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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.

The adenovirus detection rate is <10% throughout the year in South Korea; however, during the summer of 2023, it showed an unusual increase. We analyzed the adenovirus detection rate using data from the Korea Respiratory Integrated Surveillance System before and after coronavirus disease (COVID-19) collected from 2019 to week 36 of 2023. Before the COVID-19 outbreak in 2019, the mean detection rate was 8.2%, which decreased to 6.1% during the COVID-19 pandemic from 2020 to 2022. In 2023, the mean detection rate was 14.3% in week 36 and the highest in week 34, at 42.2%, and adenovirus was predominantly detected in the summer. The detection rate by age group showed substantially high activity among 0–12-yr-olds after the pandemic. This age group had a steady mean rate of 9.5% during the pandemic, without seasonality. In 2023, the detection rate surged in the 0–6-yr and 7–12-yr age groups, peaking at 61.6% and 57.1%, respectively. The dominant epidemic serotypes were HAdV-1 and HAdV-2 during and HAdV-3 after the pandemic. The multifaceted non-pharmaceutical interventions during the COVID-19 pandemic considerably impacted the prevalence of common respiratory viruses and complicated respiratory virus patterns after the pandemic. Constant surveillance is crucial for epidemic preparedness to monitor the possible surge of certain respiratory viruses. [ABSTRACT FROM AUTHOR]

Introduction Understanding the pneumococcal serotypes causing community-acquired pneumonia (CAP) is essential for evaluating the impact of pneumococcal vaccines. Methods We conducted a prospective surveillance study of adults aged ≥18 years hospitalized with CAP at 3 hospitals in Tennessee and Georgia between 1 September 2018 and 31 October 2022. We assessed for pneumococcal etiology with cultures, the BinaxNOW urinary antigen detection test, and serotype-specific urinary antigen detection assays that detect 30 pneumococcal serotypes contained in the investigational pneumococcal conjugate vaccine V116, as well as licensed vaccines PCV15 and PCV20 (except serotype 15B). The distribution of pneumococcal serotypes was calculated based on serotype-specific urinary antigen detection results. Results Among 2917 hospitalized adults enrolled with CAP, 352 (12.1%) patients had Streptococcus pneumoniae detected, including 51 (1.7%) patients with invasive pneumococcal pneumonia. The 8 most commonly detected serotypes were: 3, 22F, 19A, 35B, 9N, 19F, 23A, and 11A. Among 2917 adults with CAP, 272 (9.3%) had a serotype detected that is contained in V116, compared to 196 (6.7%) patients with a serotype contained in PCV20 (P <.001), and 168 (5.8%) patients with a serotype contained in PCV15 (P <.001). A serotype contained in V116 but not PCV15 or PCV20 was detected in 120 (4.1%) patients, representing 38.0% of serotype detections. Conclusions Approximately 12% of adults hospitalized with CAP had S. pneumoniae detected, and approximately one-third of the detected pneumococcal serotypes were not contained in PCV15 or PCV20. Development of new pneumococcal vaccines with expanded serotype coverage has the potential to prevent a substantial burden of disease. [ABSTRACT FROM AUTHOR]

Glaesserella parasuis (GPS) is an important bacterial pathogen of swine. Serotype identification has presented a bottleneck in GPS research since it was first identified as the pathogen causing Glässer's disease in pigs in 1910. This paper presents a systematic review of the history of the development and application of gel immunodiffusion (GID), indirect hemagglutination assay (IHA), and polymerase chain reaction (PCR) typing methods for GPS, and the discovery of their shared antigenic basis. It provides a systematic theoretical overview of the immunology and principles underlying the three typing methods and offers new ideas for research into the prevention and control of Glässer's disease. In 1992, GPS was first classified into serotypes 1–15 using GID based on GPS heat-stable antigens, but about 25% of the strains were found to be non-typeable, and the composition of their antigens for serotyping was unclear. In 2003, the IHA method was established based on saline-extracted antigens of GPS, whose sensitivity and typing rate were higher than for GID, although about 15% of strains were still found to be non-typeable. The results of IHA and GID typing are roughly consistent, since they share the same GPS surface polysaccharide serotyping antigens, although whether these are capsular polysaccharides, lipopolysaccharides, or other polysaccharides, remains to be determined. In 2013, the Capsular polysaccharide (CPS) synthetic gene clusters from GPS serotypes 1–15 were successfully analyzed, confirming that CPS is essential for the formation of antigens for serotyping. In 2015, primers were designed based on the specific target genes of GPS capsules to establish a PCR typing method (H-PCR) for GPS, which, however, could not identify serotypes 5 and 12. In 2017, a new PCR typing method (J-PCR) was established based on the specific target genes of GPS capsules, which could identify serotypes 5 and 12. A combination of the two PCR typing methods enables the typing of almost all GPS strains, and the consistency with GID and IHA was verified using molecular biological methods. The antigenic basis of the three typing methods was shown to involve the GPS capsule. PCR typing methods are characterized by simple operation, fast speed, and low cost, and can successfully solve many problems in GID and IHA serotyping, and so have become widely adopted. [ABSTRACT FROM AUTHOR]

Bluetongue virus (BTV) is an agriculturally and economically significant insect-borne virus that causes serious illness and death in sheep and other domestic and wild ruminants in large areas of the world. Numerous BTV serotypes exist, and distant serotypes exhibit unique neutralizing antibody profiles, which target the outermost capsid protein VP2. The predominant serotype-specific nature of the antibody response to VP2 is a barrier to the development of broad-spectrum prophylactic BTV vaccine candidates. Although VP2 is the main serotype determinant of BTV, the structural basis of serotype specificity has not been investigated. In this study, we utilized the recently available atomic structure of VP2 with a modeled tip domain to carry out in silico structural comparisons between distant serotypes BTV1 and BTV8. These analyses identified structural differences in the tip domain, positioned at the apex of VP2, and informed the design of mutant VP2 constructs. Dissection of tip domain antigenicity demonstrated that the region of structural difference between BTV1 and highly virulent BTV8 was a target of BTV neutralizing antibodies and that mutation of this region resulted in a loss of neutralizing antibody recognition. This study has for the first time provided insights into the structural differences, which underpin the serotype-specific neutralizing antibody response to BTV. [ABSTRACT FROM AUTHOR]

