Genetic characterization of methicillin-resistant / susceptible Staphylococcus aureus (MRSA/MSSA) and Staphylococcus argenteus clinical isolates in Bangladesh: Dominance of ST6-MRSA-IV/t304 and detection of cfr/fexA in ST8-MSSA/t008

Objectives

Coagulase-positive staphylococcus (CoPS), represented by Staphylococcus aureus, is a major cause of infections in humans. This study aimed to investigate molecular epidemiological characteristics, antimicrobial resistance, and their trends of CoPS in Bangladesh.

Methods

Clinical isolates of CoPS were collected from two medical institutions in Bangladesh for a 2-year period and analyzed for their species, genotypes, virulence factors, antimicrobial susceptibility, and resistance determinants.

Results

172 CoPS isolates collected were identified as S. aureus or S. argenteus (170 and two, respectively). Methicillin-resistant S. aureus (MRSA) accounted for 36% (n = 61), having Staphylococcal cassette chromosome mec (SCCmec)-IV (82%) or V (18%). Panton-Valentine leukocidin (PVL) genes were detected at higher rate in methicillin-susceptible S. aureus (MSSA) (62%) than MRSA (26%). MRSA comprised 11 STs, including a dominant type ST6 (46%) associated with mostly SCCmec-IVa/spa-t304, and one isolate had genetic features of the USA300 clone (ST8/SCCmec-IVa/coa-IIIa/spa-t008/ACME-I/ΦSa2USA). STs of CC1, CC88, and CC398 were common in MSSA, with CC88 showing the highest PVL-positive rate. One MSSA isolate (ST8/spa-t008) harbored fexA and cfr showing susceptibility to linezolid. S. argenteus was methicillin-susceptible and belonged to ST2250/coa-XId.

Conclusions

Genetic characteristics of current MRSA/MSSA in Bangladesh were revealed, with first identification of S. argenteus at low prevalence.

The Prevalence, Risk Factors, and Antimicrobial Resistance Determinants of Helicobacter pylori Detected in Dyspeptic Patients in North-Central Bangladesh

Chronic infection of Helicobacter pylori represents a key factor in the etiology of gastrointestinal diseases, with high endemicity in South Asia. The present study aimed to determine the prevalence of H. pylori among dyspeptic patients in north-central Bangladesh (Mymensingh) and analyze risk factors of infection and antimicrobial resistance (AMR) determinants in the pathogen. Endoscopic gastrointestinal biopsy samples were collected from dyspeptic patients for a one-year period from March 2022 and were checked for the presence of H. pylori via the rapid urease test and PCR and further analyzed for the status of virulence factors vacA/cagA and genetic determinants related to AMR via PCR with direct sequencing or RFLP. Among a total of 221 samples collected, 80 (36%) were positive for H. pylori, with the vacA+/cagA+ genotype being detected in almost half of them. H. pylori was most prevalent in the age group of 41-50-year-olds, with it being more common in males and rural residents with a lower economic status and using nonfiltered water, though the rates of these factors were not significantly different from those of the H. pylori-negative group. Relatively higher frequency was noted for the A2147G mutation in 23S rRNA, related to clarithromycin resistance (18%, 7/39). Amino acid substitutions in PBP-1A (T556S) and GyrA (N87K and D91N) and a 200 bp deletion in rdxA were detected in samples from some patients with recurrence after treatment with amoxicillin, levofloxacin, and metronidazole, respectively. The present study describes the epidemiological features of H. pylori infection in the area outside the capital in Bangladesh, revealing the spread of AMR-associated mutations.

Antimicrobial Susceptibility Patterns of Bacterial Isolates from Blood Culture of Pediatric Patients with Suspected Sepsis at a Tertiary Care Hospital in Mymensingh, Bangladesh

Sepsis is a serious, life-threatening condition, occurring when an infectious agent invades the body, resulting in systemic inflammatory response syndrome (SIRS). Neonates and children are among the most vulnerable population groups of developing sepsis because of their weak immune barrier. Despite major advances in prevention, diagnosis and treatment of bacterial infections, invasive infections followed by sepsis remain one of the leading causes of childhood mortality. The aim of this study was to identify bacterial agents and antimicrobial resistance patterns of aerobic bacteria among children suspected of having sepsis. This cross-sectional descriptive type of observational study was conducted in the Department of Microbiology, Mymensingh Medical College, Bangladesh from March 2021 to February 2022. Blood samples were collected from pediatric patients, suspected of having sepsis referred from inpatient facility of department of Neonatology and Pediatrics, Mymensingh Medical College Hospital (MMCH). Blood samples were inoculated into BacT/ALERT PF Plus bottles followed by sub-culture of positive samples in blood agar, MacConkey agar and chocolate agar plates. Isolated bacteria were identified by routine biochemical tests. Antimicrobial resistance pattern of all isolated bacteria was seen by disk diffusion method. MIC of vancomycin by agar dilution method was determined for isolated S. aureus and Coagulase negative Staphylococci (CoNS). The prevalence of pediatric sepsis was 31.82% with highest isolation rate 35.55% among neonates. The isolation rate of gram-positive bacteria was 62.50% where S. aureus was the most common isolate 32.15% followed by CoNS 30.36%. Out of 21 gram-negative bacteria, Pseudomonas spp. was the most frequent isolate 7(33.33%), all of which were resistant to cefuroxime, ceftriaxone and ceftazidime along with all klebsiella and Acinetobacter isolates. Out of 18 S. aureus isolates, 94.44%, 88.89% and 66.67% were resistant to Azithromycin, Penicillin-G and Ciprofloxacin respectively. The MIC of Vancomycin by agar dilution method was observed <2μg/ml against all isolated S. aureus and CoNS. All the Gram-positive isolates were sensitive to Linezolid and Vancomycin. Early detection of bacteria followed by antimicrobial susceptibility test can help by selection of appropriate antibiotic and prevent spread of infection.

