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Infectious bronchitis virus (IBV) strains of genotype GVIII have been emerging in Europe in the last decade, but no biological characterization has been reported so far. This paper reports the extensive genetic and biological characterization of IBV strain D2860 of genotype GVIII which was isolated from a Dutch layer flock that showed a drop in egg production. Whole genome sequencing showed that it has a high similarity (95%) to CK/DE/IB80/2016 (commonly known as IB80). Cross-neutralization tests with antigens and serotype-specific antisera of a panel of different non-GVIII genotypes consistently gave less than 2% antigenic cross-relationship with D2860. Five experiments using specified pathogen-free chickens of 0, 4, 29 and 63 weeks of age showed that D2860 was not able to cause clinical signs, drop in egg production, false layers or renal pathology. There was also a distinct lack of ciliostasis at both 5 and 8 days post-inoculation at any age, despite proof of infection by immunohistochemical (IHC) staining, RT–PCR and serology. IHC showed immunostaining between 5 and 8 days post inoculation in epithelial cells of sinuses and conchae, while only a few birds displayed immunostaining in the trachea. In vitro comparison of replication of D2860 and M41 in chicken embryo kidney cells at 37°C and at 41°C indicated that D2860 might have a degree of temperature sensitivity that might cause it to prefer the colder parts of the respiratory tract. [ABSTRACT FROM AUTHOR]

Salmonellosis represents a significant economic and public health concern for the poultry industry in Africa, leading to substantial economic losses due to mortality, reduced productivity, and food safety problems. However, comprehensive information on the burden of poultry salmonellosis at the continental level is scarce. To address this gap, a systematic review and meta-analysis were conducted to consolidate information on the prevalence and circulating serotypes of poultry salmonellosis in African countries. This involved the selection and review of 130 articles published between 1984 and 2021. A detailed systematic review protocol was structured according to Cochrane STROBE and PRISMA statement guideline. From the 130 selected articles from 23 different African countries, the overall pooled prevalence estimate (PPE) of poultry salmonellosis in Africa was found to be 14.4% (95% CI = 0.145–0.151). Cameroon reported the highest PPE at 71.9%. The PPE was notably high in meat and meat products at 23%. The number of research papers reporting poultry salmonellosis in Africa has shown a threefold increase from 1984 to 2021. Salmonella Enteritidis and Typhimurium were the two most prevalent serotypes reported in 18 African countries. Besides, Salmonella Kentucky, Virchow, Gallinarum, and Pullorum were also widely reported. Western Africa had the highest diversity of reported Salmonella serotypes (141), in contrast to southern Africa, which reported only 27 different serotypes. In conclusion, poultry salmonellosis is highly prevalent across Africa, with a variety of known serotypes circulating throughout the continent. Consequently, it is crucial to implement strategic plans for the prevention and control of Salmonella in Africa. RESEARCH HIGHLIGHTS The pooled sample prevalence of poultry salmonellosis in Africa is high (14.4%). The highest PPE was recorded in meat and meat products. Salmonella serotypes of zoonotic importance were found in all sample types. Salmonella Enteritidis and Typhimurium are common serotypes spreading in Africa. [ABSTRACT FROM AUTHOR]

Background: Adults living with human immunodeficiency virus (ALWHIV) receiving antiretroviral therapy (ART) exhibit higher pneumococcal carriage prevalence than adults without HIV (HIV-). To assess factors influencing high pneumococcal carriage in ALWHIV, we estimated pneumococcal carriage acquisition and clearance rates in a high transmission and disease-burdened setting at least 10 years after introducing infant PCV13 in routine immunisation. Methods: We collected longitudinal nasopharyngeal swabs from individuals aged 18–45 in Blantyre, Malawi. The study group included both HIV- individuals and those living with HIV, categorised based on ART duration as either exceeding 1 year (ART > 1y) or less than 3 months (ART < 3 m). Samples were collected at baseline and then weekly for 16 visits. To detect pneumococcal carriage, we used classical culture microbiology, and to determine pneumococcal serotypes, we used latex agglutination. We modelled trajectories of serotype colonisation using multi-state Markov models to capture pneumococcal carriage dynamics, adjusting for age, sex, number of under 5 year old (< 5y) children, social economic status (SES), and seasonality. Results: We enrolled 195 adults, 65 adults in each of the study groups. 51.8% were females, 25.6% lived with more than one child under 5 years old, and 41.6% lived in low socioeconomic areas. The median age was 33 years (IQR 25–37 years). The baseline pneumococcal carriage prevalence of all serotypes was 31.3%, with non-PCV13 serotypes (NVT) at 26.2% and PCV13 serotypes (VT) at 5.1%. In a multivariate longitudinal analysis, pneumococcal carriage acquisition was higher in females than males (hazard ratio [HR], NVT [1.53]; VT [1.96]). It was also higher in low than high SES (NVT [1.38]; VT [2.06]), in adults living with 2 + than 1 child < 5y (VT [1.78]), and in ALWHIV on ART > 1y than HIV- adults (NVT [1.43]). Moreover, ALWHIV on ART > 1y cleared pneumococci slower than HIV- adults ([0.65]). Residual VT 19F and 3 were highly acquired, although NVT remained dominant. Conclusions: The disproportionately high point prevalence of pneumococcal carriage in ALWHIV on ART > 1y is likely due to impaired nasopharyngeal clearance, which results in prolonged carriage. Our findings provide baseline estimates for comparing pneumococcal carriage dynamics after implementing new PCV strategies in ALWHIV. [ABSTRACT FROM AUTHOR]

Listeria monocytogenes is ubiquitous in nature and persistent in food‐processing facilities, farms, retail stores, and home and restaurant kitchens. Current research suggests ready‐to‐eat (RTE) products (including RTE hummus and fresh produce) to be of increasing interest and concern. These foods are typically stored at refrigeration temperatures suited to the survival of L. monocytogenes and are consumed without further processing. Since L. monocytogenes is ubiquitous in agricultural environments, the cultivation of fresh produce predisposes it to contamination. The contamination of RTE foods originates either from raw ingredients or, more commonly, from cross‐contamination within food‐processing facilities. Research on the food‐processing environment has been recommended to reduce the incidence of L. monocytogenes in foods. The consumption of contaminated foods by immunocompromised individuals causes invasive listeriosis, with a 20% to 30% fatality rate despite treatment. The emergence of antibiotic‐resistant strains has reduced the effectiveness of modern medicine and may increase morbidity and mortality. Without epidemiological surveillance and identifying trends in disease determinants, no action can be taken to improve food safety and mitigate the risk of such outbreaks. [ABSTRACT FROM AUTHOR]

Simple Summary: African swine fever is a deadly disease affecting pigs worldwide, causing major economic losses. The virus strain causing the current outbreak in Europe and Asia, known as genotype II, was first identified in Georgia in 2007. This study aimed to analyze the genetic makeup of a strain found in Thailand to better understand its characteristics and how it compares to other strains in Asia. The viral DNA from an infected pig was analyzed and was found to be almost identical to strains from Georgia and China. The Thai strain had eight unique genetic changes, including small mutations in specific genes and deletions in others. This detailed genetic analysis helps track the spread and evolution of the virus, providing important information for developing strategies to control future outbreaks. By understanding these genetic differences, improved measures to protect pig populations can be implemented, thereby reducing the economic impact on the agricultural industry. African swine fever virus (ASFV) has been responsible for the globally devastating epidemics in wild and domesticated pigs. Of the 24 identified ASFV genotypes, genotype II is the primary cause for the pandemic occurring in Europe and Asia since its emergence in Georgia in 2007. The current study aimed to characterize the full-length genomic pattern of the ASFV strain from Thailand, TH1_22/CR (Accession No. PP915735), which was then compared with genomic diversity across other Asian isolates using Georgia 2007/1 (Accession No. FR682468) as the reference. Viral DNA was isolated from the pig spleen sample following library preparation and paired-end sequencing using the MiSeq Illumina platform. The sequenced TH1_22/CR isolate spanned 189,395 nucleotides encoding 193 open reading frames (ORFs), exhibiting maximum nucleotide similarity (99.99%) with Georgian (Georgia 2007/1) and Chinese (Wuhan 2019-1 and China HLJ) isolates. Based on phylogenetic analysis, the TH1_22/CR isolate (Accession No. PP915735) was characterized as genotype II, serogroup 8, and IGR-II due to the presence of three tandem repeat sequences (TRSs). Genetic variations including SNPs and single and polynucleotide indels were identified in TH1_22/CR in agreement with other Asian isolates. For comprehensive analysis, the genome was divided into four regions (I–IV) based on gene location. Overall, the TH1_22/CR isolate demonstrated eight SNPs and indels in its genome. Two unique SNPs were reported in the coding regions of the TH1_22/CR isolate, out of which, a C-591-T substitution was seen in MGF 360-4L and a C-297-T was found in A238L, and four unique SNPs were reported in non-coding regions (NCRs). Furthermore, a 29 bp deletion was observed in the IGR between MGF 110-13La and MGF 110-13Lb, as well as 52 bp deletion in the ASFV G ACD 00350 gene. This comparative analysis establishes the foundational information for future studies on the diversity and phylogeography of this regionally significant genetic sub-group of ASFV. [ABSTRACT FROM AUTHOR]

