Molecular Epidemiological Studies Research Articles

Genetic diversity and prevalence of Blastocystis subtypes in Alborz Province, Iran: A molecular epidemiological study.

The primary objective of this study was to evaluate the genetic diversity of Blastocystis. Additionally, it aimed to explore, for the first time in Iran, the potential association between Blastocystis infection and ABO blood groups. Another focus was to examine the relationship between Blastocystis subtypes and blood groups, an often overlooked risk factor, within the population of Alborz Province, Iran. 450 stool samples were collected from diagnostic facilities across Alborz Province between June 2022 and April 2024. The presence of Blastocystis was confirmed in 64 out of 450 samples (14.22 %) using the Nested PCR-RFLP technique. Among the 64 positive samples, nine (2 %) were classified as indeterminate. Two distinct Blastocystis subtypes were identified in 55 isolates, accounting for 12.22 % of the total samples. ST1 was detected in 44 isolates (9.77 %), rendering it the most prevalent subtype, while ST3 was identified in 11 isolates (2.44 %). Phylogenetic trees were constructed using sequencing data and compared against genotypes available in GenBank. Significant differences between infected and non-infected individuals were observed regarding educational attainment, marital status, and blood type (p < 0.05). A significant association was found between ABO blood groups and the prevalence of Blastocystis infection (p = 0.019). However, when examining the correlation between Blastocystis subtypes (ST1 and ST3) and ABO blood groups, no significant overall association was observed. Nonetheless, specific associations were found for blood groups O+ and B-, with subtype ST1 being more prevalent in these groups.

The spread of molecular markers of artemisinin partial resistance and diagnostic evasion in Eritrea: a retrospective molecular epidemiology study

Eritrea was the first African country to discontinue the use of histidine rich protein 2 (HRP2)-detecting rapid diagnostic tests (RDTs) for malaria diagnosis following reports of a high prevalence of pfhrp2/3-deleted Plasmodium falciparum parasites causing false-negative results in the country. Eritrea was also the first African country to report partial artemisinin resistance due to the Pfalciparum kelch13 (pfk13) Arg622Ile mutation. We aimed tocharacterise the spatial distribution of pfk13 mutants and their interactions with pfhrp2/3 deletions in Eritrea andto assess the role of the use of HRP2-detecting RDTs and antimalarial (artesunate-amodiaquine) therapy in the spread of the two variants. We conducted a retrospective molecular epidemiological analysis of pfk13 mutations and pfhrp2/3 deletions in existing Pfalciparum-infected blood samples collected as part of previous pfhrp2/3 deletion and severe malaria studies. Samples were collected in March, 2016and between September, 2018, and January, 2020, from symptomatic patients seeking care at 15health centres in four administration zones (Semenawi Keyih Bahri, Gash Barka, Anseba, and Debub) in Eritrea. Afragment spanning the propeller region of pfk13 was amplified from samples and sequenced using Sanger sequencing or targeted amplicon sequencing to identify genetic mutations. Deletions of pfhrp2/3 genes in samples were determined using multiplex quantitative PCR. Parasite haplotypes and genetic relatedness of parasite haplotypes were determined previously using microsatellite marker typing. The primary objective was to determine the prevalence of pfk13 mutations at health centres and administrative zones. The secondary objective was to investigate whether pfk13 mutants and pfhrp2/3 deleted parasites converge. We sequenced 50samples collected in March, 2016from the Semenawi Keyih Bahri zone and identified no pfk13 mutations. By contrast, in 587samples included in this study that were collected from health centres in GashBarka, Anseba, and Debub in 2018-20, we detected five different single non-synonymous mutations: Glu605Lys, Arg622Ile, Asn657Lys, Lys658Glu, and Ser679Leu. The most prevalent mutation was pfk13 Arg622Ile, which was detected in samples collected from all nine health centres where more than five samples were available across all three administration zones, with an overall prevalence of 11·9% (70 of 587samples; range 5·9-28·0%). Weidentified 22unique pfk13 Arg622Ile mutant haplotypes among 26samples tested, of which 13 (59·1%) were genetically related, whereas the remaining nine (40·9%) were not. The prevalence of pfk13 Arg622Ile was significantly higher in parasites with a single pfhrp3 deletion (46 [18·0%] of 255samples) than in parasites withoutpfhrp2/3 deletions (ten [6·2%] of 161samples; odds ratio 3·89 [95% CI 1·59-7·61]; p=0·0006) and with dual pfhrp2/3-deleted parasites (13 [9·0%] of 145; 2·23 [1·13-4·68]; p=0·018). The geographical spread of the pfk13 Arg622Ile mutation might have initially resulted from the clonal expansion and spread of pfhrp2/3 deletions under the test-and-treat policy using HRP2-detecting RDTs. Subsequently, selective pressure from artemisinin combination therapy could have further facilitated the spread of both pfk13 Arg622Ile and pfhrp2/3 deletions. Continuous monitoring of trends in pfk13 and pfhrp2/3 variants is needed to inform effective malaria control and elimination strategies in Eritrea and other African countries. US Department of Defense Armed Forces Health Surveillance Division, Global Emerging Infections Surveillance Branch (AFHSD/GEIS), and Wellcome Trust.

