Herpesviridae and Atypical Bacteria Co-Detections in Lower Respiratory Tract Samples of SARS-CoV-2-Positive Patients Admitted to an Intensive Care Unit

Shortly after the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), cases of viral, bacterial, and fungal coinfections in hospitalized patients became evident. This retrospective study investigates the prevalence of multiple pathogen co-detections in 1472 lower respiratory tract (LRT) samples from 229 SARS-CoV-2-positive patients treated in the largest intensive care unit (ICU) in Slovenia. In addition to SARS-CoV-2, (rt)RT-PCR tests were used to detect cytomegalovirus (CMV), Epstein-Barr virus (EBV), herpes simplex virus 1 (HSV-1), herpes simplex virus 2 (HSV-2), varicella zoster virus (VZV), and atypical bacteria: Chlamydia pneumoniae, Mycoplasma pneumoniae and Legionella pneumophila/spp. At least one co-detection was observed in 89.1% of patients. EBV, HSV-1, and CMV were the most common, with 74.7%, 58.1%, and 38.0% of positive patients, respectively. The median detection time of EBV, HSV-1, and CMV after initial SARS-CoV-2 confirmation was 11 to 20 days. Bronchoalveolar lavage (BAL) and tracheal aspirate (TA) samples showed equivalent performance for the detection of EBV, CMV, and HSV-1 in patients with both available samples. Our results indicate that SARS-CoV-2 infection could be a risk factor for latent herpesvirus reactivation, especially HSV-1, EBV, and CMV. However, additional studies are needed to elucidate the clinical importance of these findings.

Swelling of inguinal lymph nodes in a patient with HIV: a case report

Lymphogranuloma venereum (LGV) is a sexually transmitted infection caused by the L1, L2, and L3 serotypes of Chlamydia trachomatis (CT). It primarily affects regional lymph nodes. Although it is not endemic in Europe and North America, recent reports indicate an increasing prevalence among men who have sex with men, with proctocolitis as the most frequently reported symptom. We report the case of a homosexual male that presented to our department with a nodular lesion on the shaft of the penis and tender, enlarged inguinal lymph nodes. Throat, urethral, and rectal swabs were collected for CT testing using real-time polymerase chain reaction. The urethral swab was positive for CT, whereas the throat and rectal swabs were negative. Subsequent testing detected the presence of LGV DNA. The patient was treated with a prolonged course of doxycycline. After 6 weeks, the urethral swab for CT returned a negative result. The patient reported complete remission 7 weeks after the start of treatment.

Clinical, Laboratory, and Radiographic Features Can Help Predict Mycoplasma pneumoniae Lower Respiratory Tract Infection in Children

Mycoplasma pneumoniae (Mp) is a common cause of lower respiratory tract infection (LRTI) in children that is difficult to distinguish from LRTI of other etiologies. We aimed to determine if a combination of clinical, laboratory, and chest radiographic features can help identify patients at higher risk of Mp LRTI. We reviewed medical charts of children referred to our tertiary hospital with suspected acute mycoplasmal LRTI. Pharyngeal swabs obtained from patients were tested by Mp PCR. We compared epidemiological and clinical data of children with positive and negative Mp PCR results. In addition, a multivariable logistic regression analysis was performed to predict Mp LRTI based on the patient's age, duration of symptoms, presence of extrapulmonary manifestations, laboratory findings, and chest radiographic findings. We included 65 children with Mp PCR-negative and 49 with Mp PCR-positive LRTI and no viral co-detection. Children with Mp LRTI were older (median age 5.8 vs. 2.2 years, p < 0.001), had a longer duration of symptoms on referral (median 7 vs. 4 days, p < 0.001), and lower median WBC (9.9 vs. 12.7 × 10⁹/L, p < 0.001). On chest radiograph, unilateral infiltrates were more frequently observed in the Mp PCR-positive group (57.5% vs. 24.1%, p = 0.001). Age, duration of symptoms, and chest radiographic findings had the highest predictive value for Mp LRTI in a multivariable logistic regression model. Our analysis suggests that a combination of clinical, laboratory, and chest radiographic features can be used to assess the likelihood of Mp LRTI and assist in decision-making for which children need further tests or macrolide antibiotic treatment.