Objectives Escherichia coli can cause infections in the urinary tract and in normally sterile body sites leading to invasive E. coli disease (IED), including bacteraemia and sepsis, with older populations at increased risk. We aimed to estimate the theoretical coverage rate by the ExPEC4V and 9V vaccine candidates. In addition, we aimed at better understanding the diversity of E. coli isolates, including their genetic and phenotypic antimicrobial resistance (AMR), sequence types (STs), O-serotypes and the bacterial population structure. Methods Blood and urine culture E. coli isolates (n  = 304) were collected from hospitalized patients ≥60 years (n = 238) with IED during a multicentric, observational study across three continents. All isolates were tested for antimicrobial susceptibility, O-serotyped, whole-genome sequenced and bioinformatically analysed. Results A large diversity of STs and of O-serotypes were identified across all centres, with O25b-ST131, O6-ST73 and O1-ST95 being the most prevalent types. A total of 45.4% and 64.7% of all isolates were found to have an O-serotype covered by the ExPEC4V and ExPEC9V vaccine candidates, respectively. The overall frequency of MDR was 37.4% and ST131 was predominant among MDR isolates. Low in-patient genetic variability was observed in cases where multiple isolates were collected from the same patient. Conclusions Our results highlight the predominance of MDR O25b-ST131 E. coli isolates across diverse geographic areas. These findings provide further baseline data on the theoretical coverage of novel vaccines targeting E. coli associated with IED in older adults and their associated AMR levels. [ABSTRACT FROM AUTHOR]

Background: This study conducted in the departments of Oueme and Plateau aims to assess the presence of the dengue virus and its different serotypes in Aedes aegypti and Aedes albopictus, as well as the epidemic risk incurred by the populations. Methods: Collections of adult mosquitoes using human landing catches (HLC) were carried out in six communes, three (Porto-Novo, Adjarra, and Avrankou) in the Oueme department and the rest (Ifangni, Kétou, and Pobè) in the Plateau department. Pools of ten Aedes mosquitoes were formed, and stored at −80°C in RNA later. RT-PCR was used to detect dengue virus, and conventional PCR for the different serotypes. Inspection of water containers and collection of Aedes larvae was performed inside and around each house to calculate the stegomyan indices. Results: In the six communes, the dengue virus was present both in Ae. aegypti and Ae. albopictus. Combined data of the two Aedes species at the communes level revealed infection rates ranging from 80.00% (95% CI: 61.43–92.29) to 96.67% (95% CI: 82.78–99.92). In all the communes, the values of stegomyan indices reached the WHO threshold, which indicates the existence of the risk of an arbovirus epidemic. In addition, the infection rates were similar for Ae. aegypti [88.19% (95% CI: 81.27–93.24)] and Ae. albopictus [86.79% (95% CI: 74.66–94.52)]. The three virus serotypes detected in the pools of Aedes were DENV-1, DENV-3, and DENV-4, with a high prevalence for the first two. Conclusion: This study revealed that three serotypes (DENV-1, DENV-3, and DENV-4) of dengue virus circulate in Ae. aegypti and Ae. albopictus in the departments of Oueme and Plateau. Moreover, the risk of transmission of arboviruses was globally high and variable from commune to commune. This information is essential for informed decision-making in the preventive control of the disease. [ABSTRACT FROM AUTHOR]

Respiratory syncytial virus (RSV) and rotavirus infections are long-standing infectious diseases that affect children worldwide. RSV and rotavirus were first discovered in clinical specimens in 1955 and 1973, respectively. From their discovery to the present day, significant progress has been made in understanding these two infections. The introduction of a simple and rapid antigen diagnostic test into clinical settings in the 1990s offered new insight into the clinical characteristics and epidemiology of these infections. Regarding therapeutics, symptomatic treatments have remained the mainstay; however, prophylactic humanized anti-RSV monoclonal antibodies have been developed and advances in structural biology may allow for more effective human anti-RSV monoclonal antibodies and novel RSV vaccines to be developed soon. For rotavirus, two vaccines have been licensed and broadly applied over the past 10 years, which have been successful clinically and have changed the epidemiology of rotavirus infections in Japan. [ABSTRACT FROM AUTHOR]

We determined the dengue virus (DENV) serotypes and genotypes in archived serum samples that were collected during the 2014–2016 and 2021 dengue outbreaks in Dire Dawa City and the Somali region in Ethiopia. DENV serotype 1 (DENV-1) was predominant followed by DENV serotype 2 (DENV-2). Thirteen of the DENV-1 strains were assigned to Genotype-I, while the remaining two were found to be Genotype-III. All three DENV-2 strains were assigned the Cosmopolitan Genotype. The DENV strains responsible for the outbreaks are genetically closely related to the DENV strains that circulated in neighboring and Asian countries. The findings also showed continued local transmission of a monophyletic lineage and a co-circulation of DENV-1 and DENV-2 during the outbreaks. There is a need to strengthen DENV genomic surveillance capacity for the early detection of circulating serotypes, and prevent devastating consequences of future outbreaks due to the co-circulation of different serotypes. [ABSTRACT FROM AUTHOR]

The escalating rates of gonorrhea globally are associated with higher numbers of disseminated gonococcal infection (DGI). Expression of the PorB1A allele of the major outer membrane porin protein, PorB, is associated with DGI. This meta-analysis shows that the odds of PorB1A strains to disseminate is 20.53 compared to PorB1B isolates. [ABSTRACT FROM AUTHOR]

In August 2023, we identified a case of dengue fever in Yantai City, which was imported from Xishuangbanna, China. To investigate its evolutionary history and population dynamics, we utilized the metatranscriptomic method to obtain the virus' whole genome sequence. Together with 367 selected dengue virus whole genome sequences from the NCBI database, we constructed a time-scaled Maximum Clade Credibility (MCC) tree. We found that our sequence exhibited a high homology with a sequence of DENV1 (OR418422.1) uploaded by the Guangzhou Center for Disease Control and Prevention in 2023, with an estimated divergence time around 2019 (95% HPD: 2017–2023), coinciding with the emergence of SARS-CoV-2. The DENV strain obtained in this study belongs to genotype I of DENV1. Its ancestors experienced a global epidemic around 2005 (95% HPD: 2002–2010), and its progeny strains have spread extensively in Southeast Asia and China since around 2007 (95% HPD: 2006–2011). The Bayesian skyline plot indicates that the current population of DENV1 has not been affected by SARS-CoV-2 and is expected to maintain stable transmission. Hence, it is imperative to track and monitor its epidemiological trends and genomic variations to prevent potential large-scale outbreaks in the post-SARS-CoV-2 era. [ABSTRACT FROM AUTHOR]

Introduction: Vibrio parahaemolyticus is a common pathogen that can cause seafood-borne gastroenteritis in humans. We determined the prevalence and characteristics of V. parahaemolyticus isolated from clinical specimens and oysters in Thailand. Methodology: Isolates of V. parahaemolyticus from clinical specimens (n = 77) and oysters (n = 224) were identified by biochemical testing, polymerase chain reaction (PCR) assays, and serotyping. The toxin genes, antimicrobial resistance, and β-lactamase production were determined. Results: A total of 301 isolates were confirmed as V. parahaemolyticus by PCR using specific primers for the toxR gene. The majority of clinical isolates carried the tdh+/trh− genotype (82.1%), and one of each isolate was tdh−/trh+ and tdh+/trh+ genotypes. One isolate from oyster contained the tdh gene and another had the trh gene. Twenty-six serotypes were characterized among these isolates, and O3:K6 was the most common (37.7%), followed by OUT:KUT, and O4:K9. In 2010, most clinical and oyster isolates were susceptible to antibiotics, with the exception of ampicillin. In 2012, clinical isolates were not susceptible to cephalothin (52.4%), streptomycin (95.2%), amikacin (66.6%), kanamycin (61.9%), and erythromycin (95.2%), significantly more frequently than in 2010. More than 95% of isolates that were not susceptible to ampicillin produced β-lactamase enzymes. Conclusions: We found toxin genes in two oyster isolates, and the clinical isolates that were initially determined to be resistant to several antibiotics. Toxin genes and antimicrobial susceptibility profiles of V. parahaemolyticus from seafood and environment should be continually monitored to determine the spread of toxin and antimicrobial resistance genes. [ABSTRACT FROM AUTHOR]

Streptococcus pneumoniae is the major cause of invasive pneumococcal disease. However, the global population structure remains largely unexplored. In this study, we investigated the spatial and temporal patterns of genetic variation of S. pneumoniae based on archived multilocus sequence typing data from PubMLST.org. Our analyses demonstrated both shared and unique distributions of sequence types (STs) and allele types among regional populations. Among the 17 915 global STs, 36 representing 15 263 isolates were broadly shared among all six continents, consistent with recent clonal dispersal and expansion of this pathogen. The analysis of molecular variance revealed that >96% genetic variations were found within individual regional populations. However, though low (<4%), statistically significant genetic differentiation among regional populations was observed. Comparisons between non-clone-corrected and clone-corrected datasets showed that localized clonal expansion contributed significantly to the observed genetic differentiations among regions. Temporal analyses of the isolates showed that implementation of pneumococcal conjugate vaccine impacted the distributions of STs, but the effect on population structure was relatively limited. Linkage disequilibrium analyses identified evidence for recombination in all continental populations; however, the inferred recombination was not random. We discussed the limitations and implications of our analyses to the global epidemiology and future vaccine developments for S. pneumoniae. [ABSTRACT FROM AUTHOR]

