Malini Shariff

Introduction: Staphylococcus aureus (S. aureus) is a facultative anaerobic bacterium that colonizes the nasal cavity, skin and other mucosal surfaces of humans. It causes a wide spectrum of infections, ranging from localized skin and soft tissue infections to severe systemic conditions such as bacteremia, endocarditis and osteomyelitis. The pathogen is a major contributor to hospital-acquired infections and the emergence of Methicillin-Resistant S. aureus (MRSA) poses significant therapeutic and epidemiological challenges. Methods: This retrospective analytical study analysed 100 archived S. aureus isolates from clinical, colonizing and environmental sources in a hospital setting. Multilocus Sequence Typing (MLST) was performed on 55 of these isolates. Fragments of seven housekeeping genes were amplified following the protocol outlined on the PUBMLST website. The resulting amplicons were sequenced and Sequence Types (STs) were assigned by comparing allele profiles with the PUBMLST database. Novel allelic combinations were designated as new STs. Results: The identified STs included ST22, ST5, ST364, ST1910, ST5939, ST5529, ST7442, ST672 and ST9162. Forty-four novel STs were submitted to the PUBMLST site and were designated new STs. Most of these isolates belonged to Clonal Complex 5 (CC5). A comparative analysis was conducted against Indian and global S. aureus isolates available in the PUBMLST database to assess phylogenetic relationships and geographic distribution. Conclusion: Understanding the molecular epidemiology and evolutionary dynamics of S. aureus through MLST provides valuable insights into strain diversity and transmission patterns. These findings underscore the importance of robust infection-control and targeted surveillance strategies to mitigate the spread of MRSA in healthcare settings.

Introduction: Staphylococcus aureus (S. aureus) is a facultative anaerobe commonly colonizing the nose, skin and other sites. It causes localized and systemic infections, is a major agent of hospital-acquired disease and methicillin resistance complicates treatment. We analyzed isolates from patients, healthy carriers and environmental sources. Materials and methods: A total of 100 S. aureus isolates were analyzed, comprising 50 clinical, 40 colonizing and 10 environmental samples. The study assessed antibiotic resistance profiles, virulence determinants and the presence of associated genetic markers. Results: Based on cefoxitin resistance testing, 46 isolates were classified as methicillin-resistant S. aureus (MRSA) and 54 as methicillin-susceptible S. aureus (MSSA). The mecA gene was detected in 36 (78%) MRSA isolates and, unexpectedly, in 27 (50%) MSSA isolates. Among clinical isolates, 22/50 (44%) were positive for Panton-Valentine Leukocidin (PVL), 34/50 (68%) for α-hemolysin (Hla), 44/50 (88%) for fibronectin-binding protein A (FnbA) and 43/50 (86%) for staphylococcal protein A (SpA) genes. In colonising isolates, the prevalence was lower for PVL (8/40, 20%), Hla (14/40, 35%) and SpA (25/40, 62.5%). However, FnbA showed a higher frequency of 39/40 (97.5%). Environmental isolates showed lower rates, with PVL present in 1/10 (10%), Hla in 5/10 (50%), FnbA in 9/10 (90%) and SpA in 2/10 (20%). Conclusion: MRSA isolates exhibiting virulence properties that are frequently encountered in hospital settings pose significant therapeutic challenges, contributing to increased morbidity and mortality. Effective infection control and robust surveillance strategies are essential to monitor and limit their transmission. Furthermore, restricting the availability of over-the-counter antibiotics is critical to curbing the spread of MRSA and may aid in its long-term control, if not eradication.