Background Lower respiratory infections and invasive disease caused by Streptococcus pneumoniae serotype 3 remain major clinical challenges around the world, despite widespread availability of updated vaccines. Methods As part of CANWARD, antimicrobial susceptibility testing and serotyping were performed on all S. pneumoniae isolates from 2007 to 2021. A subset of 226/264 (85.6%) serotype 3 isolates were selected for WGS to determine sequence type (ST)/clonal cluster (CC) and correspondence of antimicrobial resistance determinants (erm , mefAE , tetM , cat , folA , folP) with resistance phenotype. Results Of the 3,039 S. pneumoniae isolates obtained from 2007 to 2021, 8.7% (n  = 264) were serotype 3, with 64.0% of respiratory origin and 36.0% from blood. Of 226 sequenced serotype 3 isolates, 184 (81.4%) were ST180 (GPSC12). The proportion of ST8561 (single locus variant of ST180) increased from 7.2% to 16.6% during the study period. An increasing proportion of serotype 3 isolates had phenotypic resistance (P  = 0.0007) and genetic resistance determinants (P  = 0.004), comparing 2017–21 to 2007–11, largely due to a recently expanded ST180 clade with cat , tetM and mef determinants. Conclusions S. pneumoniae serotype 3 from GPSC12 continues to dominate throughout Canada, with an increase in the proportion of ST8561. The proportion of serotype 3 isolates that are phenotypically resistant and with genetic resistance determinants is increasing over time, reflecting a global increase in GPSC12 genotypes with known resistance determinants. Phylogenomic characterization of isolates collected over time and from around the world may facilitate improved treatment and enhanced prevention strategies, including new vaccines with activity against S. pneumoniae serotype 3. [ABSTRACT FROM AUTHOR]

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]

Streptococcus agalactiae, or group B streptococcus (GBS), is a Gram-positive pathogen with an extended track record of colonization in the gastrointestinal and genitourinary tracts. GBS can induce disease in individuals across all age demographics, yet it predominantly triggers infections in neonates and the elderly. Identification of the serotype is vital for effective management of the disease as it provides critical information for clinicians on the cause of the disease. In this study, we evaluated the rapid, simple, and easy-to-adopt multiplex real-time PCR technique, NovaplexTM (NovaPCR). A total of 131 clinical isolates of different serotypes were tested using NovaPCR. Observations revealed that 129 isolates showed the same observations as LA and conventional mPCR. NovaPCR accurately identified serotypes IV and V, which were first classified as serotype Ia in the LA test and mPCR, and the difference between the traditional (LA test and mPCR) and NovaPCR methods is only 1.52%. Accurate serotype identification is helpful for monitoring the epidemics and achieving optimal clinical outcomes, and NovaPCR showed a reliable, fast, easy-to-interpret, and cost-efficient performance in GBS serotyping. [ABSTRACT FROM AUTHOR]

Acute hepatopancreatic necrosis disease, which can cause 100% mortality, is one of the main threats to farming Litopenaeus vannamei. We identified seven strains of pathogenic bacteria from ponds with outbreaks of acute hepatopancreatic necrosis at a L. vannamei farm in Zhuhai, China. Among the seven bacteria strains, one strain was isolated from aquaculture water, two strains were isolated from hepatopancreas, and the other four strains were isolated from juvenile shrimp. The results of 16S rRNA sequencing and biochemical identification showed that all seven pathogenic bacteria were Vibrio parahaemolyticus and that they carried the pirA and pirB virulence genes. These bacteria showed ß-hemolysis with translucent rings, and six serotypes were identified. The regression infection results showed that the lethal rates of the three V. parahaemolyticus strains of serotypes O1:KUT and OUT:KUT to L. vannamei were significantly higher than those of the other serotypes. The three V. parahaemolyticus strains had the same growth characteristics, and they all entered the growth plateau at 4 h after inoculation. In addition, the pathogenicity of the three V. parahaemolyticus strains were similar. In the present study, V. parahaemolyticus was identified as one of the pathogenic bacteria causing acute hepatopancreatic necrosis of L. vannamei, and the O1:KUT and OUT:KUT serotypes may be the main pathogenic strains in Zhuhai. These results provided a foundation for the isolation, identification, and pathogenicity study of acute hepatopancreatic necrosis of L. vannamei, providing a reference for the prevention and control direction of L. vannamei disease. [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]

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Background: Streptococcus pneumoniae is a significant etiological agent of infection and commonly inhabits the human nasopharynx, alongside other potentially pathogenic bacteria. In this study, S. pneumoniae strains were obtained from a community population and subjected to investigation of their phenotypes, genotypes, and vaccine coverage. Methods: S. pneumoniae was isolated from nasopharyngeal swab samples of a healthy population in the Guangfu Community. Capsular serotypes and genotypes were identified using Quellung reaction and multilocus sequence typing (MLST), respectively. The antimicrobial susceptibility was tested using minimum inhibitory concentrations. Results: In total, 500 unvaccinated people were sampled. Ninety-four S. pneumoniae strains were identified. Common serotypes were 19F, 6A, and 9V. The strain coverages of PCV13 and PPV23 were 61.7% and 58.5%, respectively. About 27.6% isolates were non-susceptible to penicillin, and over 80% were resistant to erythromycin and doxycycline. Among 27 novel sequence types (STs) identified in all strains, the most common STs were ST236 (6/94, 6.4%) and ST12669 (6/94, 6.4%). Nearly half of the strains were grouped into four clone complexes (CC12665, CC271, CC6011, and CC180), of which CC271 showed the highest resistance to PEN. Conclusion: In our study, various drug-resistant clone complexes of Streptococcus pneumoniae were found in the healthy population, the elderly, and children. Consequently, pneumococcal vaccines should be included in the national immunization schedule to prevent disease spread. [ABSTRACT FROM AUTHOR]