Introduction of pneumococcal conjugate vaccines (PCVs) reduced the number of cases of pneumococcal disease (PD). However, there is an increase in clinical and economic burden of PD from serotypes that are not part of the existing pneumococcal vaccines, particularly impacting pediatric and elder population. In addition, the regions where the PCV is not available, the disease burden remains high. In this study, immunogenicity and safety of the BE's 14-valent PCV (PNEUBEVAX 14™; BE-PCV-14) containing two additional epidemiologically important serotypes (22F and 33F) was evaluated in infants in comparison to licensed vaccine, Prevenar-13 (PCV-13). This is a pivotal phase-3 single blind randomized active-controlled study conducted at 12 sites across India in 6–8 weeks old healthy infants at 6–10–14 weeks dosing schedule to assess immunogenic non-inferiority and safety of a candidate BE-PCV-14. In total, 1290 infants were equally randomized to receive either BE-PCV-14 or PCV-13. Solicited local reactions and systemic events, adverse events (AEs), serious AEs (SAEs), and medically attended AEs (MAAEs) were recorded. Immunogenicity was assessed by measuring anti-PnCPS (anti-pneumococcal capsular polysaccharide) IgG concentration and functional antibody titers through opsonophagocytic activity (OPA), one month after completing three dose schedule. Cross protection to serotype 6A offered by serotype 6B was also assessed in this study. The safety profile of BE-PCV-14 was comparable to PCV-13 vaccine. Majority of reported AEs were mild in nature. No severe or serious AEs were reported in both the treatment groups. For the twelve common serotypes and for the additional serotypes (22F and 33F) in BE-PCV-14, NI criteria was demonstrated as defined by WHO TRS-977. Primary immunogenicity endpoint was met in terms of IgG immune responses for all 14 serotypesof BE-PCV-14. Moreover, a significant proportion of subjects (69%) seroconverted against serotype 6A, even though this antigen was not present in BE-PCV-14. This indicates that serotype 6B of BE-PCV-14 cross protects serotype 6A. BE-PCV-14 also elicited comparable serotype specific functional OPA immune responses to all the serotypes common to PCV-13. BE-PCV-14 was found to be safe and induced robust and functional serotype specific immune responses to all 14 serotypes. It also elicited cross protective immune response against serotype 6B.These findings suggest that BE-PCV-14 can be safely administered to infants and achieve protection against pneumococcal disease caused by serotypes covered in the vaccine. The study was prospectively registered with clinical trial registry of India – CTRI/2020/02/023129. [ABSTRACT FROM AUTHOR]

Non-vaccine serotype (NVT) pneumococcal pneumonia in Japan has increased with the spread of pneumococcal vaccinations. However, there is no data regarding the clinical background and antimicrobial susceptibility of NVT isolates compared with those of vaccine serotype (VT) isolates in adult pneumococcal pneumonia. The serotypes and antimicrobial susceptibilities of pneumococcal isolates obtained from patients with pneumonia at the University of Occupational and Environmental Health, Japan, from January 2011 to December 2020 were retrospectively evaluated along with the patients' clinical information. In total, 252 patients with pneumococcal pneumonia (98 NVT and 154 VT isolates) were included. Among NVTs, the most common serotype was 35B, followed by 15A, 34, 6C, 23A, and 15C. The MIC 50 and MIC 90 of each antibiotic in 35B and 15A tend to be higher than those in 34, 6C, and 23A. Regarding background characteristics, the percentages of patients with dementia and liver disease were significantly higher in patients in the VT group than in those in the NVT group (p = 0.048 and p = 0.012, respectively). There were no significant differences in the severity of pneumonia and mortality rate between patients with the VT and NVT isolates. This study first demonstrated that NVT isolates included those with reduced susceptibility to antibiotics in adult pneumonia in Japan. The data of the present study can be useful in optimizing treatment strategies for pneumococcal pneumonia because of the increasing number of NVT cases in Japan. [ABSTRACT FROM AUTHOR]

In the study, rectal swabs taken from 300 ruminant animals including cattle (100), sheep (100), and goats (100) were inoculated into Mac Conkey Agar and incubated for 18 h at 37°C. Escherichia coli isolates were confirmed by biochemical tests and the BBL Crystal rapid diagnosis system. O26, O45, O103, O111, O121, O145, and O157 serotypes by PCR test following DNA isolation; ETEC (elt, Stla); EPEC (eaeA,bfpA); STEC (stx1, stx2, eaeA); EHEC (EhlyA); EAEC (CVD432) tested for virulence and/or toxigenic genes. As a result of the isolation studies, 50 E. coli from cattle feces, 92 from sheep feces, and 80 from goat feces were isolated and identified. Apart from the first 5 serotypes frequently seen in studies (O157, O26, O103, O111, and O145), higher rates were found in serogroups such as O45 and O121, and subtypes such as STECs (stx1 and stx2), EPEC (eaeA and bfpA) and EAEC (CVD432) types compared to other studies. The EAEC (CVD432) subtype was found to be very high in this study. It has been determined that serotypes and subtypes detected at high rates in cattle, sheep, and goat feces in our region may cause an increase in the incidence of some critical food-borne infections in humans. Within the framework of the concept of one health, taking the necessary precautions is important for public health. [ABSTRACT FROM AUTHOR]

Dengue virus is a flavivirus transmitted by the mosquitoes, Aedes aegypti and Aedes albopictus. Dengue infection by all four serotypes (DEN 1 to 4) is endemic globally in regions with tropical and subtropical climates, with an estimated 100–400 million infections annually. Among those hospitalized, the mortality is about 1%. Neurological involvement has been reported to be about 5%. The spectrum of neurological manifestations spans both the peripheral and central nervous systems. These manifestations could possibly be categorized into those directly related to dengue infection, i.e. acute and chronic encephalitis, indirect complications leading to dengue encephalopathy, and post-infectious syndrome due to immune-mediated reactions, and manifestations with uncertain mechanisms, such as acute transverse myelitis, acute cerebellitis and myositis. The rising trend in global dengue incidence calls for attention to a more explicit definition of each neurological manifestation for more accurate epidemiological data. The actual global burden of dengue infection with neurological manifestation is essential for future planning and execution of strategies, especially in the development of effective antivirals and vaccines against the dengue virus. In this article, we discuss the recent findings of different spectrums of neurological manifestations in dengue infection and provide an update on antiviral and vaccine development and their challenges. [ABSTRACT FROM AUTHOR]

Objective To understand the distribution, serotype, and drug resistance of Salmonella in domestic sewage in Jining city, and to analyze the whole genome sequencing so as to provide scientific basis for the prevention and control of Salmonella. Methods From February to March in 2023, two samples of sewage from the intake of 3 urban sewage plants with 500 ml each were collected continuously for 7 weeks. A total of 42 sewage samples were collected for culture, isolation, and identification of Salmonella. The isolated Salmonella was tested for serum agglutination test and fluorescent quantitative PCR serotyping. In total 41 strains of Salmonella were tested for minimum inhibitory concentration (MIC) of 17 drugs in 9 classes by microbroth dilution method, followed by genome sequencing and phylogenetic analysis. Results The isolation rate of Salmonella from domestic sewage in Jining city was high. Among 24 positive samples, 41 strains of Salmonella were isolated, belonging to 9 serotypes, mainly S.Agona and S.Kentucky. Liying and Jidong sewage treatment plants had their own unique serotypes. Only one strain of S.Give was not resistant, and the other 40 strains of Salmonella were multi-drug resistant. The resistance rates to sulfamethoxazole, tetracycline, ampicillin, and streptomycin were more than 90%, and the resistance rate to ampicillin/sulbactam was more than 80%. There were 19 kinds of drug resistance spectra, of which SXT-TET-STR-AMP-AMS ranked the first place. The resistance spectra of different serotypes of Salmonella were different. S.Kentucky, S.Gold Coast, and S.Infant were multi-drug resistant seriously. The resistance spectrum of the same serotype was also inconsistent in different sewage plants, and the resistance was the most serious in Liying sewage plant. The CARD database was used to prediet drug resistance genes, mainly predicting 18 drug resistance genes in 8 types of drug resistance families, and the drug resistance phenotypes and drug resistance genes were almost all consistent. The ST types of different serotypes of Salmonella were different, and ST13 S.Agona was dominant. The phylogenetic tree was divided into 6 clusters, and strains in different sewage plants were in different branches, indicating that their genomes were different and had different sources. Conclusion There are various serotypes of salmonella in domestic sewage in Jining city, suggesting that they might have exist and spread in the population. Almost all strains are multi-drug resistant bacteria, carrying resistance genes extensively. Some types of strains live persistently and distribute across regions, leading to the potential risk to population. It is necessary to carry out continuous monitor, and scientific prevention and control measures need to be formulated to control the epidemic of salmonella and the aggravation of drug resistance. [ABSTRACT FROM AUTHOR]

