Serotype Diversity Research Articles

Genetic and phylogenetic characterization of Shiga toxin-producing Escherichia coli and enteropathogenic E. coli from livestock in Jiangsu by using whole-genome sequencing.

There are knowledge gaps regarding STEC and EPEC strains in livestock in Jiangsu, China. This study aimed to evaluate the potential public health significance of STEC and EPEC strains isolated from livestock by determining the serotypes, virulence profiles, and genetic relationship with international STEC strains. A total of 68 STEC and 37 EPEC strains were obtained from 231 faecal sheep samples and 70 faecal cattle samples. By using whole-genome sequencing (WGS) analysis, all STEC belonged to 15 O: H serotypes, and the most prevalent serotypes were O6:H10 (19.1%), O155:H21 (14.7%), and O21:H25 (10.3%). The main Shiga toxin gene subtypes detected were stx1c (41.2%), stx1a (26.5%), stx2b (14.7%), and stx2k (14.7%). Only the STEC from cattle carried eae gene. Other adherence-associated or toxin-related genes, including lpfA (70.6%), iha (48.5%), subA (54.4%), and ehxA (33.8%), were found in STEC. All EPEC strains were bfpA-negative, and the predominant eae variants were eae-β1 (62.2%), eae-ζ (21.6%), and eae-θ (8.1%). The core-genome multi-locus sequence typing (cgMLST) analysis revealed nine scattered clusters in STEC and one dominant cluster in EPEC. The strains with the same serotypes, including O22:H8 and O43:H2 in the two towns, possessed a closely genomic distance. The core genome single-nucleotide polymorphism (cgSNP) showed that part of STEC strains in this study was clustered with isolates possessing the same serotypes from the Netherlands, Sweden, and Xinjiang of China. Five serotypes of STEC isolates were associated with the clinical STEC strains from databases. This study provided the diverse serotypes and the virulence genes profiles in STEC and EPEC strains. Local strains possessed widely diverse and scattered clusters by cgMLST. Closely genomic correlation with clinical isolates displayed that part of the STEC strains may threaten to public health. Non-O157 STEC strains act as important pathogens for human infections. This study supports the increased surveillance work of non-O157 STEC rather than just O157 STEC in this region.

Genomic Analysis of Group B Streptococcus from Neonatal Sepsis Reveals Clonal CC17 Expansion and Virulence- and Resistance-Associated Traits After Intrapartum Antibiotic Prophylaxis.

Group B Streptococcus (GBS) is a leading cause of invasive neonatal infections. This study aimed to investigate the trend of GBS serotype and genotype change and their correlation with antimicrobial resistance before and after implementation of intrapartum antibiotic prophylaxis (IAP). We performed serotyping, whole-genome sequencing, antimicrobial susceptibility testing, and single-nucleotide polymorphism (SNP)-based phylogenetic analysis on 238 invasive GBS isolates collected from October 1998 to February 2020 in Taiwan. There were 7 serotypes and 6 clonal complexes (CCs) among the 238 GBS isolates, and more than half of the isolates carried multiple antimicrobial resistance genes. The expansion of CC17 strains and the increase in late-onset disease occurred synchronously after the implementation of IAP. Analysis of the carriage isolates from pregnant women showed diverse serotype distribution in the IAP era. The antimicrobial susceptibility testing showed that all 238 strains were susceptible to ampicillin and penicillin, while the number of various resistance genes in GBS genomes was found increased with the expansion of CC17. Compared with reference genomes, 697 nonsynonymous SNPs in 443 protein-coding genes were CC17 specific. The study revealed the expansion of GBS CC17 and the increase of late-onset disease that occurred simultaneously with the implementation of IAP. Although the susceptibility of CC17 to antimicrobial agents is not different from that of other sequence types at present, GBS with phenotypic resistance to antimicrobials may emerge in the future, given the environmental selection pressure and the continued accumulation of SNP mutations.

A national study through a 'Farm-to-fork' Approach to determine Salmonella dissemination along with the Lebanese poultry production chain.

