Predominant Serotype Research Articles

Epidemiology of invasive Haemophilus influenzae infections in Belgium: 2018-2022.

Haemophilus influenzae plays a major role in invasive bacterial infections. Resistant strains are emerging, prompting the WHO to include H. influenzae on its list of priority pathogens for research and development of new antibiotics. We aimed to describe the serotypes, demographics and susceptibility profiles of invasive strains collected in Belgium. Data on invasive strains referred to the Belgian National Reference Center for H. influenzae from 2018 to 2022 were analyzed retrospectively. A total of 608 invasive strains were included. The number of notifications per year ranged from 85 to 165, with a marked decrease between 2020 and 2021. The highest incidence rate was observed in Brussels (1.56 per 100,000 inhabitants over the five year 2018-2022). Sex and age distribution were in line with global trends, as was the predominance of the non-typeable H. influenzae (NTHI). Beta-lactam resistance varies between molecules: 18.9% for ampicillin, 5.6% for amoxicillin-clavulanate. Mutations in the ftsI gene associated with decreased susceptibility to beta-lactams increased from 11.5 to 17.7% over the period studied. The COVID-19 pandemic significantly influenced the epidemiology of invasive H. influenzae infections in Belgium. Demographic analysis identified a significant male predominance among infants, with a male-to-female ratio of 2.57 in patients under one year of age, a high figure not previously reported in the literature. The continued predominance of NTHI underscores the efficacy of Hib vaccination, although the emergence of Hib in patients younger than five years in 2022 suggests an alarming serotype dynamic. The detection of meropenem resistance also highlights the growing threat of antimicrobial resistance, while the increase in ftsI gene mutations raises concerns about the efficacy of first-line treatment. This study provides a comprehensive overview of the epidemiology of invasive H. influenzae infections in Belgium, focusing on demographic changes, serotype predominance and antimicrobial resistance trends. Vigilant surveillance and research are essential to address emerging challenges and guide future interventions, including potential vaccine development.

Epidemiology and Genotype Dynamics of Dengue in Hospitalized Patients in Northern Vietnam Between 2020 and 2022.

Arboviruses, including Dengue (DENV), Zika, and chikungunya, cause recurrent outbreaks of varying intensity in tropical countries. This study aimed to investigate other arboviruses, including Zika and chikungunya, in patients clinically suspected of Dengue and to characterize the circulating Dengue serotypes and genotypes in Northern Vietnam from 2020 to 2022. To date, information on this topic in the region has been limited. Multiplex real-time polymerase chain reaction (PCR) was used to detect Dengue, Zika, and chikungunya RNA, and DENV serotypes were identified via real-time reverse transcriptase PCR from 426 clinically Dengue suspected patients. Patients were screened for NS1 antigen and anti-DENV immunoglobulin (Ig) G/IgM antibodies. Phylogenetic analysis of DENV Capsid-premembrane gene sequences was performed to investigate genotype distribution. Dengue was confirmed in 95% of cases, with no Zika or chikungunya RNA detected. DENV-2 was the predominant serotype (61%), followed by DENV-1 (31%) and DENV-4 (7%). Coinfections were observed, with DENV-1 and DENV-2 being the most common. In 2022, a high incidence of Dengue cases with warning signs and severe Dengue was observed, accompanied by elevated liver enzyme levels and reduced platelet counts. Phylogenetic analysis revealed that the DENV-1 and DENV-4 serotypes clustered with previously reported regional virus, while DENV-2 showed a shift from genotype Asian I to Cosmopolitan over the study period. This study underscores a significant rise in Dengue severity and shifts in DENV genotypes in recent years in Northern Vietnam, emphasizing the importance of understanding genotype dynamics and clinical dynamics for improving outbreak preparedness and response strategies.

Prevalence and transmission of Salmonella collected from farming to egg processing of layer production chain in Jiangsu Province, China.