Epidemiological Features and Evolutionary Analysis of Recombinant CVA24v in the Context of a Re-Emerging AHC Outbreak in China, 2023.

China experienced another outbreak of acute hemorrhagic conjunctivitis (AHC) in 2023, with a total of 195 297 recorded cases. This marks the third nationwide outbreak in nearly two decades, following previous outbreaks in 2007 and 2010. Descriptive epidemiological analysis shows that the number of cases in 2023 peaked in September, similar to the last two outbreaks. The age groups with the highest incidence rate of the three outbreaks in 2007, 2010, and 2023 are 15-20, 10-15, and 10-15 years old, respectively. Students are the main occupational group in the three outbreaks. Hainan, Guangxi, and Guangdong were the top three regions with high incidence rates in the three outbreaks. In 2023, the incidence rate in Hainan Province is the highest ever. Pathogenetic analyses show that the pathogens isolated during the 2023 outbreak were identified as the GIV genotype of CVA24v. Seven different recombination patterns were identified in the recombination analysis of the Chinese strains in 2023 and representative strains of global outbreaks since 1988. These patterns mainly involved the recombination signals of EV-C96 and PV in the 5' untranslated region and 3C and 3D regions. Although recombination events of CVA24v are rarely reported, its recombination was consistently present through systematic analysis in this study. This study comprehensively analyzed the 2023 AHC re-emerging data and isolated CVA24v sequences, providing valuable data for future CVA24v molecular epidemiology studies.

Emergence of a blaNDM-5-carrying extensively drug-resistant Enterobacter cloacae ST1718 in Saudi Arabia: Insights from comprehensive genome analysis.

Patients with severe COVID-19 may require intensive care unit (ICU) admission to manage life-threatening complications. However, ICU admission is associated with an increased risk of acquiring nosocomial infections caused by multidrug-resistant (MDR) bacteria, particularly carbapenem-resistant Enterobacterale (CRE). Enterobacter cloacae complex (ECC), a group of closely related species including Enterobacter cloacae, is a common cause of healthcare-associated infections (HAIs). The study conducted a comprehensive genomic analysis of an extensively drug-resistant (XDR) E. cloacae strain (ECloa-JZ71) isolated from the blood of a critically ill COVID-19 patient in Jazan, Saudi Arabia. ECloa-JZ71 exhibited resistance to multiple antimicrobial agents, except for amikacin, gentamycin, and fosfomycin. Whole-genome sequencing revealed that ECloa-JZ71 had a rarely reported sequence type, ST1718. Resistance to β-lactam antibiotics was primarily mediated by the genes blaCMH-3, blaTEM-1B, blaLAP-2, and blaNDM-5. The strain was found to harbor IncFIB(pECLA) and IncX3 plasmid replicons, with the latter encoding the blaNDM-5 gene. The IncX3 plasmid was identified as a significant contributor to the dissemination of the blaNDM-5 gene among Enterobacterale species The coexistence of blaNDM-5 and other carbapenem-hydrolyzing enzymes explains the reduced efficacy of β-lactam drugs in ECloa-JZ71. The coexistence of blaNDM-5 and other carbapenem-hydrolyzing enzymes explains the reduced efficacy of β-lactam drugs in ECloa-JZ71. The presence of specific virulence factors along with carbapenem resistance in ECloa-JZ71 may enhance its pathogenesis, complicating treatment and control efforts. The findings highlight the need for monitoring the spread of multidrug-resistant clones, conducting molecular epidemiological studies, and implementing effective infection control measures to prevent the dissemination of antimicrobial resistance in healthcare settings.

