Fifteen years of phenotypic and genotypic surveillance and antibiotic susceptibility pattern of Actinomycetes (Mycobacterium, Nocardia, Rhodococcus, etc.) in clinical and environmental samples of Iran

Actinomycetes, ubiquitous in the natural world, have been known to inflict infections upon both immunocompromised and healthy individuals. Interestingly enough, these species are oftentimes found residing within the microbiota of humans and animals alike. Unfortunately, these infections are frequently misdiagnosed as more sinister ailments such as malignancy or tuberculosis. Due to this issue, this review deals with 15 years of study on clinical and environmental samples to determine Actinomycetes' prevalence, isolation, identification, and antibiotic susceptibility pattern in Iran by Davood Azadi et al. According to the Davood Azadi framework, we searched the following databases: PubMed/MEDLINE, Embase, Scopus, Web of Science, SID, and Google Scholar in the period from 2007 to 2023. This review aimed to provide an overview of the most recent techniques for collecting environmental samples, cultivating them, and identifying the Actinomycetes group's members. The isolation of Actinomycetes from clinical and ecological sources is becoming more prevalent and should be a concern for health authorities in developing countries. Health centers should take action to increase awareness of diagnostic criteria and management guidelines for actinomycete diseases. Improvements in national and regional reference laboratories may also aid in accurately diagnosing these diseases.

Clinical characteristics and drug susceptibility profiles of Mycobacterium abscessus complex infection at a medical school in Thailand

OBJECTIVES

This study investigated the differences in epidemiological and clinical data, and antimicrobial susceptibilities among different subspecies of Mycobacterium abscessus complex (MABSC) clinical isolates at a medical school in Thailand.

METHODS

A total of 143 MABSC clinical isolates recovered from 74 patients were genotypically analyzed for erm(41), rrl, and rrs mutations, and antimicrobial susceptibilities were determined using a broth microdilution method. Patient characteristics and clinical outcomes were reviewed from the medical records.

RESULTS

Seventy-four patients were infected with 28/74 (37.8%) M. abscessus subspecies abscessus (MAB), 43/74 (58.1%) M. abscessus subsp. massiliense (MMA), and 3/74 (4.1%) M. abscessus subsp. bolletii (MBO). The clinical findings and outcomes were generally indistinguishable between the three subspecies. All three subspecies of MABSC clinical isolates exhibited high resistance rates to ciprofloxacin, doxycycline, moxifloxacin, TMP/SMX, and tobramycin. MAB had the highest resistance rates to clarithromycin (27.8%, 20/72) and amikacin (6.9%, 5/72) compared to MBO and MMA, with p < 0.001 and p = 0.004, respectively. In addition, the rough morphotype was significantly associated with resistance to amikacin (8.9%, 5/56), clarithromycin (26.8%, 15/56), and imipenem (76.8%, 43/56) (p < 0.001), whereas the smooth morphotype was resistant to linezolid (57.1%, 48/84) (p = 0.002). In addition, T28 of erm(41), rrl (A2058C/G and A2059C/G), and rrs (A1408G) mutations were detected in 87.4% (125/143), 16.1% (23/143), and 9.1% (13/143) of MABSC isolates, respectively.

CONCLUSIONS

Three MABSC subspecies caused a variety of infections in patients with different underlying comorbidities. The drug susceptibility patterns of the recent circulating MABSC strains in Thailand were different among the three MABSC subspecies and two morphotypes.

Clinical relevance and diagnosis of nontuberculous mycobacterial pulmonary disease in populations at risk

The lungs are the most common disease site of nontuberculous mycobacteria (NTM). However, the isolation of NTM in a respiratory specimen does not indicate lung disease (LD). Differentiation between NTM colonization and NTM-LD remains challenging. In this brief review, we summarize the clinical impact of NTM-LD on morbidity and mortality in high-risk populations. The diagnosis criteria for NTM-LD-including clinical features, radiological presentations, and microbiological evidence-are also reviewed, according to the latest American Thoracic Society (ATS)/Infectious Disease Society of America (IDSA) guideline and the British Thoracic Society (BTS) guideline. However, the diagnosis of NTM-LD does not necessitate the initiation of anti-NTM treatment. Both environmental, host, and bacterial factors should be considered to identify patients that require NTM-LD treatment.

