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Microbial Genomics Sep 2023Non-typhoidal are extremely diverse and different serovars can exhibit varied phenotypes, including host adaptation and the ability to cause clinical illness in animals...
Non-typhoidal are extremely diverse and different serovars can exhibit varied phenotypes, including host adaptation and the ability to cause clinical illness in animals and humans. In the USA, serovar Kentucky is infrequently found to cause human illness, despite being the top serovar isolated from broiler chickens. Conversely, in Europe, this serovar falls in the top 10 serovars linked to human salmonellosis. Serovar Kentucky is polyphyletic and has two lineages, Kentucky-I and Kentucky-II; isolates belonging to Kentucky-I are frequently isolated from poultry in the USA, while Kentucky-II isolates tend to be associated with human illness. In this study, we analysed whole-genome sequences and associated metadata deposited in public databases between 2017 and 2021 by federal agencies to determine serovar Kentucky incidence across different animal and human sources. Of 5151 genomes, 90.3 % were from isolates that came from broilers, while 5.9 % were from humans and 3.0 % were from cattle. Kentucky-I isolates were associated with broilers, while isolates belonging to Kentucky-II and a new lineage, Kentucky-III, were more commonly associated with cattle and humans. Very few serovar Kentucky isolates were associated with turkey and swine sources. Phylogenetic analyses showed that Kentucky-III genomes were more closely related to Kentucky-I, and this was confirmed by CRISPR-typing and multilocus sequence typing (MLST). In a macrophage assay, serovar Kentucky-II isolates were able to replicate over eight times better than Kentucky-I isolates. Analysis of virulence factors showed unique patterns across these three groups, and these differences may be linked to their association with different hosts.
Topics: Humans; Animals; Cattle; Swine; Serogroup; Salmonella enterica; Chickens; Kentucky; Multilocus Sequence Typing; Phylogeny; Genomics; Phenotype
PubMed: 37750759
DOI: 10.1099/mgen.0.001089 -
Polish Journal of Microbiology Jun 2023(pneumococcus) belongs to the Gram-positive cocci. This bacterium typically colonizes the nasopharyngeal region of healthy individuals. It has a distinct polysaccharide... (Review)
Review
(pneumococcus) belongs to the Gram-positive cocci. This bacterium typically colonizes the nasopharyngeal region of healthy individuals. It has a distinct polysaccharide capsule - a virulence factor allowing the bacteria to elude the immune defense mechanisms. Consequently, it might trigger aggressive conditions like septicemia and meningitis in immunocompromised or older individuals. Moreover, children below five years of age are at risk of morbidity and mortality. Studies have found 101 capsular serotypes, of which several correlate with clinical and carriage isolates with distinct disease aggressiveness. Introducing pneumococcal conjugate vaccines (PCV) targets the most common disease-associated serotypes. Nevertheless, vaccine selection pressure leads to replacing the formerly dominant vaccine serotypes (VTs) by non-vaccine types (NVTs). Therefore, serotyping must be conducted for epidemiological surveillance and vaccine assessment. Serotyping can be performed using numerous techniques, either by the conventional antisera-based (Quellung and latex agglutination) or molecular-based approaches (sequetyping, multiplex PCR, real-time PCR, and PCR-RFLP). A cost-effective and practical approach must be used to enhance serotyping accuracy to monitor the prevalence of VTs and NVTs. Therefore, dependable pneumococcal serotyping techniques are essential to precisely monitor virulent lineages, NVT emergence, and genetic associations of isolates. This review discusses the principles, associated benefits, and drawbacks of the respective available conventional and molecular approaches, and potentially the whole genome sequencing (WGS) to be directed for future exploration.
Topics: Child; Humans; Serotyping; Streptococcus pneumoniae; Biomedical Research; Immunocompromised Host; Multiplex Polymerase Chain Reaction
PubMed: 37314355
DOI: 10.33073/pjm-2023-023 -
Microbiology Spectrum Dec 2023This study assessed the clinical and molecular epidemiology of carbapenem-resistant Enterobacteriaceae in pediatric inpatients at three hospitals in South China by means...