This cross-sectional study was conducted to determine the prevalence of Salmonella at different stages of the broiler production chain and layer flocks in addition to their antibiotic resistance profile and molecular patterns. Over a period of 3years, different sample matrices were collected from Lebanese farms, slaughterhouses and retail markets. Out of 672 Salmonella serotyped, 514 were analysed for antimicrobial resistance and 214 for clonality using Pulsed-field gel electrophoresis (PFGE). The results highlighted an important prevalence of Salmonella, 30% in farms, 35.8% in slaughterhouses and 22.4% at retail level. A large diversity of serotypes was identified with predominance among Salmonella Infantis (32.9%), Salmonella Enteritidis (28.4%) and Salmonella Kentucky (21.4%). High resistance to nalidixic acid was revealed in all the isolates. The most prominent resistance was exhibited in S. Kentucky and S. Infantis. The latter was resistant to tetracycline (99%), streptomycin (88.2%) and remarkable multi-drug resistance (MDR) (89.7%). All S.Kentucky isolates were resistant to ciprofloxacin, MDR (62.4%) and 6% were resistant to extended-spectrum cephalosporin (ESCs). One persistent clone of S. Enteritidis was found common between poultry and humans. Similar genomic profiles were detected between farms, slaughterhouses and retail suggesting the dissemination of identical clones throughout the food chain possibly due to weak barriers preventing such transmission.

High sequence similarity between avian pathogenic E. coli isolates from individual birds and within broiler chicken flocks during colibacillosis outbreaks

Avian pathogenic E. coli (APEC) cause high first week mortality (FWM) in broiler chickens worldwide. In order to investigate the epidemiologic aspects of colibacillosis in broiler flocks it is important to develop reliable and cost-effective sampling guidelines. In this context, it is particularly important to define the minimum number of samples required to reliably identify the causative APEC clone during outbreaks of colibacillosis.This study describes the diversity of E. coli isolates between and within three flocks with high FWM due to colibacillosis. Each flock was represented by five animals, showing typical lesions of colibacillosis, and spleen, liver and one other organ from each animal was sampled for APEC. A total of 47 E. coli isolates, one per organ, and approximately 15 isolates per flock were whole genome sequenced and compared by multilocus sequence typing (MLST), serotyping and phylogenetic analysis to deduce their relationship. The results revealed that within individual birds there was little or no sequence type (ST) or serotype diversity between APEC isolates from different organs. Based on phylogenetic analysis, isolates belonging to the same ST and serotype showed a low number of single nucleotide polymorphisms (SNPs) across more than 95 % of the genome. Isolates from the liver always represented the major disease-causing APEC in individual birds, even when more than one ST was detected within an individual bird and flock. This study guides us towards an economically efficient way of sampling for future epidemiological studies on colibacillosis, by determining the causative APEC-clone at flock level.

Platform optimization for efficient AAV purification: insights from a CDMO

Over the last decade, the number of clinical trials involving recombinant adeno-associated viral (AAV) vectors has dramatically increased, the diversity of serotypes has expanded, and the demand for larger quantities of highly purified material manufactured to cGMP standards has rocketed. For contract development and manufacturing organizations (CDMOs) like Yposkesi, the manufacturing challenges are centered around flexibility, robustness, and productivity, especially with regards to purification. Universal tools able to address any serotype with minimal process adjustments are critical. In this article, we describe how POROS™ CaptureSelect™ AAVX resin can be used as a pan-affinity tool for the universal capture of AAV vectors, and how Yposkesi optimized the operational parameters to make the resin an efficient, robust, and productive purification platform that fits within the constraints faced by CDMOs.

Uncovering inter- and intra-raft dynamics of icosahedral flavivirus assemblies

Dengue virus is a mosquito-borne, icosahedral flavivirus that represents a significant threat to human health worldwide. Vaccine development for dengue has long eluded scientists due to serotype and strain diversity associated with altered viral capsid dynamics. Despite having conserved icosahedral (T=3) structures, dengue strains show unique surface fluctuations referred to as ‘breathing’. Here we describe unique dynamic signatures of dengue strains 3, 4 and related zika by amide hydrogen/deuterium exchange mass spectrometry (HDXMS).