Background and Aim: Foot-and-mouth disease (FMD) is an infectious disease of cloven-hoofed animals, including buffalo, cattle, sheep, goats, and pigs, causing major economic losses to the local farmers and, overall, to the national economy of the country. This study aimed to detect FMDV serotypes in year-round FMD outbreaks, hematological and biochemical changes, and oxidative stress in FMDV-infected cattle and buffaloes in the district of Quetta, Balochistan, Pakistan, and the socioeconomic impact of FMD outbreaks on farmers. Materials and Methods: We conducted a cross-sectional study in the district of Quetta, Balochistan, Pakistan, where FMD virus (FMDV) serotypes were detected by enzyme-linked immunosorbent assay (ELISA). Hematological, biochemical, and oxidative analyses were performed by analyzing the blood of FMDV-infected and non-infected animals. Information on the associated risk factors was obtained through a structured questionnaire by interviewing farmers in each FMD-affected farm. Results: Thirty-four out of 38 farms (89%, 95% confidence interval [CI]: 75%-97%) were positive for FMD by ELISA. Higher FMD infection was detected in farms with a herd size of <50 animals (50%, 17/34), followed by >100 animals (32%, 11/34) and 51-100 animals (18%, 6/34). Fifty-seven percent (114/200, 95% CI: 50%-64%) of animals were positive for FMD. Of these, 61% (69/114) were cattle and 39% (45/114) were buffalo. FMD positivity was higher in females (86%, 98/114) than in males (14%, 16/114) and higher in animals older than 2 years of age (52%, 59/114). On average, farmers lose U.S. dollars 3000 annually due to FMD outbreaks. Animals infected with FMDV had significantly (p ≤ 0.05) white blood cell counts and significantly (p ≤ 0.05) lower hemoglobin and total protein concentrations in buffalo and cattle, whereas infected cattle showed significantly (p ≤ 0.05) lower albumin levels. Globulin levels were lower in buffaloes infected. Alanine aminotransferase levels were lower in infected cattle (p ≤ 0.05). Creatinine levels were higher in infected buffalo (p ≤ 0.05). Urea and phosphorus concentrations were higher in FMDV-infected cattle and buffalo (p ≤ 0.05). Calcium levels were lower in infected cattle and buffalo (p ≤ 0.05). Catalase enzyme activity in infected cattle and buffaloes was significantly lower (p < 0.05). Lipid peroxidation was significantly higher in FMDV-infected cattle and buffalo (p ≤ 0.05). Conclusion: This study confirmed serotype O circulation among cattle and buffalo in year-long FMD outbreaks in the Quetta District of Balochistan. Blood analysis identified a parameter deviated from the normal level due to FMDV infection. In addition, the outbreak of FMD has a significant negative economic impact on livestock farmers. [ABSTRACT FROM AUTHOR]

Objective(s): Pneumococcal cell wall (PCW) is an inflammatory component in Streptococcus pneumoniae. The cell surface proteins and the toll-like receptors (TLR) signaling response were investigated in the human lung epithelial (A549) cells inoculated with PCW of different serotypes. Materials and Methods: The presence of genes encoding these proteins was determined using polymerase chain reaction (PCR). The structure of the cell walls was analyzed by proton nuclear magnetic resonance (1H NMR). The A549 cell line was challenged with PCW extracts of different serotypes. RNA from the infected host cells was extracted and tested against a total of 84 genes associated with TLR signaling pathways (TLR 1-6 and 10) using RT2 Profiler PCR Array. Results: Cell surface proteins; ply, lytA, nanA, nanB, and cbpD genes were present in all serotypes. The distribution and structure of surface protein genes suggest behavioral changes in the molecules, contributing to the resilience of the strains to antibiotic treatment. Conclusion: TLR2 showed the highest expression, while serotypes 1, 3, and 5 induced higher TNFα and IL-1α, suggesting to be more immunogenic than the other strains tested. [ABSTRACT FROM AUTHOR]

Background Streptococcus suis is an important pig pathogen and an emerging zoonotic agent. In a previous study, we described a high proportion of penicillin-resistant serotype 9 S. suis (SS9) isolates on pig farms in Italy. Objectives We hypothesized that resistance to penicillin emerged in some SS9 lineages characterized by substitutions at the PBPs, contributing to the successful spread of these lineages in the last 20 years. Methods Sixty-six SS9 isolates from cases of streptococcosis in pigs were investigated for susceptibility to penicillin, ceftiofur and ampicillin. The isolates were characterized for ST, virulence profile, and antimicrobial resistance genes through WGS. Multiple linear regression models were employed to investigate the associations between STs, year of isolation, substitutions at the PBPs and an increase in MIC values to β-lactams. Results MIC values to penicillin increased by 4% each year in the study period. Higher MIC values for penicillin were also positively associated with ST123, ST1540 and ST1953 compared with ST16. The PBP sequences presented a mosaic organization of blocks. Within the same ST, substitutions at the PBPs were generally more frequent in recent isolates. Resistance to penicillin was driven by substitutions at PBP2b, including K479T, D512E and K513E, and PBP2x, including T551S, while reduced susceptibility to ceftiofur and ampicillin were largely dependent on substitutions at PBP2x. Conclusions Here, we identify the STs and substitutions at the PBPs responsible for increased resistance of SS9 to penicillin on Italian pig farms. Our data highlight the need for monitoring the evolution of S. suis in the coming years. [ABSTRACT FROM AUTHOR]

In the lack of updated Tunisian epidemiological data, we sought to describe the epidemiology of Group B Streptococcus (GBS) in pregnant women and newborns. A retrospective analysis of GBS neonatal invasive infections and a cross-sectional study evaluating the prevalence of maternal GBS colonization were conducted. GBS isolates were tested for antimicrobial susceptibility, serotyped, and assessed for the appurtenance to the hypervirulent ST17 clone. Of 98 neonates with GBS, early-onset GBS disease (EOD) comprised 83.7 and 16.3% were late-onset GBS disease (LOD). The prevalence of maternal GBS colonization was 27%. All GBS isolates were susceptible to penicillin. Serotype III predominated (42.6%) for neonatal invasive infections. GBS isolates belonging to the ST17 sequence type were found only as serotype III. This study documents the frequency of GBS EOD, the high rate of maternal GBS colonization, and the predominance of the hypervirulent clone type III/ST17 in infants. [ABSTRACT FROM AUTHOR]

Background: There is only limited information on the clinical presentation, medical management, and outcomes of hospitalized sheep diagnosed with bluetongue virus (BTV) disease. Objectives: To describe the signalment, history, clinical signs, clinicopathological findings, medical management, and clinical outcomes of sheep diagnosed with BTV disease. Animals: Thirty‐five hospitalized sheep with BTV disease. Methods: Retrospective case series. Medical records from 1989 to 2021 were evaluated. History, signalment, clinical signs, laboratory test results, treatments, and outcomes were recorded. Results: BTV disease was diagnosed from July to December, with a peak proportion (43%; 15/35) of diagnoses recorded in October. Pyrexia and anorexia, respiratory disease, vasculitis, coronitis and lameness, and ulcerative mucosal lesions were present in 71%, 71%, 66%, 49%, and 22% of sheep, respectively. BTV serotypes 10, 11, 13, and 17 were identified, with serotype 17 (75%) being the most frequent. Management of cases included administration of antimicrobials (89%), anti‐inflammatories (77%), IV fluids (60%), vitamins (20%), proton‐pump inhibitors (14%), diuretics (9%), and antioxidants (9%). Six ewes were pregnant on presentation, but none aborted. Six (17%) sheep died or were euthanized because of clinical deterioration, whereas 83% were discharged. Conclusions and Clinical Importance: The proportion of sheep that survived BTV disease after treatment was relatively high. Serotyping of BTV is recommended because of the mismatch between frequently identified serotypes and the serotype present in the vaccine. [ABSTRACT FROM AUTHOR]

Salmonella is a major cause of food poisoning, and its infection and antimicrobial resistance vary regionally due to different sanitary standards and the use of antimicrobials. The aim of this study is to evaluate the microbiological contamination and antimicrobial resistance of Salmonella in Shanghai, providing references for supervision over food safety and clinical treatment. This study analysed the distribution of serotypes, the distribution of antimicrobial resistance in different poultry meats and serotype of Salmonella, the correlation between different antimicrobial resistance, and multiple drug resistance (MDR) of 139 strains of Salmonella from poultry meats. The results showed that the proportion of Salmonella detected in pigeons was high, which could cause severe diseases to humans. The most common resistance was observed to TET (about 60%), and resistance was even found to IPM. Resistance to two or more antimicrobials was accounted for 75.5%, indicating a wide spreading MDR. [ABSTRACT FROM AUTHOR]

Foot-and-mouth disease (FMD) is a contagious disease affecting cloven-hoofed animals, which has been well-documented as one of the major animal diseases that causes severe economic loss in livestock sectors. The disease is endemic in many countries, particularly in Asia and Africa. Indonesia has been declared a disease-free country since 1986, and the World Organization of Animal Health (WOAH/OIE) recognized Indonesia as an FMD-free country without vaccination in 1990. However, the FMD virus was detected in many disease outbreaks in cattle and goats in Indonesia in May 2022. This study reports the detection and identification of FMD serotype O viruses in Indonesia. Although these viruses appeared to belong to the ME-SA/Ind-2001e lineage, they formed a unique cluster with 95.3% average nucleotide sequence similarity of the FMD VP1 gene to Ind-2001e viruses from other Asia countries. The illegal trade of live animals from endemic areas in Southeast Asia is one of the possible routes regarding the incursion of FMD in Indonesia, however, it requires further investigation. [ABSTRACT FROM AUTHOR]

Bacterial coldwater disease (BCWD), caused by Flavobacterium psychrophilum, results in significant losses among multiple salmonid (family Salmonidae) species. Molecular epidemiology and serotyping studies have suggested that some variants are host specific; however, these associations have not been evaluated by cross‐challenging fish species with putatively host‐associated F. psychrophilum isolates via more natural (i.e. immersion) exposure routes. To this end, F. psychrophilum isolates US19‐COS, US62‐ATS and US87‐RBT, each originally recovered from diseased coho salmon (Oncorhynchus kisutch), Atlantic salmon (Salmo salar) or rainbow trout (O. mykiss), and belonging to a host‐associated multilocus sequence typing clonal complex (e.g. CC‐ST9, CC‐ST232 or CC‐ST10), were PCR‐serotyped, evaluated for proteolytic activity, and used to challenge adipose fin‐clipped 4‐month old Atlantic salmon, coho salmon and rainbow trout via immersion. Findings showed US87‐RBT caused disease and mortality only in rainbow trout (e.g. 56.7% survival probability). US19‐COS and US62‐ATS caused more mortality in coho salmon and Atlantic salmon but also caused disease in both other host species, albeit to a lesser extent. Observed survival differences may be due to variant antigenic/virulence determinants as differences in serotype and proteolytic activity were discovered. Collectively, results highlight the intricacies of F. psychrophilum‐host interactions and provide further in vivo evidence that some F. psychrophilum MLST variants are host specific, which may have implications for the development of BCWD prevention and control strategies. [ABSTRACT FROM AUTHOR]