Association between colonization of the respiratory tract with Ureaplasma species and bronchopulmonary dysplasia in newborns with extremely low gestational age: a retrospective study

AIM

To ascertain the incidence of respiratory tract colonization in extremely low gestational age newborns (ELGANs) with Ureaplasma parvum and Ureaplasma urealyticum and determine if there is a difference in the severity of bronchopulmonary dysplasia (BPD) between ELGANs with and without Ureaplasma species (spp) colonization.

METHODS

We reviewed the medical records of ELGANs 23 0/7-27 6/7 weeks of gestation, tested for U. parvum and U. urealyticum in our Center from January 1, 2009 to December 31, 2019. Ureaplasma spp were identified with the Mycofast Screening Revolution assay based on liquid broth cultures or with polymerase chain reaction.

RESULTS

This study enrolled 196 preterm newborns. Fifty (25.5%) newborns had Ureaplasma spp respiratory tract colonization, with U. parvum being the predominant species. The incidence rate of respiratory tract colonization with Ureaplasma spp slightly increased in the studied period. The incidence rate for 2019 was 16.2 per 100 infants. BPD severity significantly correlated with Ureaplasma spp colonization (P = 0.041). After controlling for other risk factors for BPD in a regression model, preterm infants colonized with Ureaplasma spp had 4.32 times (95% confidence interval, CI 1.20-15.49) higher odds for developing moderate-to-severe BPD.

CONCLUSIONS

U. parvum and U. urealyticum could be associated with the development of BPD in ELGANs.

Mycoplasma pneumoniae detections before and during the COVID-19 pandemic: results of a global survey, 2017 to 2021

Background

Mycoplasma pneumoniae respiratory infections are transmitted by aerosol and droplets in close contact.

Aim

We investigated global M. pneumoniae incidence after implementation of non-pharmaceutical interventions (NPIs) against COVID-19 in March 2020.

Methods

We surveyed M. pneumoniae detections from laboratories and surveillance systems (national or regional) across the world from 1 April 2020 to 31 March 2021 and compared them with cases from corresponding months between 2017 and 2020. Macrolide-resistant M. pneumoniae (MRMp) data were collected from 1 April 2017 to 31 March 2021.

Results

Thirty-seven sites from 21 countries in Europe, Asia, America and Oceania submitted valid datasets (631,104 tests). Among the 30,617 M. pneumoniae detections, 62.39% were based on direct test methods (predominantly PCR), 34.24% on a combination of PCR and serology (no distinction between methods) and 3.37% on serology alone (only IgM considered). In all countries, M. pneumoniae incidence by direct test methods declined significantly after implementation of NPIs with a mean of 1.69% (SD ± 3.30) compared with 8.61% (SD ± 10.62) in previous years (p < 0.01). Detection rates decreased with direct but not with indirect test methods (serology) (–93.51% vs + 18.08%; p < 0.01). Direct detections remained low worldwide throughout April 2020 to March 2021 despite widely differing lockdown or school closure periods. Seven sites (Europe, Asia and America) reported MRMp detections in one of 22 investigated cases in April 2020 to March 2021 and 176 of 762 (23.10%) in previous years (p = 0.04).

Conclusions

This comprehensive collection of M. pneumoniae detections worldwide shows correlation between COVID-19 NPIs and significantly reduced detection numbers.

Decreasing Pasteurization Treatment Efficiency against Amoeba-Grown Legionella pneumophila—Recognized Public Health Risk Factor

