Antimicrobial susceptibility against metronidazole and carbapenem in clinical anaerobic isolates from Pakistan

New functions of pirin proteins and a 2-ketoglutarate: Ferredoxin oxidoreductase ortholog in Bacteroides fragilis metabolism and their impact on antimicrobial susceptibility to metronidazole and amixicile

The understanding of how central metabolism and fermentation pathways regulate antimicrobial susceptibility in the anaerobic pathogen Bacteroides fragilis is still incomplete. Our study reveals that B. fragilis encodes two iron-dependent, redox-sensitive regulatory pirin protein genes, pir1 and pir2. The mRNA expression of these genes increases when exposed to oxygen and during growth in iron-limiting conditions. These proteins, Pir1 and Pir2, influence the production of short-chain fatty acids and modify the susceptibility to metronidazole and amixicile, a new inhibitor of pyruvate: ferredoxin oxidoreductase in anaerobes. We have demonstrated that Pir1 and Pir2 interact directly with this oxidoreductase, as confirmed by two-hybrid system assays. Furthermore, structural analysis using AlphaFold2 predicts that Pir1 and Pir2 interact stably with several central metabolism enzymes, including the 2-ketoglutarate:ferredoxin oxidoreductases Kor1AB and Kor2CDAEBG. We used a series of metabolic mutants and electron transport chain inhibitors to demonstrate the extensive impact of bacterial metabolism on metronidazole and amixicile susceptibility. We also show that amixicile is an effective antimicrobial against B. fragilis in an experimental model of intra-abdominal infection. Our investigation led to the discovery that the kor2AEBG genes are essential for growth and have dual functions, including the formation of 2-ketoglutarate via the reverse TCA cycle. However, the metabolic activity that bypasses the function of Kor2AEBG following the addition of phospholipids or fatty acids remains undefined. Overall, our study provides new insights into the central metabolism of B. fragilis and its regulation by pirin proteins, which could be exploited for the development of new narrow-spectrum antimicrobials in the future.

Detection of the antibiotic resistance genes content of intestinal Bacteroides, Parabacteroides and Phocaeicola isolates from healthy and carbapenem-treated patients from European countries

BACKGROUND

Bacteroides fragilis group (BFG) species are the most significant anaerobic pathogens and are also the most antibiotic-resistant anaerobic species. Therefore, surveying their antimicrobial resistance levels and investigating their antibiotic resistance mechanisms is recommended. Since their infections are endogenous and they are important constituents of the intestinal microbiota, the properties of the intestinal strains are also important to follow. The aim of this study was to investigate the main antibiotic gene content of microbiota isolates from healthy people and compare them with the gene carriage of strains isolated from infections.

RESULTS

We detected 13, mainly antibiotic resistance determinants of 184 intestinal BFG strains that were isolated in 5 European countries (Belgium, Germany, Hungary, Slovenia and Turkey) and compared these with values obtained earlier for European clinical strains. Differences were found between the values of this study and an earlier one for antibiotic resistance genes that are considered to be mobile, with higher degrees for cfxA, erm(F) and tet(Q) and with lower degrees for msrSA, erm(B) and erm(G). In addition, a different gene prevalence was found depending on the taxonomical groups, e.g., B. fragilis and NBFB. Some strains with both the cepA and cfiA β-lactamase genes were also detected, which is thought to be exceptional since until now, the B. fragilis genetic divisions were defined by the mutual exclusion of these two genes.

CONCLUSIONS

Our study detected the prevalences of a series of antibiotic resistance genes in intestinal Bacteroides strains which is a novelty. In addition, based on the current and some previous data we hypothesized that prevalence of some antibiotic resistance genes detected in the clinical and intestinal BFG strains were different, which could be accounted with the differential composition of the Bacteroides microbiota and/or the MGE mobilities at the luminal vs. mucosal sites of the intestine.

Antimicrobial resistance pattern of anaerobic bacteria causing lower respiratory tract infections

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.

A model for analysis of antibiotic usage in low-income settings

OBJECTIVES

Quantification of antibiotic usage is an important component of antimicrobial stewardship programmes. We aimed to estimate institutional antibiotic usage and costs using methodology and metrics applicable to low-income settings without electronic health records.

METHODS

The DDD per 100 patient-days (DDDs/100 PDs) of antibiotics used in a calendar year was calculated retrospectively from ward registers and inpatient drug records in general surgical wards of a tertiary hospital. The antibiotics were categorized using the Access, Watch, Reserve classification. The annual expenditure on antibiotics was estimated from price lists of the state medication procurer.

