Predominant Clade Research Articles

P-2344. Genomic Analysis of Monkeypox Virus (MPVX) Outbreak in Bangkok, Thailand in 2022-2023

Abstract Background Since early May 2022, cases of mpox (monkeypox) have been reported in countries where the disease is not endemic, alongside continued reports from endemic regions. This marks the first time that multiple mpox cases and clusters have been concurrently reported in both non-endemic and endemic countries across diverse geographical areas. As of March 8, 2024, there were 94,776 confirmed mpox cases globally, with 721 cases in Thailand—most of which were reported from Bangkok. Figure 1 The phylogenetic tree was constructed from 60 Mpox genomes collected in Bangkok, Thailand, during 2022-2023. The tree was produced using the maximum likelihood method in IQ-TREE2 with 1000 replicates of ultrafast bootstrap and HKY+F+I nucleotide substitution model and visualized by ggtree library in R. Methods We collected biological samples, mostly lesion swabs from suspected Mpox cases at STI Clinics in Bangkok, Thailand, from July 2022 to September 2023. Whole Genome Sequencing (WGS) was performed on 60 specimens from mpox cases in Bangkok, primarily lesion swabs, that were PCR-positive for MPXV with a cycle threshold (Ct) value below 30. A hybridization probe-capture–based approach was utilized for sequencing, specifically Illumina RNA Prep with Enrichment kit with the Viral Surveillance Panel. Consensus genomes were generated using an in-house pipeline based on reference mapping (BWA v0.7.17) to the Mpox reference genome from Nigeria (GenBank accession no. NC_063383. Results Phylogenetic analysis from WGS revealed that the predominant MPXV clade in Bangkok is IIb, with most specimens belonging to lineage IIb-C (48/60), followed by IIb-A (9/60) and IIb-B (3/60) as shown in Figure 1. Lineage IIb-A was detected in samples from 2022, while IIb-B and IIb-C were prominent in 2023. We identified multiple clusters with similar genomes in lineage IIb-C from different individuals, with percent identity ranging from 99.970% to 99.999% (197,184 nucleotides), suggesting ongoing community transmission. There is no clear introduction of lineage IIb-C into Thailand, however, the phylogenetic tree indicates the transmission of locally transmitted lineage to other countries. We detected the unique activity of APOBEC mRNA editing in serial samples from immunocompromised hosts. No mutations associated with resistance to tecovirimat were identified. Conclusion Our study demonstrated the introduction of MPXV from multiple countries, confirming ongoing community transmission in Bangkok during 2022-2023. Continuing genomic surveillance is crucial for tracking the epidemiology and viral evolution. Disclosures All Authors: No reported disclosures

Hepatitis Delta Virus Clade 8 Is the Predominant Clade Circulating in Botswana amongst People Living with HIV.

Hepatitis delta virus (HDV) co-infections more often result in severe hepatitis compared to hepatitis B virus (HBV) infections alone. Despite a high HDV prevalence (7.1%), information regarding circulating HDV clades is very limited in Botswana. We extracted total nucleic acid from confirmed HDV-positive samples and quantified their viral load. We then sequenced the large hepatitis delta antigen (L-HDAg) using Oxford Nanopore Technology (ONT). Genotyping was performed using the HDV Database, and HDV mutation profiling was performed on AliView. All participants with HBV genotypic information belonged to sub-genotype A1, and 80% (4/5) of them had a higher HDV viral load and a lower HBV viral load. We sequenced 75% (9/12) of the HDV-positive samples, which belonged to HDV clade 8. A total of 54 mutations were discovered, with the most prevalent being Q148R (16%), D149P (16%) and G151D (16%). Known mutations such as S117A, K131R, R139K and G151D were detected, while the other mutations were novel. Our results reveal that HDV clade 8 is the predominant clade in Botswana. The significance of all mutations remains unclear. Future studies with a larger sample size to detect other HDV clades that might be circulating in Botswana and functionally characterize the detected mutations are warranted.

The complete genome sequence of five pre-2013 Escherichia coli sequence type (ST)1193 strains reveals insights into an emerging pathogen.