Salmonella is a common foodborne pathogen found in poultry production systems. Contaminated poultry products are a major source of human salmonellosis. Understanding the conditions of contamination and the genetic relationships of Salmonella in poultry production is necessary to develop effective interventions measures for controlling Salmonella transmission. Through epidemiological investigation and whole-genome sequence (WGS) analysis, this study revealed the epidemic law, drug resistance, and genetic characteristics of Salmonella in the production chain. In total, 130 (10.77 %) Salmonella strains were isolated from the collected samples, with Salmonella Enteritidis (S. Enteritidis) and S. Infantis being the predominant serotypes. WGS analysis revealed that the Sequence Type (ST) of all the 22 strains of S. Enteritidis were ST11, and 13 strains of S. Infantis were ST32. Antimicrobial resistance gene analysis showed that 95.45 % of S. Enteritidis carried strA/strB, sul, and blaTEM-1B; 77.3 % contained tetA genes; and 100 % of S. Infantis carried aac(6')-Iaa and mdf(A), which was consistent with the drug resistance phenotype. The phylogenetic tree showed that S. Enteritidis strains with different links were distributed in the same branch which displayed the very close genetic relationship. Combined with epidemiological investigations, it was found that S. Enteritidis infection begins at the chicken breeding stage and spreads vertically and horizontally along the production chain. In addition, phylogenetic tree analysis of S. Infantis showed that the genomes of 13 strains from egg products and egg collection center were very similar and belonged to the same clone cluster. It is speculated that the S. Infantis transmitted in the industrial chain is the same strain; it can spread along the industrial chain, and cross-contamination may occur. This study indicates that Salmonella contamination in the layered industrial chain is more serious and that a cloning relationship exists among the strains of different links. Therefore, more stringent measures should be taken to control Salmonella during the chicken breeding stage, and the importance of implementing good hygiene practices at every level of production should be emphasized.

Pneumococcal pneumonia trends in adults hospitalised with community-acquired pneumonia over 10 years (2013–2023) and the role of serotype 3

BackgroundWith higher valency pneumococcal vaccines on the horizon and new adult immunisation strategies under discussion, we aimed to evaluate the contribution of individual pneumococcal serotypes to the burden of pneumococcal...

Epidemiology of Dengue - Puerto Rico, 2010-2024.

Dengue is a mosquitoborne viral illness that can cause acute febrile illness, severe disease, or death. Worldwide, the number of dengue cases is increasing. During the last dengue outbreaks in Puerto Rico throughout 2010-2013, dengue virus (DENV) serotype 1 (DENV-1) predominated, and the largest proportion of cases occurred among adolescents and young adults aged 10-19 years. Dengue case data from January 1, 2010-November 4, 2024, were obtained from the Puerto Rico Department of Health. Bivariate analyses were conducted to evaluate the distribution of cases by patient age, DENV serotype, and hospitalization status during three periods: 2010-2019, 2020-2022, and 2023-2024. During 2023-2024, the median age of dengue cases increased to 26 years (95% CI=25-27 years) compared with that during 2020-2022 (17 years; 95% CI=17-18 years) and 2010-2019 (19 years; 95% CI=19-19 years). After >10 years of DENV-1 predominance, the proportions of DENV serotypes 2 (DENV-2) and 3 (DENV-3) increased significantly during 2023-2024, with DENV-3 replacing DENV-1 as the predominant serotype. In addition, the proportion of dengue patients who were hospitalized increased from 35.7% (2010-2019) to 53.5% (2023-2024). The current dengue outbreak in Puerto Rico marks a shift in serotype predominance to DENV-3 and increasing percentages of cases in older age groups (61.7% in adults aged ≥20 years), although a high proportion of cases still occur among adolescents aged 10-19 years (29.5%). The current dengue outbreak also has a higher rate of hospitalizations than those in previous years. Understanding the changing epidemiology of dengue is crucial to guiding public health strategies for dengue control, including clinical management, surveillance and health care system resilience, and public outreach and education.

Prevalence of Different Dengue Serotypes in Northern India, 2021-2022: A Tertiary Care Hospital-Based Study.

Dengue fever is a substantial emerging and reemerging arboviral virus in tropical and subtropical areas that seriously threatens public health worldwide. India is experiencing rising dengue epidemics in urban and rural regions linked to all four serotypes. The objective is to examine the serotypes and genotypes of the circulating dengue virus (DENV) at a tertiary care center in eastern Uttar Pradesh, India, from 2020 to 2021. This retrospective cross-sectional observational study involved dengue patients from January 2021 to December 2022. The genetic analysis of the circulating DENV was conducted by amplifying the partial CprM (511-bp) gene using nested reverse transcriptase polymerase chain reaction (RT-PCR), followed by sequencing. Only those positive for NS1 antigen (n = 581) were included in the study. A total of 204 cases (35.1%) were seropositive, with 96 cases (37.4%) out of 257 in 2021 and 108 cases (33.3%) out of 324 in 2022. With 119 cases (58.3%), men were most affected. The nested RT-PCR for dengue revealed three DENV-1 to DENV-3, except for DENV-4. DENV-2 and DENV-3 were the most predominant serotypes, with 98 (48%) and 94 (46%) cases, respectively. Conversely, DENV-1 was the least prevalent with cases 3 (1.6%). Unfortunately, 35 (17.2%) of the 204 cases died. DENV-2 had the highest mortality rate, with 23 deaths (65.7%). In cases with DENV-3, nine (25.7%) died. This study revealed regional disparities in DENV serotype prevalence in India. If regional differences in the most common serotypes and genotypes are identified early in the season, molecular surveillance may predict major dengue outbreaks and severity.