This study assessed the clinical and molecular epidemiology of carbapenem-resistant Enterobacteriaceae in pediatric inpatients at three hospitals in South China by means of screening stool samples for carbapenem-resistant genes and a nested case-control study to determine risk factors for carriage of carbapenem-resistant Enterobacteriaceae. Of 4,033 fecal samples screened, 158 (3.92%) were positive for CRE, including (51.27 %), (37.97%), and (6.96%). The most common carbapenemase genes harbored by gastrointestinal CRE strains were blaNDM-5, blaNDM-1, and blaIMP-4. Hematological malignancies, respiratory diseases, otolaryngological diseases, nervous system diseases, oral administration of third-generation cephalosporins, and the combined use of two or more antibiotics were independently associated with CRE colonization.
Topics: Humans; Child; Carbapenem-Resistant Enterobacteriaceae; Enterobacteriaceae Infections; Molecular Epidemiology; Case-Control Studies; Inpatients; Bacterial Proteins; beta-Lactamases; Anti-Bacterial Agents; Klebsiella pneumoniae; Escherichia coli; Microbial Sensitivity Tests
PubMed: 37819092
DOI: 10.1128/spectrum.02839-23 -
Microbiology Spectrum Jun 2023Carbapenem-resistant Klebsiella pneumoniae (CRKP) has disseminated globally and is difficult to treat, causing increased morbidity and mortality rates in critically ill...
Carbapenem-resistant Klebsiella pneumoniae (CRKP) has disseminated globally and is difficult to treat, causing increased morbidity and mortality rates in critically ill patients. We conducted a multicenter cross-sectional study of intensive care unit (ICU) inpatients in 78 hospitals to investigate the prevalence and molecular characteristics of CRKP in Henan Province, China, a hyperepidemic region. A total of 327 isolates were collected and downsampled to 189 for whole-genome sequencing. Molecular typing revealed that sequence type 11 (ST11) of clonal group 258 (CG258) was predominant (88.9%, = 168), followed by ST2237 (5.8%, = 11) and ST15 (2.6%, = 5). We used core genome multilocus sequence typing (cgMLST) to further classified the population into 13 subtypes. Capsule polysaccharide (K-antigen) and lipopolysaccharide (LPS; O-antigen) typing revealed that K64 (48.1%, = 91) and O2a (49.2%, = 93) were the most common. We studied isolates collected from both the airway and the gut of the same patients and showed that intestinal carriage was associated with respiratory colonization (odds ratio = 10.80, < 0.0001). Most isolates (95.2%, = 180) showed multiple drug resistance (MDR), while 59.8% ( = 113) exhibited extensive drug resistance (XDR), and all isolates harbored either (98.9%, = 187) or and extended-spectrum beta-lactamases (ESBLs) (75.7%, = 143). However, most were susceptible to ceftazidime-avibactam (CZA) (94.7%, = 179) and colistin (97.9%, = 185). We found truncations in isolates conferring resistance to colistin and mutations in and OmpK35 and OmpK36 osmoporins in CZA-resistant isolates. Using a regularized regression model, we found that the aerobactin sequence type and the salmochelin sequence type, among others, were predictors of the hypermucoviscosity phenotype. In this study, we address the ongoing epidemic of carbapenem-resistant Klebsiella pneumoniae, a critical threat to public health. The alarming genotypic and phenotypic convergence of multidrug resistance and virulence highlights the increasingly aggravated threat posed by K. pneumoniae. This calls for a combined effort of physicians and scientists to study the potential mechanisms and establish guidelines for antimicrobial therapies and interventions. To this end, we have conducted a genomic epidemiology and characterization study using isolates collected in a coordinated effort of multiple hospitals. Innovative biological discoveries of clinical importance are made and brought to the attention of clinical researchers and practitioners. This study presents an important advance in the application of genomics and statistics to recognize, understand, and control an infectious disease of concern.
Topics: Humans; Klebsiella pneumoniae; Anti-Bacterial Agents; Carbapenems; Colistin; Cross-Sectional Studies; Klebsiella Infections; beta-Lactamases; Inpatients; Carbapenem-Resistant Enterobacteriaceae; Intensive Care Units; Genomics; Microbial Sensitivity Tests; Bacterial Proteins
PubMed: 37212684
DOI: 10.1128/spectrum.04197-22 -
Frontiers in Cellular and Infection... 2023A high incidence of human leptospirosis is recorded on Mayotte, an oceanic island located in southwestern Indian Ocean, but the severity of the disease appears...
INTRODUCTION
A high incidence of human leptospirosis is recorded on Mayotte, an oceanic island located in southwestern Indian Ocean, but the severity of the disease appears relatively mild in terms of mortality rate and admission to the intensive care unit. It has been proposed that mild leptospirosis may result from a limited virulence of some of the occurring species to which the population is exposed.