Top Questions in the Diagnosis and Treatment of Pulmonary M. abscessus Disease

Mycobacterium abscessus disease is particularly challenging to treat, given the intrinsic drug resistance of this species and the limited data on which recommendations are based, resulting in a greater reliance on expert opinion. We address several commonly encountered questions and management considerations regarding pulmonary Mycobacterium abscessus disease, including the role of subspecies identification, diagnostic criteria for determining disease, interpretation of drug susceptibility test results, approach to therapy including the need for parenteral antibiotics and the role for new and repurposed drugs, and the use of adjunctive strategies such as airway clearance and surgical resection.

Management of infections due to nontuberculous mycobacteria in solid organ transplant recipients-Guidelines from the American Society of Transplantation Infectious Diseases Community of Practice

These updated guidelines from the American Society of Transplantation Infectious Diseases Community of Practice review the epidemiology, diagnosis, prevention, and management of nontuberculous mycobacterial infections in the pre- and post-transplant period. NTM commonly cause one of five different clinical syndromes: pleuropulmonary disease, skin and soft tissue infection, osteoarticular infection, disseminated disease, including that caused by catheter-associated infection, and lymphadenitis. Diagnosis of these infections can be challenging, particularly when they are isolated from nonsterile spaces, owing to their ubiquity in nature. Consequently, diagnosis of pulmonary infections with these pathogens requires fulfillment of microbiologic, radiographic, and clinical criteria to address this concern. A combination of culture and molecular diagnostic techniques is often required to make a species-level identification. Treatment varies depending on the species isolated and is complex, owing to drug toxicities, need for long-term multidrug regimens, and consideration of complex drug-drug interactions between antimicrobials and immunosuppressive agents. Given these treatment challenges, efforts should be made in both the hospital and community settings to limit exposure to these pathogens to the extent feasible.

Two-Phase Hospital-Associated Outbreak of Mycobacterium abscessus: Investigation and Mitigation

Background

Nontuberculous mycobacteria (NTM) commonly colonize municipal water supplies and cause healthcare-associated outbreaks. We investigated a biphasic outbreak of Mycobacterium abscessus at a tertiary care hospital.

Methods

Case patients had recent hospital exposure and laboratory-confirmed colonization or infection with M. abscessus from January 2013 through December 2015. We conducted a multidisciplinary epidemiologic, field, and laboratory investigation.

Results

The incidence rate of M. abscessus increased from 0.7 cases per 10000 patient-days during the baseline period (January 2013-July 2013) to 3.0 cases per 10000 patient-days during phase 1 of the outbreak (August 2013-May 2014) (incidence rate ratio, 4.6 [95% confidence interval, 2.3-8.8]; P < .001). Thirty-six of 71 (51%) phase 1 cases were lung transplant patients with positive respiratory cultures. We eliminated tap water exposure to the aerodigestive tract among high-risk patients, and the incidence rate decreased to baseline. Twelve of 24 (50%) phase 2 (December 2014-June 2015) cases occurred in cardiac surgery patients with invasive infections. Phase 2 resolved after we implemented an intensified disinfection protocol and used sterile water for heater-cooler units of cardiopulmonary bypass machines. Molecular fingerprinting of clinical isolates identified 2 clonal strains of M. abscessus; 1 clone was isolated from water sources at a new hospital addition. We made several water engineering interventions to improve water flow and increase disinfectant levels.

Conclusions

We investigated and mitigated a 2-phase clonal outbreak of M. abscessus linked to hospital tap water. Healthcare facilities with endemic NTM should consider similar tap water avoidance and engineering strategies to decrease risk of NTM infection.

Public health relevance of non-tuberculous mycobacteria among AFB positive sputa

BACKGROUND

Sputum smear microscopy for acid fast bacilli (AFB) is used by most public health programmes to detect tuberculosis. While most AFB in countries endemic for tuberculosis are Mycobacterium tuberculosis (MTB), some may also be non-tuberculous mycobacteria (NTM). The inability to differentiate NTM from MTB by sputum smear microscopy may lead to erroneous diagnoses of tuberculosis, leading in turn to inappropriate therapy.

METHODS

This was a retrospective study of consecutive sputum samples received from November 2013 to March 2015 in the Department of Microbiology, Bhopal Memorial Hospital & Research Centre, Bhopal, India. Samples underwent smear microscopy, line probe assay (LPA) for MTB complex, culture, biochemical tests and LPA for NTM.