Natural Inhibitors of Salmonella MDR Efflux Pumps AcrAB and AcrD: An Integrated In Silico, Molecular, and In Vitro Investigation.

Multidrug-resistant (MDR) Salmonella remains a significant global health threat. This study aimed to explore the potential of essential oil components as novel inhibitors of the Salmonella MDR efflux pumps AcrAB and AcrD. Salmonella isolates were characterized for serotype, antibiotic resistance, and efflux pump activity. Essential oil components were screened for inhibitory effects using phenotypic and genotypic methods. In silico docking and molecular dynamics simulations were conducted to investigate binding interactions and stability. Salmonella Typhimurium was the predominant serotype with high MDR rates. Efflux pump activity was prevalent. Cumin and cinnamon oils demonstrated promising inhibitory effects on these pumps. Molecular docking simulations revealed strong binding affinities of analyzed compounds to the AcrAB and AcrD binding pocket. The 2-methyl-1-(p-tolyl)propan-2-ol exhibited higher stability within the AcrAB binding pocket compared to (1S,3R,5R)-1-isopropyl-4-methylenebicyclo[3.1.0]hexan-3-ol within the AcrD binding pocket. Treatment with these oils significantly downregulated efflux pump genes (robA, acrB, mdtB, acrF, acrD, soxS, mdsB, marA). The novel approach of combining in silico and molecular dynamics simulations with precise gene expression analysis provides a valuable framework for future studies aimed at combating MDR Salmonella efflux pumps.

Diagnostic Challenges of Arboviral Infections and Dengue Virus Serotype Distribution in Febrile Patients in East Java, Indonesia

ObjectivesArboviruses pose significant public health threats globally, with Southeast Asia being a hotspot for these infections. This study aimed to reassess the incidence of dengue, Zika, and chikungunya viruses in patients clinically diagnosed with dengue in East Java, Indonesia in 2023. MethodsThe study included 108 patients admitted to hospitals in Jember, with blood samples collected on admission. Multiplex RT-PCR was used to detect viral RNA for dengue, Zika, and chikungunya, while dengue serotypes were identified using real-time PCR. ResultsA total of n=67/108 patients (62%) tested positive for dengue virus (DENV), one patient tested positive for chikungunya and no cases of Zika were detected. Differences in laboratory parameters between DENV RNA-negative patients and confirmed dengue cases suggest possible misdiagnosis of dengue. Serotyping of DENV-positive samples revealed DENV-3 as predominant serotype in Jember, accounting for 34% of cases (n=23/67), followed by DENV-1 and DENV-2 at 19% each (n=13/67), and 6% for DENV-4 (n=4/67), while 21% (n=14/67) remained untyped. ConclusionsThis study highlights the nature of the dengue outbreak in Jember in 2023, where all four DENV serotypes were in circulation, and underlines the need for serological or nucleic acid-based methods to improve arbovirus diagnosis in the region.

Dominance of dengue virus serotype-2 in Pakistan (2023-2024): Molecular characterization of the envelope gene and exploration of antiviral targets.

Dengue virus infection, caused by a single positive-stranded RNA virus from the Flaviviridae family, represents a significant public health challenge in tropical and subtropical regions. This virus has four serotypes (DENV-1, 2, 3, and 4), primarily transmitted by Aedes mosquitoes. Despite extensive research, effective antiviral treatments and vaccines remain elusive due to the viral diversity and the complex mechanisms such as antibody-dependent enhancement (ADE). In the current study, NS1-positive serum samples from dengue cases in Pakistan (2023-2024), were analyzed to determine the predominant serotype and characterize the envelope (E) gene for further exploration of antiviral targets. Out of 100 samples, 63 (63%) tested positive for DENV-2, indicating its predominance during this period, while two samples showed mixed infections with DENV-2 and DENV-3. The envelope gene was successfully amplified using nested PCR, validated through gel electrophoresis and sanger sequencing. Phylogenetic analysis revealed high similarity of the DENV-2 isolates to strains from China and India. Computational modeling of the envelope protein structure identified potential antiviral binding sites and further molecular docking studies suggested that specific antiviral compounds like Arbidol and Quercetin can inhibit early steps in viral infection. Additionally, BepiPred-3.0 predicted several B-cell epitopes, which could be useful for vaccine development. These findings enhance our understanding of dengue epidemiology in Pakistan and contribute to the development of targeted antiviral therapies, potentially informing future vaccination strategies and outbreak management.