Purpose: Developing countries, invasive Salmonella infections can cause considerable morbidity and mortality. There is a relative lack of data on coinfection with Salmonella in HIV-infected patients in Hangzhou, China. Patients and Methods: In this study, we manually collected case data of patients aged > 18 years with HIV combined with invasive Salmonella infections admitted to Xixi Hospital in Hangzhou from January 2012 to August 2023 by logging into the Hospital Information System, and identified 26 strains of invasive Salmonella using a fully automated microbiological identification system and mass spectrometer. Serotypes were determined using Salmonella diagnostic sera based on the White-Kauffmann-Le Minor scheme. Drug sensitivity tests were performed using the automated instrumental method of the MIC method. Results: A total of 26 HIV-infected patients with invasive Salmonella coinfections were identified over 11 years; Twenty-five of the 26 patients (96.2%) were males, with a mean age of 33.5 years (26.75, 46.75). The most common type of infection was bloodstream infection (92.3%). One patient also had concomitant meningitis and osteoarthritis, followed by pneumonia (7.7%). The presence of multiple bacterial infections or even multiple opportunistic pathogens was clearly established in 7 (26.9%) patients. Three (11.6%) patients were automatically discharged from the hospital with deterioration of their condition, and one (3.8%) patient died. Salmonella enteritidis was the most common serotype in 6 patients (23.2%), and Salmonella Dublin was the most common serotype in 6 patients (23.2%). Drug sensitivity results revealed multidrug resistance in a total of 8 (30.8%) patients. Conclusion: The clinical presentation of invasive Salmonella infection in HIV patients is nonspecific and easily masked by other mixed infections. A CD4+ count < 100 cells/μL and comorbid intestinal lesions may be important susceptibility factors. Salmonella has a high rate of resistance to common antibiotics, and the risk of multidrug resistance should not be ignored. [ABSTRACT FROM AUTHOR]

Background: Streptococcus pneumoniae, a major contributor to global morbidity and mortality, disproportionately affects children, the elderly, and immunocompromised individuals. Despite vaccination efforts, the challenge of serotype replacement highlights the ongoing struggle against invasive pneumococcal diseases (IPD) in Morocco, emphasizing the need for updated public health strategies and vaccine efficacy assessments. Methods: This study was conducted at the Ibn Rochd University Hospital Center and the Mohammed VI University Hospital Center from 2019 to 2022, focusing on hospitalized children. It involved the analysis of 74 strains of IPD, assessing the distribution of pneumococcal serotypes and their antibiotic sensitivity in the post-vaccination era. Results: The prevalence of meningitis or meningo-encephalitis was found to be 66% among the study subjects, with the most frequent serotypes being 3, 19A, 6B, 14, and 11. These serotypes varied significantly by age and location. Coverage rates for the pneumococcal conjugate vaccines, PCV-10 and PCV-13, were 20.27% and 56.75%, respectively. Notably, 43% of the strains were non-vaccine serotypes, with serotypes 3 and 19 accounting for 36% of the infections in children, indicating a lack of vaccine efficacy against these types. Additionally, 31.3% of the strains were Penicillin non-susceptible Streptococcus pneumoniae (PNSP), with 81.25% associated with nonvaccine serotypes. Conclusions: This study highlights the persistence of IPD in Moroccan children, revealing significant challenges despite vaccination efforts. With the reintroduction of PCV-13, concerns about the efficacy against non-vaccine serotypes, particularly 3 and 19A, remain. Continuous surveillance and adaptable vaccination strategies are essential to combat these serotype replacements and ensure the effectiveness of future preventive measures. [ABSTRACT FROM AUTHOR]

Abstract Glaesserella parasuis (GPS) is an important bacterial pathogen of swine. Serotype identification has presented a bottleneck in GPS research since it was first identified as the pathogen causing Glässer’s disease in pigs in 1910. This paper presents a systematic review of the history of the development and application of gel immunodiffusion (GID), indirect hemagglutination assay (IHA), and polymerase chain reaction (PCR) typing methods for GPS, and the discovery of their shared antigenic basis. It provides a systematic theoretical overview of the immunology and principles underlying the three typing methods and offers new ideas for research into the prevention and control of Glässer’s disease. In 1992, GPS was first classified into serotypes 1–15 using GID based on GPS heat-stable antigens, but about 25% of the strains were found to be non-typeable, and the composition of their antigens for serotyping was unclear. In 2003, the IHA method was established based on saline-extracted antigens of GPS, whose sensitivity and typing rate were higher than for GID, although about 15% of strains were still found to be non-typeable. The results of IHA and GID typing are roughly consistent, since they share the same GPS surface polysaccharide serotyping antigens, although whether these are capsular polysaccharides, lipopolysaccharides, or other polysaccharides, remains to be determined. In 2013, the Capsular polysaccharide (CPS) synthetic gene clusters from GPS serotypes 1–15 were successfully analyzed, confirming that CPS is essential for the formation of antigens for serotyping. In 2015, primers were designed based on the specific target genes of GPS capsules to establish a PCR typing method (H-PCR) for GPS, which, however, could not identify serotypes 5 and 12. In 2017, a new PCR typing method (J-PCR) was established based on the specific target genes of GPS capsules, which could identify serotypes 5 and 12. A combination of the two PCR typing methods enables the typing of almost all GPS strains, and the consistency with GID and IHA was verified using molecular biological methods. The antigenic basis of the three typing methods was shown to involve the GPS capsule. PCR typing methods are characterized by simple operation, fast speed, and low cost, and can successfully solve many problems in GID and IHA serotyping, and so have become widely adopted.

We identified 3 clades of dengue virus serotype 3 belonging to genotype III isolated during 2019–2020 in Jamaica by using whole-genome sequencing and phylogenomic and phylogeographic analyses. The viruses likely originated from Asia in 2014. Newly expanded molecular surveillance efforts in Jamaica will guide appropriate public health responses.

Abstract 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 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.

Arbovirus-borne dengue fever remains a global public health threat. The actual burden of dengue infection may be underestimated due to undiagnosed or misdiagnosed fever cases. The distribution of dengue is influenced by both climatic and nonclimatic factors, including global warming, which affects the vector population and transmission period. Other factors, such as serotype evolution and host immunity, also contribute to the spread of the virus. Different serotypes of the dengue virus show different clinical manifestations. The prevalence of serotypes varies geographically and over time. Early diagnosis and characterization of circulating viruses at the genomic level are important for disease prevention and control.

