Anaerobic Bacteria in Clinical Specimens - Frequent, But a Neglected Lot: A Five Year Experience at a Tertiary Care Hospital

Use of pus metagenomic next-generation sequencing for efficient identification of pathogens in patients with sepsis

The positive detection rate of blood metagenomic next-generation sequencing (mNGS) was still too low to meet clinical needs, while pus from the site of primary infection may be advantageous for identification of pathogens. To assess the value of mNGS using pus in patients with sepsis, thirty-five samples were collected. Pathogen identification and mixed infection diagnosis obtained by use of mNGS or cultivation methods were compared. Fifty-three aerobic or facultative anaerobes, 59 obligate anaerobes and 7 fungi were identified by the two methods. mNGS increased the accuracy rate of diagnosing aerobic or facultative anaerobic infections from 44.4% to 94.4%; mNGS also increased the sensitivity of diagnosing obligate anaerobic infections from 52.9% to 100.0%; however, mNGS did not show any advantage in terms of fungal infections. Culture and mNGS identified 1 and 24 patients with mixed infection, respectively. For obligate anaerobes, source of microorganisms was analyzed. The odontogenic bacteria all caused empyema (n = 7) or skin and soft tissue infections (n = 5), whereas the gut-derived microbes all caused intra-abdominal infections (n = 7). We also compared the clinical characteristics of non-obligate anaerobic and obligate anaerobic infection groups. The SOFA score [9.0 (7.5, 14.3) vs. 5.0 (3.0, 8.0), P = 0.005], procalcitonin value [4.7 (1.8, 39.9) vs. 2.50 (0.7, 8.0), P = 0.035], the proportion of septic shock (66.7% vs. 35.3%, P = 0.044) and acute liver injury (66.7% vs. 23.5%, P = 0.018) in the non-obligate anaerobic infection group were significantly higher than those in the obligate anaerobic infection group. In patients with sepsis caused by purulent infection, mNGS using pus from the primary lesion may yield more valuable microbiological information.

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.

Antimicrobial Effects of Mouse Adipose-Derived Mesenchymal Stem Cells Encapsulated in Collagen-Fibrin Hydrogel Scaffolds on Bacteroides fragilis Wound Infection in vivo

Background

Anaerobes are the causative agents of many wound infections. B. fragilis is the most prevalent endogenous anaerobic bacterium causes a wide range of diseases, including wound infections. This study aimed to assess the antibacterial effect of mouse adipocyte derived-mesenchymal stem cell (AD-MSCs) encapsulated in collagen-fibrin (CF) hydrogel scaffolds on B. fragilis wound infection in an animal model.

Methods

Stem cells were extracted from mouse adipose tissue and confirmed by surface markers using flow cytometry analysis. The possibility of differentiation of stem cells into osteoblast and adipocyte cells was also assessed. The extracted stem cells were encapsulated in the CF scaffold. B. fragilis wound infection was induced in rats, and then following 24 h, collagen and fibrin-encapsulated mesenchymal stem cells (MSCs) were applied to dress the wound. One week later, a standard colony count test monitored the bacterial load in the infected rats.

Results

MSCs were characterized as positive for CD44, CD90, and CD105 markers and negative for CD34, which were able to differentiate into osteoblast and adipocyte cells. AD-MSCs encapsulated with collagen and fibrin scaffolds showed ameliorating effects on B. fragilis wound infection. Additionally, AD-MSCs with a collagen scaffold (54 CFU/g) indicated a greater effect on wound infection than AD-MSCs with a fibrin scaffold (97 CFU/g). The combined CF scaffold demonstrated the highest reduction in colony count (the bacteria load down to 29 CFU/g) in the wound infection.

Conclusion

Our findings reveal that the use of collagen and fibrin scaffold in combination with mouse AD-MSCs is a promising alternative treatment for B. fragilis.

Sonication Fluid Isolation of Peptoniphilus asaccharolyticus After Total Hip Arthroplasty

Peptoniphilus asaccharolyticus is a gram-positive anaerobic coccus found on the skin, vagina, and gut, where it acts as an opportunistic pathogen or as part of polymicrobial infections of chronic wounds or diabetic ulcers. We present a case of a 68-year-old woman who was diagnosed with a late prosthetic hip arthroplasty infection caused by P. asaccharolyticus and isolated from sonication fluid cultures. Despite the fact that evidence is scarce, its role and pathogenicity in more severe infections should not be underestimated.