Legionellae are gram-negative bacteria most commonly found in freshwater ecosystems and purpose-built water systems. In humans, the bacterium causes Legionnaires’ disease (LD) or a Pontiac fever. In this study, the different waters (drinking water, pool water, cooling towers) in which Legionella pneumophila has been isolated were studied to assess the possible risk of bacterial spreading in the population. The influence of physical and chemical parameters, and interactions with Acanthamoeba castellanii on L. pneumophila, were analyzed by Heterotrophic Plate Count, the Colony-forming units (CFU) methods, transmission electron microscopy (TEM), and Sequence-Based Typing (SBT) analysis. During the study period (2013–2019), a total of 1932 water samples were analyzed, with the average annual rate of Legionella-positive water samples of 8.9%, showing an increasing trend. The largest proportion of Legionella-positive samples was found in cooling towers and rehabilitation centers (33.9% and 33.3%, respectively). Among the isolates, L. pneumophila SGs 2–14 was the most commonly identified strain (76%). The survival of Legionella was enhanced in the samples with higher pH values, while higher electrical conductivity, nitrate, and free residual chlorine concentration significantly reduced the survival of Legionella. Our results show that growth in amoeba does not affect the allelic profile, phenotype, and morphology of the bacterium but environmental L. pneumophila becomes more resistant to pasteurization treatment.

Comparison of genovars and Chlamydia trachomatis infection loads in ocular samples from children in two distinct cohorts in Sudan and Morocco

Trachoma is a blinding disease caused by repeated conjunctival infection with different Chlamydia trachomatis (Ct) genovars. Ct B genovars have been associated with more severe trachoma symptoms. Here, we investigated associations between Ct genovars and bacterial loads in ocular samples from two distinct geographical locations in Africa, which are currently unclear. We tested ocular swabs from 77 Moroccan children (28 with trachomatous inflammation-follicular (TF) and 49 healthy controls), and 96 Sudanese children (54 with TF and 42 healthy controls) with a Ct-specific real-time polymerase chain reaction (PCR) assay. To estimate bacterial loads, Ct-positive samples were further processed by multiplex real-time qPCR to amplify the chromosomal outer membrane complex B and plasmid open reading frame 2 of Ct. Genotyping was performed by PCR-based amplification of the outer membrane protein A gene (~1120 base pairs) of Ct and Sanger sequencing. Ct-positivities among the Moroccan and Sudanese patient groups were 60·7% and 31·5%, respectively. Significantly more Sudanese patients than Moroccan patients were genovar A-positive. In contrast, B genovars were significantly more prevalent in Moroccan patients than in Sudanese patients. Significantly higher Ct loads were found in samples positive for B genovars (598596) than A genovar (51005). Geographical differences contributed to the distributions of different ocular Ct genovars. B genovars may induce a higher bacterial load than A genovars in trachoma patients. Our findings emphasize the importance of conducting broader studies to elucidate if the noted difference in multiplication abilities are genovar and/or endemicity level dependent.

We investigated the association between different Ct genovars, the approximate load of infection, and the distribution of Chlamydia genovars by comparing samples from one trachoma-endemic area (i.e., the city of El-Gadaref in Al Qadarif, Sudan) and one previously endemic area (i.e., the Zagora Province in Morocco), currently considered as non-endemic. This study is the first to reveal a significant difference between the genome copy numbers of Ct genovar A and B/Ba in children with TF. Evidence that Ct is still circulating in rural foci of countries like Morocco that are no longer considered endemic implies that the continuation of the trachoma surveillance must be warranted in future to avoid further spreading of Ct. The clinical significance of different infectious loads in the development of sequelae has to be determined as well as whether these differences are genovar specific or related to the given endemicity level.

Ongoing evolution of Chlamydia trachomatis lymphogranuloma venereum: exploring the genomic diversity of circulating strains