Prevalence and Serotype Diversity of Salmonella enterica in the Estonian Meat Production Chain in 2016-2020.

Background: Salmonella enterica represents a considerable public concern worldwide, with farm animals often recognised as an important reservoir. This study gives an overview of the prevalence and serotype diversity of Salmonella over a 5-year period in the meat production chain in Estonia. Data on human salmonellosis over the same period are provided. Methods: Salmonella surveillance data from 2016 to 2020 were analysed. Results: The prevalence of Salmonella at the farm level was 27.7%, 3.3% and 0.1% for fattening pigs, cattle and poultry, respectively. S. Derby was the most prevalent serotype at the farm level for fattening pigs and S. Dublin for cattle. The top three serotypes isolated at the slaughterhouse and meat cutting levels were S. Derby, monophasic S. Typhimurium and S. Typhimurium with proportions of 64.7%, 9.4% and 7.0%, respectively. These serotypes were the top five most common Salmonella serotypes responsible for human infections in Estonia. S. Enteritidis is the main cause (46.9%) of human salmonellosis cases in Estonia, but in recent years, Enteritidis has not been detected at the slaughterhouse or meat cutting level. Conclusion: In recent years, monophasic S. Typhimurium has become epidemiologically more important in Estonia, with the second-highest cause in human cases and third-highest among the most prevalent serotypes of Salmonella enterica in the meat chain.

1047. Development of a Next Generation 30+ Valent Pneumococcal Conjugate Vaccine (VAX-XP) Using Site-Specific Carrier Protein Conjugation

BackgroundDue to the diversity of serotypes, exacerbated by the phenomenon of serotype replacement, there remains an unmet medical need for a pneumococcal conjugate vaccine (PCV) containing additional serotypes. Using a cell-free protein synthesis (CFPS) platform to produce an enhanced carrier protein (eCRM®) based on the CRM197 sequence, Vaxcyte is developing a PCV encompassing over 30 serotypes. The eCRM carrier protein contains multiple insertions of the non-native amino acid para-azidomethyl-L-phenylalanine (pAMF) that facilitates site-specific conjugation of the pneumococcal polysaccharides (PS) to eCRM. Unlike conventional methodologies, site-selective conjugation enhances process consistency and increases capacity for inclusion of additional serotypes in a PCV without promoting carrier suppression. Using this platform, the aim of the current study was to employ CFPS technology to construct a 31-valent PCV and evaluate its immunogenicity in New Zealand White (NZW) rabbits. MethodsThe eCRM carrier protein was individually conjugated to each of 31 selected pneumococcal PSs using copper-free click chemistry to produce 31 Conjugate Drug Substances (DS), which were then mixed with aluminum phosphate to produce the VAX-XP Drug Product. 24 of the DS conjugates in VAX-XP were generated at manufacturing scale. Two doses of VAX-XP were administered to NZW rabbits at 0 and 21 days to assess its ability to elicit anti-capsular IgG antibodies. Additionally, rabbits were also administered either Prevnar13 or a mixture of Pneumovax 23 and 8 incremental PS in isotonic saline, as comparators.ResultsVAX-XP showed conjugate-like immune responses for all 31 serotypes, as demonstrated by superior responses to PS-based vaccines and comparable responses to Prevnar13. IgG responses for VAX-XP compared with Prevnar13 and Pneumovax 23 at 14 days post dose 2 ConclusionThese results demonstrate that increasing the number of pneumococcal serotypes does not result in immunological attenuation in any of the serotypes contained in VAX-XP relative to the current standard of care. Furthermore, the data confirm the scalability and reproducibility of the CFPS platform in the production of VAX-XP conjugates, creating the foundation for a next generation broad-valency PCV.Disclosures Chris Behrens, PhD, Vaxcyte, Inc. (Employee) Jeff Fairman, PhD, Vaxcyte, Inc. (Employee) Paresh Agarwal, PhD, Vaxcyte, Inc. (Employee) Shylaja Arulkumar, MS, Vaxcyte, Inc. (Employee) Sandrine Barbanel, MS, Vaxcyte, Inc. (Employee) Leslie Bautista, n/a, Vaxcyte, Inc. (Employee) Aym Berges, PhD, Vaxcyte, Inc. (Employee) John Burky, BS, Vaxcyte, Inc. (Employee) Peter Davey, MS, Vaxcyte, Inc. (Employee) Chris Grainger, PhD, Vaxcyte, Inc. (Employee) Sherry Guo, PhD, Vaxcyte, Inc. (Employee) Sam Iki, MS, Vaxcyte, Inc. (Employee) Mark Iverson, BS, Vaxcyte, Inc. (Employee) Neeraj Kapoor, PhD, Vaxcyte, Inc. (Employee) Olivier Marcq, PhD, Vaxcyte, Inc. (Employee) Thi-Sau Migone, PhD, Vaxcyte, Inc. (Employee) Lucy Pill, MS, Vaxcyte, Inc. (Employee) Mohammed Sardar, n/a, Vaxcyte, Inc. (Employee) Paul Sauer, MBA, Vaxcyte, Inc. (Employee) James Wassil, MS MBA, Vaxcyte, Inc. (Employee)