RESULTS

Annual usage of IV co-amoxiclav, cefuroxime and metronidazole was significantly higher than other antibiotics and certain wards showed outlier use of the same. The IV formulations of co-amoxiclav (5-fold), metronidazole (3-fold) and ciprofloxacin (2-fold) were used in excess of the oral formulation. Proportionate antibiotic usage based on the AWaRe category did not vary significantly between wards. Two wards were outliers for annual expenditure/100 PDs. IV clindamycin and meropenem combined accounted for 43.8% of expenditure on antibiotics.

CONCLUSIONS

This study demonstrated intra-institutional variations of annual antibiotic usage and related costs. The metric DDD/100 PDs and the methodology used here are suitable for intra- and inter-institutional analyses of antibiotic usage, particularly in low-income settings.

Anaerobic Gram-Negative Bacteria: Role as a Reservoir of Antibiotic Resistance

BACKGROUND

Anaerobic Gram-negative bacteria (AGNB) play a significant role as both pathogens and essential members of the human microbiota. Despite their clinical importance, there remains limited understanding regarding their antimicrobial resistance (AMR) patterns. This knowledge gap poses challenges in effectively managing AGNB-associated infections, as empirical treatment approaches may not adequately address the evolving resistance landscape. To bridge this research gap, we conducted a comprehensive study aimed at exploring the role of human AGNB as a reservoir of AMR. This can provide valuable insights for the prevention and management of anaerobic infections.

METHODS

We studied the prevalence of AMR and AMR determinants conferring resistance to metronidazole (nimE), imipenem (cfiA), piperacillin-tazobactam (cepA), cefoxitin (cfxA), clindamycin (ermF), chloramphenicol (cat) and mobile genetic elements (MGEs) such as cfiA^IS and IS1186 associated with the cfiA and nim gene expression. These parameters were studied in Bacteroides spp., Fusobacterium spp., Prevotella spp., Veillonella spp., Sutterella spp., and other clinical AGNB.

RESULTS

Resistance to metronidazole, clindamycin, imipenem, piperacillin-tazobactam, cefoxitin and chloramphenicol was 29%, 33.5%, 0.5%, 27.5%, 26.5% and 0%, respectively. The presence of resistance genes, viz., nim, ermF, cfiA, cepA, cfxA, was detected in 24%, 33.5%, 10%, 9.5%, 21.5% isolates, respectively. None of the tested isolates showed the presence of a cat gene and MGEs, viz., cfiA^IS and IS1186. The highest resistance to all antimicrobial agents was exhibited by Bacteroides spp. The association between resistant phenotypes and genotypes was complete in clindamycin, as all clindamycin-resistant isolates showed the presence of ermF gene, and none of the susceptible strains harbored this gene; similarly, all isolates were chloramphenicol-susceptible and also lacked the cat gene, whereas the association was low among imipenem and piperacillin-tazobactam. Metronidazole and imipenem resistance was seen to be dependent on insertion sequences for the expression of AMR genes. A constrained co-existence of cepA and cfiA gene in B. fragilis species was seen. Based on the absence and presence of the cfiA gene, we divided B. fragilis into two categories, Division I (72.6%) and Division II (27.3%), respectively.

CONCLUSION

AGNB acts as a reservoir of specific AMR genes, which may pose a threat to other anaerobes due to functional compatibility and acquisition of these genes. Thus, AST-complying standard guidelines must be performed periodically to monitor the local and institutional susceptibility trends, and rational therapeutic strategies must be adopted to direct empirical management.

Phenotypic and Genotypic Correlation of Antimicrobial Susceptibility of Bacteroides fragilis: Lessons Learnt

Background Bacteroides fragilis is an opportunistic pathogen causing severe infections, including bacteremia. There have been increased reports of antimicrobial resistance in B. fragilis. However, phenotypic testing of susceptibility is time consuming and not cost effective for anaerobes. The present study investigates the correlation of phenotypic susceptibility with genotypic markers; to determine if these could be considered for deciding empirical therapy for B. fragilis. Material and methods Bacteroides fragilis isolates from various clinical samples including exudates, tissue, and body fluids were collected between November 2018 and January 2020 in the Department of Clinical Microbiology, Christian Medical College (CMC) Vellore. Species identification was done by Matrix Assisted Laser Desorption Ionization time of flight mass spectrometry (MALDI TOF) according to the manufacturer's instructions. A total number of 51 B. fragilis isolates were tested against metronidazole, clindamycin, piperacillin/tazobactam, and meropenem phenotypically by agar dilution method using Clinical & Laboratory Standards Institute (CLSI) 2019 guidelines and minimum inhibitory concentrations (MIC) were interpretated. The genotypic markers for antimicrobial resistance genes (nim, emrF, and cfiA) were studied by polymerase chain reaction (PCR) assay as per the standard protocol on all isolates to detect resistance genes. Results B. fragilis isolates in this study expressed 45%, 41%, and 16% phenotypic resistance to clindamycin, metronidazole, and meropenem, respectively, with least resistance to piperacillin/tazobactam (6%). Among the metronidazole resistant isolates, 52% harbored nim gene. Nim gene was also present in 76% (23/30) of the metronidazole susceptible isolates. Similarly, cfiA was present in all eight meropenem resistant isolates in addition to 22% (9/41) of the susceptible isolates. All cfiA negative isolates were phenotypically susceptible. Interestingly, 74% (17/23) of the clindamycin resistant isolates were positive for ermF. Conclusions Detection of a limited set of genes does not always correlate with phenotypic resistance to metronidazole and clindamycin due to the reported influence of insertion sequence (IS) elements, efflux, and other genetic determinants. Certainly, the absence of the cfiA gene can be employed to rule out meropenem resistance. However, redundant use of antibiotics such as meropenem along with metronidazole could be avoided for B. fragilis, which might otherwise elevate meropenem resistance. Recommendation of metronidazole requires prior phenotypic testing due to the reported 41% resistance.