Lactococcosis, caused by Lactococcus garvieae, is an acute hemorrhagic septicemia in fish recorded in marine and freshwater aquaculture during the summer months. In 2020–2021, several sea cage Pompano farms recorded sudden fish mortality events. Based on the results of phenotypic and biochemical tests, L. garvieae was predicted to be the cause. PCR with L. garvieae specific primers (pLG1 and pLG2) targeting the 16S rRNA region further confirmed the etiological agent as L. garvieae after amplifying an 1100 base pairs (bp) product. Furthermore, the 16S rRNA sequences of the two representative strains (AOD109‐196‐2B and AOD110‐215‐2B) shared 99.81% identity with L. garvieae (GenBank accession number: MT597707.1). The genetic profiles of the strains were classified using pulsed‐field gel electrophoresis after digestion with SmaI and ApaI, which clustered our strains under the same pulsotype. Multiplex PCR targeting the capsule gene cluster and serotype‐specific PCR collectively showed that the strains were non‐capsulated; thus, they belonged to serotype I. An experimental infection was designed to fulfil Koch's postulates by infecting healthy Pompano with case‐driven L. garvieae strains (AOD109‐196‐2B and AOD110‐215‐2B) with a cumulative mortality of 70%. Overall, L. garvieae infection in Pompano emphasizes the need for better monitoring and control procedures in aquaculture settings. [ABSTRACT FROM AUTHOR]

Objective To investigate the serotype distribution and antimicrobial resistance of invasive Streptococcus pneumoniae isolated from children in Suzhou. Methods The invasive Streptococcus pneumoniae isolates were systematically collected from Children’s Hospital of Soochow University between 2010 to 2020. The susceptibility of antibiotics was detected with Kirby-Bauer disk diffusion and E-test method， and the isolates were serotyped by Quellung reactions. Results A total of 215 invasive pneumococci isolates were collected during the study period，28.4% of which were from children with meningitis. The non-susceptibility rate to penicillin G was 35.9%. The coverage of the 13-valent pneumococcal conjugate vaccine （PCV13） was 93.2%， and the common serotypes were 6B，14，19F， 19A and 23F. In recent years， the non-susceptibility rate of Cefotaxime and Trimethoprimsulphamethoxazole has decreased， and the proportion of serotypes 6B and 14 has decreased significantly， while the proportion of serotypes 19F and 23F has increased significantly. Conclusion The coverage of PCV13 vaccine serotypes was high among the invasive isolates Streptococcus pneumoniae isolated from children in Suzhou， and the invasive pneumococci were moderately sensitive to penicillin. There were differences in serotypes and antimicrobial resistance between different times and different sources of disease. [ABSTRACT FROM AUTHOR]

Introduction: In the year 2022, a Dengue virus outbreak occurred nationwide in Bangladesh, including Chattogram, a port city. The purpose of this study was to identify and document the serotypes of Dengue virus and to measure the viral load of the virus positive specimens. Methods: This observational study was conducted in a tertiary care hospital of Chattogram during a period of six months from June through December, 2022. A total of 74 patients with symptoms suggestive of Dengue Fever(DF) and NS1 or IgM/IgG positive dengue patients were recruited into the study. From them clinicopathological data was collected on a case record form(CRF). Ten ml of venous whole blood was drawn in EDTA tubes then centrifuged and was sent to the laboratory at SlieaGen L.L.C in Austin, Texas, USA, for Dengue serotyping and viral load analysis by qPCR-LDT method. A total of 73 specimens were analyzed, one specimen was excluded. Ethical clearance was obtained from the hospital ethical review board, written informed consents were also taken from all subjects. Serotyping and qPCR testing data was shared by SlieaGen LLC once analysis was completed. Results: Amongst the 74 patients most were male 57(77%) and most [20(40.5%)] patients were young at 21-30 years. All had history of fever(100%), followed by body aches 67(90.5%), headache 49(66.2%) and weakness 55(74.3%). Positive NS1, IgM Dengue Ab and IgG Dengue Ab were found in 68(91.9%), 8(10.8%) and 3(4.1%) cases respectively. Frequency of serotype distributions revealed DENV 1 and DENV 3 were the most common serotypes 25(33.8%) and 16(21.6%) respectively also DENV 2 was 3(4.1%) and DENV 4 was 1(1.4%). Among 27 virus positive cases single infection DENV 1 was found in 10(13.51%) samples, DENV 3 and DENV 4 found in 1(1.4%) samples each, doubly infected (DENV 1 + DENV 2) was found in 12(16.2%) samples, triple infected (DENV 1 + DENV 2 + DENV 3) was found in 3(4.1%) samples. No virus was detected in 46(62.16%) samples. Viral load (Mean ± SD) found in DENV 1(890974.48 ± 4156206)cp/ml, DENV 2 (33423.00 ± 9088.35)cp/ml, DENV 3(23991.12 ± 51250.18)cp/ml and DENV 4 (822.00cp/ml) in virus detected samples. Conclusions: All four serotypes were found in the 2022 Dengue outbreak in Chittagong and DENV 1 and DENV 3 were common serotype. Simultaneous double and triple serotype infection in the same patients may be related with different unusual clinical features which need further documentations in future. [ABSTRACT FROM AUTHOR]

Flavobacterium psychrophilum is a pathogenic bacterium affecting Chilean salmonid farms. High antigenic and genetic diversity exists among Chilean F. psychrophilum isolates, but the distribution thereof among farms is poorly understood. These epidemiological data are key for developing isolate‐specific vaccines. The present study isolated F. psychrophilum in diseased Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss) from five freshwater farms between 2018 and 2019. Each farm only raised one salmonid species and was geographically separated from and did not share culturing water with the other farms. Antigenic and genetic analyses were conducted to shed light on the possibility of isolates coexisting within the same farm during outbreaks. A total of 68 Chilean F. psychrophilum isolates were recovered from skin lesions, gills, fins, kidney and spleen of moribund and live fish. Among the 68 Chilean isolates, mPCR‐serotyping indicated three major serotypes (i.e. 23.5% type 0; 47.1% type 2; and 26.5% type 4) and, to a lesser degree, serotype 1 (2.9%). Sixteen antigenic groups were detected by slide agglutination. Genetic characterizations by 16S rRNA alleles identified 71% of the isolates as the virulent genogroup CSF259‐93 allele. A predominant serotype was associated with each farm, with types 0 and 4 related to Atlantic salmon and types 1 and 2 to rainbow trout. Notwithstanding, several antigenic groups coexisted within some farms. Likewise, the experimental intramuscular challenges (n = 20) demonstrated that the type‐2 isolates from rainbow trout were the most pathogenic among isolates recovered from infectious outbreaks in Atlantic salmon, especially as compared to those from types‐0 and ‐4. These results allow us to suggest that prevention measures, specifically vaccines, should be developed according to dominant isolates and with specificity to each farm, that is the use of autogenous or site‐specific vaccines. [ABSTRACT FROM AUTHOR]

Fowl adenovirus (FAdV) is reported to pose a severe risk to the poultry industry, affecting food and nutrient security nationally and globally. FAdV is identified as the primary pathogen for inclusion body hepatitis (IBH) disease in avians during outbreaks in farms. Numerous interventions have been employed to reduce the chicken’s mortality rate in future outbreaks, such as local autogenous vaccine production that has yet to be successfully commercialised. Fibre and hexon protein are two out of the three major components of the adenoviral capsid, identified to contribute towards FAdV virulence. Hence, this study aims to determine the fibre and hexon gene molecular changes of a local isolate, FAdV UPMT1901, in Malaysia’s recent IBH outbreak and identify the evolutionary relationship with known FAdV strains. Propagation of FAdV UPMT1901 was performed in specific pathogen-free embryonated chicken prior to genomic extraction. The genes were amplified, and the retrieved nucleotide sequences were aligned with the published FAdV sequences. The phylogenetic tree analysis showed that UPMT1901 partial fibre and hexon genes are 99% similar to other known FAdV serotype 8b (FAdV-8b) species, especially the published Malaysian FAdV-8b isolates. Interestingly, the amino acid residue analysis further supported consistent residues amongst Malaysian isolates at fibre positions T176A, Q195H, D213E, S243T, A258V, F335Y, and F353V and hexon position T422M. These findings elucidate the structural proteins’ functional capacity and molecular diversity, specifically amongst Malaysian FAdV isolates and FAdV-8b, while contributing to global initiatives to establish biosecurity, such as a vaccine or antiviral production against future outbreaks. [ABSTRACT FROM AUTHOR]

All four serotypes of the dengue virus (DENV1–4) cause a phenotypically similar illness, but serial infections from different serotypes increase the risk of severe disease. Thus, genomic surveillance of circulating viruses is important to detect serotype switches that precede community outbreaks of disproportionate magnitude. A phylogenetic analysis was conducted on near full length DENV genomes sequenced from serum collected from a prospective cohort study from the Colombo district, Sri Lanka during a 28-month period using Oxford nanopore technology, and the consensus sequences were analyzed using maximum likelihood and Bayesian evolutionary analysis. From 523 patients, 328 DENV sequences were successfully generated (DENV1: 43, DENV2: 219, DENV3:66). Most circulating sequences originated from a common ancestor that was estimated to have existed from around 2010 for DENV2 and around 2015/2016 for DENV1 and DENV3. Four distinct outbreaks coinciding with monsoon rain seasons were identified during the observation period mostly driven by DENV2 cosmopolitan genotype, except for a large outbreak in 2019 contributed by DENV3 genotype I. This serotype switch did not result in a more clinically severe illness. Phylogeographic analyses showed that all outbreaks started within Colombo city and then spread to the rest of the district. In 2019, DENV3 genotype I, previously, rarely reported in Sri Lanka, is likely to have contributed to a disease outbreak. However, this did not result in more severe disease in those infected, probably due to pre-existing DENV3 immunity in the community. Targeted vector control within Colombo city before anticipated seasonal outbreaks may help to limit the geographic spread of outbreaks. [ABSTRACT FROM AUTHOR]