Streptococcus pneumoniae carriage in school children

Purpose. To investigate the serotype distribution, clonal structure and antimicrobial resistance of pneumococci isolated from schoolchildren.Materials and methods. During the period from 2012 to 2018 we examined 498 healthy school children aged 6 to 17 years. Oropharyngeal swab was taken from each child for culture, after that all S. pneumoniae strains were genotyped for serotype and ST-type deduction (PCR and sequencing, respectively). Antimicrobial resistance was also determined.Results. Pneumococcal culture was positive in 10.6 % of children. S. pneumoniae isolates belonged to seven serogroups and seven serotypes. Serogroup 6 and serotype 19F strains (15.1% each), and serogroup 9 strains (13.2%) were the most prevalent. S. pneumoniae33FA/37 and 3 (9.4 and 5.7%), serogroups 15 and 18 (7.6 and 5.7%), and 10A serotype (3.8%) were determined at a lower frequency. 20 detected ST-types belonged to 14 clonal complexes (CCs); CC156, CC447, and CC320 were predominant. 1.9% of isolates were penicillin-resistant; 13.2% – macrolide-, clindamycin-, and tetracycline-resistant. S. pneumoniae antibiotic resistant strains belonged to multidrug-resistant CCs 320, 315, and 156.Conclusion. S. pneumoniae prevalence in school children is not high. Pneumococcal population is characterized by serotype and clonal diversity including ‘invasive’ serotypes and genotypes. Most of strains are susceptible to antimicrobials.

Pneumococcal capsule blocks protection by immunization with conserved surface proteins

Vaccines targeting Streptococcus pneumoniae (Spn) are limited by dependence on capsular polysaccharide and its serotype diversity. More broadly-based approaches using common protein antigens have not resulted in a licensed vaccine. Herein, we used an unbiased, genome-wide approach to find novel vaccine antigens to disrupt carriage modeled in mice. A Tn-Seq screen identified 198 genes required for colonization of which 16 are known to express conserved, immunogenic surface proteins. After testing defined mutants for impaired colonization of infant and adult mice, 5 validated candidates (StkP, PenA/Pbp2a, PgdA, HtrA, and LytD/Pce/CbpE) were used as immunogens. Despite induction of antibody recognizing the Spn cell surface, there was no protection against Spn colonization. There was, however, protection against an unencapsulated Spn mutant. This result correlated with increased antibody binding to the bacterial surface in the absence of capsule. Our findings demonstrate how the pneumococcal capsule interferes with mucosal protection by antibody to common protein targets.