Fluoroquinolone-resistant Escherichia coli sequence type (ST)1193 is a profound, emerging lineage associated with systemic, urinary tract and neonatal infections. Humans, companion animals and the environment are reservoirs for ST1193, which has been disseminated globally. Following its detection in 2007, ST1193 has been identified repeatedly amongst fluoroquinolone-resistant clones in Australia. However, despite the growing importance of ST1193, only three complete genomes are published in the literature, none of which are from Australia. Here we expand on the available ST1193 resources with the complete genomes of five ST1193 strains sequenced using Oxford Nanopore Technologies and Illumina. Using in silico genotyping, we found that all strains were multi-drug resistant, including resistances to fluoroquinolones and cephalosporins. In vitro antibiotic susceptibility testing mostly correlated with individual genotypes. The exception was MS8320, which had additional in vitro resistance to piperacillin/tazobactam, ampicillin/sulbactam, cefazolin and doripenem (carbapenem). Further investigation identified seven additional copies of an IS26 transposable unit carrying a bla TEM-1B beta-lactamase gene, suggesting this tandem amplification is associated with extended resistance phenotypes. Uropathogenicity factors, including three separate siderophore-encoding loci, were conserved in chromosomal and plasmid regions. Using all complete genomes, we further elucidated the recombination events surrounding the previously described K5/K1 capsular locus switch. Phenotypic confirmation of differing capsules in Australian ST1193 strains, coupled with genetic analysis revealing insertions downstream of the capsular locus, underscored the genetic distinctions between K5 and K1 capsule encoding strains. This study provides five new reference ST1193 genomes from Australia. These include the earliest complete K5-capsule ST1193 genomes on record (collected 2007), alongside our reference genome (MS10858), a clinical isolate obtained early during the ST1193 expansion and representative of the predominant K1-associated clade. These findings lay the foundations for further genomic and molecular analyses that may help understand the underlying reasons for the rapid global expansion of ST1193.

Plasmid-mediated acquisition and chromosomal integration of blaCTX-M-14 in a subclade of Escherichia coli ST131-H30 clade C1.

Escherichia coli ST131 is a multidrug-resistant lineage associated with the global spread of extended-spectrum β-lactamase-producing organisms. Particularly, ST131 clade C1 is the most predominant clade in Japan, harboring blaCTX-M-14 at a high frequency. However, the process of resistance gene acquisition and spread remains unclear. Here, we performed whole-genome sequencing of 19 E. coli strains belonging to 12 STs and 12 fimH types collected between 1997 and 2016. Additionally, we analyzed the full-length genome sequences of 96 ST131-H30 clade C0 and C1 strains, including those obtained from this study and those registered in public databases, to understand how ST131 clade C1 acquired and spread blaCTX-M-14. We detected conjugative IncFII plasmids and IncB/O/K/Z plasmids carrying blaCTX-M-14 in diverse genetic lineages of E. coli strains from the 1990s to the 2010s, suggesting that these plasmids played an important role in the spread of blaCTX-M-14. Molecular phylogenetic and molecular clock analyses of the 96 ST131-H30 clade C0 and C1 strains identified 8 subclades. Strains harboring blaCTX-M-14 were clustered in subclades 4 and 5, and it was inferred that clade C1 acquired blaCTX-M-14 around 1993. All 34 strains belonging to subclade 5 possessed blaCTX-M-14 with ISEcp1 upstream at the same chromosomal position, indicating their common ancestor acquired blaCTX-M-14 in a single ISEcp1-mediated transposition event during the early formation of the subclade around 1999. Therefore, both the horizontal transfer of plasmids carrying blaCTX-M-14 to diverse genetic lineages and chromosomal integration in the predominant genetic lineage have contributed to the spread of blaCTX-M-14.

Soil texture contributes to shaping comammox Nitrospira communities in rice-wheat rotation soils

Complete ammonia oxidizers (comammox Nitrospira) are intriguing discoveries that mark a significant milestone in the global nitrogen cycle. While numerous soil physiochemical variables have been identified as key influencers of comammox Nitrospira distribution, the role of soil texture in shaping these communities remains largely uncertain. Here, we explored the diversity, community structure of comammox Nitrospira, and their driving factors, including soil texture in 237 rice-wheat rotation soils. The results indicated that soil pH and texture were the primary factors influencing the Shannon diversity and richness of comammox Nitrospira. Comammox Nitrospira Shannon diversity and richness were positively associated with soil pH and silt content, but negatively correlated with clay content, suggesting that finer-textured soils harbored lower comammox Nitrospira diversity. Additionally, silt content emerged as the second most influential factor, after pH, shaping comammox Nitrospira community structure. Clade A.2 was found as the predominant comammox Nitrospira clade in rice-wheat rotation soils, representing 59.3 % of the total sequences. Clade A.2 exhibited a positive correlation with sand and clay contents but a negative association with silt content. Conversely, Clades A.3 and B demonstrated the opposite pattern. Overall, our study underscores the critical role of soil texture as a mediator of comammox Nitrospira diversity and community structure, emphasizing the need to consider soil texture in investigations of comammox Nitrospira.