The Epidemiological Impact of Dengue in Colombia: A Systematic Review.

Dengue is the most important viral vector-borne disease in the tropics, with Colombia being one of the most affected countries. In this context, it is essential to identify and synthesize the existing evidence on the epidemiology of dengue in Colombia. A systematic review (PROSPERO CRD42021257985) was conducted by searching for epidemiological data in populations with suspected or confirmed dengue in Colombia from 2012 to 2020. We searched PubMed, EMBASE, the Cochrane Library, the LILACS, and SciELO databases, and 104 publications out of 1,234 records were selected. The dengue annual incidence rate varied through the years without a clear trend. The lowest annual incidence rate was observed in 2017 (90.7 per 100,000 population) and the highest in 2013 (476.2 per 100,000 population). The proportion of severe cases in the same period ranged between 0.89% in 2016 and 2.7% in 2012. The four dengue virus (DENV) serotypes co-circulated in the country, and DENV-2 was the predominant serotype. Fifty percent of dengue cases occurred in people under 20 years, and those between 5 and 14 years had the highest incidence rate. The mortality rate for all dengue cases ranged from 0.07% in 2020 to 0.16% in 2012 and 2015. In conclusion, dengue is a hyperendemic disease in Colombia with the circulation of four serotypes. New strategies must be implemented to prevent the contagion and impact of the disease on the population at risk.

Genomic epidemiology of ceftriaxone-resistant non-typhoidal Salmonella enterica strain in China

Non-typhoidal Salmonella (NTS) is one of the top causes of diarrhea worldwide. Ceftriaxone is commonly recommended as the initial treatment option for Salmonella infections due to its antibacterial effectiveness. The objective of this study was to investigate the molecular epidemiological characteristics of NTS and to compare the phenotypic and genotypic profiles of antimicrobial resistance in multidrug-resistant Salmonella strains by sequencing 329 NTS strains collected from a county-level hospital between 2018 and 2021. Multi-locus sequence typing (MLST), antimicrobial resistance genes and plasmid types were identified by BacWGSTdb 2.0 webserver. Phylogenetic analysis of all NTS strains was carried out using Snippy and Gubbins software. The transferability of ceftriaxone resistant plasmids was confirmed through plasmid conjugation assays, and verified by S1-PFGE-Southern blot assays. The predominant serotypes among all NTS strains were Typhimurium (161/329), Enteritidis (49/329) and London (45/329). The most common sequence type observed was ST34 (86/329), followed by ST19 (72/329) and ST11 (47/329). The antimicrobial resistance of Salmonella to a wide range of antimicrobials showed an overall increase. Out of these 37 (11.24%) ceftriaxone-resistant strains, with the majority of them (33/37) being blaCTX−M. The predominant plasmid types identified were IncHI2 (14/21) and IncI1 (6/21), ranging in size from 70 kb to 360 kb. The conjugation efficiency was calculated with the high conjugation efficiency of 1.1 × 10− 5 to 9.3 × 10− 2. The strains varied widely, ranging from 3 to 45,024 single nucleotide polymorphisms (SNPs). There are close linkages observed among the predominant lineage, with an average of 78 SNPs between each pair of ST34 strains. The findings contribute to our understanding of the transmission and resistance mechanisms of multidrug-resistant Salmonella, thereby facilitating the development of effective control strategies.

Cryptic transmission and novel introduction of Dengue 1 and 2 genotypes in Colombia.

Dengue fever remains as a public health challenge in Colombia, standing as the most prevalent infectious disease in the country. The cyclic nature of dengue epidemics, occurring approximately every 3years, is intricately linked to meteorological events like El Niño Southern Oscillation (ENSO). Therefore, the Colombian system faces challenges in genomic surveillance. This study aimed to evaluate local dengue virus (DENV) transmission and genetic diversity in four Colombian departments with heterogeneous incidence patterns (department is first-level territorial units in Colombia). For this study, we processed 266 serum samples to identify DENV. Subsequently, we obtained 118 genome sequences by sequencing DENV genomes from serum samples of 134 patients infected with DENV-1 and DENV-2 serotypes. The predominant serotype was DENV-2 (108/143), with the Asian-American (AA) genotype (91/118) being the most prevalent one. Phylogenetic analysis revealed concurrent circulation of two lineages of both DENV-2 AA and DENV-1 V, suggesting ongoing genetic exchange with sequences from Venezuela and Cuba. The continuous migration of Venezuelan citizens into Colombia can contribute to this exchange, emphasizing the need for strengthened prevention measures in border areas. Notably, the time to most recent common ancestor analysis identified cryptic transmission of DENV-2 AA since approximately 2015, leading to the recent epidemic. This challenges the notion that major outbreaks are solely triggered by recent virus introductions, emphasizing the importance of active genomic surveillance. The study also highlighted the contrasting selection pressures on DENV-1 V and DENV-2 AA, with the latter experiencing positive selection, possibly influencing its transmissibility. The presence of a cosmopolitan genotype in Colombia, previously reported in Brazil and Peru, raises concerns about transmission routes, emphasizing the necessity for thorough DENV evolution studies. Despite limitations, the study underscores genomic epidemiology's crucial role in early detection and comprehension of DENV genotypes, recommending the use of advanced sequencing techniques as an early warning system to help prevent and control dengue outbreaks in Colombia and worldwide.