Extensive Drug-Resistant Salmonella enterica Isolated From Poultry and Humans: Prevalence and Molecular Determinants Behind the Co-resistance to Ciprofloxacin and Tigecycline.

The emergence of extensive drug-resistant (XDR) Salmonella in livestock animals especially in poultry represents a serious public health and therapeutic challenge. Despite the wealth of information available on Salmonella resistance to various antimicrobials, there have been limited data on the genetic determinants of XDR Salmonella exhibiting co-resistance to ciprofloxacin (CIP) and tigecycline (TIG). This study aimed to determine the prevalence and serotype diversity of XDR Salmonella in poultry flocks and contact workers and to elucidate the genetic determinants involved in the co-resistance to CIP and TIG. Herein, 115 Salmonella enterica isolates of 35 serotypes were identified from sampled poultry (100/1210, 8.26%) and humans (15/375, 4.00%), with the most frequent serotype being Salmonella Typhimurium (26.96%). Twenty-nine (25.22%) Salmonella enterica isolates exhibited XDR patterns; 25 out of them (86.21%) showed CIP/TIG co-resistance. Exposure of CIP- and TIG-resistant isolates to the carbonyl cyanide 3-chlorophenylhydrazone (CCCP) efflux pump inhibitor resulted in an obvious reduction in their minimum inhibitory concentrations (MICs) values and restored the susceptibility to CIP and TIG in 17.24% (5/29) and 92% (23/25) of the isolates, respectively. Molecular analysis revealed that 89.66% of the isolates contained two to six plasmid-mediated quinolone resistance genes with the predominance of qepA gene (89.66%). Mutations in the gyrA gene were detected at codon S83 (34.62%) or D87 (30.77%) or both (34.62%) in 89.66% of XDR Salmonella. The tet(A) and tet(X4) genes were detected in 100% and 3.45% of the XDR isolates, respectively. Twelve TIG-resistant XDR Salmonella had point mutations at codons 120, 121, and 181 in the tet(A) interdomain loop region. All CIP and TIG co-resistant XDR Salmonella overexpressed ramA gene; 17 (68%) out of them harbored 4-bp deletion in the ramR binding region (T-288/A-285). However, four CIP/TIG co-resistant isolates overexpressed the oqxB gene. In conclusion, the emergence of XDR S. enterica exhibiting CIP/TIG co-resistance in poultry and humans with no previous exposure to TIG warrants an urgent need to reduce the unnecessary antimicrobial use in poultry farms in Egypt.

Genetic diversity of Dengue virus serotypes circulating among Aedes mosquitoes in selected regions of northeastern Nigeria

The flaviviruses are mosquito borne pathogens that continue to pose a considerable public health risk to animals and humans. The members of this group includes, Dengue virus (DENV), Yellow fever virus (YVF), Japanese encephalitis virus (JEV), West Nile virus (WEV) and Zika virus (ZKV). The DENV mosquito vector is endemic to tropical and subtropical climates, placing ∼40% of the world's population at direct risk of dengue infection. Currently, in Nigeria the status of DENV serotypes circulating among mosquito vectors is unknown. Our study was designed to identify and characterize the DENV serotypes circulating in Aedes mosquito populations collected in selected sites in Nigeria. The mosquitoes were collected and identified morphologically to species level using colored identification keys of Rueda. Generally, each species identified was tested in pools of 20 individuals of each Aedes species. RT-PCR and semi nested PCR were used to detect DENV serotypes in mosquitoes and characterized using Sanger sequencing methods. The results showed that DENV serotypes were detected in 58.54% (24/41) of the pools of Aedes mosquitoes from Mubi, Numan and Yola screened. All DENV1-4 serotypes were detected in Ae. aegypti. While DENV 1, 2 and 4 were detected in Ae. albopictus. And only DENV 2 was detected in Ae. galloisi with DENV4 serotype being reported for the first time in Nigeria. DENV2 (37.8%) was the most detected serotypes, while double and triple co-infections of serotypes were detected in 24.4% of the pools. Phylogenetic analysis revealed a strong evolutionary relatedness of DENV serotypes in our study with that of South and Southeast Asia, North America, and other African countries. This is the first reports on the natural DENV serotypes co-infection among Aedes species pools in Nigeria, which can create possible interaction with other flaviviruses causing animal and human diseases. In addition, our study postulates the possible linkage between DENV serotypes infection and human febrile flu-like disease burden being experienced by host communities in northeastern Nigeria.