In this study, we aimed to clarify the risk factors associated with unfavorable outcomes in adults with pneumococcal meningitis (PnM). Surveillance was conducted between 2006 and 2016. Adults with PnM (n = 268) were followed up for outcomes within 28 days after admission using the Glasgow Outcome Scale (GOS). After classifying the patients into the unfavorable (GOS1–4) and favorable (GOS5) outcome groups, i) the underlying diseases, ii) biomarkers at admission, and iii) serotype, genotype, and antimicrobial susceptibility for all isolates were compared between both groups. Overall, 58.6% of patients with PnM survived,15.3% died, and 26.1% had sequelae. The number of living days in the GOS1 group was highly heterogeneous. Motor dysfunction, disturbance of consciousness, and hearing loss were the commonest sequelae. Of the underlying diseases identified in 68.9% of the PnM patients, liver and kidney diseases were significantly associated with unfavorable outcomes. Of the biomarkers, creatinine and blood urea nitrogen, followed by platelet and C-reactive protein had the most significant associations with unfavorable outcomes. There was a significant difference in the high protein concentrations in the cerebrospinal fluid between the groups. Serotypes 23F, 6C, 4, 23A, 22F, 10A, and 12F were associated with unfavorable outcomes. These serotypes were not penicillin-resistant isolates possessing three abnormal pbp genes (pbp1a , 2x , and 2b), except for 23F. The expected coverage rate of the pneumococcal conjugate vaccine (PCV) was 50.7% for PCV15 and 72.4% for PCV20. In the introduction of PCV for adults, the risk factors for underlying diseases should be prioritized over age, and serotypes with unfavorable outcomes should be considered. [ABSTRACT FROM AUTHOR]

Objectives: Chlamydia trachomatis infects the urogenital tract and eyes. Anatomical tropism is correlated with serovars which are characterized according to the variation in the major outer membrane proteins encoded by the ompA gene. The aim of the present study was to determine the distribution of C. trachomatis serovars among patients with follicular conjunctivitis in Iran. Materials and Methods: A total of 68 conjunctival specimens from symptomatic adults were studied for the presence of C. trachomatis using polymerase chain reaction (PCR) analysis. Serovars were determined by Omp1 PCR-RFLP analysis. Results: C. trachomatis was detected in 38 (55.9%) of patients with follicular conjunctivitis, with higher C. trachomatis prevalence in the younger age groups. Twenty-six (38.2%) of these patients had a history of urinary tract infection. Four distinct serovars were identified in the conjunctiva samples using molecular genotyping. The most prevalent was serovar E, followed by G, I, and F. Conclusion: Our serovar distribution indicated that chlamydial follicular conjunctivitis usually has a genital source. Genital serovars may cause eye diseases, especially in sexually active adults. On the other hand, conjunctivitis might be the only sign of sexually transmitted infection. Therefore, genotyping C. trachomatis in ocular and genital specimens could be beneficial for acquiring more detailed epidemiological information about the etiology of the disease and monitoring treatment success. [ABSTRACT FROM AUTHOR]

Foot and mouth disease is endemic in nearly all countries of Africa. The highest prevalence of FMD was detected in Mauritius and Comoros while the lowest prevalence was reported in Mozambique, Namibia, Angola, Malawi, South Africa, Mauritania, Botswana, and Uganda. Serotype A was circulated in 11 African countries. The results showed that serotype A was more prevalent in the northern and eastern parts of Africa than in the southern and western parts. The highest prevalence of serotype A was found in Algeria, Egypt, and Tunisia, while the lowest prevalence was observed in Uganda. Co-circulation of serotype A with other serotypes has been observed in some countries, such as Egypt, Algeria, Tunisia, Libya, Sudan, Zambia, Democratic Republic of the Congo, Eritrea, Ethiopia, and Kenya. This is likely due to the illegal movement of livestock between these countries. Serotype O was the most predominant serotype in Africa. The results found that serotype O was more prevalent in the northern, eastern, and western parts of Africa than in the southern part. The highest prevalence of serotype O was recorded in Mauritius and Comoros, while the lowest prevalence was found in Eritrea, Egypt, Ethiopia, Kenya, Sudan, and Zambia. Unlike Serotype A and O, SAT1 was distributed in 6 African countries. The results revealed that serotype SAT1 was more prevalent in the eastern and southern parts of Africa than in the western and northern parts. The highest prevalence of serotype SAT1 was reported in Zimbabwe, while the lowest prevalence was in Botswana and South Africa. the study also found that the circulating serotype SAT1 was the same genetically in Zimbabwe, Tanzania, Kenya, and South Africa. This suggests that the virus is being transmitted between these countries, either through the illegal movement of livestock or through the movement of wild animals. Serotype SAT2 was widely distributed across African countries. The highest probability of infection of serotype SAT2 was found in Egypt, while the lowest probability of infection was observed in Mozambique, Angola, Namibia, Malawi, Zambia, Mauritania, Botswana, and South Africa. SAT3 serotype being the lowest circulating serotype of FMDV in Africa, it was distributed only in 3 African countries. The results stated that serotype SAT3 was only found in three African countries: Namibia, South Africa, and Zimbabwe. Based on the raster risk map, northern, eastern, and southern African countries were determined to have the highest predicted risk of FMD spatial occurrence during the study period. [ABSTRACT FROM AUTHOR]

Morganella morganii is a Gram-negative opportunistic Enterobacteriaceae pathogen inherently resistant to colistin. This species causes various clinical and community-acquired infections. This study investigated the virulence factors, resistance mechanisms, functional pathways, and comparative genomic analysis of M. morganii strain UM869 with 79 publicly available genomes. The multidrug resistance strain UM869 harbored 65 genes associated with 30 virulence factors, including efflux pump, hemolysin, urease, adherence, toxin, and endotoxin. Additionally, this strain contained 11 genes related to target alteration, antibiotic inactivation, and efflux resistance mechanisms. Further, the comparative genomic study revealed a high genetic relatedness (98.37%) among the genomes, possibly due to the dissemination of genes between adjoining countries. The core proteome of 79 genomes contains the 2692 core, including 2447 single-copy orthologues. Among them, six were associated with resistance to major antibiotic classes manifested through antibiotic target alteration (PBP3, gyrB) and antibiotic efflux (kpnH, rsmA, qacG; rsmA; CRP). Similarly, 47 core orthologues were annotated to 27 virulence factors. Moreover, mostly core orthologues were mapped to transporters (n = 576), two-component systems (n = 148), transcription factors (n = 117), ribosomes (n = 114), and quorum sensing (n = 77). The presence of diversity in serotypes (type 2, 3, 6, 8, and 11) and variation in gene content adds to the pathogenicity, making them more difficult to treat. This study highlights the genetic similarity among the genomes of M. morganii and their restricted emergence, mostly in Asian countries, in addition to their growing pathogenicity and resistance. However, steps must be taken to undertake large-scale molecular surveillance and to direct suitable therapeutic interventions. [ABSTRACT FROM AUTHOR]

Background: Streptococcus suis is a zoonotic pathogen that causes substantial economic losses in the pig industry and contributes to human infections worldwide, especially in Southeast Asia. Recently, a multiplex polymerase chain reaction (PCR) process was developed to distinguish disease-associated and non-disease-associated pathotypes of S. suis European strains. Herein, we evaluated the ability of this multiplex PCR approach to distinguish pathotypes of S. suis in Thailand. Results: This study was conducted on 278 human S. suis isolates and 173 clinically healthy pig S. suis isolates. PCR identified 99.3% of disease-associated strains in the human isolates and 11.6% of non-disease-associated strains in the clinically healthy pig isolates. Of the clinically healthy pig S. suis isolates, 71.1% were classified as disease-associated. We also detected undetermined pathotype forms in humans (0.7%) and pigs (17.3%). The PCR assay classified the disease-associated isolates into four types. Statistical analysis revealed that human S. suis clonal complex (CC) 1 isolates were significantly associated with the disease-associated type I, whereas CC104 and CC25 were significantly associated with the disease-associated type IV. Conclusion: Multiplex PCR cannot differentiate non-disease-associated from disease-associated isolates in Thai clinically healthy pig S. suis strains, although the method works well for human S. suis strains. This assay should be applied to pig S. suis strains with caution. It is highly important that multiplex PCR be validated using more diverse S. suis strains from different geographic areas and origins of isolation. [ABSTRACT FROM AUTHOR]