Surveillance of pathogenic yeasts in hospital environments in Taiwan in 2020

BackgroundA predominate azole-resistant Candida tropicalis clade 4 genotype causing candidemia has been detected in not only Taiwan but also China, Singapore, and Australia. It can also be detected on fruit surfaces. In addition to determining distribution and drug susceptibilities of pathogenic yeasts in environments of intensive care units of 25 hospitals in Taiwan, we would also like to investigate whether the azole-resistant C. tropicalis exists in Taiwan's hospital environment. MethodsThe swabs of hospital environments were collected from August to November in 2020 and were cultured for yeasts. The yeasts were identified by rDNA sequence and the antifungal susceptibilities of those isolates were determined by the broth microdilution method. ResultsThe average yeast-culture rate of hospitals was 9.4% (217/2299). Sinks had the highest yeast-positive culture rate (32.7%), followed by bedside tables (28.9%), floors (26.0%), water-dispenser buttons (23.8%), and TV controller/touch panels (19.0%). Of 262 identified isolates, Candida parapsilosis was the most common species, accounting for 22.1%, followed by Filobasidium uniguttulatum (18.3%), Candida albicans (9.5%), C. tropicalis (8.0%), Candida glabrata (Nakaseomyces glabratus) (6.9%), and 30 other species (35.1%). Of the 21 C. tropicalis isolates from 11 units in 9 hospitals, 15 diploid sequence types (DSTs) were identified. The two DST506 fluconazole-resistant ones belonged to clade 4. ConclusionWe detected not only various pathogenic yeast species but also the predominant clade 4 genotype of azole-resistant C. tropicalis. Our findings highlight and re-emphasize the importance of regular cleaning and disinfection practices.

Molecular Epidemiology and Antifungal Susceptibility Profile in Nakaseomyces glabrata Species Complex: A 5-Year Countrywide Study.

The current study aimed to identify Iranian Nakaseomyces (Candida) glabrata complex species in the clinical isolates and determine their antifungal susceptibility profile. In total, 320 N. glabrata clinical isolates were collected from patients hospitalized in different geographical regions of Iran. The initial screening was performed by morphological characteristics on CHROMagar Candida. Each isolate was identified by targeting the D1/D2 rDNA using a multiplex-PCR method. To validate the mPCR method and determine genetic diversity, the ITS-rDNA region was randomly sequenced in 40 isolates. Additionally, antifungal susceptibility was evaluated against nine antifungal agents following the CLSI M27-A4 guidelines. All clinical isolates from Iran were identified as N. glabrata. The analysis of ITS-rDNA sequence data revealed the presence of eight distinct ITS clades and 10 haplotypes among the 40 isolates of N. glabrata. The predominant clades identified were Clades VII, V, and IV, which respectively accounted for 22.5%, 17.5%, and 17.5% isolates. The widest MIC ranges were observed for voriconazole (0.016-8 μg/mL) and isavuconazole (0.016-2 μg/mL), whereas the narrowest ranges were seen with itraconazole and amphotericin B (0.25-2 μg/mL). Haplotype diversity can be a valuable approach for studying the genetic diversity, transmission patterns, and epidemiology of the N. glabrata complex.

Long-Term Co-Circulation of Host-Specialist and Host-Generalist Lineages of Group B Streptococcus in Brazilian Dairy Cattle with Heterogeneous Antimicrobial Resistance Profiles.