Prevalence of antimicrobial resistant genes in Bacteroides spp. isolated in Oita Prefecture, Japan

INTRODUCTION

Bacteroides spp. are the most common anaerobic bacteria isolated from the human gastrointestinal tract. Several resistant genes are present in Bacteroides spp. However, most studies have focused on the prevalence of the cfiA gene in Bacteroides fragilis alone. We assessed the susceptibility to antimicrobial agents and the prevalence of cepA, cfiA, cfxA, ermF, nim, and tetQ genes in Bacteroides strains isolated from clinical specimens in our hospital.

METHODS

We isolated 86 B. fragilis and 58 non-fragilis Bacteroides strains from human clinical specimens collected from January 2011 to November 2021. Resistance against piperacillin (PIPC), cefotaxime (CTX), cefepime (CFPM), meropenem (MEPM), clindamycin, and minocycline was determined.

RESULTS

The resistant rates of penicillins and cephalosporins in non-fragilis isolates were significantly higher than those in B. fragilis isolates. In B. fragilis isolates, the resistant rates of PIPC, CTX, and CFPM in cfxA-positive isolates were significantly higher than those in cfxA-negative isolates (71% vs. 16%, 77% vs. 19%, and 77% vs. 30%, respectively). Thirteen B. fragilis isolates harbored the cfiA gene, two of which were resistant to MEPM. Six of the 13 cfiA-positive B. fragilis isolates were heterogeneously resistant to MEPM.

CONCLUSION

It is important to evaluate the use of MEPM as empirical therapy for Bacteroides spp. infections, considering the emergence of carbapenem resistance during treatment, existence of MEPM-resistant strains, and heterogeneous resistance.

High prevalence of cfiA positive Bacteroides fragilis isolates collected at a teaching hospital in Hohhot, China

OBJECTIVES

Carbapenem-resistant Bacteroides fragilis has emerged globally and cfiA is the key underlying factor. However, the prevalence of cfiA-positive carbapenem-resistant B. fragilis varies among countries. Therefore, we investigated the prevalence of cfiA-positive B. fragilis clinical isolates in a tertiary hospital in China.

METHODS

Carbapenem-resistant cfiA-positive B. fragilis isolates were identified using polymerase chain reaction. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was used to identify the characteristic mass spectra of cfiA-positive B. fragilis.

RESULTS

The prevalence of cfiA among 153 B. fragilis isolates was 22.2% (34/153), when 20.6% (7/34) cfiA-positive B. fragilis strains were isolated from pediatric patients. Twenty-one carbapenem-resistant B. fragilis isolates were identified and were all positive with cfiA gene. Two characteristic peaks (4825 and 9642 Da) were identified using MALDI-TOF MS, and the sensitivity, specificity, and both the positive and negative predictive values of these two peaks were 100%. A new peak shift from 9627 Da for cfiA-negative isolates to 9642 Da for cfiA-positive isolates was observed.

CONCLUSIONS

A high prevalence of cfiA was observed among B.fragilis isolates in this study, especially those isolated from pediatric patients. Characteristic MS spectra can accurately discriminate cfiA-positive and -negative B. fragilis isolates and can contribute to the rapid screening of cfiA-positive B. fragilis isolates in clinical laboratories.