Clinico-microbiological spectrum of anaerobic pyogenic infections in an Indian tertiary care teaching hospital: A two-year study

Introduction:

Anaerobes are important however the most neglected pathogens. Timely isolation of anaerobes can guide the clinician about the correct course of clinical treatment and thus reduce the mortality and also the problem of antimicrobial resistance.

Materials and Methods:

Tissue and/or pus aspirates were collected aseptically from infectious sites in the Robertson's cooked meat medium (RCM) and sent to anaerobic bacteriology laboratory for culture. Subcultures from RCM for each sample were done on neomycin blood agar and 5% sheep blood agar along with metronidazole disc (5μg). The plates were incubated in an anaerobic jar using GasPak for 72 hrs. The preliminary identification was performed by standard biochemical tests for both obligate and facultative anaerobic isolates. Speciations of obligate anaerobes were performed by Vitek 2 automated system.

Results:

Obligate anaerobes either single or polymicrobial were obtained in 38/216 (14.5 %) samples processed during the study period. Polymicrobial infections were reported in 21/216 (55.26%) samples and most commonly with obligate anaerobic gramnegative bacilli i.e. Prevotella-Porphyromonas and Bacteroides fragilis group. Most common monomicrobial anaerobic infections were observed with Veillonella spp. (n=4) and Porphyromonas spp. (n=4) followed by Bacteroides fragilis (n=3). Obligate anaerobes were predominantly isolated from skin and soft tissue infections (n=14) followed by surgical site infections (n=8).

Conclusion:

Although most of the infections are polymicrobial, a rise in the incidence of monomicrobial anaerobic infections has been noticed. Therefore, the performance of anaerobic cultures along with aerobic cultures is much needed for complete bacterial work-up of specimens from infectious sites and better patient management.

Anaerobic infections in patients admitted in various surgical units of a tertiary care hospital of north India: neglected but important

Background and Objectives:

Anaerobic infections are usually caused by the host’s endogenous flora due to a breach in the anatomical barriers and Bacteroides spp. are the most notorious organisms associated with anaerobic infections. The identification of anaerobes has been a challenge since times. MALDI-TOF-MS is a boon for aiding the rapid detection of anaerobic organisms and has helped us to enlist the distribution of various anaerobic pathogens.

Materials and Methods:

This retrospective analysis (January 2018 to December 2019) was carried out in a tertiary care hospital in North India, in which the anaerobic microbiological profile of all patients admitted to surgical wards, ICU, and OPD of various departments (Orthopedics, Surgery, Gynecology, and Obstetrics) was reviewed. Samples received were immediately processed aerobically (5% sheep blood agar and Mac Conkeyagar) as well as anaerobically (RCM and freshly prepared sheep blood agar) as per the laboratory protocols.

Results:

Bacteroides fragilis (19.12%) was the most common anaerobe whereas among aerobes Escherichia coli (30.2%) followed by Klebsiella pneumoniae (10.34%) were most commonly isolated. The majority of patients were males (56%) and the most common presentation was with abscesses (21.4%). Polymicrobial infections (69.51%) outnumbered monomicrobial ones (30.48%).

Conclusion:

There is a paucity of literature on anaerobe isolation from surgical infections from our country which motivated us to study anaerobic infections and the high sample size in our institute enabled us to study surgical infections from an anaerobic perspective. This will add to the knowledge of microbiologists and clinicians. MALDI-TOF MS helped in rapid and accurate identification and hence we could report a wider spectrum of organisms in our study.

Genome Characterization of a Novel Wastewater Bacteroides fragilis Bacteriophage (vB_BfrS_23) and its Host GB124

Bacteroides spp. are part of the human intestinal microbiota but can under some circumstances become clinical pathogens. Phages are a potentially valuable therapeutic treatment option for many pathogens, but phage therapy for pathogenic Bacteroides spp. including Bacteroides fragilis is currently limited to three genome-sequenced phages. Here we describe the isolation from sewage wastewater and genome of a lytic phage, vB_BfrS_23, that infects and kills B. fragilis strain GB124. Transmission electron microscopy identified this phage as a member of the Siphoviridae family. The phage is stable when held at temperatures of 4 and 60°C for 1 h. It has a very narrow host range, only infecting one host from a panel of B. fragilis strains (n = 8). Whole-genome sequence analyses of vB_BfrS_23 determined it is double-stranded DNA phage and is circularly permuted, with a genome of 48,011 bp. The genome encodes 73 putative open reading frames. We also sequenced the host bacterium, B. fragilis GB124 (5.1 Mb), which has two plasmids of 43,923 and 4,138 bp. Although this phage is host specific, its isolation together with the detailed characterization of the host B. fragilis GB124 featured in this study represent a useful starting point from which to facilitate the future development of highly specific therapeutic agents. Furthermore, the phage could be a novel tool in determining water (and water reuse) treatment efficacy, and for identifying human fecal transmission pathways within contaminated environmental waters and foodstuffs.