Group B Streptococcus (GBS) is a major cause of contagious bovine mastitis (CBM) in Brazil. The GBS population is composed of host-generalist and host-specialist lineages, which may differ in antimicrobial resistance (AMR) and zoonotic potential, and the surveillance of bovine GBS is crucial to developing effective CBM control and prevention measures. Here, we investigated bovine GBS isolates (n = 156) collected in Brazil between 1987 and 2021 using phenotypic testing and whole-genome sequencing to uncover the molecular epidemiology of bovine GBS. Clonal complex (CC) 61/67 was the predominant clade in the 20th century; however, it was replaced by CC91, with which it shares a most common recent ancestor, in the 21st century, despite the higher prevalence of AMR in CC61/67 than in CC91, and high selection pressure for AMR from indiscriminate antimicrobial use in the Brazilian dairy industry. CC103 also emerged as a dominant CC in the 21st century, and a considerable proportion of herds had two or more GBS strains, suggesting poor biosecurity and within-herd evolution due to the chronic nature of CBM problems. The majority of bovine GBS belonged to serotype Ia or III, which was strongly correlated with CCs. Ninety-three isolates were resistant to tetracycline (≥8 μg/mL; tetO = 57, tetM = 34 or both = 2) and forty-four were resistant to erythromycin (2.0 to >4 μg/mL; ermA = 1, ermB = 38, mechanism unidentified n = 5). Only three isolates were non-susceptible to penicillin (≥8.0 μg/mL), providing opportunities for improved antimicrobial stewardship through the use of narrow-spectrum antimicrobials for the treatment of dairy cattle. The common bovine GBS clades detected in this study have rarely been reported in humans, suggesting limited risk of interspecies transmission of GBS in Brazil. This study provides new data to support improvements to CBM and AMR control, bovine GBS vaccine design, and the management of public health risks posed by bovine GBS in Brazil.

Modified laminar bone did not stop sauropods from achieving large body sizes

ABSTRACT An almost complete dinosaur femur found in the Baynshire Formation (late Cenomanian to Santonian; Mongolia) in 1963 during the Polish–Mongolian Paleontological Expeditions is described here for the first time. The morphology of the femur and bone histology suggest that the specimen was a representative of the Titanosauriformes, the predominant sauropod clade during the Cretaceous. Bone tissue exclusive to this clade, modified laminar bone that indicates a reduced growth rate, is identified in the thin sections taken from the femur. Based on its bone histology, the already ca. 20-meter-long specimen appears to be a subadult. This specimen achieved a significantly larger size compared with other Titanosauriformes with modified lamellar bone at a similar growth stage.

Treponema pallidum genetic diversity and its implications for targeted vaccine development: A cross-sectional study of early syphilis cases in Southwestern Colombia.

Venereal syphilis, caused by the spirochete Treponema pallidum subsp. pallidum (TPA), is surging worldwide, underscoring the need for a vaccine with global efficacy. Vaccine development requires an understanding of syphilis epidemiology and clinical presentation as well as genomic characterization of TPA strains circulating within at-risk populations. The aim of this study was to describe the clinical, demographic, and molecular features of early syphilis cases in Cali, Colombia. We conducted a cross-sectional study to identify individuals with early syphilis (ES) in Cali, Colombia through a city-wide network of public health centers, private sector HIV clinics and laboratory databases from public health institutions. Whole blood (WB), skin biopsies (SB), and genital and oral lesion swabs were obtained for measurement of treponemal burdens by polA quantitative polymerase chain reaction (qPCR) and for whole-genome sequencing (WGS). Among 1,966 individuals screened, 128 participants met enrollment criteria: 112 (87%) with secondary (SS), 15 (12%) with primary (PS) and one with early latent syphilis; 66/128 (52%) self-reported as heterosexual, while 48 (38%) were men who have sex with men (MSM). Genital ulcer swabs had the highest polA copy numbers (67 copies/μl) by qPCR with a positivity rate (PR) of 73%, while SS lesions had 42 polA copies/μl with PR of 62%. WB polA positivity was more frequent in SS than PS (42% vs 7%, respectively; p = 0.009). Isolation of TPA from WB by rabbit infectivity testing (RIT) was achieved in 5 (56%) of 9 ES WB samples tested. WGS from 33 Cali patient samples, along with 10 other genomic sequences from South America (9 from Peru, 1 from Argentina) used as comparators, confirmed that SS14 was the predominant clade, and that half of all samples had mutations associated with macrolide (i.e., azithromycin) resistance. Variability in the outer membrane protein (OMP) and vaccine candidate BamA (TP0326) was mapped onto the protein's predicted structure from AlphaFold. Despite the presence of mutations in several extracellular loops (ECLs), ECL4, an immunodominant loop and proven opsonic target, was highly conserved in this group of Colombian and South American TPA isolates. This study offers new insights into the sociodemographic and clinical features of venereal syphilis in a highly endemic area of Colombia and illustrates how genomic sequencing of regionally prevalent TPA strains can inform vaccine development.

Epidemiological and Molecular Characteristics of Hypermucoviscous and Hypervirulent Klebsiella pneumoniae Isolates in Community Patients in Shanghai, China.