Sodium New Houttuyfonate Inhibits Cancer-Promoting Fusobacterium nucleatum (Fn) to Reduce Colorectal Cancer Progression

Colorectal cancer (CRC) is a major cause of morbidity and mortality worldwide. Recent studies showed that the common anaerobe Fusobacterium nucleatum (Fn) is closely associated with a higher risk for carcinogenesis, metastasis, and chemoresistance of CRC. However, there is no specific antimicrobial therapy for CRC treatment. Herbal medicine has a long history of treating diseases with remarkable effects and is attracting extensive attention. In this study, we tested six common phytochemicals for their antimicrobial activities against Fn and whether anti-Fn phytochemicals can modulate CRC development associated with Fn. Among these antimicrobials, we found that SNH showed the highest antimicrobial activity and little cytotoxicity toward cancer cells and normal cells in vitro and in vivo. Mechanistically, SNH may target membrane-associated FadA, leading to FadA oligomerization, membrane fragmentation and permeabilization. More importantly, SNH blocked the tumor-promoting activity of Fn and Fn-associated cancer-driven inflammation, thus improving the intestinal barrier damaged by Fn. SNH reduced Fn load in the CRC-cells-derived mice xenografts with Fn inoculation and significantly inhibited CRC progression. Our data suggest that SNH could be used for an antimicrobial therapy that inhibits Fn and cancer-driven inflammation of CRC. Our results provide an important foundation for future gut microbiota-targeted clinical treatment of CRC.

Time for Some Group Therapy: Update on Identification, Antimicrobial Resistance, Taxonomy, and Clinical Significance of the Bacteroides fragilis Group

Bacteroides fragilis group (BFG) species are common members of the human microbiota that provide several benefits to healthy hosts, yet BFG are also the most common anaerobes isolated from human infections, including intra-abdominal infections, abscesses, and bloodstream infection. Compared to many other anaerobes associated with disease, members of the BFG are more likely to be resistant to commonly used antimicrobials, including penicillin (>90% resistant), carbapenems (2 to 20% resistant), and metronidazole (0.2 to 4% resistant). As a result, infection with BFG bacteria can be associated with poor clinical outcomes. Here, we discuss the role of BFG in human health and disease, proposed taxonomic reclassifications within the BFG, and updates in methods for species-level identification. The increasing availability of whole-genome sequencing (WGS) supports recent proposals that the BFG now span two families (Bacteroidaceae and "Tannerellaceae") and multiple genera (Bacteroides, Parabacteroides, and Phocaeicola) within the phylum Bacteroidota. While members of the BFG are often reported to "group" rather than "species" level in many clinical settings, new reports of species-specific trends in antimicrobial resistance profiles and improved resolution of identification tools support routine species-level reporting in clinical practice. Empirical therapy may not be adequate for treatment of serious infections with BFG, warranting susceptibility testing for serious infections. We summarize methods for antimicrobial susceptibility testing and resistance prediction for BFG, including broth microdilution, agar dilution, WGS, and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). We examine global trends in BFG antimicrobial resistance and review genomics of BFG, revealing insights into rapid activation and dissemination of numerous antimicrobial resistance mechanisms.

Anaerobic bloodstream infections in Italy (ITANAEROBY): A 5-year retrospective nationwide survey

INTRODUCTION

A lack of updated data on the burden and profile of anaerobic bloodstream infections (ABIs) exists. We assessed the incidence of ABIs and trends in antimicrobial resistance in anaerobes isolated from blood in Italy.

MATERIAL AND METHODS

We conducted a retrospective study on 17 Italian hospitals (2016-2020). Anaerobes isolated from blood culture and their in vitro susceptibility profiles (EUCAST-interpreted) were registered and analyzed.

RESULTS

A total of 1960 ABIs were identified. The mean age of ABIs patients was 68.6 ± 18.5 years, 57.6% were males. The overall incidence rate of ABIs was 1.01 per 10.000 patient-days. Forty-seven% of ABIs occurred in medical wards, 17% in ICUs, 14% in surgical wards, 7% in hemato-oncology, 14% in outpatients. The three most common anti-anaerobic tested drugs were metronidazole (92%), clindamycin (89%) and amoxicillin/clavulanate (83%). The three most common isolated anaerobes were Bacteroides fragilis (n = 529), Cutibacterium acnes (n = 262) and Clostridium perfringens (n = 134). The lowest resistance rate (1.5%) was to carbapenems, whereas the highest rate (51%) was to penicillin. Clindamycin resistance was >20% for Bacteroides spp., Prevotella spp. and Clostridium spp. Metronidazole resistance was 9.2% after excluding C. acnes and Actinomyces spp. Bacteroides spp. showed an increased prevalence of clindamycin resistance through the study period: 19% in 2016, 33% in 2020 (p ≤ 0.001).

CONCLUSIONS

Our data provide a comprehensive overview of the epidemiology of ABIs in Italy, filling a gap that has existed since 1995. Caution is needed when clindamycin is used as empirical anti-anaerobic drug.