Historical Investigation of Fowl Adenovirus Outbreaks in South Korea from 2007 to 2021: A Comprehensive Review.

Fowl adenoviruses (FAdVs) have long been recognized as critical viral pathogens within the poultry industry, associated with severe economic implications worldwide. This specific group of viruses is responsible for a broad spectrum of diseases in birds, and an increasing occurrence of outbreaks was observed in the last ten years. Since their first discovery forty years ago in South Korea, twelve antigenically distinct serotypes of fowl adenoviruses have been described. This comprehensive review covers the history of fowl adenovirus outbreaks in South Korea and updates the current epidemiological landscape of serotype diversity and replacement as well as challenges in developing effective broadly protective vaccines. In addition, transitions in the prevalence of dominant fowl adenovirus serotypes from 2007 to 2021, alongside the history of intervention strategies, are brought into focus. Finally, future aspects are also discussed.

Genetic diversity and molecular evolution of human adenovirus serotype 41 strains circulating in Beijing, China, during 2010-2019.

Human adenovirus serotype 41 (HAdV-F41) is an important pathogen that causes diarrhea in children. However, the data on its molecular genetic characteristics and evolutionary history are still neither comprehensive nor sufficient. Four capsid protein genes from 58 HAdV-F41-positive specimens taken from diarrheal children in Beijing during 2010-2019 were amplified and analyzed. Variant amino acids in the hexon gene (18 sites) and short fiber gene (4 sites) clustered these strains into two clades and four subclades. The deletion of 15 amino acids found in the gene seemed to have little effect on the genomic strain cluster same as to penton gene. The HAdV-F41 strains had high diversity, as assessed from the intraspecific recombination of hexon, short fiber and long fiber. The molecular evolutionary rate of HAdV-F41's concatenated genes was 4.07×10-5 substitutions/site/year, and it diverged from the most recent common ancestor in 1720. Apart from in the penton gene, positive selection codons were predicted in the other three genes, which may play a synergistic role in the evolution of HAdV-F41. These results provide new insights for understanding the characteristics of infectivity and developing vectors and vaccine vehicles for HAdV-F41.

Infectious Bronchitis Disease in Poultry its Diagnosis, Prevention and Control Strategies

Avian Infectious bronchitis (IB) is profoundly one of the main diseases associated with respiratory syndrome in domestic poultry causing significant economic losses to poultry production. Avian Infectious Bronchitis (IB) has a place with Coronaviridae family, which causes respiratory illness, diminished creation of flying creatures, nephrotic Syndrome, and unsalvageable harm to oviduct, which can cause the crenation of anomalous eggs. Inoculation programs currently are pointless because of the outrageous hereditary varieties of IBV. Consequently, an exact and fast serotype assurance is a significant factor in controlling IBV. Compelling analytic instruments are likewise expected to analyze IB diseases in the field and to distinguish diverse serotypes and variations. Ideal administration for forestalling IB in flying creatures incorporates ideal inoculation with live or inactivated Vaccines containing flowing strains and severe disconnection of the contaminated fowls. Great administration and sterile practices in poultry units can handle the spread of IB among groups by and large. The idea of DNA vaccination with spike protein quality has altered the idea of IB immune prophylaxis as it has been found to evoke an adequate invulnerable reaction. Atomic science-based identification and control procedures must be created alongside the up degree of customary strategies to handle the developing danger presented by this microorganism the sickness can be adequately controlled in the years.

Otitis media with ANCA-associated vasculitis: A retrospective study of 30 patients.