ObjectiveTo monitor the molecular epidemiology and antimicrobial resistance pattern of Salmonella isolates recovered from the clinical and the food sources in Shaoxing City， the genomic characterization of some clinical strains were analyzed.MethodsSlide agglutination method was used to determine the serovars. PFGE method was applied to study molecular classification. Broth microdilution method was performed to carry out drug resistance testing. Whole genome data were sequenced. Whole genome single nucleotide polymorphism （wgSNP） classification was performed by BioNumerics V7.6 software. The sequence types （ST）， drug resistant genes and virulence genes were predicted with Pubmlst， ResFinder 4.1 and VFDB software， respectively.ResultsTwenty-four serotypes， 109 different PFGE fingerprints， 80 resistant patterns were detected in 135 clinical and the 10 food isolates of Salmonella. The predominant serovars were Salmonella typhimurium， Salmonella enteritidis and Salmonella london. The main serotypes in food were Salmonella london and Salmonella paratyphi B. Salmonella had high resistance to ampicillin， tetracycline and streptomycin. The multiple drug resistance rate reached 73.79% （107/145）. The main drug resistance in food were ampicillin， cefazolin， tetracycline and nalidixic acid. A total of 11 diverse ST types were identified from the 30 clinical strains. Phylogenetic wgSNP comparisons demonstrated that four Salmonella enteritidis from ST11 types were genetically similar and clustered together. A total of 31 different antimicrobial resistance genes among these isolates were identified. The most common antimicrobial resistance genes were the aminoglycosides resistance gene aac（6'）-Iaa （100%， 30/30）， the β-lactams resistance gene blaTEM-1B （70%， 21/30） and so on. A total of 224 virulence genes were also identified， and 107 of these existed among all isolates.ConclusionSalmonella in Shaoxing had a variety of serotypes and PFGE fingerprints， a complex resistant patterns， a high proportion of multiple drug resistance. The findings showed that selected raw poultry was not a direct source of local Salmonella infection. Part of the clinical strains had a high carrying rate of antimicrobial resistance genes and virulence genes.

ObjectiveTo provide scientific basis for the prevention and control of foodborne diseases and clinical treatment， the serological， drug resistance and molecular typing characteristics of Salmonella isolated from patients with foodborne diarrhea in Wenzhou City was investigated.MethodsA total of 567 Salmonella strains isolated from foodborne diarrhea cases in Wenzhou City from 2017 to 2021 were sorted out and serotyped. The susceptibility tests to 15 antimicrobial agents were performed using the broth microdilution method. Pulsed field gel electrophoresis （PFGE） was used for molecular typing.ResultsAmong the 567 patients of Salmonella， 326 were male and 241 were female， accounting for 57.5% and 42.5%， respectively. Most of them were children under 6 years old， and 119 strains were isolated， accounting for 21.0%. Next was the elderly over 60 years old， 111 strains of Salmonella were isolated， accounting for 19.6%. The 567 isolates of Salmonella were divided into 50 serotypes， among which the top two serotypes were Salmonella typhimurium （33.5%， 190/567） and Salmonella enteritidis （23.6%， 134/567）. The results showed that the resistance rate to ampicillin was the highest （73.5%， 417/567）. It was followed by tetracycline （63.3%， 359/567）. Salmonella typhimurium had the highest resistance to tetracycline （84.2%， 160/190）， and Salmonella enteritidis had the highest resistance to nalidixic acid （95.5%， 128/134） among 15 antibiotics. Among 567 strains of Salmonella， 178 kinds of drug resistance spectrum were found， the rate of multiple drug resistance was 62.6%and the highest proportion was AMP-AMS-CFZ-CT-NAL. The 201 strains of Salmonella typhimurium and the monophasic varieties of Salmonella typhimurium produced 70 band types. The band types varied greatly and the similarity was between 1.5% and 100%. One hundred and twenty-seven strains of Salmonella enteritidis obtained a total of 32 band types with the similarity between 35.8% and 100%. Fifty strains of Salmonella london obtained a total of 24 band types by PFGE， and the similarity was between 40.0% and 100%.ConclusionFoodborne Salmonella strains isolated in Wenzhou displayed diverse serotypes， varying degrees of drug resistance， and multi-drug resistance. To effectively prevent and control foodborne diseases caused by Salmonella， enhancing monitoring of Salmonella among foodborne diarrhea patients was essential. Timely understanding of Salmonella serotype distribution trends and drug resistance patterns in the region， followed by appropriate measures， was imperative.

The aim of the study was to investigate the prevalence and resistance of biofilm-forming Salmonella strains on poultry farms in Kazakhstan, Latvia, and Turkey. During the study, samples of faeces, tissues (liver and intestines) and water from drinkers were collected and analysed from January to December 2023. Salmonella strains were isolated and identified using standard microbiological methods. A total of 150 Salmonella strains were isolated and identified, of which 90 strains were obtained from faecal samples, 40 from tissue samples and 20 from water samples. The distribution of strains by country showed that in Kazakhstan, Latvia and Turkey, the largest number of strains were isolated from faecal samples. Of the 80 Salmonella Enteritidis strains, most showed the ability to form biofilms, as determined by the crystal violet method, with subtypes SE1 and SE2 showing the highest propensity for biofilm formation. Among the Salmonella Typhimurium strains, a significant biofilm formation ability was found in the ST1 subtype. Antibiotic resistance was determined using the disc diffusion method. The biofilm-forming strains showed higher antibiotic resistance compared to the non-biofilm-forming strains. Of the 150 strains isolated, 105 showed resistance to at least one of the antibiotics tested, with the highest level of resistance among Salmonella Typhimurium strains. Correlation analysis revealed a significant positive relationship between the level of biofilm formation and antibiotic resistance. The results demonstrate the need to introduce the development of new methods of control and prevention of infections on poultry farms, which would take into account the peculiarities of biofilm formation and antibiotic resistance of certain strains

This study presents a retrospective epidemiological analysis of foot and mouth disease (FMD) in ruminants in Palestine from 2006 to 2023. Data from the Palestinian Central Bureau of Statistics, the Annual Agricultural Census, and reports from the World Organization for Animal Health indicated the endemic nature of FMD in Palestine throughout the study period. The findings unveil FMD's consistent presence, reporting outbreaks every year. The comprehensive analysis encompasses 202 outbreaks, involving 5635 cases and 84 deaths, underscoring the disease's substantial impact. The average morbidity, mortality, and case fatality rates were 17.0, 2.2 and 1.49%, respectively. Serotypes O, A, Asia 1, and SAT 2 were identified, each exerting varying effects on morbidity, mortality, and susceptible livestock. Annual trends displayed unpredictable fluctuations in outbreaks, emphasizing the erratic nature of FMD occurrences. Vaccination efforts exhibited fluctuating coverage levels, hinting at potential shifts in strategies or challenges in maintaining consistent programs. Concerningly, recent years witnessed a decline in vaccination, signaling a need for sustained vigilance and strengthened vaccination initiatives to manage FMD's impact on susceptible animal populations effectively. To control disease spread, the study advocates for improved data recording, heightened owner awareness, increased FMD vaccine utilization, and the implementation of a systematic disease monitoring and serotyping program.