Clinical characteristics of pediatric patients with pneumonia and Streptococcus pneumoniae serotype distribution at Hai Phong Children’s Hospital, Vietnam

Streptococcus pneumoniae (S. pneumoniae) is a major cause of pneumonia in pediatric health concerns. Effective vaccination strategies depend on understanding serotype distribution and its correlation with clinical manifestations. This study aims to describe the serotype distribution of Streptococcus pneumoniae strains at Hai Phong Children’s Hospital, Vietnam. Conducted at Hai Phong Children’s Hospital in Vietnam from November 2022 to September 2023, our cross-sectional study enrolled 428 pediatric pneumonia patients. Nasopharyngeal fluid specimens were collected to isolate S. pneumoniae by culture and confirmed by Real-time PCR. S. pneumoniae serotyping was performed by realtime PCR. Medical records provided symptom and medical history data. Out of 428 samples, 66.8% tested positive for S. pneumoniae. Among confirmed cases by real-time PCR, 82.6% were typeable, with predominant serotypes being 6A/B (16.4%), 19F (14.9%), 15B/C (11.4%), 19A (11.0%), and 15A/15F (7.8%). Notably, 70.7% of strains belonged to vaccine-covered serotypes. Cough (96.5%), tachypnea (78.7%), fever (56.1%), and wheezing (52.8%) were the most frequent symptoms. Notably, cough, tachypnea, wheezing, and chest indrawing (29.0%) significantly correlated with pneumococcal pneumonia. Positive S. pneumoniae cultures also correlated with chest X-ray findings. Our study reveals a high prevalence of S. pneumoniae in pediatric patients with pneumonia in Vietnam. Insights into serotype distribution, clinical characteristics of pneumonia cases offer valuable guidance for optimizing vaccination programs and enhancing disease management.

Assessing the Impact of Pneumococcal Conjugate Vaccine Immunization Schedule Change From 3+0 to 2+1 in Australian Children: A Retrospective Observational Study.

In mid-2018, the Australian childhood 13-valent pneumococcal conjugate vaccine schedule changed from 3+0 to 2+1, moving the third dose to 12 months of age, to address increasing breakthrough cases of invasive pneumococcal disease (IPD), predominantly in children aged >12 months. This study assessed the impact of this change using national IPD surveillance data. Pre- and postschedule change 3-dose 13-valent pneumococcal conjugate vaccine breakthrough cases were compared by age group, serotype, and clinical syndrome. Annual rates of breakthrough cases were calculated (per 100 000) using respective birth cohort sizes and 3-dose vaccine coverage. Using time-series modelling, observed IPD rates in children aged <12 years were compared to that expected if the 3+0 schedule were continued. Over 2012-2022, rate of 3-dose breakthrough cases in children aged >12 months was 2.8 per 100 000 (n = 557; 11 birth cohorts). Serotype 3 replaced 19A as predominant breakthrough serotype (respectively, 24% and 65% in 2013 to 60% and 20% in 2022) followed by 19F. In breakthrough cases, the most frequent clinical phenotype was bacteremic pneumonia (69%), with meningitis accounting for 3%-4%. In cohorts eligible for 2+1 versus 3+0 schedules, rate of breakthrough cases was lower for all vaccine serotypes, except type 3 (incidence rate ratio, 0.50 [95% confidence interval, .28-.84] and 1.12 [0.71-1.76], respectively). Observed compared to expected IPD was 51.7% lower (95% confidence interval, -60.9 to -40.7%) for vaccine serotypes, but the change for nonvaccine types was not significant 12% (-9.6 to 39.7). The 2+1 schedule is likely superior to 3+0 for overall IPD control, a finding that may be worth consideration for other countries considering or using 3+0 PCV schedules.