Otitis media with antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis (OMAAV) is a new category of otitis media in which cases of otitis media due to ANCA-associated vasculitis (AAV) are classified, regardless of ANCA variant or ANCA serotype. We aimed to describe the clinical features and course of patients with OMAAV and identify factors associated with hearing outcomes. We retrospectively analysed 30 patients with OMAAV, classified based on the criteria proposed by the Japan Otological Society in 2016. Single-positive myeloperoxidase-ANCA, single-positive proteinase 3-ANCA, double-positive ANCA, and double-negative ANCA were identified in 47%, 33%, 7%, and 13% of the patients, respectively. All patients subjected to audiometry showed hearing impairments, and 85% were affected bilaterally. Mixed- and sensorineural-type hearing impairments were identified in 80% and 20% of impaired ears, respectively. Hypertrophic pachymeningitis (HPM) was identified in 37% of the patients. Immunosuppressive therapy was administered to 93% of patients, and the median air conduction hearing levels at pre- and post-treatment were 66.1 dB and 43.4 dB, respectively, indicating significant hearing improvements. HPM and a long interval between disease onset and treatment initiation were significantly correlated with poor hearing prognosis. OMAAV develops under any type of ANCA-serology and typically causes mixed or sensorineural bilateral hearing loss. The early initiation of immunosuppressive therapy and the absence of HPM were associated with good hearing outcomes.

Serotype and genotype diversity of dengue viruses circulating in India: a multi-centre retrospective study involving the Virus Research Diagnostic Laboratory Network in 2018

A retrospective study was undertaken to investigate the circulating dengue virus (DENV) serotypes and genotypes in India in 2018. In total, 4963 samples referred to virus research diagnostic laboratories (n=21), the Indian Council of Medical Research-National Institute of Virology (ICMR-NIV) and ICMR-NIV field units (n=2) for diagnosis of dengue in 2018 were tested using a real-time reverse transcription polymerase chain reaction assay for the presence of DENV serotypes. Representative samples were sequenced for the envelope (E) gene. Regional diversity was observed with regard to the dominant circulating serotypes. DENV-2 was found to be the most common serotype in many states. Thrombocytopenia, petechiae and malaise were associated with DENV-2 infection. Phylogenetic analyses of DENV E gene sequences revealed the circulation of genotypes I and V of DENV-1, two lineages of DENV-2 genotype IV, DENV-3 genotype III and DENV-4 genotype I. This study found regional differences in the prevalence of circulating DENV serotypes in India, and provides baseline data for continuous molecular surveillance. Molecular surveillance may have implications for predicting large-scale outbreaks of dengue if regional shifts in the predominantly circulating serotypes and genotypes are detected during the early phase of the dengue season.

Lack of effectiveness of 13-valent pneumococcal conjugate vaccination against pneumococcal carriage density in Papua New Guinean infants

BackgroundPapua New Guinea (PNG) introduced the 13-valent pneumococcal conjugate vaccine (PCV13) in 2014, with administration at 1, 2, and 3 months of age. PCV13 has reduced or eliminated carriage of vaccine types in populations with low pneumococcal carriage prevalence, carriage density and serotype diversity. This study investigated PCV13 impact on serotype-specific pneumococcal carriage prevalence, density, and serotype diversity in PNG infants, who have some of the highest reported rates of pneumococcal carriage and disease in the world. MethodsNasopharyngeal swabs were collected at 1, 4 and 9 months of age from PCV13-vaccinated infants (n = 57) and age-/season-matched, unvaccinated infants (at approximately 1 month, n = 53; 4 months, n = 57; 9 months, n = 52). Serotype-specific pneumococcal carriage density and antimicrobial resistance genes were identified by qPCR and microarray. ResultsPneumococci were present in 89% of swabs, with 60 different serotypes and four non-encapsulated variants detected. Multiple serotype carriage was common (47% of swabs). Vaccine type carriage prevalence was similar between PCV13-vaccinated and unvaccinated infants at 4 and 9 months of age. The prevalence of non-vaccine type carriage was also similar between cohorts, with non-vaccine types present in three-quarters of samples (from both vaccinated and unvaccinated infants) by 4 months of age. The median pneumococcal carriage density was high and similar at each age group (~7.0 log10genome equivalents/mL). PCV13 had no effect on overall pneumococcal carriage density, vaccine type density, non-vaccine type density, or the prevalence of antimicrobial resistance genes. ConclusionPNG infants experience dense and diverse pneumococcal colonisation with concurrent serotypes from 1 month of age. PCV13 had no impact on pneumococcal carriage density, even for vaccine serotypes. The low prevalence of vaccine serotypes, high pneumococcal carriage density and abundance of non-vaccine serotypes likely contribute to the lack of PCV13 impact on carriage in PNG infants. Indirect effects of the infant PCV programs are likely to be limited in PNG. Alternative vaccines with broader coverage should be considered.