Paraphocaeicola brunensis gen. nov., sp. nov., Carrying Two Variants of nimB Resistance Gene from Bacteroides fragilis, and Caecibacteroides pullorum gen. nov., sp. nov., Two Novel Genera Isolated from Chicken Caeca

Three difficult-to-cultivate, strictly anaerobic strains, AN20^T, AN421^T, and AN502, were analyzed within a project studying possible probiotics for newly hatched chickens. Phylogenetic analyses showed that strains AN20^T, AN421^T, and AN502 formed two well-separated phylogenetic lineages in all phylogenetic and phylogenomic trees comprising members of the family Bacteroidaceae. Comparison to reference genomes of type species Bacteroides fragilis NCTC 9343^T, Phocaeicola abscessus CCUG 55929^T, and Capsularis zoogleoformans ATCC 33285^T showed low relatedness based on the calculated genome-to-genome distance and orthologous average nucleotide identity. Analysis of fatty acid profiles showed iso-C_15:0, anteiso-C_15:0, C_16:0, C_18:1ω9c, and iso-C_17:0 3OH as the major fatty acids for all three strains and additionally C_16:0 3OH for AN421^T and AN502. A specific combination of respiratory quinones different from related taxa was found in analyzed strains, MK-5 plus MK-11 in strain AN20^T and MK-5 plus MK-10 in strains AN421^T and AN502. Strains AN421^T and AN502 harbor complete CRISPR loci with CRISPR array, type II-C, accompanied by a set of cas genes (cas9, cas1, and cas2) in close proximity. Interestingly, strain AN20^T was found to harbor two copies of nimB gene with >95% similarity to nimB of B. fragilis, suggesting a horizontal gene transfer between these taxa. In summary, three isolates characterized in this study represent two novel species, which we proposed to be classified in two novel genera of the family Bacteroidaceae, for which the names Paraphocaeicola brunensis sp. nov. (AN20^T = CCM 9041^T = DSM 111154^T) and Caecibacteroides pullorum sp. nov. (AN421^T= CCM 9040^T = DSM 111155^T) are proposed.

IMPORTANCE This study represents follow-up research on three difficult-to-cultivate anaerobic isolates originally isolated within a project focused on strains that are able to stably colonize newly hatched chickens, thus representing possible probiotics. This project is exceptional in that it successfully isolates several miscellaneous strains that required modified and richly supplemented anaerobic media, as information on many gut-colonizing bacteria is based predominantly on metagenomic studies. Superior colonization of newly hatched chickens by Bacteroides spp., Phocaeicola spp., or related taxa can be considered of importance for development of future probiotics. Although different experiments can also be performed with provisionally characterized isolates, precise taxonomical definition is necessary for subsequent broad communication. The aim of this study is therefore to thoroughly characterize these isolates that represent novel genera and precisely determine their taxonomic position among related taxa to facilitate further research and communication involving these strains.

Antimicrobial susceptibility patterns of anaerobic bacteria at an Irish University Hospital over a ten-year period (2010-2020)

OBJECTIVES

In recent years various clinical studies have demonstrated poor outcomes in infections caused by anaerobic bacteria due to inappropriate therapy, directly due to emergence of resistant strains. This is a concern given that many anaerobic infections are treated empirically with metronidazole or a beta-lactam/beta-lactamase inhibitor combinations (e.g., co-amoxiclav, piperacillin-tazobactam). To date there is a paucity of available data on antimicrobial resistance trends of anaerobic bacteria in Ireland, and our study aims to determine such patterns among isolates processed at our institution over the last ten years.

METHODS

Significant anaerobic bacteria isolated from clinical specimens processed at our laboratory from January 2010 to January 2020 inclusive were reviewed. Bacteria were identified using MALDI-TOF, with E-tests used for antimicrobial susceptibility testing. Data was processed through WHONET.

RESULTS

A total of 2098 clinically significant anaerobic bacterial isolates from blood cultures (31%), theatre/intraoperative specimens (30%), aspirates and drain fluid (22%) and wound swabs (17%) were reviewed during the study period; with the majority of isolates being Bacteroides spp (32.79%, n = 688) and Clostridium spp (18.68%, n = 392). With isolates demonstrating well-recognised or inherent resistances excluded, overall resistance to tested antimicrobials was 6.40% to penicillin, 1.71% to metronidazole, 1.43% to co-amoxiclav, 13.63% to clindamycin, 0.43% to piperacillin-tazobactam and 0% to meropenem.

CONCLUSION

Metronidazole and beta-lactam/beta-lactamase inhibitor combinations remain highly efficacious against the majority of anaerobic isolates reviewed, and can safely be used as empiric therapy in suspected anaerobic infections. However, periodic surveillance of resistance trends remains important.