Background and Aim: Salmonellosis is a significant foodborne disease that causes serious illness in the gastrointestinal of humans and it is a public health problem worldwide. This study aimed to determine Salmonella spp. in animal feeds, its characteristic, serovar identification, genotyping, and drug sensitivity. Materials and Methods: Salmonella spp. from animal feedstuffs was collected from January 1 to December 31, 2017, with 657 samples. Serogroup classification was performed by using the slide agglutination test. Then, the samples were analyzed for genotype patterns using pulsed-field gel electrophoresis (PFGE) for DNA fingerprint and antibiotic sensitivity by Vitek? 2 techniques. Results: A total of 80 samples (12.17 %) were found to be Salmonella positive; commercial feed compounds of 60 samples (75%); soybean meal of 10 samples (12.5%); pork meal of 5 samples (6.25%); a fish meal of three samples (3.75%) and poultry meal of 2 samples (2.5%). Serogroups B, C, D, and E were found in this study; 8 samples (10%), 39 samples (48.75%), 8 samples (10%), and 13 samples (16.25%), respectively. A total of 12 samples (15%) were not determined by serogrouping. The most common serovars were Salmonella Rissen (10%), Salmonella Mbandaka (8.75%), and Salmonella Livingstone (6.25%), which belong to serogroup C. Nine of eleven pulsotypes were detected when analyzed by PFGE, showed similarity index between 40.8 and 100 %. Antimicrobial susceptibility tests by Vitek? 2 compact for 11 strains were classified into three groups: resistance to 4, 8, and 11 antibiotics, out of 20 antibiotics. Conclusion: This study revealed annual variation of Salmonella spp. Serovar, genotype, and phenotype from commercial feed compounds and raw materials of which involved people must be aware. [ABSTRACT FROM AUTHOR]

Background: The World Health Organization views dengue fever as a significant worldwide public health threat in the tropics and subtropics. Dengue virus has four serotypes, DENG 1 to 4, which were responsible for outbreaks that occurred in other parts of the world from the 1980s until now. Aims and Objectives: Clinical manifestations and molecular and serological studies help determine the inflammatory response events associated with dengue severity. This study aimed to define the profiles of some cytokines and chemokines, as well as their molecular serotyping. Materials and Methods: Blood serum samples are collected, followed by serodiagnosis (NS1 and IgM) through ELISA, molecular serotyping detection of dengue by real-time PCR through SyBr green, and an immunological study of cytokines tumor necrosis factor-alpha and interferon-gamma (IFN-γ) on mother-hand chemokines CCL26 and MCP1 by ELISA. Statistical analysis was performed by SPSS (version 22). Results: The study examined 70 dengue seropositive samples, of which five were NS1 positive and 55 were IgM positive. After accounting for comorbidities and patients’ demographic classifications, the 21–30 age group has a maximum positivity of 30%. The mean concentration level of IFN-γ is elevated at 1544.438 pg/mL. Conclusion: Dengue-positive patients have a high ischemic heart disease rate, among other diseases. An elevated circulating level of osteopetrosis may cause cancer, tuberculosis, and other serious diseases. In immunological aspects, IFN-γ elevation can be used to predict the severity of dengue infection. [ABSTRACT FROM AUTHOR]

Background: Streptococcus pneumoniae (pneumococcus) represents an important human pathogen, responsible for respiratory and invasive infections in the community. The efficacy of polysaccharide conjugate vaccines formulated against pneumococci is reduced by the phenomenon of serotype replacement in population of this pathogen. The aim of the current study was to obtain and compare complete genomic sequences of two pneumococcal isolates, both belonging to ST320 but differing by the serotype. Results: Here, we report genomic sequences of two isolates of important human pathogen, S. pneumoniae. Genomic sequencing resulted in complete sequences of chromosomes of both isolates, 2,069,241 bp and 2,103,144 bp in size, and confirmed the presence of cps loci specific for serotypes 19A and 19F. The comparative analysis of these genomes revealed several instances of recombination, which involved not only S. pneumoniae but also presumably other streptococci as donors. Conclusions: We report the complete genomic sequences of two S. pneumoniae isolates of ST320 and serotypes 19A and 19F. The detailed comparative analysis of these genomes revealed the history of several recombination events, clustered in the region including the cps locus. [ABSTRACT FROM AUTHOR]

Background: Surface polysaccharides (SPs), such as lipopolysaccharide (O antigen) and capsular polysaccharide (K antigen), play a key role in the pathogenicity of Escherichia coli (E. coli). Gene cluster for polysaccharide antigen biosynthesis encodes various glycosyltransferases (GTs), which drive the process of SP synthesis and determine the serotype. Results: In this study, a total of 7,741 E. coli genomic sequences were chosen for systemic data mining. The monosaccharides in both O and K antigens were dominated by D-hexopyranose, and the SPs in 70–80% of the strains consisted of only the five most common hexoses (or some of them). The linkages between the two monosaccharides were mostly α-1,3 (23.15%) and β-1,3 (20.49%) bonds. Uridine diphosphate activated more than 50% of monosaccharides for glycosyltransferase reactions. These results suggest that the most common pathways could be integrated into chassis cells to promote glycan biosynthesis. We constructed a database (EcoSP, http://ecosp.dmicrobe.cn/) for browse this information, such as monosaccharide synthesis pathways. It can also be used for serotype analysis and GT annotation of known or novel E. coli sequences, thus facilitating the diagnosis and typing. Conclusions: Summarizing and analyzing the properties of these polysaccharide antigens and GTs are of great significance for designing glycan-based vaccines and the synthetic glycobiology. [ABSTRACT FROM AUTHOR]

Background: Pregnancy increases a woman's risk of severe dengue. To the best of our knowledge, the moderation effect of the dengue serotype among pregnant women has not been studied in Mexico. This study explores how pregnancy interacted with the dengue serotype from 2012 to 2020 in Mexico. Method: Information from 2469 notifying health units in Mexican municipalities was used for this cross-sectional analysis. Multiple logistic regression with interaction effects was chosen as the final model and sensitivity analysis was done to assess potential exposure misclassification of pregnancy status. Results: Pregnant women were found to have higher odds of severe dengue [1.50 (95% CI 1.41, 1.59)]. The odds of dengue severity varied for pregnant women with DENV-1 [1.45, (95% CI 1.21, 1.74)], DENV-2 [1.33, (95% CI 1.18, 1.53)] and DENV-4 [3.78, (95% CI 1.14, 12.59)]. While the odds of severe dengue were generally higher for pregnant women compared with non-pregnant women with DENV-1 and DENV-2, the odds of disease severity were much higher for those infected with the DENV-4 serotype. Conclusion: The effect of pregnancy on severe dengue is moderated by the dengue serotype. Future studies on genetic diversification may potentially elucidate this serotype-specific effect among pregnant women in Mexico. [ABSTRACT FROM AUTHOR]

Listeria monocytogenes is an ubiquitously occurring foodborne bacterial pathogen known to contaminate foods during the production processes. To assess the presence and persistence of L. monocytogenes in Danish ready-to-eat (RTE) food production companies in response to a Listeria awareness campaign, the production environment of selected companies were sampled in 2016 and in 2020. Whole genome sequencing (WGS) was performed to characterize the isolates (n = 50, plus 35 isolates obtained from the routine surveillance during 2016–2020), including investigation of the presence of virulence, persistence and resistance genes. The number of companies that tested positive by culture was 17/39 (43.6%) in 2016 and 11/34 (32.4%) in 2020, indicating a limited effect of the campaign. WGS analyses of the 85 isolates showed that the most common sequence types (STs) were ST8 and ST121. The single nucleotide polymorphism (SNP) analysis showed that isolates coming from the same company and belonging to the same ST exhibited <10 SNP differences regardless of the sampling year and whether the samples came from the environment or products, indicating the persistence of the specific STs. Several prevalent STs were found in clinical cases concurrently, including genetically similar isolates. This highlights the issue of persistent L. monocytogenes in the food production environment and the need for improved risk communication and mitigation strategies. [ABSTRACT FROM AUTHOR]

Despite scientific discoveries in the field of gene and cell therapy, some diseases still have no effective treatment. Advances in genetic engineering methods have enabled the development of effective gene therapy methods for various diseases based on adeno-associated viruses (AAVs). Today, many AAV-based gene therapy medications are being investigated in preclinical and clinical trials, and new ones are appearing on the market. In this article, we present a review of AAV discovery, properties, different serotypes, and tropism, and a following detailed explanation of their uses in gene therapy for disease of different organs and systems. [ABSTRACT FROM AUTHOR]

Accurate detection of all Salmonella serovars present in a sample is important in surveillance programs. Current detection protocols are limited to detection of a predominant serovar, missing identification of less abundant serovars in a sample. An alternative method, called CRISPR-SeroSeq, serotyping by sequencing of amplified CRISPR spacers, was employed to detect multiple serovars in a sample without the need of culture isolation. The CRISPR-SeroSeq method successfully detected 34 most frequently reported Salmonella serovars in pure cultures and target serovars at 104 CFU/mL in 27 Salmonella-negative environmental enrichment samples post-spiked with one of 15 different serovars, plus 2 additional serovars at 1 log CFU/mL higher abundance. When the method was applied to 442 naturally contaminated environmental samples collected from 192 poultry farms, 25 different serovars were detected from 430 of the samples. In 73.1% of the samples, 2 to 7 serovars were detected, with Salmonella Kiambu (55.7%), Salmonella Infantis (48.4%), Salmonella Kentucky (27.1%), Salmonella Livingstone (26.6%), and Salmonella Mbandaka/Montevideo (23.4%) being the most prevalent on the farms. Single isolates from 384 samples were also analyzed using a traditional serotyping method, and the same serovar identified by culture was detected by CRISPR-SeroSeq in 96.1% (369/384) of samples, with the former missing detection of additional and sometimes critical serovars. The surveillance data obtained via CRISPR-SeroSeq revealed a significant emergence of Salmonella Kiambu and Salmonella Rissen on poultry farms in Ontario. The results highlight the effectiveness of the CRISPR-SeroSeq approach in detecting multiple Salmonella serovars in poultry environmental samples under applied conditions, providing updated surveillance information on Salmonella serovars on poultry farms in Ontario. IMPORTANCE The CRISPR-SeroSeq method represents an alternative molecular tool to the traditional culture-based serotyping method that can detect multiple Salmonella serovars in a sample and provide rapid serovar results without the need of selective enrichment and culture isolation. The evaluation results can facilitate implementation of the method in routine Salmonella surveillance on poultry farms and in outbreak investigations. The application of the method can increase the accuracy of current serovar prevalence information. The results highlight the effectiveness of the validated method and the need for monitoring Salmonella serovars in poultry environments to improve current surveillance programs. The updated surveillance data provide timely information on emergence of different Salmonella serovars on poultry farms in Ontario and support on-farm risk assessment and risk management of Salmonella. [ABSTRACT FROM AUTHOR]