Acinetobacter baumannii (A. baumannii) is an important nosocomial pathogen responsible for a wide range of human infections. The emergence of multidrug resistance (MDR) causes life-threatening nosocomial infections. Also, the formation of biofilm helps it survive on abiotic surfaces and is transferred through healthcare workers, thereby causing nosocomial infections. Hence, we study the current antibiotic resistance patterns and virulence factors in our clinical and colonizing isolates. A total of 92 isolates (44 colonizing and 48 clinical) of A. baumannii were included in the study. Antibiotic susceptibility testing was performed by VITEK 2. Biofilm formation was assessed by the tissue culture plate method. Polymerase chain reaction (PCR) for oxacillinases, MBLs and biofilm-associated genes were performed. Meropenem resistance was found in 42 (87.5%) of the clinical and 44 (97.7%) of the colonizing isolates. A strongly adherent biofilm was produced by 11 (22.91%) of the clinical and 12 (27.27%) of the colonizing isolates. Biofilm-associated genes, ompA, bap and csuE were present in 45 (93.7%), 47 (97.9%) and 44 (91.6%) of the clinical isolates, respectively and in all the colonizing isolates. bla_OXA23-like was more prevalent in colonizing than clinical isolates. bla_OXA-58-like and bla_OXA-24-like were present in very few isolates. The presence of metallo beta-lactamase (MBLs) was observed to be lower than oxacillinases. NDM1 was present in 15.29%, SIM in 27%, GIM in 14.11%, VIM in 32.9%, SPM in 5.8%, and IMP in 1.2% of the meropenem-resistant isolates. Carbapenem resistance (XDR) is increasing in A.baumannii. Biofilm formation is an important virulence factor responsible for its survival in the hospital environment and causes nosocomial infections. Biofilm-producing isolates were also found to be carbapenem-resistant. Strict disinfection procedures are to be followed to prevent its spread in the hospital.

To establish the epidemiological correlation between the study isolates, Indian and World isolates of Acinetobacter baumannii by performing Multilocus Sequence typing. A total of 181 isolates (Sputum (n = 116), lower respiratory tract other than sputum (n = 36), upper respiratory tract (n = 20), Environment (medical) (n = 4), and Blood (n = 5) of Acinetobacter baumannii were retrieved from our repository. DNA was isolated and Multilocus Sequence Typing was performed according to the Pasteur scheme. The amplified fragments were sequenced by outsourcing, and the locus and the sequence types were determined as given in the PUBMLST site. The clonal complexes were assigned using eBURST. Of the 181 isolates, 20 were colonizers and 4 were from hospital environments. All the study isolates were multidrug-resistant (MDR) and 4 of them were extensively drug-resistant (XDR). 23 sequence types were unique and were assigned new sequence types. Among them, 2125 (n = 12), an SLV (Single Locus Variant) of 2, was the commonest followed by 2126 (n = 2) which was a DLV (Double Locus Variant) of 2 and an SLV of 2125. Others were singletons. Among the known STs, 149 (n = 72) was the commonest followed by ST 2 (n = 62) & 415 (n = 5), ST 10 (n = 4), ST 15, ST622 and ST1482 (3 each). ST149 had 1SLV ST1482 (n = 3). ST 2 has 5 SLVs (415, 1555, 2125, 2128, & 2131, and 2 DLVs (2130 & 2126). eBURST analysis of the study isolates showed three groups: Group I (86 isolates) with ST 2 as the primary founder, group II (6 isolates) and group III (79 isolates) with ST 149 as the primary founder. All the other 11 isolates were singletons. There was no difference in antimicrobial sensitivity or sequence types of clinical and colonizing isolates. The sequence types of study isolates were compared to the world isolates in the PUBMLST database. To conclude, MLST is an important tool for establishing isolates’ phylogenetic relationships. Acinetobacter baumannii being an important nosocomial pathogen should be routinely screened for the frequent changes in the sequence types to demonstrate the emerging resistance patterns and other changes.

Chronic obstructive pulmonary disease (COPD) represents an important public health challenge and is a major cause of morbidity and mortality throughout the world. The chronic course of COPD is often accompanied by acute exacerbations of COPD (AECOPD) where 70% of exacerbations are caused by infection due to aerobic bacteria, 30% due to viruses and 5-10 % by atypical bacteria, most commonly Mycoplasma pneumoniae (M. pneumoniae), Chlamydia pneumoniae (C. pneumoniae) and Legionella pneumophila (L. pneumophila). Identification of these atypical microorganism is challenging, however, with the availability of newer molecular diagnostic techniques such as PCR and Real time PCR (RT-PCR) the sensitivity in detecting these pathogens has improved and can be tested simultaneously. So, the present prospective study was undertaken to determine the atypical pathogens in patients with COPD by PCR and RT-PCR in the clinical samples. 196 hospitalized patients were included in the study. They were categorized into different stages of COPD and AECOPD using GOLD and Anthonisen criteria. Clinical samples such as throat swab, nasopharyngeal swab, sputum, were collected. Atypical bacteria were identified by using PCR and RT-PCR methods. All these patients showed varying degree of exacerbation. Majority, 78/196 (39.79%) of the patients belonged to severe COPD category. Whereas, 96/193(49.74%) patients had only mild exacerbation. PCR was found to be positive in 11 and 22 numbers for M. pneumoniae and L.pneumophila. None of the samples were positive for Chlamydia pneumophila. Presence of pathogens, atypical bacteria did not show any correlation with the staging of AECOPD. The results were not statistically significant. No one method is suitable for the detection of atypical bacteria. Hence, a combination of tests for identification of Atypical pathogens is required for better sensitivity.