Progress on the national action plan of Pakistan on antimicrobial resistance (AMR): a narrative review and the implications

Introduction: The emergence of antimicrobial resistance (AMR) is a threat to public health. In 2015, the World Health Organization (WHO) introduced a global action plan to tackle AMR in the World Health Assembly. Pakistan's national action plan (NAP) for AMR was released in May 2017 by the Ministry of National Health Services. Based on the NAP, strategies have been initiated on a national and provincial scale in Pakistan.Areas covered: This narrative review of the five components of the Pakistan NAP has been undertaken to discuss some of the challenges in implementation of the NAP for AMR in Pakistan including different opinions and views of key stakeholders, combined with suggestions on potential ways to reduce the burden of the AMR.Expert opinion: Going forward, healthcare authorities should focus on screening and monitoring of all the objectives of the NAP by establishing proper policies as well as promoting antimicrobial stewardship interventions and Infection prevention and control (IPC) practices. Overall, the comprehensive strengthening of the healthcare system is required to adequately implement the NAP, tackle continued inappropriate antimicrobial use and high AMR rates in Pakistan.

Phenotypic and genotypic antimicrobial resistance in clinical anaerobic isolates from India

BACKGROUND

Antimicrobial resistance (AMR) in anaerobes remains a neglected field. The laborious procedures, non-compliance with the standard methodology and differences in interpretive breakpoints add variation in resistance data.

OBJECTIVES

To assess the phenotypic and genotypic resistance among clinically important anaerobes to six antibiotics frequently used as empirical therapy for anaerobic infections.

METHODS

A total of 150 anaerobic isolates were recovered from clinical specimens. The antimicrobial susceptibility was determined by the breakpoint agar dilution method as per CLSI guidelines. The presence of genes encoding resistance to metronidazole (nim gene), imipenem (cfiA gene) and mobilizable insertion sequence (IS) elements was detected to comprehend their association with phenotypic resistance.

RESULTS

This is a first study of its kind from the Indian subcontinent looking at the AMR and associated genes in anaerobes. Resistance to metronidazole, clindamycin, imipenem, piperacillin/tazobactam and cefoxitin was 32.6%, 42.6%, 0.6%, 38% and 35.3%, respectively. No resistance was observed to chloramphenicol. The nim gene was detected in 24.6% of isolates, of which 70.2% were resistant by phenotype. On sequencing, the PCR products of six random nim genes showed a close similarity to nimE of Bacteroides fragilis with 99% nucleotide and 100% amino acid sequence similarity. The cfiA gene, associated with imipenem resistance, was detected in 16% of isolates.

CONCLUSIONS

The possibility of isolates carrying AMR genes to become resistant to antibiotics by acquisition of IS elements mandates attention to periodically monitor the resistance patterns and geographic distribution of these genes and IS elements to understand the trends of AMR in anaerobes.

Molecular characterization of metronidazole resistant Bacteroides strains from Kuwait

Eleven metronidazole resistant Bacteroides and one newly classified Phocaeicola dorei strain from Kuwait were investigated for their resistance mechanisms and the emergence of their resistant plasmids. All but one strain harbored nimE genes on differently sized plasmids. Of the 11 nimE genes, 9 were preceded by full copies of the prototype ISBf6 insertion sequence element, one carried a truncated ISBf6 and one was activated by an additional copy of IS612B. Nucleotide sequencing results showed that the nimE ISBf6 distances were constant and all five different plasmids shared a common region, suggesting that (i) the nimE-ISBf6 configuration was inserted into an undisclosed common genetic element, (ii) over time, this common element was mutated by insertions and deletions, spreading the resultant plasmids. Of the 10 B. fragilis strains in this collection, 6 were also cfiA-positive, one with full imipenem resistance, indicating a tendency for multidrug resistance (MDR) among such isolates. The significant number of metronidazole resistant Bacteroides spp. and P. dorei strains with the MDR phenotype warns of difficulties in treatment and suggests promoting adherence to antibiotic stewardship recommendations in Kuwait.

Antibiotic resistance in Pakistan: a systematic review of past decade

Background

During the last six decades, extensive use of antibiotics has selected resistant strains, increasing the rate of fatal infectious diseases, and exerting an economic burden on society. This situation is widely accepted as a global problem, yet its degree is not well elucidated in many regions of the world. Up till now, no systemic analysis of Antimicrobial resistance (AMR) in Pakistan has been published. The current study aims to describe the antibiotic-resistance scenario of Pakistan from human samples of the last 10 y, to find the gaps in surveillances and methodology and recommendations for researchers and prescribers founded on these outcomes.

Methods

Original research articles analyzed the pattern of Antibiotic resistance of any World Health Organization (WHO) enlisted priority pathogens in Pakistan (published onward 2009 till March 2020), were collected from PubMed, Google scholar, and PakMedi Net search engines. These articles were selected based on predefined inclusion and exclusion criteria. Data about the study characteristics and antibiotic-resistance for a given bacterium were excluded from literature. Antibiotic resistance to a particular bacterium was calculated as a median resistance with 95% Confidence Interval (CI).