Background Monitoring changes in pharyngeal carriage of pneumococcus in children following 13-valent pneumococcal conjugate vaccine (PCV13) introduction in the United Kingdom in 2010 informs understanding of patterns of invasive pneumococcal disease (IPD) incidence. Methods Nasopharyngeal swabs from healthy children vaccinated with PCV13 according to schedule (2, 4, and 12 months) were cultured and serotyped. Results for children aged 13–48 months were compared between 2014–2015 and 2017–2019 and with children aged 6–12 months (2017–2020). Blood was obtained from a subset of children for pneumococcal serotype-specific immunoglobulin G (IgG). Results Total pneumococcal carriage at 13–48 months was 47.9% (473/988) in 2014–2015 and 51.8% (412/795) in 2017–2019 (P =.10); at age 6–12 months this value was 44.6% (274/615). In 2017–2019, 2.9% (95% confidence interval, 1.8%–4.3%) of children aged 13–48 months carried PCV13 serotypes (mainly 3 [1.5%] and 19A [0.8%]) and >20% carried the additional 20-valent PCV (PCV20) serotypes. Similar proportions of children had IgG ≥0.35 IU/mL for each serotype in 2014–2015 and 2017–2019. Serotype 7C carriage increased significantly (P <.01) between 2014–2015 and 2017–2019. Carriage of PCV20 serotypes 8 and 12F, both major causes of IPD, was rare. Conclusions Introduction of PCV20, if licensed for children, could significantly change the composition of pneumococcal serotypes carried in the pharynx of UK children. Clinical Trials Registration NCT03102840. [ABSTRACT FROM AUTHOR]

Background: Streptococcus pneumoniae remains a leading cause of morbidity and mortality worldwide. In this study, we sought to analyze serotype distributions, antibiotic resistance, and genetic relationships of 106 clinical invasive pneumococcal isolates recovered in Tunisia between 2012 and 2018, prior to the routine use of pneumococcal conjugate vaccines (PCV). Methods: We used multiplex PCR, the disk diffusion method and/or E-test, and multi-locus sequence typing (MLST). Results: The most frequent serotypes were 14 (17%), 19F (14.2%), and 3 (11.3%). Of the 106 S. pneumoniae isolates, 67.9% were penicillin non-susceptible (29.4% were resistant), 45.3% were amoxicillin non-susceptible (17% were resistant), and 16% were cefotaxime non-susceptible. For antibiotics other than β-lactams, resistance rates to erythromycin, tetracycline, cotrimoxazole, and chloramphenicol were 62.3, 33, 22.6, and 4.7%, respectively. Two isolates were non-susceptible to levofloxacin. Among 66 erythromycin-resistant pneumococci, 77.3% exhibited the cMLSB phenotype, and 87.9% carried ermB gene. All tetracycline-resistant strains harbored the tetM gene. The potential coverage by 7-, 10-, and 13-valent pneumococcal conjugate vaccines were 55.7, 57.5, and 81.1%, respectively. A multilocus sequence typing analysis revealed great diversity. Fifty different sequence types (STs) were identified. These STs were assigned to 10 clonal complexes and 32 singletons. The most common STs were 179, 2918, 386, and 3772 – related mainly to 19F, 14, 6B/C, and 19A serotypes, respectively. Conclusions: This study demonstrated that the majority of the serotypes of invasive pneumococci in the Tunisian population were 14, 19F, and 3. Moreover, we noted a high degree of genetic diversity among invasive S. pneumoniae isolates. The highest proportions of antibiotic non-susceptible isolates were for penicillin, erythromycin, and tetracycline. Further molecular characteristics are required to monitor the genetic variations and to follow the emergence of resistant pneumococci for the post-vaccination era in Tunisia. [ABSTRACT FROM AUTHOR]

Background: Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease associated with loss of upper and lower motor neurones. It leads to death by respiratory failure and has a typical prognosis of 2–3 years. The immune system has been shown to play a role in the pathophysiology of ALS. Some of the most important immune genes are within the human leukocyte antigen (HLA) region, and a recent genome-wide association study (GWAS) has identified a risk allele for ALS within the HLA region. Older studies have also suggested an HLA association with ALS, with certain HLA alleles showing differing expression between patients and controls. This systematic review and meta-analysis examines the previous studies performed in this field. Methods: We used established publication search engines. Findings were excluded if they did not meet the selection criteria. We then undertook statistical meta-analysis on the eligible papers, using a fixed effects model. Results: There were eight eligible papers. There were three statistically significant meta-analysis findings, although these would not be significant after correction for multiple comparisons. The frequencies of HLA-A9 and HLA-DR4 genotypes were lower in ALS subjects than controls, and HLA-B35 was higher in ALS subjects. Discussion: This systematic review and meta-analysis do not confirm all the previously reported associations of HLA with ALS, but shows three alleles of interest. However, there are limitations to the studies, which include the use of older serotyping methodology and the small numbers of subjects. Given the recent GWAS association with HLA, further modern HLA studies are warranted. [ABSTRACT FROM AUTHOR]

Background Extraintestinal pathogenic Escherichia coli (ExPEC) is the leading cause of bacteremia worldwide, with older populations having increased risk of invasive bacterial disease. Increasing resistance to first-line antibiotics and emergence of multidrug-resistant (MDR) strains represent major treatment challenges. ExPEC O serotypes are key targets for potential multivalent conjugate vaccine development. Therefore, we evaluated the O serotype distribution and antibiotic resistance profiles of ExPEC strains causing bloodstream infections across 4 regions. Methods Blood culture isolates from patients aged ≥60 years collected during 5 retrospective E. coli surveillance studies in Europe, North America, Asia-Pacific, and South America (2011–2017) were analyzed. Isolates were O serotyped by agglutination; O genotyping was performed for nontypeable isolates. Antimicrobial susceptibility testing was also conducted. Results Among 3217 ExPEC blood culture isolates, the most ubiquitous O serotype was O25 (n = 737 [22.9%]), followed by O2, O6, O1, O75, O15, O8, O16, O4, O18, O77 group, O153, O9, O101/O162, O86, and O13 (prevalence of ≥1%). The prevalence of these O serotypes was generally consistent across regions, apart from South America; together, these 16 O serotypes represented 77.6% of all ExPEC bacteremia isolates analyzed. The overall MDR frequency was 10.7%, with limited variation between regions. Within the MDR subset (n = 345), O25 showed a dominant prevalence of 63.2% (n = 218). Conclusions Predominant O serotypes among ExPEC bacteremia isolates are widespread across different regions. O25 was the most prevalent O serotype overall and particularly dominant among MDR isolates. These findings may inform the design of multivalent conjugate vaccines that can target the predominant O serotypes associated with invasive ExPEC disease in older adults. [ABSTRACT FROM AUTHOR]

Background: Streptococcus pneumoniae (S. pneumoniae), remains a major cause of mortality and morbidity worldwide. The objective of this study was to determine the trends of invasive pneumococcal diseases (IPD) in adult and elderly population in Casablanca (Morocco) before and after introduction of pneumococcal conjugate vaccine (PCV) by determining the distribution of pneumococcal serotypes and antibiotic resistance profile of isolated strains. Method: The proposed study is a retrospective laboratory-based surveillance of IPD in hospitalized adult (15–59 years old) and elderly (≥ 60 years old) patients in Ibn Rochd University Hospital Centre from 2007 to 2019 (13 years). All the 250 non-duplicate clinical invasive isolates from adult and elderly patients, confirmed as S. pneumoniae according to the laboratory standard identification procedures, are included in this study. Results: A significant decrease of the overall incidence in IPD was observed only in adults from 0.71 to 0.54/100000 populations (P = 0.02) and to 0.47/100000 populations (P = 0.0137) in the early and mature post-vaccine period respectively compared to the pre-vaccine period. Our results also showed a significant reduction in the overall prevalence of vaccine serotypes from 28.17 to 6.90% (P = 0.0021) for the PCV-10 serotypes, and from 46.48 to 25.86% (P = 0.0164) for the PCV-13 serotypes only in the mature post-vaccine period (2015–2019). In parallel, the rate of non-vaccine serotypes did not significantly change in the early post-vaccine period (2011–2014) while it increased considerably from 54 to 74.14% (P = 0.0189) during the mature post-vaccine period. The rate of penicillin non-susceptible pneumococcal isolates decreased significantly from 23.94 to 8.77% (P = 0.02) in adult patients, and the rate of cotrimoxazole non-susceptible pneumococcal isolates significantly decreased from 29.58 to 8.77% in the early post-vaccine period (P = 0.003) and to 7.24% in the mature post-vaccine period (P = 0.0007). Conclusion: Although childhood vaccination has considerably reduced the incidence of IPD in adult population through the herd effect, IPD remain a real public health problem due to the alarming increase in non-vaccine serotypes (NVS) and the lack of herd effect among elderly population. The rate of antibiotic resistance was relatively low. Nevertheless, resistance constitutes a serious problem to the therapeutic arsenal due to the known capacity for genetic dissemination in the pneumococcus. [ABSTRACT FROM AUTHOR]