Different RT-PCR Protocol used in SARS-Cov2 PCR Laboratory of Mymensingh Medical College, Bangladesh

The novel corona virus (SARS CoV-2) was first detected on Wuhan, China. After that it spread worldwide and has caused many deaths till now. This virus is also known as novel corona virus because of being newly discovered. Scientifically it is named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It has positive-single stranded RNA and several proteins such as spike (S), envelope (E), membrane (M), nucleocapsid (N) and the other helper proteins. On the basis of phylogenic evidence, it is the new member of beta corona viruses and this group of viruses causes respiratory illness in human. This virus is detected in laboratory by using RT-PCR, by which different target gene such as E gene, S gene, N gene and RdRP (ORF1a-ORF1b) etc. are detected. This study was carried out at Mymensingh Medical College from April 2020 to December 2020. Around 65000 samples (nasopharyngeal swab) were tested during this period by three PCR protocols. By Sansure PCR kit N and ORF1a target genes were detected, Basphore's target genes were E and ORF and by Neoplex PCR kit N and RdRp genes were detected. Most of samples were tested by Sansure kit (62500), 2000 samples were screened by Bosphore kit and 500 samples by Neoplex. Among them, 6876(11.0%) samples were positive by Sansure, 120(6.0%) by Bosphore and 66(13.2%) by Neoplex. Among the positive samples, N gene 6188(90.0%) was mostly found by Sansure kit, whereas ORF was 120(100.0%) mostly found by Bosphore.

Molecular insights into the SARS-CoV-2 Omicron variant from Bangladesh suggest diverse and continuous evolution

The study analyzed the molecular dynamics of the circulating SARS-CoV-2 Omicron variant from its identification in November 2021 to January 2023. The SARS-CoV-2 sequences from Bangladesh revealed three distinct waves of the Omicron variant. More than 50 sub-lineages of Omicron variant were introduced into the country, with the majority belonging to the major lineages of BA.1-like (24.91%), BA.2-like (43.35%), BA.5-like (5.76%), XBB (10.47%), and "Others and Unassigned" (18.64%). Furthermore, the relative frequencies over time revealed that Omicron lineages existed for a short period of time before being replaced by other sub-lineages. Many potential mutations were found in the receptor binding domain of the Spike protein including G339D/H, S371 L/F, K417 N, T478K, E484A, Q493R, Q498R, and N501Y. In conclusion, the SARS-CoV-2 Omicron variant from Bangladesh showed diverse genetic features and continuous evolution. Therefore, the choice of vaccine and monitoring of hospitalized patients is important alongside genetic characterization of the circulating SARS-CoV-2.

Ear Infections by Non albicans Candida Species with Isolation of Rare Drug Resistant Species in a Tertiary Care Hospital of Bangladesh

Otomycosis, a fungal infection of external ear, is challenging for both patients and otolaryngologist as it requires long term treatment and follow up. Candida spp. is second common organism causing otomycosis with Aspergillus being first. Among Candida species, C. albicans is considered as most common but in recent years there is increasing incidence of Non albicans Candida (NAC) species with greater resistance and recurrence. This descriptive type of observational study was planned to determine the species distribution and antifungal susceptibility of Candida spp. causing otomycosis. From March 2021 to February 2022, 60 patients clinically suspected of Candida associated otomycosis at Mymensingh Medical College Hospital, Bangladesh were enrolled. Specimens were taken by an otorhinolaryngologist. After culture and microscopic examination, isolated Candida species were identified by phenotypic and genotypic method and antifungal susceptibility was determined at Department of Microbiology, Mymensingh Medical College. From 60 samples 18(30.0%) were positive for Candida on microscopy and culture. Of the isolates, C. albicans were 2(11.11%) and Non albicans Candida (NAC) 16(88.89%). Five different NAC species were identified of which C. parapsilosis was predominant 5(27.77%) followed by C. tropicalis 4(22.22%) and C. famata 3(16.67%). Rare species of C. ciferrii 2(11.11)%, Kodamaea ohmeri 2(11.11%) were isolated. Candida spp. showed highest resistance to Clotrimazole 8(44.0%) followed by Itraconazole 6(33.0%), Nystatin 4(22.0%) and Fluconazole 3(17.0%). C. ciferrii and Kodamaea ohmeri showed resistance to all antifungals except Nystatin. Outcomes from this study showed a different picture of species distribution, with isolation of rare and emerging drug resistant threatening species like C. ciferri and Kodamea ohmeri which necessitates more detailed survey.