Results

Studies published in the last 10 y showed that Urinary Tract Infection (UTI) is the most reported clinical diagnosis (16.1%) in Pakistan. E. coli were reported in 28 (30.11%) studies showing high resistance to antibiotics’ first line. Methicillin-resistant Staphylococcus aureus (MRSA) was found in 49% of S. aureus’ total reported cases. Phenotypic resistance pattern has mostly been evaluated by Disk Diffusion Method (DDM) (82.8%), taken Clinical Laboratory Standards Institute (CLSI) as a breakpoint reference guideline (in 79.6% studies). Only 28 (30.11%) studies have made molecular identification of the resistance gene. blaTEM (78.94% in Shigella spp) and blaNDM-1 (32.75% in Klebsiella spp) are the prominent reported resistant genes followed by VanA (45.53% in Enterococcus spp), mcr-1 (1.61% in Acinetobacter spp), and blaKPC-2 (31.67% in E. coli). Most of the studies were from Sindh (40.86%), followed by Punjab (35.48%), while Baluchistan’s AMR data was not available.

Conclusion

Outcomes of our study emphasize that most of the pathogens show high resistance to commonly used antibiotics; also, we find gaps in surveillances and breaches in methodological data. Based on these findings, we recommend the regularization of surveillance practice and precise actions to combat the region’s AMR.

A Pattern of Antibiotic Resistance in Gram-Negative Rods Causing Urinary Tract Infection in Adults

Background and aim Gram-negative rods (GNR) are the most common pathogens associated with urinary tract infections (UTI). The resistance of these gram-negative rods to various antibiotics is increasing with time. The study aimed to determine the pattern of resistance to antibiotics in GNR causing urinary tract infection in adults. Material and methods This is a cross-sectional study conducted during six months (1st December 2019 to 1st June 2020) among adult patients admitted to Russells Hall Hospital Dudley, UK. Urine cultures of 156 patients admitted with urinary tract infection were collected and reviewed. Sources of urine included midstream urine (MSU), catheter specimen urine (CSU), and others from nephrostomy bags and urine bags. Sensitivity and resistance were checked using Clinical and Laboratory Standards Institute (CLSI) guidelines. Results were analyzed using SPSS version 13.  Results Altogether 156 patients were included in the study. Males were 40.4% of the patients were males, and 59.6% were females. The mean age was 78 with a standard deviation (SD) of 13.15. Most of the samples (67.3%) were urine MSU, 23.1% catheter urine, and 9.6% were others, like from nephrostomy bags or unspecified. Resistance to amoxicillin was found in 61.7%, trimethoprim in 36.2%, nitrofurantoin in 13.2%, ciprofloxacin in 25.6%, fosfomycin in 10.7%, co-amoxiclav in 36.2%, gentamicin in 12.8%, piperacillin-tazobactam in 7.1%, cephalexin in 44.4%, and meropenem in 0% of patients. Conclusion Resistance to gram-negative rods causing urinary tract infection is increasing; a particular concern is increased resistance to beta-lactams, trimethoprim, and quinolones.

Comparative analysis of Bacterial Vaginosis microbiota among pregnant and non-pregnant females and isolation of phages against Enterococcus faecalis, Enterococcus faecium, and Shigella flexneri strains

BACKGROUND AND OBJECTIVES

Bacterial vaginosis (BV) is the most common vaginal infection in women of reproductive age. It shifts the paradigms of the vagina from healthy, beneficial microbiota to facultative and strict anaerobes. BV remains one of the most arduous and controversial challenges in modern-day clinical microbiology because of its high prevalence and relapse rates. A lot of research has been carried out on it. Still, its etiology is unknown, which gave this infection global importance. The current study was designed to investigate and compare the microbiota of pregnant and non-pregnant females suffering from BV, and phages were isolated against BV microbiota.

MATERIAL AND METHODS

The samples were collected from the vagina by using a speculum, and swabs were streaked on different media to isolate bacteria. The microbiological analysis was performed by microscopy, biochemical testing, and antibiotic susceptibility was determined by using Metronidazole and Clindamycin. Furthermore, the phages were isolated and characterized against BV strains.

RESULTS AND CONCLUSION

The Gram staining showed high prevalence of Staphylococcus (36% vs. 33%), followed by Streptococcus (31% vs. 14%) and Enterococcus (7% vs. 14%) in non-pregnant and pregnant females' respectively. However, the exception was observed in non-pregnant BV positive females, who had Shigella flexneri in their samples. The antibiotic sensitivity showed Metronidazole was resistant against all BV microbiota, and Clindamycin showed susceptibility against 3 strains. Phages were isolated against three bacterial strains, i.e. E. faecalis, E. faecium, and S. flexneri. Bacterial reduction assay showed bacterial growth decreases in the presence of phage suspension, pH stability showed phages' maximum lytic activity at pH 7 for E. faecalis and E. faecium and pH 9 for S. flexneri. However, the thermal stability showed phages' highest lytic activity at 55 °C for E. faecalis, 70 °C for E. faecium, and 40 °C for S. flexneri. Phage genome isolation showed that all phages nucleic acid was DNA in nature and between 15 and 20kbp. SEM analysis showed they were circular in shape and might belong to the Podoviridae family. This study provides an understanding of pathogens involved in BV and helps the doctors to treat the patients accordingly. Furthermore, this study showed that Bacterial Vaginosis and BV secondary bacteria have associations. BV secondary microbiota is also involved in the pathogenesis of this infection, whereas bacteriophage therapy has the potential to be used as an alternative treatment to antibiotics.