Hybrid and/or mixed infection by pig and human Ascaris in a Guarani indigenous village in southern Brazil.

Ascaris lumbricoides and Ascaris suum are nematode parasites that infect millions of people and pigs worldwide, respectively. Reports of cross-infection and hybridization between the two species has stimulated molecular epidemiological studies of the Ascaris genus. In this study, we evaluated the dynamics of Ascaris transmission between Guarani indigenous schoolchildren, pigs, and the environment of a village in the state of Paraná, southern Brazil. Parasitological and molecular analyses of fecal samples from humans and pigs, and soil samples from the village were carried out. Eggs of Ascaris spp. were observed in 8.4% (7/83) of human samples, 44.4% (8/18) of pig samples, and 8.9% (6/68) of soil samples. PCR amplification of the ITS-1 locus of the rDNA gene in samples that were positive in the parasitological examination revealed mixed infection and/or hybrids of the two species, A. lumbricoides and A. suum, in human and swine hosts. The soil, which was contaminated by both human and swine feces, also contained eggs of the two Ascaris species and hybrids, thus constituting a source of Ascaris infection for both hosts. DNA from A. lumbricoides and A. suum, individually, was detected in samples from humans and pigs, respectively, and the soil, while DNA from hybrid and/or Ascaris spp. was detected in samples from both hosts and the soil. The results of this study confirm the necessity of a One Health approach with the correct disposal of both human and animal feces to control the spread of human and swine ascariasis.

P-303. Mupirocin Resistance is Common in Tampa, Florida Staphylococcus aureus Clinical Isolates

Abstract Background Mupirocin (Mup) is a topical drug used to decolonize carriers of Staphylococcus aureus (SA) to prevent later SA infection. A spot survey of SA isolates at Tampa General Hospital (TGH) revealed a prevalence in Mup resistance of ∼40%, leading to a change of decolonization protocol from mupirocin to povidone iodine in January 2020, just prior to the COVID pandemic. We determined the prevalence of Mup resistance in a random sampling of clinical isolates before and after change in decolonization protocol. Methods A total of 211 PreCOVID (before 2020) and 173 PostCOVID (after 2021) samples from various sources (blood, bone, eye, fluid, respiratory, urine, and wound) were tested with minimum inhibitory concentration for Mup resistance using literature values for susceptible, low resistance, and high resistance. Oxacillin sensitivity, to verify MRSA isolates, was tested in parallel. Results were analyzed via χ² for significance (p=0.05). Results Comparison of Mup resistance levels between the Pre- and PostCOVID time points showed no significant difference (p=0.460). PreCOVID: 71.1% susceptible, 8.1% low resistance, 20.9% high resistance. PostCOVID: 74.0% susceptible, 9.8% low resistance, and 16.2% high resistance. MRSA status correlated with Mup resistance in both Pre- (p&amp;lt; 0.001) and PostCOVID samples (p=0.001). Blood vs Non-Blood samples differed in Mup resistance in the PreCOVID period (20.7% blood vs 34.1% non-blood, p=0.037), whereas samples in the PostCOVID period showed no significant difference in Mup resistance (22.8% blood vs 28.7% non-blood, p=0.375). Notably, 46.2% PreCOVID Respiratory were resistant to Mup (p=0.016). 26.3% PostCOVID Respiratory were resistant to Mup (p=0.651). Conclusion Change in decolonization protocol did not influence the overall prevalence of Mup resistance. Respiratory samples made up a significant proportion of the resistant samples in the PreCOVID time point, suggesting differences in prevalence of Mup resistance in different clinical sites. Further molecular epidemiological studies are needed to determine if specific sites of infection or specific patient groups are more likely to be colonized with Mup resistant SA isolates. Disclosures All Authors: No reported disclosures

Molecular epidemiology of chicken and turkey parvovirus in Turkiye: high risk, genetic recombination signals, and first complete genome analysis.