METHODS
Clinical and biological data of patients admitted to the Centre Hospitalier de Mayotte were collected and the infecting species were determined through molecular typing.
RESULTS
interrogans was detected in the minority of admitted patients but most of these patients suffered from severe forms, with 50% admitted to intensive care unit and suffering from organ failures. Nineteen percent of patients infected with borgpetersenii were admitted to the intensive care, with 13% displaying organ failures, and one patient died. mayottensis was found in 28% of the patients and not a single severe case was observed.
DISCUSSION
The distribution of species in patients was not different from that reported 10-15 years ago and bacterial genotypes were very closely related to those previously reported. These results highlight the importance of the diversity of pathogenic circulating on Mayotte island and are in keeping with distinct outcome of the disease depending on the infecting . Altogether, presented data support that the infecting species is an important driver of disease severity in humans.
Topics: Humans; Leptospirosis; Leptospira; Leptospira interrogans; Genotype; Molecular Typing; Comoros
PubMed: 37953799
DOI: 10.3389/fcimb.2023.1259599 -
BMC Microbiology Nov 2023Ventilator-associated pneumonia (VAP) and pyogenic liver abscess (PLA) due to Klebsiella pneumoniae infection can trigger life-threatening malignant consequences,...
Ventilator-associated pneumonia (VAP) and pyogenic liver abscess (PLA) due to Klebsiella pneumoniae infection can trigger life-threatening malignant consequences, however, there are few studies on the strain-associated clinical pathogenic mechanisms between VAP and PLA. A total of 266 patients consist of 129 VAP and 137 PLA were included for analysis in this study. We conducted a comprehensive survey for the two groups of K. pneumoniae isolates, including phenotypic experiments, clinical epidemiology, genomic analysis, and instrumental analysis, i.e., to obtain the genomic differential profile of K. pneumoniae strains responsible for two distinct infection outcomes. We found that PLA group had a propensity for specific underlying diseases, especially diabetes and cholelithiasis. The resistance level of VAP was significantly higher than that of PLA (78.57% vs. 36%, P < 0.001), while the virulence results were opposite. There were also some differences in key signaling pathways of biochemical processes between the two groups. The combination of iucA, rmpA, hypermucoviscous phenotype, and ST23 presented in K. pneumoniae infection is more important and highly prudent for timely treatment. The present study may contribute a benchmark for the K. pneumoniae clinical screening, epidemiological surveillance, and effective therapeutic strategies.
Topics: Humans; Klebsiella pneumoniae; Virulence Factors; Pneumonia, Ventilator-Associated; Multilocus Sequence Typing; Liver Abscess; Phenotype; Klebsiella Infections
PubMed: 37957579
DOI: 10.1186/s12866-023-03022-5 -
VBCG: 20 validated bacterial core genes for phylogenomic analysis with high fidelity and resolution.Microbiome Nov 2023Phylogenomic analysis has become an inseparable part of studies of bacterial diversity and evolution, and many different bacterial core genes have been collated and used...
BACKGROUND
Phylogenomic analysis has become an inseparable part of studies of bacterial diversity and evolution, and many different bacterial core genes have been collated and used for phylogenomic tree reconstruction. However, these genes have been selected based on their presence and single-copy ratio in all bacterial genomes, leaving out the gene's 'phylogenetic fidelity' unexamined.
RESULTS
From 30,522 complete genomes covering 11,262 species, we examined 148 bacterial core genes that have been previously used for phylogenomic analysis. In addition to the gene presence and single-copy rations, we evaluated the gene's phylogenetic fidelity by comparing each gene's phylogeny with its corresponding 16S rRNA gene tree. Out of the 148 bacterial genes, 20 validated bacterial core genes (VBCG) were selected as the core gene set with the highest bacterial phylogenetic fidelity. Compared to the larger gene set, the 20-gene core set resulted in more species having all genes present and fewer species with missing data, thereby enhancing the accuracy of phylogenomic analysis. Using Escherichia coli strains as examples of prominent bacterial foodborne pathogens, we demonstrated that the 20 VBCG produced phylogenies with higher fidelity and resolution at species and strain levels while 16S rRNA gene tree alone could not.