RESULTS

Of 4095 sputum samples, 2886 were AFB smear positive (70.5%). Of these, MTB complex was detected in 2611 (90.5%) samples by LPA. Of the remaining 275 samples, 47 grew AFB on culture. Nine strains belonged to the MTB complex. The remaining 38 (1.3%) were NTM, and could be speciated in 26 strains; 14 (53.8 %) were M. abscessus; 10 (38.4%) M. intracellulare, one (3.8%) M. kansasii and one (3.8%) M. fortuitum. The remaining 12 NTM could not be speciated.

CONCLUSION

NTM were present in at least 1.3% of all smear positive samples. It is important for public health programs to recognize the avoidable burden on logistics, infrastructure and finances caused by this. Detection and quantification of this burden would help design an appropriate strategy for optimal tuberculosis control.

Investigation of a Candida guilliermondii Pseudo-outbreak Reveals a Novel Source of Laboratory Contamination

Candida guilliermondii was isolated from sterile specimens with increasing frequency over a several-month period despite a paucity of clinical evidence suggesting true Candida infections. However, a health care-associated outbreak was strongly considered due to growth patterns in the microbiology laboratory that were more consistent with true infection than environmental contamination. Therefore, an extensive investigation was performed to identify its cause. With the exception of one case, patient clinical courses were not consistent with true invasive fungal infections. Furthermore, no epidemiologic link between patients was identified. Rather, extensive environmental sampling revealed C. guilliermondii in an anaerobic holding jar in the clinical microbiology laboratory, where anaerobic plates were prereduced and held before inoculating specimens. C. guilliermondii grows poorly under anaerobic conditions. Thus, we postulate that anaerobic plates became intermittently contaminated. Passaging from intermittently contaminated anaerobic plates to primary quadrants of aerobic media during specimen planting yielded a colonial growth pattern typical for true specimen infection, thus obscuring laboratory contamination. A molecular evaluation of the C. guilliermondii isolates confirmed a common source for pseudo-outbreak cases but not for the one true infection. In line with Reason's model of organizational accidents, active and latent errors coincided to contribute to the pseudo-outbreak. These included organism factors (lack of growth in anaerobic conditions obscuring plate contamination), human factors (lack of strict adherence to plating order, leading to only intermittent observation of aerobic plate positivity), and laboratory factors (novel equipment). All of these variables should be considered when evaluating possible laboratory-based pseudo-outbreaks.

Mycobacterium abscessus infection in cystic fibrosis: molecular typing and clinical outcomes

Mycobacterium abscessus is a significant pathogen in the cystic fibrosis patient population. PCR amplification and sequencing can provide accurate subspecies identification, and can predict macrolide susceptibility, which is becoming increasingly important for patient management. Molecular techniques for further typing of isolates provide tools for the ongoing investigations into the clinical impact of particular M. abscessus strains. Whole-genome sequencing is likely to be the only technique that provides sufficient resolution for investigating transmission events between patients.

An outbreak of Mycobacterium abscessus infection in a Pediatric Intensive Care Unit in Kuwait

BACKGROUND

Mycobacterium abscessus has been associated with respiratory tract infections, localized skin and soft tissue infections and sepsis. However, outbreaks of M. abscessus are rare.

AIM

to report an outbreak of M. abscessus causing respiratory tract infections in a Pediatric Intensive Care Unit (PICU) in Kuwait, its investigation and control measures.

METHODS

Respiratory secretions were obtained from ventilator-dependent patients showing signs of sepsis, including fever, malaise and weight loss. The specimens were cultured on appropriate routine media. After the results of the sample taken from the index case as acid-fast bacilli positive, all patients were screened for M. abscessus carriage. Isolates were identified by INNO-LiPA Mycobacteria v2 line probe assay and DNA sequencing. Molecular fingerprinting DiversiLab strain typing was performed on the isolates. Epidemiologic investigation was conducted during the outbreak.

FINDINGS

the outbreak affected 5 patients, 4 of whom had severe infections including 1 patient with septicemia. Asymptomatic carriage of outbreak strain was found in 1 patient. All environmental samples were negative for M. abscessus but some were positive for M. gordonae and M. fortuitum. The source could not be identified. Stringent infection control measures were put in place, including reemphasizing hand hygiene and closure of the Pediatric Intensive Care Unit to new admissions. A year later, no further case has occurred after the last case.

CONCLUSION

To our knowledge, this is the first report of a hospital-acquired outbreak of respiratory tract infection caused by M. abscessus in a Pediatric Intensive Care Unit. In the absence of definite source identification, reinforcement of standard infection control guidelines was successful in containing the outbreak.