The occurrence and dissemination of hypermucoviscous and hypervirulent Klebsiella pneumoniae (hm-hvKp) isolates in clinical settings are a critical public health problem in the world. However, the data on these isolates in community populations are limited. This study aims to understand the prevalence and molecular characteristics of hm-hvKp isolates in community patients in Shanghai, China. In 2018, an active surveillance system focused on hm-hvKp in community diarrhoeal cases was implemented in Pudong New Area, Shanghai, China, involving 12 sentinel hospitals. The antimicrobial susceptibility of hm-hvKp isolates from fecal samples was tested, and whole-genome sequencing (WGS) was performed to predict the serotypes and sequence types and to identify antimicrobial resistance determinants, virulence determinants, and phylogenetic clusters. The overall prevalence of hm K. pneumoniae isolates was 2.48% (31/1252), with the proportions of 1.76% (22/1252) for hm-hvKp and 0.72% (9/1252) for hm not hv K. pneumoniae. The prevalence of hm-hvKp isolates among different age groups and different months was statistically significant. All the 22 hm-hvKp isolates were susceptible to 20 antimicrobial agents and only carried bla SHV gene, and KL1 and KL2 accounted for eight (36.36%) cases and seven (31.82%) cases, respectively. The eight ST23/KL1 isolates belonged to the predominant CG23-I clade, which typically possessed the virulence determinants profile of rmpA/rmpA2-iro-iuc-ybt-irp-clb. The five ST86/KL2 isolates were assigned to the global clusters ST86/KL2-1 (n=2), ST86/KL2-2 (n=2), ST86/KL2-3 (n=1), all lack of the clb gene. Shanghai ST23/KL1 and ST86/KL2 isolates were closely related to the global isolates from liver abscesses, blood, and urine. Hm-hvKp is carried by the community population of Shanghai, with ST23/KL1 and ST86/KL2 isolates predominant. Hm-hvKp isolates of different continents, different sources, and different virulence levels were closely related. Ongoing surveillance of hm-hvKp isolates in the community population is warranted.

Quest for Nitrous Oxide-reducing Bacteria Present in an Anammox Biofilm Fed with Nitrous Oxide

N2O-reducing bacteria have been examined and harnessed to develop technologies that reduce the emission of N2O, a greenhouse gas produced by biological nitrogen removal. Recent investigations using omics and physiological activity approaches have revealed the ecophysiologies of these bacteria during nitrogen removal. Nevertheless, their involvement in‍ ‍anammox processes remain unclear. Therefore, the present study investigated the identity, genetic potential, and activity‍ ‍of N2O reducers in an anammox reactor. We hypothesized that N2O is limiting for N2O-reducing bacteria‍ ‍and an‍ ‍exogeneous N2O supply enriches as-yet-uncultured N2O-reducing bacteria. We conducted a 1200-day incubation of N2O-reducing bacteria in an anammox consortium using gas-permeable membrane biofilm reactors (MBfRs), which efficiently supply N2O in a bubbleless form directly to a biofilm grown on a gas-permeable membrane. A 15N tracer test indicated that the supply of N2O resulted in an enriched biomass with a higher N2O sink potential. Quantitative PCR and 16S rRNA amplicon sequencing revealed Clade II nosZ type-carrying N2O-reducing bacteria as protagonists of N2O sinks. Shotgun metagenomics showed the genetic potentials of the predominant Clade II nosZ-carrying bacteria, Anaerolineae and Ignavibacteria in MBfRs. Gemmatimonadota and non-anammox Planctomycetota increased their abundance in MBfRs despite their overall lower abundance. The implication of N2O as an inhibitory compound scavenging vitamin B12, which is essential for the synthesis of methionine, suggested its limited suppressive effect on the growth of B12-dependent bacteria, including N2O reducers. We identified Dehalococcoidia and Clostridia as predominant N2O sinks in an anammox consortium fed exogenous N2O because of the higher metabolic potential of vitamin B12-dependent biosynthesis.

Complex norovirus transmission dynamics at hospital wards revealed by deep sequencing.

Detailed knowledge regarding norovirus transmission within hospitals is limited. We investigated a norovirus hospital outbreak affecting 65 patients at five different wards. PCR showed that 61 (94%) of the patients were infected with genotype II.4 strains. Successful Ion Torrent deep sequencing of GII.4 positive samples from 59 patients followed by phylogenetic analysis revealed that all sequences but two clustered into four distinct clades. Two of the clades belonged to GII.4 Sydney 2012, while the other two belonged to GII.4 New Orleans 2009. One of the clades was predominant at two wards, while two clades were predominant at one ward each. The fourth clade was found in sporadic cases at several wards. Thus, at four out of five wards, variants from one clade were predominant. At one ward, a single clade accounted for all cases, while at three wards the predominant clade accounted for 60%-71% of cases. Analysis of quasispecies variation identified positions that could further discriminate between variants from separate wards. The results illustrate a complex transmission of healthcare-associated norovirus infections and show that sequencing can be used to discriminate between related and unrelated cases.