Lymphogranuloma venereum (LGV), the invasive infection of the sexually transmissible infection (STI) Chlamydia trachomatis, is caused by strains from the LGV biovar, most commonly represented by ompA-genotypes L2b and L2. We investigated the diversity in LGV samples across an international collection over seven years using typing and genome sequencing. LGV-positive samples (n=321) from eight countries collected between 2011 and 2017 (Spain n=97, Netherlands n=67, Switzerland n=64, Australia n=53, Sweden n=37, Hungary n=31, Czechia n=30, Slovenia n=10) were genotyped for pmpH and ompA variants. All were found to contain the 9 bp insertion in the pmpH gene, previously associated with ompA-genotype L2b. However, analysis of the ompA gene shows ompA-genotype L2b (n=83), ompA-genotype L2 (n=180) and several variants of these (n=52; 12 variant types), as well as other/mixed ompA-genotypes (n=6). To elucidate the genomic diversity, whole genome sequencing (WGS) was performed from selected samples using SureSelect target enrichment, resulting in 42 genomes, covering a diversity of ompA-genotypes and representing most of the countries sampled. A phylogeny of these data clearly shows that these ompA-genotypes derive from an ompA-genotype L2b ancestor, carrying up to eight SNPs per isolate. SNPs within ompA are overrepresented among genomic changes in these samples, each of which results in an amino acid change in the variable domains of OmpA (major outer membrane protein, MOMP). A reversion to ompA-genotype L2 with the L2b genomic backbone is commonly seen. The wide diversity of ompA-genotypes found in these recent LGV samples indicates that this gene is under immunological selection. Our results suggest that the ompA-genotype L2b genomic backbone is the dominant strain circulating and evolving particularly in men who have sex with men (MSM) populations.

Ureaplasma parvum ventriculitis related to surgery and ventricular peritoneal drainage

Ureaplasma spp. usually causes genitourinary infections; few reports in the literature describe extragenital infections, usually in immunocompromised patients. We present a case of Ureaplasma parvum ventriculitis in an immunocompetent patient related to ventriculoperitoneal drainage and surgery. Ureaplasma parvum was detected with broad range 16S rRNA PCR and cultured on A8 agar.

Substantial underdiagnosis of lymphogranuloma venereum in men who have sex with men in Europe: preliminary findings from a multicentre surveillance pilot

Objectives

Understanding the public health impact of lymphogranuloma venereum (LGV) in Europe is hampered by inadequate diagnostics and surveillance systems in many European countries. We developed and piloted LGV surveillance in three European countries without existing systems and performed a preliminary investigation of LGV epidemiology, where little evidence currently exists.

Methods

We recruited STI or dermatovenereology clinics and associated laboratories serving men who have sex with men (MSM) in Austria, Croatia and Slovenia, using the UK for comparison. We undertook centralised LGV testing of Chlamydia trachomatis (CT)-positive rectal swabs collected between October 2016 and May 2017 from MSM attending these clinics. Stored specimens from Austria (2015–2016) and Croatia (2014) were also tested. Clinical and sociodemographic data were collected using a standardised proforma. The ompA gene of LGV-positive specimens was sequenced.

Results

In total, 500 specimens from CT-positive MSM were tested, and LGV positivity was 25.6% (128/500; 95% CI 22.0% to 29.6%) overall, and 47.6% (79/166; 40.1% to 55.2%) in Austria, 20.0% (3/15; 7.1% to 45.2%) in Croatia, 16.7% (1/6; 3.0% to 56.4%) in Slovenia and 14.4% (45/313; 10.9% to 18.7 %) in the UK. Proformas were completed for cases in Croatia, Slovenia and in the UK; proformas could not be completed for Austrian cases, but limited data were available from line listings. Where recorded, 83.9% (78/93) of LGV-CT cases were HIV-positive compared with 65.4% (149/228) of non-LGV-CT cases; MSM with LGV-CT were more likely to have proctitis (Austria, 91.8% vs 40.5%, p<0.001; Croatia, 100% vs 25%, p=0.04; UK, 52.4% vs 11.7%, p<0.001) than those with non-LGV-CT. Six different ompA sequences were identified, including three new variants; the L2 ompA sequence predominated (58.6%, 51/87).

Conclusions

LGV is substantially underdiagnosed in MSM across Europe. Unified efforts are needed to overcome barriers to testing, establish effective surveillance, and optimise diagnosis, treatment and prevention.