Abstract Background Escherichia. coli is the most frequent host for New Delhi metallo-β-lactamase (NDM) which hydrolyzes almost all β-lactams except aztreonam. The worldwide spread of blaNDM-carrying E. coli heavily threatens public health. Objective This study aimed to explore the global genomic epidemiology of blaNDM- carrying E. coli isolates, providing information for preventing the dissemination of such strains. Methods Global E. coli genomes were downloaded from NCBI database and blaNDM was detected using BLASTP. Per software was used to extract meta information on hosts, resources, collection data, and countries of origin from GenBank. The sequence types (STs) and distribution of antimicrobial resistance gene (ARG) were analyzed by CLC Workbench; Plasmid replicons, serotypes and virulence genes (VFs) were analyzed by submitting the genomes to the websites. Statistical analyses were performed to access the relationships among ARGs and plasmid replicons. Results Until March 2023, 1,774 out of 33,055 isolates collected during 2003–2022 were found to contain blaNDM in total. Among them, 15 blaNDM variants were found with blaNDM-5 (74.1%) being most frequent, followed by blaNDM-1 (16.6%) and blaNDM-9 (4.6%). Among the 213 ARGs identified, 27 blaCTX-M and 39 blaTEM variants were found with blaCTX-M-15 (n = 438, 24.7%) and blaTEM-1B (n = 1092, 61.6%) being the most frequent ones, respectively. In addition, 546 (30.8%) plasmids mediated ampC genes, 508 (28.6%) exogenously acquired 16 S rRNA methyltransferase encoding genes and 262 (14.8%) mcr were also detected. Among the 232 distinct STs, ST167 (17.2%) were the most prevalent. As for plasmids, more than half of isolates contained IncFII, IncFIB and IncX3. The VF terC, gad, traT and iss as well as the serotypes O101:H9 (n = 231, 13.0%), O8:H9 (n = 115, 6.5%) and O9:H30 (n = 99, 5.6%) were frequently observed. Conclusions The study delves into the intricate relationship between plasmid types, virulence factors, and ARGs, which provides valuable insights for clinical treatment and public health interventions, and serves as a critical resource for guiding future research, surveillance, and implementation of effective strategies to address the challenges posed by blaNDM-carrying E. coli. The findings underscore the urgent need for sustained global collaboration, surveillance efforts, and antimicrobial stewardship to mitigate the impact of these highly resistant strains on public health.

Abstract Flavobacterium psychrophilum, the causative agent of bacterial cold-water disease, is a devastating, worldwide distributed, fish pathogen causing significant economic loss in inland fish farms. Previous epidemiological studies showed that prevalent clonal complexes (CC) differ in fish species affected with disease such as rainbow trout, coho salmon and ayu, indicating significant associations between particular F. psychrophilum genotypes and host species. Yet, whether the population structure is driven by the trade of fish and eggs or by host-specific pathogenicity is uncertain. Notably, all F. psychrophilum isolates retrieved from ayu belong to Type-3 O antigen (O-Ag) whereas only very few strains retrieved from other fish species possess this O-Ag, suggesting a role in outbreaks affecting ayu. Thus, we investigated the links between genotype and pathogenicity by conducting comparative bath infection challenges in two fish hosts, ayu and rainbow trout, for a collection of isolates representing different MLST genotypes and O-Ag. Highly virulent strains in one host species exhibited low to no virulence in the other. F. psychrophilum strains associated with ayu and possessing Type-3 O-Ag demonstrated significant variability in pathogenicity in ayu, ranging from avirulent to highly virulent. Strikingly, F. psychrophilum strains retrieved from rainbow trout and possessing the Type-3 O-Ag were virulent for rainbow trout but not for ayu, indicating that Type-3 O-Ag alone is not sufficient for pathogenicity in ayu, nor does it prevent pathogenicity in rainbow trout. This study revealed that the association between a particular CC and host species partly depends on the pathogen’s adaptation to specific host species.

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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]

Background: Salmonellosis is a widespread zoonotic disease that poses a significant threat to livestock and public health. This study aimed to serotype 20 Salmonella isolates obtained from sixty retail chicken meats, assess Salmonella contamination from eggs, and evaluate antibiotic resistance profiles. Methods and results: Twenty eggs were randomly collected in the new Borg El Arab market. Bacterial isolation was carried out utilizing both traditional culture, biochemical, and PCR methods. Among the twenty eggs analyzed, three (15%) tested positive for Salmonella, while the remaining seventeen (85%) were confirmed as negative. Genotyping through multiplex PCR revealed the presence of two S. Enteritidis and other serovar, with the use of three specific gene sets: a random sequence for Salmonella spp., sdfI gene for S. Enteritidis, and flagellin (fliC gene) for S. Typhimurium. Out of the 20 isolates obtained from chicken meat, five (25%) were identified as S. Typhimurium, and three (15%) were classified as S. Enteritidis. All isolates sourced from chicken meat exhibited resistance to Rifampicin and Amoxicillin, with 90% displaying sensitivity to cefotaxime, gemifloxacin, and Erythromycin. Importantly, S. Blegdam, identified via serological methods, displayed resistance to all tested antibiotics. For the three isolates obtained from eggs, 66.6% showed sensitivity to cefotaxime, erythromycin, cefuraxime, and cefaclor, while displaying complete resistance (100%) to Amoxicillin, rifampicin, clarithromycin, and cefadroxil. Notably, one serovar exhibited absolute resistance to all tested drugs. Conclusion: Stakeholders must implement strict control measures and rationalize antibiotic use in veterinary and human medicine due to the rise of antibiotic-resistant strains. [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]