Current methods in the molecular typing of Mycobacterium tuberculosis and other mycobacteria

In the epidemiology of tuberculosis (TB) and nontuberculous mycobacterial (NTM) diseases, as in all infectious diseases, the key issue is to define the source of infection and to disclose its routes of transmission and dissemination in the environment. For this to be accomplished, the ability of discerning and tracking individual Mycobacterium strains is of critical importance. Molecular typing methods have greatly improved our understanding of the biology of mycobacteria and provide powerful tools to combat the diseases caused by these pathogens. The utility of various typing methods depends on the Mycobacterium species under investigation as well as on the research question. For tuberculosis, different methods have different roles in phylogenetic analyses and person-to-person transmission studies. In NTM diseases, most investigations involve the search for environmental sources or phylogenetic relationships. Here, too, the type of setting determines which methodology is most suitable. Within this review, we summarize currently available molecular methods for strain typing of M. tuberculosis and some NTM species, most commonly associated with human disease. For the various methods, technical practicalities as well as discriminatory power and accomplishments are reviewed.

Pseudo-outbreak of Klebsiella oxytoca spontaneous bacterial peritonitis attributed to contamination of multidose vials of culture medium supplement

OBJECTIVE

To determine the source of a cluster of Klebsiella oxytoca isolates cultured from peritoneal fluid of 3 patients with cirrhosis on a single day.

DESIGN

Outbreak investigation and before-after study.

SETTING

A Veterans Affairs medical center.

METHODS

Epidemiologic investigation, analysis of antimicrobial susceptibility testing results and molecular typing of K. oxytoca isolates with repetitive sequence-based polymerase chain reaction (rep-PCR), review of microbiology laboratory procedures for processing peritoneal fluid cultures, and comparison of peritoneal fluid contamination rates 18 months before and after modification of laboratory procedures for culturing peritoneal fluid.

RESULTS

Each of the peritoneal fluid samples that grew K. oxytoca was inoculated into blood culture bottles by different clinicians at different hospital locations. None of the patients had clinical findings suggestive of peritonitis or elevated polymorphonuclear cell counts in peritoneal fluid (range, 3-25 cells/μL). Molecular typing with rep-PCR demonstrated that the K. oxytoca isolates were genetically related (greater than 95% similarity). Laboratory procedures included the routine addition of a culture medium supplement of yeast extract and dextrose from a multidose vial into blood culture bottles with peritoneal fluid. After discontinuing use of the culture medium supplement, there was a marked reduction in the number of peritoneal fluid cultures deemed as contaminants (14.3% vs 0.9%; [Formula: see text]).

CONCLUSION

A pseudo-outbreak of K. oxytoca peritonitis and high rates of contamination of peritoneal fluid were attributable to contamination of a multidose culture medium supplement. This article highlights the importance of discouraging the use of multidose vials in all clinical settings.

Identification of non-tuberculous mycobacteria isolated from clinical specimens at a tertiary care hospital: a cross-sectional study

Background

Non-tuberculous mycobacteria (NTM) are opportunistic pathogens in immuno-compromised patients. They are also increasingly recognized as pathogens in immuno-competent individuals. Globally, an increase in NTM isolation is being reported with a varied geographic prevalence of different species around the world. There is lack of data on species distribution of these organisms from Pakistan. Treatment options differ according to the species isolated and its susceptibility profile. Knowledge of local species variation would help targeted therapy. This study was performed to determine frequencies of different NTM species isolated from various clinical specimens submitted at a tertiary care hospital laboratory.

Methods

NTM isolated from 25955 clinical specimens over a period of two years (2010 to 2011) were included. All NTM were identified using conventional tests. Drug susceptibility testing (DST) was performed by broth microdilution and interpreted according to Clinical and Laboratory Standards Institute’s document M24-A2.

Results

A total of 104 NTM were included in the study. Of these, 76% (54/71) rapidly growing mycobacteria (RGM) and 57.6% (19/33) slow growing mycobacteria (SGM) could be further identified. Mycobacterium fortuitum (21/54) was the commonest NTM identified among RGM followed by M. mucogenicum (12/54) and M. smegmatis (11/54). Among SGM, M. avium complex (MAC) was the most frequent (14/19). Clinical significance could be assessed in a limited number (52/104) of NTM isolates and MAC appeared to be the commonest significant NTM. Three extra-pulmonary cases were found to be healthcare associated infections. DST results for RGM showed susceptibility to amikacin (100%), clarithromycin (100%, except M. fortuitum where it is not reportable), linezolid (90%) and moxifloxacin (75%). Whereas SGM were susceptible to clarithromycin (100%), linezolid (58.8%) and moxifloxacin (64.7%).

