Identification and pathogenicity analysis of a novel non-tuberculous mycobacterium clinical isolate with nine-antibiotic resistance

With mycobacteriosis increasing, the study of non-tuberculous mycobacteria is imperative for clinical therapy and management. Nontuberculous mycobacteria are naturally resistant to most anti-tuberculosis drugs. Accordingly, it is important to decipher the biology of the novel non-tuberculous mycobacteria through complete genomic analysis of novel pathogenic mycobacteria. We describe Mycobacterium sinense JDM601, a novel, slow-growing mycobacterium of the Mycobacterium terrae complex resistant to nine antibiotics, by clinical presentation, cultural and biochemical characteristics, minimal inhibitory concentrations, and genome-sequencing analysis. JDM601 is closest to Mycobacterium nonchromogenicum according to mycolic acid composition, but closest to Mycobacterium algericum sp. nov according to 16S rDNA. JDM601 is resistant to isoniazid, streptomycin, rifampin, euteropas, protionamide, capromycin, ciprofloxacin, amikacin and levofloxacin but not ethambutol. The clinical information, mycolic acid composition, and virulence genes indicate that JDM601 is an opportunistic pathogen.     

Nontuberculous mycobacterial infection after lung transplantation: A single-center experience in South Korea

PurposeNontuberculous mycobacteria (NTM) infection is an important issue after lung transplantation. However, a large-scale epidemiological study on this issue in Korea is lacking. We aimed to evaluate the epidemiology of NTM infection after lung transplant surgery in Korea.MethodsBetween October 2012 and December 2018, we retrospectively evaluated lung transplant recipients in a referral hospital in South Korea. A total of 215 recipients were enrolled. The median age at transplantation was 56 years (range, 17–75), and 62% were men. Bronchoscopy was performed according to the surveillance protocol and clinical indications. A diagnosis of NTM infection was defined as a positive NTM culture from a bronchial washing, bronchoalveolar lavage sample, or two separate sputum samples. We determined NTM pulmonary disease (NTM-PD) according to the American Thoracic Society/Infectious Disease Society of America 2007 guidelines. The Kaplan–Meier method and log-rank test were used for conditional survival analysis in patients with follow-up of ≥12 months.ResultsFourteen patients (6.5%) were diagnosed with NTM infection at a median of 11.8 months (range, 0.3–51.4) after transplantation. Nine patients (4.2%) were diagnosed with NTM-PD, and the incidence rate was 1980/100,000 person-years. Mycobacterium abscessus was the most common species causing NTM-PD (66%), followed by M. avium complex (33%). The presence of NTM infection did not influence all-cause mortality among those who underwent follow-up for ≥12 months (N = 133, log-rank P = 0.816).ConclusionThe incidence of NTM-PD was considerably high among lung-transplant recipients. M. abscessus was the most common causative species of NTM-PD after lung transplantation.     

Predictive value of Escherichia coli susceptibility in strains causing asymptomatic bacteriuria for women with recurrent symptomatic urinary tract infections receiving prophylaxis

A significant proportion of women develop a recurrence following an initial urinary tract infection (UTI). In women with recurrent UTI, the predictive value of asymptomatic bacteriuria (ASB) for the development of a subsequent UTI has not yet been established and it is not known whether information from an asymptomatic sample is useful in guiding antimicrobial therapy. To address these questions, we used data that originated from the ‘Non-antibiotic prophylaxis for recurrent urinary tract infections’ (NAPRUTI) study: two randomized controlled trials on the prevention of recurrent UTI in non-hospitalized premenopausal and postmenopausal women (n = 445). During 15 months of follow-up, no difference was observed in the time to a subsequent UTI between women with and without ASB at baseline (hazard ratio: 1.07, 95% CI 0.80–1.42). The antimicrobial susceptibility and pulsed-field gel-electrophoresis (PFGE) pattern of 50 Escherichia coli strains causing a UTI were compared with those of the ASB strain isolated 1 month previously. The predictive values of the susceptibility pattern of the ASB strain, based on resistance prevalence at baseline, were ≥76%, except in the case of nitrofurantoin-and amoxicillin-clavulanic acid-resistance. Asymptomatic and symptomatic isolates had similar PFGE patterns in 70% (35/50) of the patients. In the present study among women with recurrent UTI receiving prophylaxis, ASB was not predictive for the development of a UTI. However, the susceptibility pattern of E. coli strains isolated in the month before a symptomatic E. coli UTI can be used to make informed choices for empirical antibiotic treatment in this patient population.     