The aim of this study was to detect chicken parvovirus (ChPV) and turkey parvovirus (TuPV) on Turkish poultry farms and examine the molecular epidemiology of these viruses. In 2023, a total of 1,060 fecal samples were collected from 76 broiler farms and 30 turkey farms across various regions of Turkiye. The overall positivity rate was 72.3% (55/76) in broiler flocks and 70% (21/30) in turkey flocks. Among these, the positivity rate was 35% (7/20) in birds showing no signs of enteritis. The findings of this study suggest that, depending on the genetic variability of regional strains or the viral load, nested-PCR-based methods may prove more effective than single-step PCR for detecting ChPV and TuPV cases. Therefore, it is recommended to incorporate nested PCR in molecular epidemiological studies to minimize the risk of overlooking positive cases. Phylogenetic analysis of the VP1, VP2, and complete genome sequences of TUR/2023/ChPV and TR/2023/TuPV revealed that both strains clustered with American strains in distinct lineages. Analysis using the recombination detection programs RDP4.0 and SimPlot 3.5.1 strongly suggested that TUR/2023/ChPV may be a recombinant of strains from China and Brazil. Despite the observed genetic variability in the VP2 protein, an examination of B-cell epitopes showed a high degree of similarity between ChPV and TuPV strains. This study represents the first documentation of the emergence and prevalence of TuPVs in Turkiye, providing complete genome sequences for both ChPV and TuPV. Given the high prevalence and genetic diversity of these viruses and their presence in clinically asymptomatic birds, it is crucial for stakeholders in the poultry industry to implement regular flock screenings for these and similar viral pathogens. Proactive measures like these are essential for mitigating the economic impact of these important pathogens and developing effective preventive strategies.

Genetic analysis reveals the genetic diversity and zoonotic potential of Streptococcus dysgalactiae isolates from sheep

Streptococcus dysgalactiae (S. dysgalactiae ) is a common pathogen of humans and various animals. However, the phylogenetic position of animal S. dysgalactiae isolates and their zoonotic potential remain unclear. Most molecular epidemiological studies explicate beta-hemolytic streptococci according to their MLST and M protein gene (emm) types. Although human S. dysgalactiae isolates are relatively well characterized, the data concerning animal isolates are scarce. Here, we report the molecular characteristics and antimicrobial resistance of S. dysgalactiae strains recovered from sheep and their genetic relationship with isolates from other animal hosts and humans. Overall, 11 PFGE pulsotypes, five MLST sequence types (STs), and two emm types were distinguished, with ST248 and stL1376 being the most prevalent, indicating genetic diversity among tested 17 ovine isolates. Some isolates exhibited resistance to doxycycline (59%), erythromycin (6%), ciprofloxacin (6%), and trimethoprim/sulfamethoxazole (6%), harboring various resistance determinants. Phylogenetic analysis showed that studied ovine isolates grouped together with human S. dysgalactiae isolates from the cases of zoonotic infections. Moreover, some ovine isolates shared identical STs and emm gene sequences with human non-invasive and invasive S. dysgalactiae strains. These findings suggest a possible link between human and ovine isolates and indicate the zoonotic potential of this pathogen.

Systematic review of multidrug-resistant Klebsiella pneumoniae in the Arabian Peninsula: molecular epidemiology and resistance patterns