Diversity of Dengue Virus Serotypes in Dhaka City: From 2017 to 2021

This is a retrospective observational study aimed to search the alteration of circulating dengue virus (DENV) serotypes in Dhaka City for five consecutive years (2017-2021) along with disease outcome.
 Methods: Routine dengue NS1 or PCR positive dengue samples from patients who visited Evercare Hospital Dhaka (ex. Apollo Hospitals Dhaka) were selected for serotype determination by serotype specific real time reverse transcriptase PCR (RT-PCR).
 Results: In 2017, predominant serotype was DENV-2 (91.3%) with less than 5% of DENV-1 and DENV-3 among 161 cases. In 2018, among127 cases, DENV-2 was the predominant serotype (40.95%) followed by DENV-3 (33.07%) and DENV-1 (25.98%). In 2019, predominance of DENV-2 was totally replaced by DENV-3 (91.86%) and DENV-1 (8.14%). In 2021, only DENV-3 serotype was detected among 178 samples. Regarding serotype association with disease outcome, more severe cases (Dengue Hemorrhagic Fever/Dengue Shock Syndrome) were observed from 2019 with notable shifting of serotype dominance to DENV-3 from DENV-2 in previous years. In our cohort, the prevailing age group was 1-20 years which is analogous with many studies in Asia.
 Conclusion: Dominance of DENV serotype shifted to DENV-3 in 2019 from prolonged persistence of DENV-2 and DENV-1. Continuous surveillance for circulating DENV serotype is needed for preparedness of potential outbreaks and occurrence of severe cases.
 Bangladesh J Med Microbiol 2021; 15 (2): 23-29

Siphoviridae phage PH669 capable of lysing some strains of O3 and O4 serotypes in Vibrio parahaemolyticus

Vibrio parahaemolyticus, especially serotypes O3 and O4, is a common foodbrone pathogen existing both in contaminate seafood and environment. The prevention and control of this pathogen are often limited to its geographic distribution and serotype diversity. Phage can be used as disinfectant and therapeutic agent from farm to fork. In this study, a phage named PH669 that can lyse V. parahaemolyticus was isolated from domestic sewage. The test of host range showed that PH669 has multiple serotypes lyse spectrum, including some O3 and O4 serotypes of V. parahaemolyticus strains as well as other serotypes. Biological characters revealed that PH669 has a wide range of temperature stability (from 4 °C to 50 °C) and pH stability (from 3 to 11), indicating it can be used in different environments. In addition, PH669 can effectively inhibit the growth of host bacteria starting from 30 min when the MOI (Optimal Multiplicity of Infection) is 1. PH669 is judged to belong to siphoviridae of bacteriophag based on its morphology. Genomic analysis showed that PH669 has a genome size of 58,644 bp, a G + C content of 46.3%, and 83 putative open reading frames (ORFs). Furthermore, no virulence or lysogen formation genes were predicted by the virulence factor database (VFDB) and Prophage Hunter in PH669 genome, respectively. The current results indicate that PH669 could be a potential agent both for phage therapy and disinfectant against pathogenic V. parahaemolyticus.