Correlation Between Microbiological Profiles of Adenoid Tissue and Nasal Discharge in Children with Co-existent Chronic Adenoiditis and Chronic Rhinosinusitis

Chronic adenoiditis leading to adenoid hypertrophy is common in children. Many cases would also have co-existing chronic rhinosinusitis (CRS). Infact, long lasting bacterial infection of the adenoids has been hypothesized to be the cause for CRS in these children. A cross-sectional study was conducted in the departments of ENT and Micro-biology at Kasturba Hospital, Manipal, India between 2016 and 2017. 20 subjects who were diagnosed with CRS and adenoid hypertrophy took part in the study. Aerobic, anaerobic and fungal culture sensitivity of adenoid tissue was done along with aerobic and fungal culture sensitivity of nasal swabs from middle meatus. 2 out of 20 adenoid samples showed positive culture for aerobes and 19 adenoid samples grew anaerobic organisms. 7 out of 20 nasal swabs grew some aerobes and 2 were positive for fungal organisms. The correlation of microorganisms between adenoid hypertrophy and CRS was seen only in one patient in which methicillin resistant Staphylococcus aureus was grown. The present study showed mixed flora in the adenoid samples with anaerobic predominance. Aerobes were predominantly grown in nasal swabs from patients with CRS along with fungal colonizers. Though the study does not establish any bacteriological association with the CRS in our cohorts, the significant growth of the anaerobes from the core of the inflamed adenoids has prompted us to suggest the inclusion of the antibiotics against the anaerobes in the medical management of these children, whenever feasible. We think the addition of specific antibiotics to tackle anaerobes helps by hampering the further inflammatory hypertrophy of adenoid tissue.

The surgical wound in infrared: thermographic profiles and early stage test-accuracy to predict surgical site infection in obese women during the first 30 days after caesarean section

Background

Prophylactic antibiotics are commonly prescribed intra-operatively after caesarean section birth, often at high doses. Even so, wound infections are not uncommon and obesity increases the risk. Currently, no independent wound assessment technology is available to stratify women to low or high risk of surgical site infection (SSI).Study Aim: to investigate the potential of non-invasive infrared thermography (IRT), performed at short times after surgery, to predict later SSI.

Methods

IRT was undertaken in hospital on day 2 with community follow up (days 7, 15, 30) after surgery. Thermal maps of wound site and abdomen were accompanied by digital photographs, the latter used for wound assessment by six experienced healthcare professionals. Confirmatory diagnosis of SSI was made on the basis of antibiotic prescribing by the woman's community physician with logistic regression models derived to model dichotomous outcomes.

Results

Fifty-three women aged 21-44 years with BMI 30.1-43.9 Kg.m- 2 were recruited. SSI rate (within 30 days) was 28%. Inter-rater variability for 'professional' opinion of wound appearance showed poor levels of agreement. Two regions of interest were interrogated; wound site and abdomen. Wound site temperature was consistently elevated (1.5 °C) above abdominal temperature with similar values at days 2,7,15 in those who did and did not, develop SSI. Mean abdominal temperature was lower in women who subsequently developed SSI; significantly so at day 7. A unit (1 °C) reduction in abdominal temperature was associated with a 3-fold raised odds of infection. The difference between the sites (wound minus abdomen temperature) was significantly associated with odds of infection; with a 1 °C widening in temperature associated with an odds ratio for SSI of 2.25 (day 2) and 2.5 (day 7). Correct predictions for wound outcome using logistic regression models ranged from 70 to 79%.

Conclusions

IRT imaging of wound and abdomen in obese women undergoing c-section improves upon visual (subjective) wound assessment. The proportion of cases correctly classified using the wound-abdominal temperature differences holds promise for precision and performance of IRT as an independent SSI prognostic tool and future technology to aid decision making in antibiotic prescribing.