BackgroundThe rapid emergence of multidrug-resistant Klebsiella pneumoniae (MDR K. pneumoniae) is a major public health and economic burden worldwide. Various resistance mechanisms complicate treatment, leading to increased morbidity and mortality. Despite numerous studies conducted in Gulf Health Council (GHC) countries, the molecular epidemiology of MDR K. pneumoniae remains not clearly defined. This systematic review aims to analyze the emergence of antimicrobial resistance genes in MDR K. pneumoniae across GHC countries.MethodsA systematic search was conducted using PubMed, ScienceDirect, and OpenMD for articles published up to March 15, 2023. The search strategy focused on the bacterial name, drug-resistance genotypes, and GHC countries. The review followed PRISMA guidelines, with two independent reviewers assessing the risk of bias using NIH Study Quality Assessment tools.ResultsThe primary search yielded 1,663 studies, of which 67 met the inclusion criteria. Saudi Arabia contributed the most studies, with 41 (61.1%), followed by Kuwait with 7 (10.4%), and the UAE with 6 (9%) studies. Oman and Qatar each contributed 4 studies (6%), and Bahrain contributed three studies (4.5%). The remaining 4 studies (4.4%) were from multiple GHC countries. The studies exhibited considerable heterogeneity in detection methods, target genes, and resistance mechanisms. Notably, only one environmental study was conducted in the UAE, and one community-based study in Kuwait, while the remaining studies focused on clinical samples. Various resistance mechanisms and patterns were observed between countries and across different years within the same country. The review highlighted the widespread prevalence of ESBL genes, particularly blaTEM and blaCTX-M-15, and the emergence of carbapenemase genes such as blaOXA-48 and blaNDM-1 and blaKPC-2. Additionally, colistin resistance through the mcr-1 gene and mgrB mutations was reported in Saudi Arabia and the UAE, posing a significant public health challenge.ConclusionData from GHC countries shows significant gaps, particularly in community and environmental and molecular epidemiology studies. Limited molecular and genome-based investigations hinder comprehensive AMR surveillance. Implementing standardized methodologies and fostering molecular and genome-based AMR surveillance programs at both national and regional levels within the GHC are essential for effectively combating the spread of MDR K. pneumoniae and improving public health outcomes in the region.

Molecular epidemiology and phylogenetic insights of lumpy skin disease in cattle from diverse agro-ecological regions of Punjab, Pakistan.

Lumpy skin disease (LSD) is an emerging, highly contagious transboundary disease of bovines caused by the Lumpy skin disease virus (LSDV), responsible for substantial economic losses to the dairy, meat, and leather industries in Pakistan as well as various countries around the world. Epidemiological information on LSD is scarce in Punjab, Pakistan. Therefore, a molecular epidemiological study was conducted in two agro-ecologically diverse districts (Bhakkar and Jhang) of Punjab, Pakistan. A total of 800 blood samples were randomly collected from the jugular vein of clinically suspected cattle with nodular lesions using a multistage cluster sampling technique. The sampling unit was indigenous, crossbred, and exotic breeds of cattle. Four hundred samples were collected from each district. Ten union councils (UC) were selected from each district, and two villages were selected from each union council. From each village, twenty cattle were selected for sample collection. The PCR-based overall prevalence of LSDV in clinically suspected cattle using the P32 gene was 36.25% (36.25%; 290/800). The multivariable logistic regression analysis indicated that animals who were not treated with acaricide (P = 0.014; OR = 1.459; C.I = 1.079-1.972), body condition score (emaciated animals; P = 0.019; OR = 1.573; CI = 1.076-2.301), and gender (female; (P = 0.016; OR = 1.435; CI = 1.072-1.969) were significantly at higher risk for LSDV infection in cattle. The phylogenetic insights revealed that our isolates were linked to Kenya, China, Russia, Egypt, India, Zimbabwe, Iraq, and Iran. It can be concluded that LSD is widely distributed in the study area, with evidence of genetic diversity. Further studies are required on genetic composition using variable genetic markers for effective control and eradication of LSDV in Pakistan.

Interpreting the Epidemiological Characteristics of HIV-1 in Heterosexually Transmitted Population Based on Molecular Transmission Network in Kunming, Yunnan: A Retrospective Cohort Study.

Heterosexuals have become the most prevalent group of HIV-1 in Kunming, Yunnan Province. Utilizing the principle of genetic similarity between their gene sequences, we built a molecular transmission network by gathering data from earlier molecular epidemiological studies. This allowed us to analyze the epidemiological features of this group and offer fresh concepts and approaches for the prevention and management of HIV-1 epidemics. Cytoscope was used to visualize and characterize the network following the processing of the sample gene sequences by BioEdit and HyPhy. The number of possible links and the size of the clusters were investigated as influencing factors using a zero-inflated Poisson model and a logistic regression model, respectively. A scikit-learn-based prediction model was developed to account for the dynamic changes in the HIV-1 molecular network. Six noteworthy modular clusters with network scores ranging from 4 to 9 were found from 150 clusters using Molecular Complex Detection analysis at a standard genetic distance threshold of 0.01. The size of the number of possible links and the network's clustering rate were significantly impacted by sampling time, marital status, and CD4+ T lymphocytes (all p < 0.05). The gradient boosting machine (GBM) model had the highest area under the curve value, 0.884 ± 0.051, according to scikit-learn. Though not all cluster subtypes grew equally, the network clusters were relatively specific and aggregated. The largest local transmission-risk group for HIV-1CRF08_BC is now the heterosexual transmission population. The most suitable model for constructing the HIV-1 molecular network dynamics prediction model was found to be the GBM model.