Distinct Red Blotch Disease Epidemiological Dynamics in Two Nearby Vineyards.

Grapevine red blotch virus (GRBV) causes red blotch disease and is transmitted by the three-cornered alfalfa hopper, Spissistilus festinus. GRBV isolates belong to a minor phylogenetic clade 1 and a predominant clade 2. Spatiotemporal disease dynamics were monitored in a 1-hectare 'Merlot' vineyard planted in California in 2015. Annual surveys first revealed disease onset in 2018 and a 1.6% disease incidence in 2022. Ordinary runs and phylogenetic analyses documented significant aggregation of vines infected with GRBV clade 1 isolates in one corner of the vineyard (Z = -4.99), despite being surrounded by clade 2 isolates. This aggregation of vines harboring isolates from a non-prevalent clade is likely due to infected rootstock material at planting. GRBV clade 1 isolates were predominant in 2018-2019 but displaced by clade 2 isolates in 2021-2022, suggesting an influx of the latter isolates from outside sources. This study is the first report of red blotch disease progress immediately after vineyard establishment. A nearby 1.5-hectare 'Cabernet Sauvignon' vineyard planted in 2008 with clone 4 (CS4) and 169 (CS169) vines was also surveyed. Most CS4 vines that exhibited disease symptoms one-year post-planting, likely due to infected scion material, were aggregated (Z = -1.73). GRBV isolates of both clades were found in the CS4 vines. Disease incidence was only 1.4% in non-infected CS169 vines in 2022 with sporadic infections of isolates from both clades occurring via secondary spread. Through disentangling GRBV infections due to the planting material and S. festinus-mediated transmission, this study illustrated how the primary virus source influences epidemiological dynamics of red blotch disease.

Genomic analysis of 1710 surveillance-based Neisseria gonorrhoeae isolates from the USA in 2019 identifies predominant strain types and chromosomal antimicrobial-resistance determinants.

This study characterized high-quality whole-genome sequences of a sentinel, surveillance-based collection of 1710 Neisseria gonorrhoeae (GC) isolates from 2019 collected in the USA as part of the Gonococcal Isolate Surveillance Project (GISP). It aims to provide a detailed report of strain diversity, phylogenetic relationships and resistance determinant profiles associated with reduced susceptibilities to antibiotics of concern. The 1710 isolates represented 164 multilocus sequence types and 21 predominant phylogenetic clades. Common genomic determinants defined most strains' phenotypic, reduced susceptibility to current and historic antibiotics (e.g. bla TEM plasmid for penicillin, tetM plasmid for tetracycline, gyrA for ciprofloxacin, 23S rRNA and/or mosaic mtr operon for azithromycin, and mosaic penA for cefixime and ceftriaxone). The most predominant phylogenetic clade accounted for 21 % of the isolates, included a majority of the isolates with low-level elevated MICs to azithromycin (2.0 µg ml-1), carried a mosaic mtr operon and variants in PorB, and showed expansion with respect to data previously reported from 2018. The second largest clade predominantly carried the GyrA S91F variant, was largely ciprofloxacin resistant (MIC ≥1.0 µg ml-1), and showed significant expansion with respect to 2018. Overall, a low proportion of isolates had medium- to high-level elevated MIC to azithromycin ((≥4.0 µg ml-1), based on C2611T or A2059G 23S rRNA variants). One isolate carried the penA 60.001 allele resulting in elevated MICs to cefixime and ceftriaxone of 1.0 µg ml-1. This high-resolution snapshot of genetic profiles of 1710 GC sequences, through a comparison with 2018 data (1479 GC sequences) within the sentinel system, highlights change in proportions and expansion of select GC strains and the associated genetic mechanisms of resistance. The knowledge gained through molecular surveillance may support rapid identification of outbreaks of concern. Continued monitoring may inform public health responses to limit the development and spread of antibiotic-resistant gonorrhoea.

Detection of Sporadic Outbreaks of Rift Valley Fever in Uganda through the National Viral Hemorrhagic Fever Surveillance System, 2017-2020.