The aim of the study was to investigate the prevalence and resistance of biofilm-forming Salmonella strains on poultry farms in Kazakhstan, Latvia, and Turkey. During the study, samples of faeces, tissues (liver and intestines) and water from drinkers were collected and analysed from January to December 2023. Salmonella strains were isolated and identified using standard microbiological methods. A total of 150 Salmonella strains were isolated and identified, of which 90 strains were obtained from faecal samples, 40 from tissue samples and 20 from water samples. The distribution of strains by country showed that in Kazakhstan, Latvia and Turkey, the largest number of strains were isolated from faecal samples. Of the 80 Salmonella Enteritidis strains, most showed the ability to form biofilms, as determined by the crystal violet method, with subtypes SE1 and SE2 showing the highest propensity for biofilm formation. Among the Salmonella Typhimurium strains, a significant biofilm formation ability was found in the ST1 subtype. Antibiotic resistance was determined using the disc diffusion method. The biofilm-forming strains showed higher antibiotic resistance compared to the non-biofilm-forming strains. Of the 150 strains isolated, 105 showed resistance to at least one of the antibiotics tested, with the highest level of resistance among Salmonella Typhimurium strains. Correlation analysis revealed a significant positive relationship between the level of biofilm formation and antibiotic resistance. The results demonstrate the need to introduce the development of new methods of control and prevention of infections on poultry farms, which would take into account the peculiarities of biofilm formation and antibiotic resistance of certain strains. [ABSTRACT FROM AUTHOR]

We performed whole genome sequencing (WGS) of 15 Palyam serogroup virus (PALV) strains isolated from cattle or Culicoides biting midges in Japan from 1984 to 2018. We found that the PALV strains consisted of Chuzan (Kasba) virus (CHUV), D'Aguilar virus (DAGV), Bunyip Creek virus, and another PALV, Marrakai virus (MARV). The Japanese MARV strains isolated in 1997 were closely related to Australian PALV strains isolated in 1968–1976 in genome segments 2 and 10, but they were most closely related to other Japanese PALV strains in the other genome segments. Our data suggest that the Japanese MARV strains were reassortant viruses between Asian and Australian PALVs. In addition to the WGS, we developed a real-time reverse-transcription polymerase chain reaction assay that can broadly detect PALV and specifically detect CHUV and DAGV, utilizing the data obtained by the WGS in this study. We detected the DAGV gene in bovine stillborn fetuses and congenitally abnormal calves in 2019 using the newly developed assay. To our knowledge, this is the first report of isolation of MARV outside of Australia and the first report of detection of PALV in bovine fetuses or calves with congenital abnormality outside of Africa. [ABSTRACT FROM AUTHOR]

Background: Escherichia. coli is the most frequent host for New Delhi metallo-β-lactamase (NDM) which hydrolyzes almost all β-lactams except aztreonam. The worldwide spread of blaNDM-carrying E. coli heavily threatens public health. Objective: This study aimed to explore the global genomic epidemiology of blaNDM- carrying E. coli isolates, providing information for preventing the dissemination of such strains. Methods: Global E. coli genomes were downloaded from NCBI database and blaNDM was detected using BLASTP. Per software was used to extract meta information on hosts, resources, collection data, and countries of origin from GenBank. The sequence types (STs) and distribution of antimicrobial resistance gene (ARG) were analyzed by CLC Workbench; Plasmid replicons, serotypes and virulence genes (VFs) were analyzed by submitting the genomes to the websites. Statistical analyses were performed to access the relationships among ARGs and plasmid replicons. Results: Until March 2023, 1,774 out of 33,055 isolates collected during 2003–2022 were found to contain blaNDM in total. Among them, 15 blaNDM variants were found with blaNDM-5 (74.1%) being most frequent, followed by blaNDM-1 (16.6%) and blaNDM-9 (4.6%). Among the 213 ARGs identified, 27 blaCTX-M and 39 blaTEM variants were found with blaCTX-M-15 (n = 438, 24.7%) and blaTEM-1B (n = 1092, 61.6%) being the most frequent ones, respectively. In addition, 546 (30.8%) plasmids mediated ampC genes, 508 (28.6%) exogenously acquired 16 S rRNA methyltransferase encoding genes and 262 (14.8%) mcr were also detected. Among the 232 distinct STs, ST167 (17.2%) were the most prevalent. As for plasmids, more than half of isolates contained IncFII, IncFIB and IncX3. The VF terC, gad, traT and iss as well as the serotypes O101:H9 (n = 231, 13.0%), O8:H9 (n = 115, 6.5%) and O9:H30 (n = 99, 5.6%) were frequently observed. Conclusions: The study delves into the intricate relationship between plasmid types, virulence factors, and ARGs, which provides valuable insights for clinical treatment and public health interventions, and serves as a critical resource for guiding future research, surveillance, and implementation of effective strategies to address the challenges posed by blaNDM-carrying E. coli. The findings underscore the urgent need for sustained global collaboration, surveillance efforts, and antimicrobial stewardship to mitigate the impact of these highly resistant strains on public health. [ABSTRACT FROM AUTHOR]

Flavobacterium psychrophilum, the causative agent of bacterial cold-water disease, is a devastating, worldwide distributed, fish pathogen causing significant economic loss in inland fish farms. Previous epidemiological studies showed that prevalent clonal complexes (CC) differ in fish species affected with disease such as rainbow trout, coho salmon and ayu, indicating significant associations between particular F. psychrophilum genotypes and host species. Yet, whether the population structure is driven by the trade of fish and eggs or by host-specific pathogenicity is uncertain. Notably, all F. psychrophilum isolates retrieved from ayu belong to Type-3 O antigen (O-Ag) whereas only very few strains retrieved from other fish species possess this O-Ag, suggesting a role in outbreaks affecting ayu. Thus, we investigated the links between genotype and pathogenicity by conducting comparative bath infection challenges in two fish hosts, ayu and rainbow trout, for a collection of isolates representing different MLST genotypes and O-Ag. Highly virulent strains in one host species exhibited low to no virulence in the other. F. psychrophilum strains associated with ayu and possessing Type-3 O-Ag demonstrated significant variability in pathogenicity in ayu, ranging from avirulent to highly virulent. Strikingly, F. psychrophilum strains retrieved from rainbow trout and possessing the Type-3 O-Ag were virulent for rainbow trout but not for ayu, indicating that Type-3 O-Ag alone is not sufficient for pathogenicity in ayu, nor does it prevent pathogenicity in rainbow trout. This study revealed that the association between a particular CC and host species partly depends on the pathogen's adaptation to specific host species. [ABSTRACT FROM AUTHOR]