Molecular epidemiology and clinical characterization of carbapenemase-producing Enterobacter spp. from an international cohort.

Despite the global public health threat posed by carbapenem-resistant Enterobacter spp., clinical and molecular epidemiological studies on international isolates remain scarce. Historically, the taxonomy of Enterobacter has been challenging, limiting our understanding of the clinical characteristics and outcomes of carbapenemase-producing Enterobacter spp. infections. Hospitalized patients enrolled in the CRACKLE-2 study (ClinicalTrials.gov, NCT03646227) from 2016-2018 with cultures positive for carbapenemase-producing Enterobacter spp. were included. Clinical and microbiologic data were collected from health records. Whole genome sequencing was performed, and the population structures of selected predominant clones were analyzed. We enrolled 136 hospitalized patients with carbapenemase-producing Enterobacter spp. from 30 hospitals in 7 countries. Among the 136 isolates, eleven Enterobacter species were identified, with most isolates belonging to E. xiangfangensis (n=81, 60%) and E. hoffmannii (n=17, 13%), and carrying blaKPC (n=106, 78%) and blaNDM (n=12, 9%). Clinical characteristics and outcomes were similar among patients with E. xiangfangensis, E. hoffmannii or the other Enterobacter spp. 30-day mortality was 20% and older age at enrollment (adjusted odds ratio 1.42, 95% confidence interval 1.08-1.87) was associated with increased mortality. Sequence type (ST)171 E. xiangfangensis, ST78 E. hoffmannii, and ST93 E. xiangfangensis were the predominant clones, and the acquisition of fluoroquinolone resistance-associated mutations and carbapenemase-encoding plasmids contributed to their formation and global dissemination. Our findings demonstrated that E. xiangfangensis and E. hoffmannii are common species among international carbapenemase-producing Enterobacter spp., potentially linked to the clonal spread of a few predominant clones that have acquired fluoroquinolone resistance and carbapenemase-encoding plasmids.

RT-RPA as a dual tool for detection and phylogenetic analysis of epidemic arthritogenic alphaviruses

Chikungunya (CHIKV), o’nyong-nyong (ONNV), and Mayaro (MAYV) viruses are transmitted by mosquitoes and known to cause a debilitating arthritogenic syndrome. These alphaviruses have emerged and re-emerged, leading to outbreaks in tropical and subtropical regions of Asia, South America, and Africa. Despite their prevalence, there persists a critical gap in the availability of sensitive and virus-specific point-of-care (POC) diagnostics. Traditional immunoglobulin-based tests such as enzyme-linked immunosorbent assay (ELISA) often yield cross-reactive results due to the close genetic relationship between these viruses. Molecular diagnostics such as quantitative polymerase chain reaction (qPCR) offer high sensitivity but are limited by the need for specialized laboratory equipment. Recombinase polymerase amplification (RPA), an isothermal amplification method, is a promising alternative to qPCR, providing rapid results with minimal equipment requirements. Here, we report the development and validation of three virus-specific RT-RPA-based rapid tests for CHIKV, ONNV, and MAYV. These tests demonstrated both speed and sensitivity, capable of detecting 10–100 viral copies within 20 min of amplification, without exhibiting cross-reactivity. Furthermore, we evaluated the clinical potential of these tests using serum and tissue samples from CHIKV, ONNV, and MAYV-infected mice, as well as CHIKV-infected human patients. We demonstrate that the RPA amplicons derived from the patient samples can be sequenced, enabling cost-effective molecular epidemiological studies. Our findings highlight the significance of these rapid and specific diagnostics in improving the early detection and management of these arboviral infections, particularly in resource-limited settings.