Improved diagnosis of mycobacterial infections in formalin-fixed and paraffin-embedded sections with nested polymerase chain reaction

Traditional histological diagnosis of mycobacterial infection in formalin-fixed and paraffin-embedded (FFPE) tissues is insensitive and poorly specific. To improve this, we developed nested polymerase chain reaction (PCR) protocols for detecting a Mycobacterium genus-specific 65-kDa heat shock protein (HSP65) sequence and the M. tuberculosis complex-specific insertion sequence IS6110 in FFPE sections. Protocols were optimized on tissues from 20 patients with a final clinical diagnosis of mycobacterial infection. Amplicons were controlled by sequencing and restriction endonuclease digestion. PCR could detect as few as three mycobacterial genomes per reaction. Assays showed 100% sensitivity and specificity for both M. tuberculosis complex and M. avium complex infection. Paraffin blocks from a second group of 26 patients with histological evidence of necrotizing granulomas of unknown etiology were then analyzed as a surrogate group to test the assay under conditions similar to those applying during routine diagnosis. Twenty-three of these blocks contained amplifiable DNA; nine were positive for M. tuberculosis complex DNA and four for other types of mycobacterial DNA. Furthermore, digestion of HSP65 amplicons with NarI could distinguish M. tuberculosis from M. avium complex. In conclusion, our nested PCR assays can be used as reliable tools for the detection of mycobacterial infections in FFPE tissues. The assays are simple and rapid to perform and show improved sensitivity and specificity compared to previously reported protocols.     

Microbiological profile of canaliculitis and their antibiotic susceptibility patterns: A 11-year review at a referral eye care centre

PurposeTo analyze the microbiological profile and in vitro antibiotic susceptibility patterns of bacterial isolates in canaliculitis, an infection of the lacrimal drainage system of the eye.MethodsThe laboratory records of patients presenting with canaliculitis from whom specimens were obtained for microbiological investigations at our tertiary eye care centre in South India from January 2010 to December 2020, were reviewed.ResultsA total of 130 canalicular pus samples were collected from 112 patients and submitted for microbiological studies during the study period. A total of 183 micro-organisms were isolated from 115 culture-positive specimens. The micro-organisms isolated were predominantly aerobic Gram-positive bacteria (83.44%), with Coagulase-negative Staphylococci (CoNS/Other Staphylococcus spp) (31.69%), Corynebacterium spp (15.3%), Staphylococcus aureus (9.84%) and Viridans Streptococci (9.84%) accounting for a majority of the isolates. Actinomyces spp (6.56%) was the most common anaerobic bacterium isolated. Our study revealed several bacteria not previously associated with canaliculitis namely Ottowia spp, Elizabethkingia meningoseptica, Aeromonas salmonicida, Capnocytophaga ochracea and Campylobacter gracilis. Polymicrobial aetiology was observed in 39.13% of culture-positive samples. Analysis of antibiotic susceptibility patterns of the isolates revealed a high proportion of Gram-positive bacteria susceptible to chloramphenicol (90.16%) compared to fluoroquinolones including ciprofloxacin (74.42%), norfloxacin (64.15%) and gatifloxacin (60.49%).ConclusionThis study represents the largest series of canaliculitis reporting the microbiological profile and antibiotic susceptibilities of the isolated micro-organisms, till date. Gram-positive bacteria accounted for a majority of isolates, predominated by Staphylococcus spp. The increasing resistance of Gram-positive bacteria to fluoroquinolones warrants antibiotic treatment in canaliculitis is based on in vitro antimicrobial susceptibility patterns.     