Conclusion

This is the first study reporting NTM species and their clinical significance isolated from clinical specimens from Pakistan. Isolation of NTM from clinical specimens should prompt to evaluate their clinical significance.

Plumbing of hospital premises is a reservoir for opportunistically pathogenic microorganisms: a review

Several bacterial species that are natural inhabitants of potable water distribution system biofilms are opportunistic pathogens important to sensitive patients in healthcare facilities. Waterborne healthcare-associated infections (HAI) may occur during the many uses of potable water in the healthcare environment. Prevention of infection is made more challenging by lack of data on infection rate and gaps in understanding of the ecology, virulence, and infectious dose of these opportunistic pathogens. Some healthcare facilities have been successful in reducing infections by following current water safety guidelines. This review describes several infections, and remediation steps that have been implemented to reduce waterborne HAIs.

Point-of-use membrane filtration and hyperchlorination to prevent patient exposure to rapidly growing mycobacteria in the potable water supply of a skilled nursing facility

BACKGROUND

Healthcare-associated outbreaks and pseudo-outbreaks of rapidly growing mycobacteria (RGM) are frequently associated with contaminated tap water. A pseudo-outbreak of Mycobacterium chelonae-M. abscessus in patients undergoing bronchoscopy was identified by 2 acute care hospitals. RGM was identified in bronchoscopy specimens of 28 patients, 25 of whom resided in the same skilled nursing facility (SNF). An investigation ruled out bronchoscopy procedures, specimen collection, and scope reprocessing at the hospitals as sources of transmission.

OBJECTIVE

To identify the reservoir for RGM within the SNF and evaluate 2 water system treatments, hyperchlorination and point-of-use (POU) membrane filters, to reduce RGM.

DESIGN

A comparative in situ study of 2 water system treatments to prevent RGM transmission.

SETTING

An SNF specializing in care of patients requiring ventilator support.

METHODS

RGM and heterotrophic plate count (HPC) bacteria were examined in facility water before and after hyperchlorination and in a subsequent 24-week assessment of filtered water by colony enumeration on Middlebrook and R2A media.

RESULTS

Mycobacterium chelonae was consistently isolated from the SNF water supply. Hyperchlorination reduced RGM by 1.5 log(10) initially, but the population returned to original levels within 90 days. Concentration of HPC bacteria also decreased temporarily. RGM were reduced below detection level in filtered water, a 3-log(10) reduction. HPC bacteria were not recovered from newly installed filters, although low quantities were found in water from 2-week-old filters.

CONCLUSION

POU membrane filters may be a feasible prevention measure for healthcare facilities to limit exposure of sensitive individuals to RGM in potable water systems.

Worldwide Outbreak Database: the largest collection of nosocomial outbreaks

Epidemiological findings of a single outbreak event may not be generalized; however, the characteristics of a typical outbreak can be determined on the basis of a large number of similar events. The Outbreak Database (http://www.outbreak-database.com) is the largest collection of nosocomial outbreaks currently available—and is still expanding. Articles are filed systematically, enabling those on a specific parameter of interest to be retrieved quickly. As such, this database is an extremely valuable tool on many medically related fronts, such as for educating other medical personnel, providing relevant information during the investigation of an acute outbreak, or addressing scientific-oriented questions. Several systematic reviews on a wide range of subjects, including sources of infections, types of pathogens, routes of transmission, appropriate infection control measures, and patients at risk of infection, have already been published based on information contained in this database. As this database may be used free of charge, all medical staff in the field of infection control, hygiene, and hospital epidemiology should be aware of its existence.

Pseudo-outbreak of Rhizobium radiobacter infection resulting from laboratory contamination of saline solution

We report a pseudo-outbreak of Rhizobium radiobacter infections resulting from contamination by a saline dispenser in the microbiology laboratory. Isolates from clinical specimens had identical antimicrobial susceptibilities and electrophoretic fingerprints. The episode resolved with autoclaving of the dispenser. This demonstrates the importance of timely, thorough investigation of unusual organisms, particularly when they appear as a cluster.