Introduction: A distinct strain of Klebsiella pneumoniae (K. pneumoniae) referred to as hypervirulent (hvKp) is associated with invasive infections such as pyogenic liver abscess in young and healthy individuals. In South Africa, limited information about the prevalence and virulence of this hvKp strain is available. The aim of this study was to determine the prevalence of hvKp and virulence-associated factors in K. pneumoniae isolates from one of the largest tertiary hospitals in a South African province. Methods: A total of 74 K. pneumoniae isolates were received from Pelonomi Tertiary Hospital National Health Laboratory Service (NHLS), Bloemfontein. Virulence-associated genes (rmpA, capsule serotype K1/K2, iroB and irp2) were screened using Polymerase Chain Reaction (PCR). The iutA (aerobactin transporter) gene was used as a primary biomarker of hvKp. The extracted DNAs were sequenced using the next-generation sequencing pipeline and the curated sequences were used for phylogeny analyses using appropriate bioinformatic tools. The virulence of hvKp vs. classical Klebsiella pneumoniae (cKp) was investigated using the Caenorhabditis elegans nematode model. Results: Nine (12.2%) isolates were identified as hvKp. Moreover, hvKp was significantly (p < 0.05) more virulent in vivo in Caenorhabditis elegans relative to cKp. The virulence-associated genes [rmpA, iroB, hypermucoviscous phenotype (hmv) phenotype and capsule K1/K2] were significantly (p < 0.05) associated with hvKp. A homology search of the curated sequences revealed a high percentage of identity between 99.8 and 100% with other homologous iutA gene sequences of other hvKp in the GenBank. Conclusion: Findings from this study confirm the presence of hvKp in a large tertiary hospital in central South Africa. However, the low prevalence and mild to moderate clinical presentation of infected patients suggest a marginal threat to public health. Further studies in different settings are required to establish the true potential impact of hvKp in developing countries. [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]

Dengue, a mosquito‐borne viral disease, poses a significant public health challenge in Pakistan, with a significant outbreak in 2023, prompting our investigation into the serotype and genomic diversity of the dengue virus (DENV). NS‐1 positive blood samples from 153 patients were referred to the National Institute of Health, Pakistan, between July and October 2023. Among these, 98 (64.1%) tested positive using multiplex real‐time PCR, with higher prevalence among males (65.8%) and individuals aged 31‐40. Serotyping revealed DENV‐1 as the predominant serotype (84.7%), followed by DENV‐2 (15.3%). Whole‐genome sequencing of 18 samples (DENV‐1 = 17, DENV‐2 = 01) showed that DENV‐1 (genotype III) samples were closely related (>99%) to Pakistan outbreak samples (2022), and approx. > 98% with USA (2022), Singapore and China (2016), Bangladesh (2017), and Pakistan (2019). The DENV‐2 sequence (cosmopolitan genotype; clade IVA) shared genetic similarity with Pakistan outbreak sequences (2022), approx. > 99% with China and Singapore (2018−2019) and showed divergence from Pakistan sequences (2008−2013). No coinfection with dengue serotypes or other viruses were observed. Comparisons with previous DENV‐1 sequences highlighted genetic variations affecting viral replication efficiency (NS2B:K55R) and infectivity (E:M272T). These findings contribute to dengue epidemiology understanding and underscore the importance of ongoing genomic surveillance for future outbreak responses in Pakistan. [ABSTRACT FROM AUTHOR]

Objective To analyze the etiological characteristics of Vibrio parahaemolyticus (VP) isolated from food-borne outbreaks in Fuqing City between 2021 and 2023, and to explore its distribution characteristics and epidemic types. Methods The serotypes, virulence genes (tlh, tdh, trh), and drug resistance profiles of 23 VP strains isolated from 4 food- borne disease outbreaks were tested by agglutination, multiple real-time PCR, and broth microdilution methods. Pulsed-field gel electrophoresis (PFGE) was used for molecular typing to analyze homology. Results From 2021 to 2023, four food-borne disease outbreaks occurred in Fuqing City, leading to the isolation and identification of 23 VP strains. Among these, 19 clinical strains were divided into two serotypes: O10:K4 type, comprising 13 strains (68.4%), and O4:KUT type, comprising 6 strains (31.6%); the tdh gene carrying rate was 100.0%, and no trh gene was detected. The serotypes of the four food isolates were O3: K4, O10:K24, O11:KUT, and O3:K37, respectively, all differing from the clinical strains, with two strains coming from the same food item without tdh and trh genes detected. The resistance rate of all isolates to cefazolin was the highest (87.0%), with two strains (8.7%) from different sources showing multidrug resistance. The PFGE genotypes of 19 case isolates were clustered and correlated with their serotypes and drug resistance profiles; strains isolated from the same outbreak event showed high similarity, whereas food strains exhibited polymorphism in PFGE genotypes. Conclusions The predominant serotype causing the four outbreaks was O10:K4, with some strains showing multidrug resistance; all clinical strains carried the tdh gene. The high correlation between strains from the same outbreak event suggests they are homologous. Special attention should be paid to the risk of outbreaks and pandemics caused by the O10:K4 type strain again. Additionally, food safety risk monitoring and assessment should be strengthened to provide an effective basis for epidemic prevention and control and early identification and warning. [ABSTRACT FROM AUTHOR]

Listeria (L.) monocytogenes is an opportunistic foodborne pathogen that causes listeriosis in humans and animals, reaching up to 30% case mortality. There are only a few reports in Mexico about the L. monocytogenes strains found in various foods. The aim of this study was to determine the prevalence of L. monocytogenes, serogroups, virulence genes, and antimicrobial resistance in different foods from Reynosa, Tamaulipas, Mexico. L. monocytogenes strains were characterized by microbiological and molecular methods. Susceptibility to 12 antibiotics was determined according to CLSI and EUCAST. A total of 300 samples of seafood, pasteurized and raw milk, cheese, beef, and chicken were collected from supermarkets and retail markets. The presence of L. monocytogenes was detected in 5.6% of the samples. Most strains belonged to serogroups 4b, 4d, and 4e (68.4%). All strains presented a minimum of four virulence genes; the most common were actA, hly, and plcB (92.1%). A high percentage of antimicrobial susceptibility was observed, with resistance only to STX-TMP (78.9%), STR (26.3%), MEM (21.0%), and E (2.6%). These results show that the foods in Reynosa, Tamaulipas, are a reservoir of L. monocytogenes and represent a potential health risk. [ABSTRACT FROM AUTHOR]