Phenotypic and molecular characterization of Streptococcus agalactiae colonized in Chinese pregnant women: predominance of ST19/III and ST17/III

Streptococcus agalactiae (GBS) remains a major cause of invasive infections in neonates and pregnant women. Our aim was to evaluate the phenotypic and molecular characteristics of GBS isolates in order to reveal potential relationships among molecular characteristics and differences in genotype-phenotype characteristics between ST17 and ST19. A total of 104 GBS isolates were collected from pregnant women. All isolates were tested for antibiotic susceptibility by disk diffusion method and molecular characteristics, including antibiotic-resistant genes, virulence genes, serotypes and STs. The prevalence of GBS colonization in pregnant women was 4.9%. All isolates were susceptible to penicillin, but a high prevalence of resistance was observed for tetracycline (76.9%) and erythromycin (72.1%), with the predominant resistant genes being tet(M), tet(O), erm(B) and mef (A/E). The most frequent serotypes were III, Ia and V, and the predominant STs were ST19, ST17, ST12, ST10 and ST651. A potential correlation existed between STs, serotypes and alp genes, with ST19/III/rib and ST17/III/rib as the most prevalent clones. Notably, we observed significant differences in phenotypic and genotypic characteristics between ST17 [levofloxacin-susceptible and tet(O)-positive] and ST19 [levofloxacin-resistant and tet(O)-negative]. Our findings reveal a high prevalence of ST19/III and ST17/III and significant characteristic differences between them.     

Investigating infection management and antimicrobial stewardship in surgery: a qualitative study from India and South Africa

ObjectivesTo investigate the drivers for infection management and antimicrobial stewardship (AMS) across high-infection-risk surgical pathways.MethodsA qualitative study—ethnographic observation of clinical practices, patient case studies, and face-to-face interviews with healthcare professionals (HCPs) and patients—was conducted across cardiovascular and thoracic and gastrointestinal surgical pathways in South Africa (SA) and India. Aided by Nvivo 11 software, data were coded and analysed until saturation was reached. The multiple modes of enquiry enabled cross-validation and triangulation of findings.ResultsBetween July 2018 and August 2019, data were gathered from 190 hours of non-participant observations (138 India, 72 SA), interviews with HCPs (44 India, 61 SA), patients (six India, eight SA), and case studies (four India, two SA). Across the surgical pathway, multiple barriers impede effective infection management and AMS. The existing implicit roles of HCPs (including nurses and senior surgeons) are overlooked as interventions target junior doctors, bypassing the opportunity for integrating infection-related care across the surgical team. Critically, the ownership of decisions remains with the operating surgeons, and entrenched hierarchies restrict the inclusion of other HCPs in decision-making. The structural foundations to enable staff to change their behaviours and participate in infection-related surgical care are lacking.ConclusionsIdentifying the implicit existing HCP roles in infection management is critical and will facilitate the development of effective and transparent processes across the surgical team for optimized care. Applying a framework approach that includes nurse leadership, empowering pharmacists and engaging surgical leads, is essential for integrated AMS and infection-related care.     

Time-dependent differences in management and microbiology of orthopaedic internal fixation-associated infections: an observational prospective study with 229 patients

Objectives

Little information has been published on orthopaedic internal fixation-associated infections. We aimed to analyse time-dependent microbiology, treatment, and outcome.

Cysticercosis of the eye in South India--a case series

Purpose: To study the clinical presentation and treatment outcome of patients with ocular cysticercosis in southern India. Methods: This study included 10 patients who were diagnosed to have ocular or adnexal cysticercosis over a period of one year in Pondicherry, India. The clinical presentation, results of investigation and treatment outcome of the cases were analysed retrospectively. Results: Age of these patients ranged from 12 to 55 years. Four presented with loss of vision, two with a swelling in the eyelid, one with proptosis, one with diplopia and two with conjunctival involvement. ELISA for cysticercus antibodies in serum was positive in all cases. Albendazole and prednisolone were given for the treatment of these cases. Two patients responded well to treatment and were completely cured of the disease. There was partial improvement in 6 cases. Surgery in the form of excision was performed in two cases following a course of medical therapy. There was no significant change in visual acuity in eyes with intraocular cysticercosis following treatment. Conclusion: Ultrasonography B scan and ELISA for anticysticercal antibodies help to establish the diagnosis of ocular cysticercosis. A combination of oral albendazole and corticosteroids is found to be effective in confirmed cases. Intraocular cysticercosis is associated with a poor prognosis for vision.     