CONCLUSION
The 20 validated core gene set improves the fidelity and speed of phylogenomic analysis. Among other uses, this tool improves our ability to explore the evolution, typing and tracking of bacterial strains, such as human pathogens. We have developed a Python pipeline and a desktop graphic app (available on GitHub) for users to perform phylogenomic analysis with high fidelity and resolution. Video Abstract.
Topics: Humans; Phylogeny; Genes, Bacterial; RNA, Ribosomal, 16S; Genome, Bacterial; Bacteria
PubMed: 37936197
DOI: 10.1186/s40168-023-01705-9 -
The Journal of Maternal-fetal &... Dec 2024This study was aimed to investigate the serotypes, antibiotic susceptibilities, and multi-locus sequence type (MLST) profiles of group B (GBS) in the Beijing area.
OBJECTIVE
This study was aimed to investigate the serotypes, antibiotic susceptibilities, and multi-locus sequence type (MLST) profiles of group B (GBS) in the Beijing area.
METHODS
Lower vaginal and rectal swabs were obtained from pregnant women of 35-37 gestational weeks (GWs) who attended the Beijing Obstetrics and Gynecology Hospital. All GBS isolates were identified with Gram staining, catalase reaction assays, and CAMP tests, followed by antibiotic susceptibility testing, serotype identification, multilocus sequence typing and erythromycin resistance gene analysis ( and ).
RESULTS
From July 2020 to June 2022, 311 (5.17%) of 6012 pregnant women that were screened for GBS colonization were detected positive. Of the eight serotypes identified (III, Ia, Ib, IV, II, VIII, V, and NT), serotypes III (43.09%), Ia (34.08%) and Ib (17.04%) were the predominant species. In the antimicrobial susceptibility experiments, the resistant rates measured for erythromycin, clindamycin, levofloxacin, and tetracycline were 76.21%, 63.99%, 50.80%, and 81.03%, respectively, and 7.6% of GBS isolates showed inducible clindamycin in resistance (D-test phenotype). Meanwhile, the multilocus sequence typing analysis showed that sequence type 19 (ST19) (30.34%) and ST10 (18.62%) were the dominant sequence types. Among the 237 erythromycin-resistant isolates, 176 harbored (128, 54.00%) or (48, 20.30%) gene alone.
CONCLUSION
The infection rates, serotypes or MSLT distribution, and antimicrobial resistance of GBS in Beijing area were investigated, which may be applied in analyses of the epidemiological characteristics of GBS. This contributes to the basic knowledge required for successful GBS vaccine development suited for disease prevention and treatment in China, as well as the implementation of effective clinical antimicrobials.
Topics: Female; Humans; Pregnancy; Anti-Bacterial Agents; Serogroup; Pregnant Women; Clindamycin; Streptococcal Infections; Multilocus Sequence Typing; Drug Resistance, Bacterial; Erythromycin; Streptococcus agalactiae; China; Microbial Sensitivity Tests
PubMed: 38124302
DOI: 10.1080/14767058.2023.2295805 -
Communicable Diseases Intelligence... Aug 2023In Australia, both probable and laboratory-confirmed cases of invasive meningococcal disease (IMD) are reported to the National Notifiable Diseases Surveillance System...
In Australia, both probable and laboratory-confirmed cases of invasive meningococcal disease (IMD) are reported to the National Notifiable Diseases Surveillance System (NNDSS). Compared to 2021, the number of IMD notifications in 2022 increased by 81% to 127, alongside the easing of COVID-19 containment measures. Laboratory confirmation occurred in 95% of these cases, with 51% (62/121) diagnosed by bacterial culture and 49% (59/121) by nucleic acid amplification testing. The serogroup was determined for 97% of laboratory-confirmed cases (117/121): serogroup B (MenB) accounted for 83% of infections (100/121); MenW for 4% (5/121); MenY for 10% (12/121); no infections were attributed to MenC disease. Fine typing was available on 67% of the cases for which the serogroup was determined (78/117). In MenB isolates, 27 porA types were detected, the most prevalent of which were P1.7-2,4 (18%;11/62), P1.22,14 (15%; 9/62), P1.18-1,34 (10%; 6/62) and P1.7,16-26 (10%; 6/62). All five MenW infections identified as porA type P1.5,2 with different MLST sequence types (ST): 11, 574, 1287, 12351, 13135 all belonging to clonal complex 11, the hypervirulent strain reported in outbreaks in Australia and overseas. In MenY, the predominant porA type was P1.5-1,10-1 (73%; 8/11), ST 1655 and from clonal complex 23. Children less than 5 years of age and people aged 15-19 years were overrepresented with IMD notifications, accounting for 22% (27/121) and 23% (28/121) of laboratory-confirmed cases respectively. Fifteen percent of laboratory-confirmed notifications (18/121) were in persons aged 45-64 years. MenB infections were detected in all age groups but predominated in persons aged 15-19 years (93% of IMD in this age group; 26/28) and comprised 89% (24/27) of infections in children aged less than 5 years. MenW infections were markedly reduced in 2022, accounting for two IMD detections in children 1-4 years (2/16) and sporadic detections in other older age groups. MenY infections were largely detected in adults aged 45-64 years, accounting for 28% of IMD in this age group (5/18). All 62 cultured IMD isolates had antimicrobial susceptibility testing performed. Minimum inhibitory concentration (MIC) values were categorised using Clinical Laboratory Standards Institute (CLSI) interpretative criteria: 5% (3/62) were defined as penicillin resistant (MIC value ≥ 0.5 mg/L); 71% (44/62) had intermediate susceptibility to penicillin (MIC values 0.125 and 0.25 mg/L) and 24% (15/62) were susceptible to penicillin. All isolates were susceptible to ceftriaxone, ciprofloxacin and rifampicin.