Anaerobic resistance: should we be worried?

PURPOSE OF REVIEW

Anaerobic bacteria are implicated in a broad range of infections and can cause significant morbidity and mortality. As such, development of antimicrobial resistance (AMR) increases the risk of worse clinical outcomes and death.

RECENT FINDINGS

Anaerobe AMR is highly variable according to region and species included in the survey. The overall trend is to increasing resistance, particularly in Europe and Asia, and in the Bacteroides fragilis group and Clostridium sp. Conversely, with the decline in RT027, resistance in Clostridiodes difficile is decreasing. Resistance to moxifloxacin and clindamycin has reached 30-50%, whereas prevalence of metronidazole and carbapenem resistance is generally low. Infections due to multidrug anaerobes have been increasingly reported, with clinical studies demonstrating adverse clinical outcomes, including higher mortality, with anaerobic resistance or inappropriate therapy. The role of antimicrobial stewardship in the setting of increasing anaerobe resistance is yet to be fully elucidated.

SUMMARY

These findings highlight the importance of continuous surveillance in monitoring emerging trends in anaerobe AMR. Mean inhibitory concentrations should be reported due to variable susceptibility breakpoints and for detection of isolates with reduced susceptibility. At a local level, the clinical microbiology laboratory has a key role in identifying and undertaking susceptibility testing to inform individual patient management, develop local antibiograms and liaise with antimicrobial stewardship teams. A greater understanding of the clinical impact of anaerobic resistance and the role of antimicrobial stewardship in preventing resistance is required.

Antimicrobial susceptibility and prevalence of resistance genes in Bacteroides fragilis isolated from blood culture bottles in two tertiary care hospitals in Japan

The in vitro susceptibilities of Bacteroides fragilis to antimicrobial agents, especially to carbapenem, are a major concern in the treatment of patients with bloodstream infections. In this study, 50 isolates of B. fragilis were obtained from positive blood bottles from 2014 to 2019 in Saitama, Japan. Their susceptibility to ampicillin/sulbactam was reduced to 70.0% compared with a previous report, whereas they were still sufficiently susceptible to piperacillin/tazobactam (94.0%). Five cfiA-positive isolates (5/50, 10.0%) were identified that were resistant to doripenem and meropenem, and two of them carried an insertion sequence located upstream of the cfiA-coding region. In particular, imipenem should be considered as a first-line carbapenem for the empirical treatment of B. fragilis infection because only insertion sequence and cfiA double-positive strains showed resistance to imipenem. Thirty-six percent of the isolates had a reduced minimum inhibitory concentration for moxifloxacin. In addition, metronidazole should still be considered as an active agent for B. fragilis because all isolates were susceptible to this antibiotic and the prevalence of the nim gene was low in Japan.

The effect of intervention by an antimicrobial stewardship team on anaerobic bacteremia

The effect of antimicrobial stewardship (AS) on anaerobic bacteremia is uncertain. This study aimed to assess the effect of interventions by the AS team (AST) on clinical and microbiological outcomes and antimicrobial use. An AS program was introduced at Osaka City University Hospital in January 2014; an interdisciplinary AST was established. We enrolled patients with anaerobic bacteremia between January 2009 and December 2018. Patients were classified into the pre-intervention group (from January 2009 to December 2013) and the post-intervention group (from January 2014 to December 2018). A significant decrease in definitive carbapenem use (P = 0.0242) and an increase in empiric tazobactam/piperacillin use (P = 0.0262) were observed in the post-intervention group. The de-escalation rate increased significantly from 9.38% to 32.7% (P = 0.0316) in the post-intervention group. The susceptibility of Bacteroides species and 30-day mortality did not worsen in the post-intervention group. These results showed that interventions by an AST can reduce carbapenem use and increase the de-escalation rate without worsening patient outcomes.

The Role of Microbiology Testing in Controlling Infection and Promoting Antimicrobial Stewardship

This chapter discusses the Role of Microbiology Testing in Controlling Infection and Promoting Antimicrobial Stewardship. It details the role that culture and sensitivity testing has played in creating the ‘objective’ evidence base that facilitated and nurtured midwifery empowerment, task shifting and multi-disciplinary team working. The chapter presents findings of resistance patterns of isolates from women with suspected sepsis.