Cytologic features of mycobacterial pleuritis: logistic regression and statistical analysis of a blinded,case-controlled study

Tuberculous pleural effusions are characterized by lymphocytosis; the significance of mesothelial cells is uncertain, as are the cytologic features in concurrent human immunodeficiency virus (HIV) infection. This blinded study compared 38 culture-positive pleural fluids (6 HIV⁺) with 38 controls from benign exudative processes. Logistic regression analysis selected mature lymphocytes as most predictive of positive culture, and mesothelial cells and eosinophils as negative predictors. Mesothelial cells were scant (<10% of nucleated cells) in 36/38 cases with mycobacteria (sensitivity 95%); if these cells were <10%, tuberculosis was virtually ruled out in HIV⁻ patients. Specificity was maximized (82%) when mesothelial cells <10% were combined with lymphocytes <50%; positive predictive value with this combination was 76%, but was raised to 96% if moderate/marked cellularity was also identified. Among tuberculosis cases, reactive mesothelial cells differentiated HIV⁺ from HIV⁻ patients; there was no other significant difference. Diagn. Cytopathol. 1998;19:173–176. © 1998 Wiley-Liss, Inc.     

Utility of prior cultures in predicting antibiotic resistance of bloodstream infections due to Gram-negative pathogens: a multicentre observational cohort study

ObjectivesAppropriate empiric antibiotic therapy in patients with bloodstream infections due to Gram-negative pathogens can improve outcomes. We evaluated the utility of prior microbiologic results for guiding empiric treatment in Gram-negative bloodstream infections.MethodsWe conducted a multicentre observational cohort study in two large health systems in Canada and the United States, including 1832 hospitalized patients with Gram-negative bloodstream infection (community, hospital and intensive care unit acquired) from April 2010 to March 2015.ResultsAmong 1832 patients with Gram-negative bloodstream infection, 28% (n = 504) of patients had a documented prior Gram-negative organism from a nonscreening culture within the previous 12 months. A most recent prior Gram-negative organism resistant to a given antibiotic was strongly predictive of the current organism's resistance to the same antibiotic. The overall specificity was 0.92 (95% confidence interval (CI) 0.91–0.93), and positive predictive value was 0.66 (95% CI 0.61–0.70) for predicting antibiotic resistance. Specificities and positive predictive values ranged from 0.77 to 0.98 and 0.43 to 0.78, respectively, across different antibiotics, organisms and patient subgroups. Increasing time between cultures was associated with a decrease in positive predictive value but not specificity. An heuristic based on a prior resistant Gram-negative pathogen could have been applied to one in four patients and in these patients would have changed therapy in one in five.ConclusionsIn patients with a bloodstream infection with a Gram-negative organism, identification of a most recent prior Gram-negative organism resistant to a drug of interest (within the last 12 months) is highly specific for resistance and should preclude use of that antibiotic.     

A quantitative study of the classification and stability of ocular dominance in the cat's visual cortex

Summary We recorded from single cells in the cat's visual cortex to quantitatively evaluate (1) the reliability of subjective assessments of ocular dominance (101 cells) and (2) the stability of ocular dominance over time (25 cells). We found that the correlation between subjective and objective measures of this variable was poorer than expected, and was worst for cells with low overall response strengths. This result appears to reflect variability in the subjective assessment procedure. For the second part of the study, we recorded from single cortical cells of 5-week-old kittens, and made repeated objective measurements of ocular dominance over time. Twenty-four of the twenty-five cells examined were quite stable in ocular dominance for periods so long as 8 h. One unit was encountered which showed substantial progressive shifts in ocular dominance over time.Supported by grant EY01175 and Research Career Development Award EY00029 from the US National Eye Institute to R.D. Freeman     