Human papillomavirus as a potential etiological factor and biomarker in bladder carcinogenesis: A molecular epidemiological study

Human papillomavirus as a potential etiological factor and biomarker in bladder carcinogenesis: A molecular epidemiological study

Molecular Identification of OXA Carbapenemase-Encoding Genes in Acinetobacter baumannii Isolated from Patients in Critical Care in Egypt.

Background: The emergence of carbapenem-resistant Acinetobacter baumannii (CRAB) in hospitals, particularly within critical care units, has garnered substantial global concern. CRAB commonly arises from the degradation by various ß-lactamases. Objective: We aimed to assess OXA-type carbapenemases in clinical isolates of A. baumannii obtained from an Egyptian tertiary care facility. Patients and Methods: This study examined 25 distinct A. baumannii strains collected from various clinical samples of patients in intensive care unit. Bacterial identification was conducted utilizing both traditional methods and the Vitek2 system. Antibiotic resistance profiles were assessed according to the European Committee on Antimicrobial Susceptibility Testing standards using the Vitek2 Compact automated system. Additionally, multiplex real-time polymerase chain reaction was used to identify the presence of blaOXA23, blaOXA24, blaOXA51, and blaOXA58 carbapenemase genes. Colistin susceptibility was assessed utilizing the broth microdilution method. Results: Carbapenem resistance was identified in 100% of the studied isolates. The blaOXA51 gene was detected in all A. baumannii strains. The gene blaOXA23 was identified in 22 strains (88%), whereas blaOXA24 and blaOXA58 were present in 15 strains (60%). All isolates, except one, co-harbored two or more OXA encoding genes. Colistin resistance was detected in 4 of 25 strains (16%). Conclusion: Our findings demonstrate the widespread distribution of CRAB isolates that co-harbor multiple carbapenemase-encoding genes. Molecular epidemiological studies and the surveillance of antibiotic resistance profiles may aid in identifying and tracing the origins of resistant bacteria, thereby limiting their spread.

The Characterisation of Carbapenem-Resistant Acinetobacter baumannii and Klebsiella pneumoniae in a Teaching Hospital in Malaysia.

Background/Objectives: The emergence and dissemination of carbapenem-resistant organisms, particularly Acinetobacter baumannii and Klebsiella pneumoniae, pose a significant threat to healthcare systems worldwide. This retrospective study aims to characterise carbapenem-resistant Acinetobacter baumannii (CRAB) and carbapenem-resistant Klebsiella pneumoniae (CRKP) strains in a teaching hospital and to determine the risk factors associated with patients' in-hospital mortality. Methods: A total of 90 CRAB and 63 CRKP were included in this study. Carbapenemase genes and MLST types of CRAB and CRKP were determined using specific primers. Risk factors associated with in-hospital mortality were analysed with collected data. Results: All the CRAB strains consisted of OXA carbapenemase genes, with 98% of the strains co-harbouring blaOXA-23-like and blaOXA-51-like carbapenemase genes. Conversely, blaNDM is the predominant carbapenemase gene in CRKP, followed by blaOXA-48-like carbapenemase genes. ST2 and ST20 are the dominant MLST types in CRAB and CRKP, respectively. In CRAB, multivariate analysis identified age, ethnicity, the presence of a mechanical ventilator, and patients who experienced previous exposure to clindamycin in the last 90 days as associated with an increased risk of in-hospital mortality. In contrast, older age, male, ICU admission, and the presence of an indwelling urinary catheter were significantly associated with an increased risk of mortality for patients with CRKP. Conclusions: Both CRAB and CRKP lead to high rates of mortality. The MLST profile showed that the genomic patterns of CRKP were highly diverse, whereas CRAB strains had low genetic diversity. To tackle these challenging pathogens, robust surveillance and an in-depth understanding of molecular epidemiology and genomics studies are needed to tailor infection control strategies and individualise treatment approaches.

Molecular epidemiological study on tick-borne pathogens in Qinghai Province, northwestern China

Molecular epidemiological study on tick-borne pathogens in Qinghai Province, northwestern China

Expanded HPV Genotyping by Single-Tube Nested-Multiplex PCR May Explain HPV-Related Disease Recurrence.