Rift Valley fever (RVF) is a zoonotic disease of public health and economic importance. Uganda has reported sporadic outbreaks of RVF in both humans and animals across the country, especially in the southwestern part of the "cattle corridor" through an established viral hemorrhagic fever surveillance system. We report 52 human cases of laboratory-confirmed RVF from 2017 to 2020. The case fatality rate was 42%. Among those infected, 92% were males and 90% were adults (≥ 18 years). Clinical symptoms were characterized by fever (69%), unexplained bleeding (69%), headache (51%), abdominal pain (49%), and nausea and vomiting (46%). Most of the cases (95%) originated from central and western districts that are part of the cattle corridor of Uganda, where the main risk factor was direct contact with livestock (P = 0.009). Other predictors of RVF positivity were determined to be male gender (P = 0.001) and being a butcher (P = 0.04). Next-generation sequencing identified the predominant Ugandan clade as Kenya-2, observed previously across East Africa. There is need for further investigation and research into the effect and spread of this neglected tropical disease in Uganda and the rest of Africa. Control measures such as promoting vaccination and limiting animal-human transmission could be explored to reduce the impact of RVF in Uganda and globally.

Clinical outcomes and phylogenetic analysis in reflection with three predominant clades of SARS-CoV-2 variants.

The pandemic of coronavirus disease 2019 (COVID-19) has a broad spectrum of clinical manifestations. The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) undergoes continuous evolution, resulting in the emergence of several variants. Each variant has a different severity and mortality rate. In this study, 1174 COVID-19 patients were studied for mortality and severity over three SARS-CoV-2 predominating variant periods in 2021 and 2022 in Sulaimani Province, Iraq. In each period, a representative, variant virus was subjected to phylogenetic and molecular and clinical analysis. Phylogenetic analysis revealed three SARS-CoV-2 variants, belonging to: Delta B.1.617.2, Omicron BA.1.17.2, and Omicron BA.5.6. The Delta variants showed more severe symptoms and a lower PCR-Ct value than Omicron variants regardless of gender, and only 4.3% of the cases were asymptomatic. The mortality rate was lower with Omicron (.5% for BA.5.2 and 1.3% for BA.1.17.2) compared with Delta variants (2.5%). The higher mortality rate with Delta variants was in males (2.84%), while that with Omicron BA1.17.2 and BA.5.2 was in females, 1.05% and .0%, respectively. Age group (≥70) years had the highest mortality rate; however, it was (.0%) in the age group (30-49) years with Omicron variants, compared with (.96%) in Delta variants. There has been a surge in COVID-19 infection in the city due to the predominant lineages of SARS-CoV-2, B.1.617, Omicron BA.1.17.2 and Omicron BA.5.6, respectively. A higher PCR-Ct value and severity of the Delta variant over Omicron BA.1.17.2 and/or BA.5.2 variants were significantly correlated with a higher death rate in the same order.

Genomic Analysis Reveals New Integrative Conjugal Elements and Transposons in GBS Conferring Antimicrobial Resistance.

Streptococcus agalactiae or group B streptococcus (GBS) is a leading cause of neonatal sepsis and increasingly found as an invasive pathogen in older patient populations. Beta-lactam antibiotics remain the most effective therapeutic with resistance rarely reported, while the majority of GBS isolates carry the tetracycline resistance gene tet(M) in fixed genomic positions amongst five predominant clonal clades. In the UK, GBS resistance to clindamycin and erythromycin has increased from 3% in 1991 to 11.9% (clindamycin) and 20.2% (erythromycin), as reported in this study. Here, a systematic investigation of antimicrobial resistance genomic content sought to fully characterise the associated mobile genetic elements within phenotypically resistant GBS isolates from 193 invasive and non-invasive infections of UK adult patients collected during 2014 and 2015. Resistance to erythromycin and clindamycin was mediated by erm(A) (16/193, 8.2%), erm(B) (16/193, 8.2%), mef(A)/msr(D) (10/193, 5.1%), lsa(C) (3/193, 1.5%), lnu(C) (1/193, 0.5%), and erm(T) (1/193, 0.5%) genes. The integrative conjugative elements (ICEs) carrying these genes were occasionally found in combination with high gentamicin resistance mediating genes aac(6')-aph(2″), aminoglycoside resistance genes (ant(6-Ia), aph(3'-III), and/or aad(E)), alternative tetracycline resistance genes (tet(O) and tet(S)), and/or chloramphenicol resistance gene cat(Q), mediating resistance to multiple classes of antibiotics. This study provides evidence of the retention of previously reported ICESag37 (n = 4), ICESag236 (n = 2), and ICESpy009 (n = 3), as well as the definition of sixteen novel ICEs and three novel transposons within the GBS lineage, with no evidence of horizontal transfer.