Surveillance of chronic haemodialysis-associated infections in southern Israel

During a 12-month surveillance period, haemodialysis (HD) patients in southern Israel were categorised according to the type of vascular access site (VAS), i.e., arteriovenous (AV) fistula, synthetic AV graft, and cuffed or non-cuffed vascular catheters. Endpoints, expressed as cases/100 patient-months, were: incidence of hospital admission; antibiotic therapy; bloodstream infection (BSI); and VAS infection. These were compared to Centers for Disease Control (CDC) surveillance data, overall and by VAS type. In total, 2568 patient-months were analysed. The VAS distribution differed significantly from CDC data for fistulas (72% vs. 31%), grafts (12% vs. 41%), cuffed catheters (11% vs. 25%) and non-cuffed catheters (5% vs. 3%) (p < 0.0001 in all cases). Of 151 admissions, 32% resulted from infection, for which 112 antibiotic courses (22% vancomycin) were given. There were 16 BSIs, three involving resistant strains. The incidences of admission, antibiotic therapy, BSI and VAS infection were significantly lower overall, compared to CDC rates, as were most VAS-specific endpoints. These differences may be explained by VAS type distribution, although other factors may also be involved. Reporting regional or national surveillance data may allow a standardised comparison of the incidence of HD-associated infections.     

Serological and molecular study of Leptospira in pediatric patients at a tertiary care centre of northern India

Leptospirosis is considered as one of the most neglected zoonotic tropical diseases. Animals and humans acquire this infection through direct contact with contaminated urine or body fluids of infected animals. This prospective study was undertaken to know the proportion of leptospirosis in pediatric patients presented with acute febrile illness at the Post Graduate Department of Microbiology, King George's Medical University, Lucknow, Uttar Pradesh. Blood samples were collected over a period of one year from January to December 2018 from 70 pediatric patients aged up to 0–12 years presented with febrile illness for 3–14 days. Out of the 70 samples, 7 (10%) samples were found positive by IgM ELISA, 4 (5.7%) samples were positive by MAT and 3(4.3%) were found positive by PCR. Risk factors such as contact with infected animals and contaminated environment were highly associated with seropositivity of leptospirosis. Clinical symptoms such as fever, chills, myalgia, headache, abdominal pain and cough were significantly associated (p < 0.05) with the seropositivity of leptospirosis.     

Antibiotic resistance of Escherichia coli from community-acquired urinary tract infections in relation to demographic and clinical data

This prospective study determined the antibiotic susceptibility of 164 isolates of Escherichia coli from the urine of 164 patients (112 female, 52 male; mean age of 54.12 years) with community-acquired urinary tract infection (UTI). Half of the isolates were from uncomplicated UTI and half from complicated UTI (52 males and 34 females). Overall, 57.3% of isolates were resistant to ampicillin, 25% to co-trimoxazole, 20.1% to nalidixic acid, 14% to norfloxacin and ciprofloxacin, and 0% to fosfomycin and nitrofurantoin. Of the 82 isolates from complicated UTI, 16 (19.5%) were resistant to norfloxacin and ciprofloxacin, compared with seven (8.5%) from uncomplicated UTI (p 0.043). Isolates from patients aged >50 years were significantly more resistant than those from patients aged <50 years for nalidixic acid (p 0.007) and the fluoroquinolones tested (p 0.015). Resistance to fluoroquinolones was 25% (13/52) in males and 9% (10/112) in females (p 0.006). For patients with and without previous antimicrobial therapy, there was a significant difference only for resistance to nalidixic acid (p < 0.001) and the fluoroquinolones (p 0.011). There were adequate susceptibility rates to fosfomycin, nitrofurantoin and the fluoroquinolones for empirical use in the treatment of acute uncomplicated UTI. In order to interpret cumulative susceptibility data from the primary healthcare setting, it is necessary to take into account the type of UTI (uncomplicated vs. complicated), previous antimicrobial therapy, and the sex and age of each patient.     