Topics: Child; Adult; Humans; Aged; Adolescent; Young Adult; Anti-Bacterial Agents; Multilocus Sequence Typing; Genotype; Australia; Neisseria meningitidis; Meningococcal Infections; Penicillins
PubMed: 37817314
DOI: 10.33321/cdi.2023.47.44 -
Microbiology Spectrum Aug 2023The global dissemination of methicillin-resistant Staphylococcus aureus (MRSA) is associated with the emergence and establishment of clones in specific geographic areas....
The global dissemination of methicillin-resistant Staphylococcus aureus (MRSA) is associated with the emergence and establishment of clones in specific geographic areas. The Chilean-Cordobes clone (ChC) (ST5-SCCI) has been the predominant MRSA clone in Chile since its first description in 1998, despite the report of other emerging MRSA clones in recent years. Here, we characterize the evolutionary history of MRSA from 2000 to 2016 in a Chilean tertiary health care center using phylogenomic analyses. We sequenced 469 MRSA isolates collected between 2000 and 2016. We evaluated the temporal trends of the circulating clones and performed a phylogenomic reconstruction to characterize the clonal dynamics. We found a significant increase in the diversity and richness of sequence types (STs; Spearman = 0.8748, < 0.0001) with a Shannon diversity index increasing from 0.221 in the year 2000 to 1.33 in 2016, and an effective diversity (Hill number; q = 2) increasing from 1.12 to 2.71. The temporal trend analysis revealed that in the period 2000 to 2003 most of the isolates (94.2%; = 98) belonged to the ChC clone. However, since then, the frequency of the ChC clone has decreased over time, accounting for 52% of the collection in the 2013 to 2016 period. This decline was accompanied by the rise of two emerging MRSA lineages, ST105-SCCII and ST72-SCCVI. In conclusion, the ChC clone remains the most frequent MRSA lineage, but this lineage is gradually being replaced by several emerging clones, the most important of which is clone ST105-SCCII. To the best of our knowledge, this is the largest study of MRSA clonal dynamics performed in South America. Methicillin-resistant Staphylococcus aureus (MRSA) is a major public health pathogen that disseminates through the emergence of successful dominant clones in specific geographic regions. Knowledge of the dissemination and molecular epidemiology of MRSA in Latin America is scarce and is largely based on small studies or more limited typing techniques that lack the resolution to represent an accurate description of the genomic landscape. We used whole-genome sequencing to study 469 MRSA isolates collected between 2000 and 2016 in Chile providing the largest and most detailed study of clonal dynamics of MRSA in South America to date. We found a significant increase in the diversity of MRSA clones circulating over the 17-year study period. Additionally, we describe the emergence of two novel clones (ST105-SCCII and ST72-SCCVI), which have been gradually increasing in frequency over time. Our results drastically improve our understanding of the dissemination and update our knowledge about MRSA in Latin America.
Topics: Humans; Methicillin-Resistant Staphylococcus aureus; Staphylococcal Infections; Chile; Phylogeny; Tertiary Care Centers; Anti-Bacterial Agents
PubMed: 37338398
DOI: 10.1128/spectrum.05351-22