Prevalence and antimicrobial susceptibility pattern of Vibrio cholerae isolates from cholera outbreak sites in Ethiopia

BackgroundCholera is an acute infectious disease caused by ingestion of contaminated food or water with Vibrio cholerae. Cholera remains a global threat to public health and an indicator of inequity and lack of social development. The aim of this study was to assess the prevalence and antimicrobial susceptibility pattern of V. cholerae from cholera outbreak sites in Ethiopia.MethodsAcross-sectional study was conducted from May 2022 to October 2023 across different regions in Ethiopia: Oromia National Regional State, Amhara National Regional State and Addis Ababa City Administration. A total of 415 fecal samples were collected from the three regions. Two milliliter fecal samples were collected from each study participants. The collected samples were cultured on Blood Agar, MacConkey Agar and Thiosulfate Citrate Bile Salt Sucrose Agar. A series of biochemical tests Oxidase test, String test, Motility, Indole, Citrate, Gas production, H2S production, Urease test were used to identify V. cholerae species. Both polyvalent and monovalent antisera were used for agglutination tests to identify and differentiate V. cholerae serogroup and serotypes. In addition, Kirby-Bauer Disk diffusion antibiotic susceptibility test method was done. Data were registered in epi-enfo version 7 and analyzed by Statistical Package for Social Science version 25. Descriptive statistics were used to determine the prevalence of Vibrio cholerae. Logistic regression model was fitted and p-value < 0.05 was considered as statically significant.ResultsThe prevalence of V. cholerae in the fecal samples was 30.1%. Majority of the isolates were from Oromia National Regional State 43.2% (n = 54) followed by Amhara National Regional State 31.2% (n = 39) and Addis Ababa City Administration 25.6% (n = 32). Most of the V. cholerae isolates were O1 serogroups 90.4% (n = 113) and Ogawa serotypes 86.4% (n = 108). Majority of the isolates were susceptible to ciprofloxacin 100% (n = 125), tetracycline 72% (n = 90) and gentamycin 68% (n = 85). More than half of the isolates were resistant to trimethoprim-sulfamethoxazole 62.4% (n = 78) and ampicillin 56.8% (n = 71). In this study, participants unable to read and write were about four times more at risk for V. cholerae infection (AOR: 3.8, 95% CI: 1.07–13.33). In addition, consumption of river water were about three times more at risk for V. cholerae infection (AOR: 2.8, 95% CI: 1.08–7.08).Conclusionour study revealed a high prevalence of V. cholerae from fecal samples. The predominant serogroups and serotypes were O1 and Ogawa, respectively. Fortunately, the isolates showed susceptible to most tested antibiotics. Drinking water from river were the identified associated risk factor for V. cholerae infection. Protecting the community from drinking of river water and provision of safe and treated water could reduce cholera outbreaks in the study areas.

Geographical distribution, disease association and diversity of Klebsiella pneumoniae K/L and O antigens in India: roadmap for vaccine development.

Klebsiella pneumoniae poses a significant healthcare challenge due to its multidrug resistance and diverse serotype landscape. This study aimed to explore the serotype diversity of 1072 K. pneumoniae and its association with geographical distribution, disease severity and antimicrobial/virulence patterns in India. Whole-genome sequencing was performed on the Illumina platform, and genomic analysis was carried out using the Kleborate tool. The analysis revealed a total of 78 different KL types, among which KL64 (n=274/1072, 26 %), KL51 (n=249/1072, 24 %), and KL2 (n=88/1072, 8 %) were the most prevalent. In contrast, only 13 distinct O types were identified, with O1/O2v1 (n=471/1072, 44 %), O1/O2v2 (n=353/1072, 33 %), and OL101 (n=66/1072, 6 %) being the predominant serotypes. The study identified 114 different sequence types (STs) with varying serotypes, with ST231 being the most predominant. O serotypes were strongly linked with STs, with O1/O2v1 predominantly associated with ST231. Simpson's diversity index and Fisher's exact test revealed higher serotype diversity in the north and east regions, along with intriguing associations between specific serotypes and resistance profiles. No significant association between KL or O types and disease severity was observed. Furthermore, we found the specific association of virulence factors yersiniabactin and aerobactin (P<0.05) with KL types but no association with O antigen types (P>0.05). Conventionally described hypervirulent clones (i.e. KL1 and KL2) in India lacked typical virulent markers (i.e. aerobactin), contrasting with other regional serotypes (KL51). The cumulative distribution of KL and O serotypes suggests that future vaccines may have to include either ~20 KL or four O types to cover >85 % of the carbapenemase-producing Indian K. pneumoniae population. The results highlight the necessity for comprehensive strategies to manage the diverse landscape of K. pneumoniae strains across different regions in India. Understanding regional serotype dynamics is pivotal for targeted surveillance, interventions, and tailored vaccine strategies to tackle the diverse landscape of K. pneumoniae infections across India. This article contains data hosted by Microreact.