Background: Anaerobes are normal flora of the human body. However, they can cause serious infections in humans. Anaerobic bacteria are known to cause respiratory infections like pneumonia and acute exacerbation of chronic lower airway infections. These are often missed due to the complexity of their isolation and identification. Hence, this study aimed to study anaerobes causing respiratory tract infections and determine their antibiotic susceptibility. Materials & methods: Clinical specimens such as bronchial aspirates and pleural aspirates collected from patients with respiratory diseases attending Vallabhbhai Patel Chest Institute were processed, the anaerobes isolated were identified, and their susceptibilities to various groups of antimicrobials were studied using standard microbiological methods. Results: Three hundred and fourteen patients were included in the study, 154 males and 160 females. Of these 314 patients, 148 (47%) yielded anaerobes in their clinical samples. Seventy patients had more than one type of anaerobic organism. Hence, 235 isolates were recovered belonging to as many as 17 genera. The MIC of seven antibiotics on 154 isolates was tested. The isolates belonged mostly to the genera Bacteroides, Prevotella, Veillonella, and Actinomyces. Variable resistance was observed to most classes of antibiotics by many genera. Conclusions: Metronidazole is commonly used against anaerobes, but the study showed that the isolates were 20–30% resistant to the antibiotic. Starting this as an empirical therapy might lead to treatment failure.

Background Anaerobes are indigenous flora of the human body but have the potential to cause serious diseases. Anaerobic bacteria are involved in all morbid conditions of respiratory infections, and the frequencies of isolation are high in pneumonia and at the time of acute exacerbation of chronic lower airway infection. These are often missed due to the complexity of their isolation and identification. Hence, this study aimed to study anaerobes causing respiratory tract infections and determine their antibiotic susceptibility. Materials & Methods Clinical specimens such as bronchial aspirates and pleural aspirates collected from patients with respiratory diseases attending Vallabhbhai Patel Chest Institute were processed, the anaerobes isolated were identified, and their susceptibilities to various groups of antimicrobials were studied using standard microbiological methods. Results Three hundred forty-four patients were included in the study, 124 males and 147 females. Of these 344 patients, 165 yielded anaerobes in their clinical samples. Ninety patients had more than one type of anaerobic organism. Hence, a total of 271 isolates were recovered belonging to as many as 16 genera. The MIC of seven antibiotics on 154 isolates was tested. The isolates belonged to the genera Bacteroides, Prevotella, Veillonella, and Actinomyces, among others. Variable resistance was observed to most classes of antibiotics by many genera. Conclusions Metronidazole is commonly used against anaerobes, but the study showed that the isolates were 20–30% resistant to the antibiotic. Starting this as an empirical therapy might lead to treatment failure.

Little is known about the molecular basis of antibiotic resistance among uropathogens in Southeast Nigeria. The aim of the study was to characterize enterobacterial uropathogens with respect to drug resistance. One hundred (100) enterobacterial uropathogens were studied. Their antibiotic susceptibility patterns were evaluated using disk diffusion, screened, and confirmed phenotypically for the presence ofβ-lactamases: ESBL, AmpC, carbapenemase, and MBLs. Screen positives were further tested for variousβ-lactamase genes by PCR. Our isolates showed variable resistance to most drugs tested. Out of the 58 ESBL screen positiveE. coli,35 were confirmed positive with PCR. The predominant ESBL gene was bla_TEMwhile bla_SPMwas the most prevalent among MBL genes. Forty-six percentage of the screen positiveSalmonellaisolates coharbored bla_{TEM + SHV}genes. Nine of the 10 ESBL screen positiveK. pneumoniaewere phenotypically and PCR positive. Three isolates ofK. pneumoniaewere positive for MBL genes. All the 10 C. freundiiwere positive for ESBL genes. The study showed high prevalence of drug-resistant genes among the enterobacterial uropathogens. Majority of the uropathogens harbored >1 antibiotic-resistant gene, and the most predominant gene was ESBL (bla_TEM) followed by the MBL (SPM) gene.