineage L6.5, which originated from Chinese smooth colony strains and possibly emerged circa 1977. Among the mrdar variants, upregulation of the csgDEFG operons is observed, probably due to a distinct point mutation (-44G > T) in the csgD gene promoter. Pangenome and genome-wide association analyses identify 87 specific accessory genes and 72 distinct single nucleotide polymorphisms associated with the mrdar morphotype.

Multidrug-resistant atypical variants of Shigella flexneri in China.

We identified 3 atypical Shigella flexneri varieties in China, including 92 strains with multidrug resistance, distinct pulse types, and a novel sequence type. Atypical varieties were prevalent mainly in developed regions, and 1 variant has become the dominant Shigella spp. serotype in China. Improved surveillance will help guide the prevention and control of shigellosis.