Species Identification and Antifungal Susceptibility Pattern of Candida Isolates in Patients with Vulvovaginitis from Mymensingh, Bangladesh

Vulvovaginal Candidiasis (VVC), a frequent and cumbersome reproductive tract infection affects women's physical and mental health. Although Candida albicans was reported as the most common agent of VVC yet, recently there are significant changes in the pattern of Candida species causing VVC with varying antifungal susceptibility pattern. Therefore this cross-sectional, descriptive type of observational study conducted to identify the spectrum of Candida species associated with VVC and assesses their antifungal susceptibility pattern from March 2021 to February 2022. High vaginal swabs from 175 patients clinically suspected of VVC were collected and cultured on Sabouraud dextrose agar with Chloramphenicol. Species were identified by phenotypic methods like- germ tube test, sub-culture in chromogenic agar media and genotypic methods like- Polymerase chain reaction (PCR), Restriction fragment length polymorphism (RFLP). Antifungal susceptibility was done by disk diffusion method. Out of 175 patients, 52(29.7%) were positive for Candida species. Of the isolates- C. albicans 34(65.0%), Non albicans Candida (NAC) 18(35.0%). Among NAC, C. glabrata 5(9.6%), C. tropicalis 5(9.6%), C. parapsilosis 4(7.7%) and each of C. krusei, C. kefyr, C. ciferrii, C. dubliniensis were 1(1.9%). On susceptibility testing highest resistance was to Clotrimazole 31.0% followed by Nystatin 13.0%, Itraconazole 12.0% and Fluconazole 10.0%. Resistance to azole was higher in NAC than in albicans. Of these patients, 16(31.0%) had history of recurrent VVC (RVVC) of which 12(75.0%) were by NAC, predominantly C. glabrata 5(32.0%). The results showed the increasing incidence of NAC associated vaginitis with higher resistance and recurrence that should be considered in gynecology clinics.

Clonal Diversity of Candida auris, Candida blankii, and Kodamaea ohmeri Isolated from Septicemia and Otomycosis in Bangladesh as Determined by Multilocus Sequence Typing

Candida auris, Candida blankii, and Kodamaea ohmeri have been regarded as emerging fungal pathogens that can cause infections with high mortality. For genotyping of C. auris, a multilocus sequence typing (MLST) scheme based on four locus sequences has been reported, while there is no typing scheme for C. blankii and K. ohmeri. In the present study, the existing MLST scheme of C. auris was modified by adding more locus types deduced from sequence data available in the GenBank database. Furthermore, MLST schemes of C. blankii and K. ohmeri were developed using the four cognate loci (ITS, RPB1, RPB2, D1/D2) and similar sequence regions to those of C. auris. These MLST schemes were applied to identify the ST (sequence type) of clinical isolates of C. auris (n = 7), C. blankii (n = 9), and K. ohmeri (n = 6), derived from septicemia or otomycosis in Bangladesh in 2021. All the C. auris isolates were classified into a single ST (ST5) and clade I, having a Y132F substitution in ERG11p, which is associated with azole resistance. Similarly, all the C. blankii isolates belonged to a single type (ST1). In contrast, six K. ohmeri isolates were assigned to five types (ST1-ST5), suggesting its higher genetic diversity. These findings revealed the availability of MLST schemes for these three fungal species for understanding their clonal diversity among clinical isolates.

Prevalence and Antifungal Susceptibility of Clinically Relevant Candida Species, Identification of Candida auris and Kodamaea ohmeri in Bangladesh

Candida species are major fungal pathogens in humans. The aim of this study was to determine the prevalence of individual Candida species and their susceptibility to antifungal drugs among clinical isolates in a tertiary care hospital in Bangladesh. During a 10-month period in 2021, high vaginal swabs (HVSs), blood, and aural swabs were collected from 360 patients. From these specimens, Candida spp. was isolated from cultures on Sabouraud dextrose agar media, and phenotypic and genetic analyses were performed. A total of 109 isolates were recovered, and C. albicans accounted for 37%, being derived mostly from HVSs. Among non-albicans Candida (NAC), C. parapsilosis was the most frequent, followed by C. ciferrii, C. tropicalis, and C. glabrata. Three isolates from blood and two isolates from aural discharge were genetically identified as C. auris and Kodamaea ohmeri, respectively. NAC isolates were more resistant to fluconazole (overall rate, 29%) than C. albicans (10%). Candida isolates from blood showed 95% susceptibility to voriconazole and less susceptibility to fluconazole (67%). Two or three amino acid substitutions were detected in the ERG11 of two fluconazole-resistant C. albicans isolates. The present study is the first to reveal the prevalence of Candida species and their antifungal susceptibility in Bangladesh.