Enrichment culture evaluation and characterization of Streptococcus agalactiae among pregnant women in Japan.

Introduction. Maternal screening tests and prophylactic antibiotics are important to prevent neonatal and infant group B streptococcal (GBS) infections.Hypothesis/Gap Statement. The performance of enrichment broth media for GBS screening that are available in Japan is unclear. Whole-genome data of GBS isolates from pregnant women in Japan is lacking.Aim. The aim of this study was to compare the protocol performance of six enrichment broths and two subculture agar plates, which were all available in Japan, for GBS detection. In addition, we showed whole-genome data of GBS isolates from pregnant women in Japan.Methodology. We collected 133 vaginal-rectal swabs from pregnant women visiting clinics and hospitals in Nagasaki Prefecture, Japan, and compared the protocol performance of 6 enrichment broths and 2 subculture agar plates. All GBS isolates collected in this study were subjected to whole-genome sequencing analysis.Results. We obtained 133 vaginal-rectal swabs from pregnant women at 35-37 weeks of gestation from 8 private clinics and 2 local municipal hospitals within Nagasaki Prefecture, Japan. The detection rate of the protocol involving the six enrichment broths and subsequent subcultures varied between 95.5 and 100 %, depending on the specific choice of enrichment broth. The GBS carriage rate among pregnant women in this region was 18.8 %. All 25 isolates derived from the swabs were susceptible to penicillin, whereas 48 and 36 % of the isolates demonstrated resistance to erythromycin and clindamycin, respectively. The distribution of serotypes was highly diverse, encompassing seven distinct serotypes among the isolates, with the predominant serotype being serotype V (n = 8). Serotype V isolates displayed a tendency towards increased resistance to erythromycin and clindamycin, with all resistant isolates containing the ermB gene.Conclusion. There was no difference in performance among the culture protocols evaluated in this study. GBS strains isolated from pregnant women appeared to have greater genomic diversity than GBS strains detected in neonates/infants with invasive GBS infections. To confirm this result, further studies with larger sample sizes are needed.

Resurgence of Dengue Virus Serotype 2: Findings from the 2023 Bangladesh Outbreak.

Bangladesh experienced the largest and deadliest dengue outbreak in 2023, after the virus had reappeared in the country 2 decades earlier. A total of 1,705 people died in Bangladesh, representing the highest case fatality rate (0.5%) due to dengue in the world for that year. The severity of dengue infection is to some extent related to the emergence of new circulating serotypes. To identify the possible predominant serotype in 2023, the reverse transcription polymerase chain reaction-based identification technique was used on stored serum samples of suspected dengue patients during the period between July and December 2023. The overall result of molecular serotyping showed that dengue virus (DENV-2) reappeared as the predominant serotype (74.1%), followed by a moderate number of samples with DENV-1 (19.8%) and DENV-3 (6.1%), in 2023. However, DENV-1 was found to be dominant in a few rural areas of Cox's Bazar districts. During the 2019 outbreak, DENV-3 was the dominant serotype, which seemed to be replaced by the DENV-2 serotype; this may have impacted the increased case fatality in 2023.

Colistin-, cefepime-, and levofloxacin-resistant Salmonella enterica serovars isolated from Egyptian chicken carcasses