Drug susceptibility of rapid and slow growing non-tuberculous mycobacteria isolated from symptomatics for pulmonary tuberculosis,Central India

Background: Non-tuberculous mycobacteria (NTM) are emerging as important pathogens. Their treatment also differs from that of Mycobacterium tuberculosis. In India, any datum on them is scarce as species identification and drug susceptibility are not performed in most laboratories. Susceptibility also differs from one geographic area to another, and in our country, there are no data even to guide the clinicians to start treatment empirically. Methodology: The present study endeavours to generate drug susceptibility data on NTM isolated from sputum samples collected and stored from 6445 symptomatics for pulmonary tuberculosis during a prevalence survey and from specimens received from the hospital. Isolates were not necessarily associated with the disease. Species were identified and antibiotic susceptibility was performed using micro-broth dilution technique as per the standard Clinical and Laboratory Standards Institute guidelines. Results: A total of 65 NTM with 11 species were identified, of which 27 belonged to Mycobacterium fortuitum complex, 14 Mycobacterium gordonae, 9 Mycobacterium avium, 7 Mycobacterium flavescens, 4 Mycobacterium scrofulaceum and one each of others. Sensitivity to amikacin for M. fortuitum was 95.22% (20 out of 21), followed by ciprofloxacin (76.19%) and clarithromycin (71.42%). All the 9 M. avium isolates, 11 of M. gordonae (78.57%), 5 of M. flavescens and 2 of M. scrofulaceum were sensitive to clarithromycin. All NTM were resistant to first-line antitubercular drugs except 8, which were sensitive to streptomycin. Conclusions: Drug sensitivity of NTM varies from species to species. While amikacin was the best for rapidly growing mycobacteria, clarithromycin was the most active drug against M. avium and other slow growers.     

单中心2006至2009年血流感染病原菌的临床分布特征及耐药性分析

了解引起血流感染(BSI)病原菌的临床分布特征及耐药性,为指导临床合理用药提供依据。方法 用BacT/ALERT 3D微生物全自动检测系统对血进行培养检测。用VITEK-2全自动微生物鉴定仪对病原菌进行鉴定及药物敏感性检测。以Whonet 5.4软件进行数据统计分析,通过查阅病历了解住院患者的临床资料。结果 2006至2009年中山大学孙逸仙纪念医院共收检血培养标本10462份,检出病原菌830株,阳性率为7.9％,其中革兰阴性杆菌442株,占53.3％(442/830),以大肠埃希菌为主,占33.7％(149/442);革兰阳性球菌275株占33.2％(275/830),以凝固酶阴性葡萄球菌(CoNS)为主,占44.4％(122/275);真菌113株,占13.6％(113/830),以热带念珠菌为主,占24.8％(28/113)。引起BSI的病原菌中,大肠埃希菌居首位(18.0％),其次为凝固酶阴性葡萄球菌(14.7％)、肺炎克雷伯菌(8.2％)。产超广谱β-内酰胺酶大肠埃希菌和肺炎克雷伯菌分别为67.5％和49.1％。碳青酶烯类及阿米卡星对肠杆菌科细菌有较好的抗菌活性,左氧氟沙星对常见非发酵菌的体外抗菌活性较好。耐甲氧西林金黄色葡萄球菌和耐甲氧西林凝固酶阴性葡萄球菌的检出率分别为53.2％和88.5％,未发现耐万古霉素革兰阳性球菌。血流感染患者临床分布以ICU、儿科和血液科为主,分别为25.5％、22.2％和12.4％,其基础疾病以恶性肿瘤、血液病多见,分别为26.8％、20.6％。结论 该院血流感染病原菌主要为大肠埃希菌,其次是凝固酶阴性葡萄球菌和肺炎克雷伯菌。万古霉素、替考拉宁、利奈唑烷及奎奴普丁或达福普汀对革兰阳性球菌有较好的抗菌活性;碳青酶烯类及左氧氟沙星对革兰阴性杆菌有较好的抗菌活性。有恶性肿瘤、血液病等基础疾病者易发生血流感染。     

皮肤软组织偶发分枝杆菌感染的病理学观察

目的：探讨皮肤软组织偶发分枝杆菌（MF）感染的临床病理学特征。方法：对59例局部注射后发生皮肤软组织MF感染病例进行详细的临床及病理学分析。结果：皮肤软组织MF感染具有局部表现重,病程长,治疗困难,病理改变多样化等特点;积极进行综合治疗是治愈本病的关键。结论：皮肤软组织MFMF感染无论在诊断和治疗上都具有特殊性,应加深认识和进行更深入的研究。