The role of the human papillomavirus (HPV) in the establishment of cervical cancer has driven studies to find more effective methods of viral detection so that early intervention strategies can be performed. However, the methods still have limitations, especially regarding detecting the different genotypes simultaneously. We have developed a high-throughput system using a single-tube nested-multiplex polymerase chain reaction (NMPCR) for the detection of 40 HPV genotypes using capillary electrophoresis. The NMPCR assay was compared to the Hybrid Capture 2 assay (HC2) with 40 women from the Northeast of Brazil (São Luis, MA), a high endemic region, where the HPV positivity was 75% and 37.5%, respectively. These results were validated by performing a molecular epidemiological study on 5223 Brazilian women undergoing gynecological examinations from 2009 to 2017, who presented with an HPV prevalence of 59%. Multiple infections were found in 62.5% and 58% of the patients from the endemic region and from the Brazilian women population, respectively, mostly presenting high-risk genotypes (90.5% and 60%, respectively). Considering cervical intraepithelial neoplasia and adenocarcinomas, the sensitivity and specificity were 97.5% and 100%, respectively. The NMPCR assay was also capable of identifying viral subtypes in cases of multiple infections, even with low viral loads (10-6 ng/µL of HPV DNA). The NMPCR test is a promising and robust tool for HPV diagnostics and a screening tool for prevention of cervical cancer.

Unraveling the dynamics of drug resistance: Insights from molecular epidemiology

Abstract. Drug-resistant bacterial strains pose significant challenges to public health worldwide. Molecular epidemiology studies employing cutting-edge techniques such as whole-genome sequencing and pulsed-field gel electrophoresis have shed light on the genetic diversity, transmission dynamics, and evolution of drug resistance mechanisms. This review explores the current state of knowledge in this field, highlighting key findings on genetic diversity, transmission dynamics within healthcare facilities and communities, and factors influencing resistance evolution. By elucidating the intricate interplay between genetic determinants, transmission pathways, and selective pressures, molecular epidemiology provides critical insights for guiding infection control measures and developing strategies to mitigate the spread of drug resistance. Embracing a One Health perspective and strengthening global surveillance efforts are essential for addressing the transboundary dissemination of drug-resistant pathogens and preserving antimicrobial efficacy.

Transmission of MRSA, ESBL E. coli, and C. difficile within a tertiary care hospital and across surrounding facilities in Japan: a molecular epidemiological study with the PCR-based Open-reading frame typing.

To determine the regional impact of transmission of multidrug-resistant organisms (MRDOs) and Clostridioides difficile (C. difficile) among a tertiary care hospital and surrounding facilities including long-term care facilities (LTCFs). Retrospective cohort study. Patients admitted to a tertiary care hospital from July 2019 to July 2021 were recruited if their clinically collected cultures grew the following pathogens: Methicillin-resistant Staphylococcus aureus (MRSA), Extended-Spectrum Beta-Lactamase (ESBL) producing Enterobacterales, Pseudomonas aeruginosa with difficult-to-treat resistance, Carbapenem-resistant Enterobaterales, Vancomycin-resistant Enterococci, and C. difficile. Patient characteristics including admission and discharge pathway were collected. For the isolates of MRSA, ESBL-producing Escherichia coli (E. coli), and C. difficile, a molecular epidemiological analysis was conducted, utilizing the PCR-based Open-Reading Frame Typing (POT) method. Three hundred-five patients were identified with a total of 332 culture specimens of the target pathogens. The top three were 132 MRSA isolates (43.3%, out of 305), 97 ESBL E. coli (31.8%), and 32 ESBL Enterobacterales (non-E. coli) (10.5%). The target pathogens were more detectable within 3 days among patients admitted from LTCFs or other hospitals than those admitted from home (Odds Ratio 4.6, 95% confidence interval 2.8-7.6, p-value < 0.001). The molecular epidemiological analysis suggested the transmissions of MRSA, ESBL E. coli and C. difficile occurred 52 out of 111 patients within the in-hospital environment, and 7 out of 128 within the prehospital environment, respectively. MDROs/C. difficile transmission is prevalent within a tertiary care hospital and further complicated by its inter-facility transmission across surrounding LTCFs and hospitals in Japan.