ObjectivesThe emergence of multidrug-resistant (MDR) Salmonella strains, especially resistant ones toward critically important antimicrobial classes such as fluoroquinolones and third- and fourth-generation cephalosporins, is a growing public health concern. The current study, therefore, aimed to determine the prevalence, and existence of virulence genes (invA, stn, and spvC genes), antimicrobial resistance profiles, and the presence of β-lactamase resistance genes (blaOXA, blaCTX-M1, blaSHV, and blaTEM) in Salmonella strains isolated from native chicken carcasses in Egypt marketed in Mansoura, Egypt, as well as spotlight the risk of isolated MDR, colistin-, cefepime-, and levofloxacin-resistant Salmonella enterica serovars to public health.MethodsOne hundred fifty freshly dressed native chicken carcasses were collected from different poultry shops in Mansoura City, Egypt between July 2022 and November 2022. Salmonella isolation was performed using standard bacteriological techniques, including pre-enrichment in buffered peptone water (BPW), selective enrichment in Rappaport Vassiliadis broth (RVS), and cultivating on the surface of xylose-lysine-desoxycholate (XLD) agar. All suspected Salmonella colonies were subjected to biochemical tests, serological identification using slide agglutination test, and Polymerase Chain Reaction (PCR) targeting the invasion A gene (invA; Salmonella marker gene). Afterward, all molecularly verified isolates were screened for the presence of virulence genes (stn and spvC). The antimicrobial susceptibility testing for isolated Salmonella strains towards the 16 antimicrobial agents tested was analyzed by Kirby–Bauer disc diffusion method, except for colistin, in which the minimum inhibition concentration (MIC) was determined by broth microdilution technique. Furthermore, 82 cefotaxime-resistant Salmonella isolates were tested using multiplex PCR targeting the β-lactamase resistance genes, including blaOXA, blaCTX-M1, blaSHV, and blaTEM genes.ResultsSalmonella enterica species were molecularly confirmed via the invA Salmonella marker gene in 18% (27/150) of the freshly dressed native chicken carcasses. Twelve Salmonella serotypes were identified among 129 confirmed Salmonella isolates with the most predominant serotypes were S. Kentucky, S. Enteritidis, S. Typhimurium, and S. Molade with an incidence of 19.4% (25/129), 17.1% (22/129), 17.1% (22/129), and 10.9% (14/129), respectively. All the identified Salmonella isolates (n = 129) were positive for both invA and stn genes, while only 31.8% (41/129) of isolates were positive for the spvC gene. One hundred twenty-one (93.8%) of the 129 Salmonella-verified isolates were resistant to at least three antibiotics. Interestingly, 3.9%, 14.7%, and 75.2% of isolates were categorized into pan-drug-resistant, extensively drug-resistant, and multidrug-resistant, respectively. The average MAR index for the 129 isolates tested was 0.505. Exactly, 82.2%, 82.2%, 63.6%, 51.9%, 50.4%, 48.8%, 11.6%, and 10.1% of isolated Salmonella strains were resistant to cefepime, colistin, cefotaxime, ceftazidime/clavulanic acid, levofloxacin, ciprofloxacin, azithromycin, and meropenem, respectively. Thirty-one out (37.8%) of the 82 cefotaxime-resistant Salmonella isolates were β-lactamase producers with the blaTEM as the most predominant β-lactamase resistance gene, followed by blaCTX-M1 and blaOXA genes, which were detected in 21, 16, and 14 isolates respectively).ConclusionThe high prevalence of MDR-, colistin-, cefepime-, and levofloxacin-resistant Salmonella serovars among Salmonella isolates from native chicken is alarming as these antimicrobials are critically important in treating severe salmonellosis cases and boost the urgent need for controlling antibiotic usage in veterinary and human medicine to protect public health.Graphical

Phenotypic and genotypic characterization of antimicrobial resistance of non-typhoidal Salmonella from retail meat in California

Antimicrobial resistance (AMR) is a global emerging problem for food safety and public health. Retail meat is one of the vehicles that may transmit antimicrobial resistant bacteria to humans. Here we assessed the phenotypic and genotypic resistance of non-typhoidal Salmonella from retail meat collected in California in 2019 by the National Antimicrobial Resistance Monitoring System (NARMS) Retail Food Surveillance program. A total of 849 fresh meat samples were collected from randomly selected grocery stores in Northern and Southern California from January to December 2019. The overall prevalence of Salmonella was 15.31 %, with a significantly higher occurrence in Southern (28.38%) than in Northern (5.22 %) California. The prevalence of Salmonella in chicken (24.01 %) was higher (p < 0.001) compared to ground turkey (5.42 %) and pork (3.08 %) samples. No Salmonella were recovered from ground beef samples. The prevalence of Salmonella in meat with reduced antibiotic claim (20.35 %) was higher (p < 0.001) than that with conventional production (11.96 %). Salmonella isolates were classified into 25 serotypes with S. Kentucky (47.73 %), S. typhimurium (11.36 %), and S. Alachua (7.58 %) as predominant serotypes. Thirty-two out of 132 (24.24 %) Salmonella isolates were susceptible to all tested antimicrobial drugs, while 75.76 % were resistant to one or more drugs, 62.88 % to two or more drugs, and 9.85 % to three or more drugs. Antimicrobials that Salmonella exhibited high resistance to were tetracycline (82/132, 62.12 %) and streptomycin (79/132, 59.85 %). No significant difference was observed between reduced antibiotic claim and conventional production in the occurrence of single and multidrug resistance. A total of 23 resistant genes, a D87Y mutation of gyrA, and 23 plasmid replicons were identified from resistant Salmonella isolates. Genotypic and phenotypic results were well correlated with an overall sensitivity of 96.85 %. S. infantis was the most resistant serotype which also harbored the IncFIB (pN55391) plasmid replicon and gyrA (87) mutation. Data from Northern and Southern California in this study helps us to understand the AMR trends in Salmonella from retail meat sold in the highly populous and demographically diverse state of California.