Objective: The purpose of the paper was to monitor the disease incidence in farm and wild animals in some areas of Kazakhstan, which are most susceptible to leptospirosis, and the typification of isolated pathogens, carried out under the scientific and technical program "Studying the epizootological characteristics of the country territory on particularly dangerous diseases and developing veterinary and sanitary measures to improve their effectiveness" in 2021-2023. Materials and Methods: The material included the reports of veterinary laboratories on leptospirosis in recent years, as well as laboratory tests on samples carried out at the "SANA" research and development enterprise. During this period, 6,701 serum samples from farm animals and 86,651 serum samples from rodents were tested by enzyme-linked immunosorbent assay. Results: The serological results showed antibody titers in the blood of 6.32% of cattle, 5.4% of sheep, 4.2% of horses, and 1.8% of pigs. The highest number of positive samples were found in Turkestan (12.3%), Almaty (11.7%), and Kyzylorda (11.4%) regions. Infection in rodents was lower and ranged from 0.34% to 0.07% during these years. The population of leptospira-causing diseases of animals on the territory of the country is represented by 8 serogroups. Studies in 2022 on the detection of pathogenic leptospires by polymerase chain reaction in 350 samples of blood serum from animals and 350 samples of biomaterial from rodents from different regions of Kazakhstan were negative. Conclusion: Studies conducted as part of this work will help reduce the incidence of disease among the population and animals in Kazakhstan. [ABSTRACT FROM AUTHOR]

Listeria monocytogenes is a foodborne pathogen that lives in nature as a saprophyte. Two of the three most common serotypes that cause foodborne listeriosis are 1/2a and 4b. Within serotype 4b, there is a variant called 4bv-1. In the last decade, several produce-related outbreaks (linked to leafy salad, caramel apples, and stone fruit) were linked to 4bv-1 strains, specifically those of Sequence Type 382. This study assessed the fitness of ST 382 strains on lettuce leaf sections to determine if they are more fit on produce than strains of other serotypes. Strains of serotypes 1/2a, 4b, and ST 382 were inoculated as mixtures onto lettuce and incubated at 4 °C for 7 days or 25 °C for 24 h. Thirty L. monocytogenes colonies resulting from the growth on each lettuce piece were characterized for serotype by multiplex PCR, and the percentages of each serotype recovered were compared. In the individual mixtures with three strains, none of the ST 382 strains showed better fitness for growth on lettuce at either 4 °C or 25 °C. Overall, ST 382 strains showed better recovery from lettuce sections grown at 4 °C than at 25 °C. Statistical analysis of the recovery of twelve strains tested in competition experiments indicated that ST 382 strains were less fit for lettuce growth when competing against the other serotypes. The data indicate that ST 382 strains do not have a competitive fitness advantage on cut lettuce sections.

Objective: The purpose of the paper was to monitor the disease incidence in farm and wild animals in some areas of Kazakhstan, which are most susceptible to leptospirosis, and the typifi¬cation of isolated pathogens, carried out under the scientific and technical program "Studying the epizootological characteristics of the country territory on particularly dangerous diseases and developing veterinary and sanitary measures to improve their effectiveness" in 2021–2023. Materials and Methods: The material included the reports of veterinary laboratories on leptospi¬rosis in recent years, as well as laboratory tests on samples carried out at the "SANA" research and development enterprise. During this period, 6,701 serum samples from farm animals and 86,651 serum samples from rodents were tested by enzyme-linked immunosorbent assay. Results: The serological results showed antibody titers in the blood of 6.32% of cattle, 5.4% of sheep, 4.2% of horses, and 1.8% of pigs. The highest number of positive samples were found in Turkestan (12.3%), Almaty (11.7%), and Kyzylorda (11.4%) regions. Infection in rodents was lower and ranged from 0.34% to 0.07% during these years. The population of leptospira-causing diseases of animals on the territory of the country is represented by 8 serogroups. Studies in 2022 on the detection of pathogenic leptospires by polymerase chain reaction in 350 samples of blood serum from animals and 350 samples of biomaterial from rodents from different regions of Kazakhstan were negative. Conclusion: Studies conducted as part of this work will help reduce the incidence of disease among the population and animals in Kazakhstan. [J Adv Vet Anim Res 2024; 11(2.000): 439-448]

ABSTRACTThis study aimed to provide data for the clinical features of invasive pneumococcal disease (IPD) and the molecular characteristics of Streptococcus pneumoniae isolates from paediatric patients in China. We conducted a multi-centre prospective study for IPD in 19 hospitals across China from January 2019 to December 2021. Data of demographic characteristics, risk factors for IPD, death, and disability was collected and analysed. Serotypes, antibiotic susceptibility, and multi-locus sequence typing (MLST) of pneumococcal isolates were also detected. A total of 478 IPD cases and 355 pneumococcal isolates were enrolled. Among the patients, 260 were male, and the median age was 35 months (interquartile range, 12–46 months). Septicaemia (37.7%), meningitis (32.4%), and pneumonia (27.8%) were common disease types, and 46 (9.6%) patients died from IPD. Thirty-four serotypes were detected, 19F (24.2%), 14 (17.7%), 23F (14.9%), 6B (10.4%) and 19A (9.6%) were common serotypes. Pneumococcal isolates were highly resistant to macrolides (98.3%), tetracycline (94.1%), and trimethoprim/sulfamethoxazole (70.7%). Non-sensitive rates of penicillin were 6.2% and 83.3% in non-meningitis and meningitis isolates. 19F-ST271, 19A-ST320 and 14-ST876 showed high resistance to antibiotics. This multi-centre study reports the clinical features of IPD and demonstrates serotype distribution and antibiotic resistance of pneumococcal isolates in Chinese children. There exists the potential to reduce IPD by improved uptake of pneumococcal vaccination, and continued surveillance is warranted.