The genetic diversity, replication, and transmission of 2009 pandemic H1N1 viruses in China.

The 2009 pandemic H1N1 influenza A virus (pdm09) continue to evolve, and few studies have systemically analyzed the evolution, replication, and transmission of pmd09 viruses in China. To better understand the evolution and pathogenicity of pdm09 viruses, we systematically analyzed viruses that were confirmed in 2009-2020 in China and characterized their replication and transmission ability. We extensively analyzed the evolution characteristics of pdm/09 in China over the past decades. The replication ability of 6B.1 and 6B.2 lineages on Madin-Darby canine kidney (MDCK) and human lung adenocarcinoma epithelial (A549) cells and their pathogenicity and transmission in guinea pigs were also compared. In total, 3,038 pdm09 viruses belonged to clade 6B.1 (62% of all pdm09 viruses) and clade 6B.2 (4%). Clade 6B.1 pdm09 viruses are the predominant clade, with proportions of 54.1%, 78.9%, 57.2%, 58.6%, 61.7%, 76.3%, and 66.6% in the North, Northeast, East, Central, South, Southwest, and Northeast regions in China, respectively. The isolation proportion of clade 6B.1 pdm/09 viruses was 57.1%, 74.3%, 96.1%, 98.2%, 86.7%, and 78.5% in 2015-2020, respectively. A clear differentiation time point appeared in 2015 before which the evolution trend of pdm09 viruses in China was similar to that in North America but then showed a different trend after that point. To characterize pdm09 viruses in China after 2015, we further analyzed 33 pdm09 viruses isolated in Guangdong in 2016-2017, among which A/ Guangdong/33/2016 and A/Guangdong/184/2016 (184/2016) belonged to clade 6B.2, and the other 31 strains belonged to clade 6B.1. A/Guangdong/887/2017 (887/2017) and A/Guangdong/752/2017 (752/2017) (clade 6B.1), 184/2016 (clade 6B.2) and A/California/04/2009 (CA04) replicated efficiently in MDCK cells and A549 cells, as well as the turbinates of guinea pigs. 184/2016 and CA04 could transmit among guinea pigs through physical contact. Our findings provide novel insights into the evolution, pathogenicity, and transmission of pdm09 virus. The results show that enhancing surveillance of pdm09 viruses and timely evaluation of their virulence are essential.

MDR carbapenemase-producing Klebsiella pneumoniae of the hypervirulence-associated ST23 clone in Poland, 2009-19.

To characterize carbapenemase-producing isolates of the Klebsiella pneumoniae hypervirulent (hvKp) clone ST23 in Poland. Fifteen K. pneumoniae ST23 isolates were identified by the Polish surveillance of carbapenemase-producing Enterobacterales. These comprised a cluster with KPC-2 + NDM-1 (n = 7), KPC-2 (n = 1) or NDM-1 (n = 1) enzymes from one hospital from 2018, and sporadic isolates with KPC-2 (n = 1), NDM-1 (n = 1), VIM-1 (n = 1) or OXA-48 (n = 3), recovered from 2009 to 2019 in different towns. The isolates were sequenced by Illumina MiSeq, followed by MinION for six representatives. Clonality, phylogeny, serotypes, virulomes, resistomes and plasmids of the isolates were analysed and compared with international ST23 strains, using various bioinformatic tools. Only two diverse isolates with KPC-2 or VIM-1 were of typical hvKp ST23 serotypes K1 and O1v.2, and its predominant phylogenetic clade. These contained multiple chromosomal (ybt, clb) and pK2044/KpVP-1 plasmid (iuc, iro, rmpADC, rmpA2) virulence loci, whereas carbapenemase and other antimicrobial resistance (AMR) genes were on single additional plasmids. All remaining isolates were of K57 and O2v.2 serotypes, and a minor, distant clade of unclear phylogeny, including also ∼10 isolates from other European countries. These had fewer virulence loci (ybt, iuc, rmpADC, rmpA2) but abounded in plasmids, which with several chromosomal AMR mutations conferred more extensive MDR phenotypes than in K1 O1v.2. Lower clonal diversity than in K1, and numerous common characteristics of the isolates supported the hypothesis of the emerging character of the ST23 K57 clade. A new MDR ST23 lineage has emerged in Europe, causing a potential threat to public health.