Unilateral brachial plexopathy, a rare complication of Mycoplasma pneumoniae infection

Few reports in the literature describe isolated peripheral neuropathies in relation to Mycoplasma pneumoniae infection without concurrent damage to the central nervous system. To our knowledge only a single case of mononeuritis multiplex with brachial plexus neuropathy coincident with M. pneumoniae has been documented until now. Here we present the first clinical case of lobar M. pneumoniae pneumonia in a 19-year-old female patient, where coincident neurological complications manifested as unilateral brachial plexus neuropathy, affecting axillar and suprascapular nerves. Isolated M. pneumoniae from sputum belonged to P1 type 2 and to MLVA type 3-6-6-2. No mutation associated with macrolide resistance in domain V of the 23S rRNA gene was detected. Serological testing of a GM1 antibody showed positive results, which might support the role of immunologic mechanisms in the pathogenesis of peripheral neuropathies related to M. pneumoniae infection.

Genetic diversity and macrolide resistance of Mycoplasma pneumoniae isolates from two consecutive epidemics in Slovenia

Two nationwide Mycoplasma pneumoniae epidemics occurred in Slovenia between 2006 and 2016. The aim of this study was to assess which M. pneumoniae genotypes were present in our area during the selected timeframe, whether the origin of the epidemics was monoclonal or polyclonal and whether the proportion between detected genotypes changed over time. We were also interested in the presence of macrolide resistance (MR) and whether it could be linked to specific genotypes. We performed pyrosequencing of the P1 gene and multiple-locus variable-number tandem repeat (VNTR) analysis (MLVA) typing from 872 M. pneumoniae isolates obtained from respiratory tract infections (RTI)-suffering patients. Additionally, isolates were tested for the presence of MR implicated mutations in the 23S rRNA gene. The MLVA typing results revealed that three main genotypes, MLVA-3,5,6,2, MLVA-3,6,6,2 and MLVA-4,5,7,2, were constantly present and occasionally joined by less abundant, short-lived genotypes, which were detected mostly, but not exclusively, during epidemics. We also noticed a switch in abundance from MLVA-3,5,6,2 and MLVA-3,6,6,2, which dominated in the first epidemic (77.0%; 97/126), to MLVA-4,5,7,2 (71.6%; 428/598), which dominated in the second. Similar to this finding, the dominant P1 type also shifted from type 2 to type 1, although a complete P1 type shift was not observed, since both types remained in circulation. MR was detected in 0.8% (7/872) of M. pneumoniae isolates. Our results seem to suggest that MR remains sporadic in Slovenia at this point in time and that both recent epidemics were polyclonal in nature and, possibly, to some extent, fuelled by the P1 type dominance change.

Under-reporting of sexually transmitted infection with chlamydia trachomatis - a revision of surveillance system is required

INTRODUCTION

To consider whether a revision of the national chlamydia surveillance system is needed, the objectives were to estimate the proportion of laboratory confirmed cases at the Institute of Microbiology and Immunology (IMI) not reported to the National Institute of Public Health (NIPH), and to assess the completeness of reporting for individual data items.

METHODS

The dataset with information about the cases diagnosed at the IMI during 2007-2010, and the national chlamydia surveillance data at the NIPH, were linked using SOUNDEX code and the date of birth as unique identifier. The proportion of unreported cases was calculated. The proportions of records with missing data for individual variables were estimated for all reported cases during the same period. Chlamydia testing and reported rates for the period 2002-2010 were presented.

RESULTS

Of 576 laboratory confirmed chlamydia cases at the IMI during 2007-2010, 201 were reported to the NIPH, corresponding to 65.1% of the overall underreporting (50.4% among dermatovenerologists, 90.1% among gynaecologist and 100% among other specialists). Item response was above 99% for demographic variables and from 69% to 81% for sexual behaviour variables. Higher testing rates corresponded to higher diagnosed rates.

CONCLUSIONS

Surveillance data underestimated diagnosed chlamydia infection rates. Mandatory reporting of cases by laboratories with less variables, including unique identifier, gender, date of diagnosis, and reporting physician specialty, together with numbers of tests performed (for estimating testing and positivity rates) would simplify the surveillance system and eliminate underreporting of laboratory confirmed cases, while still providing necessary information for public health policies.

Confirmed inguinal lymphogranuloma venereum genovar L2c in a man who had sex with men, Slovenia, 2015

A laboratory-confirmed lymphogranuloma venereum (LGV) case in Slovenia was reported in 2015, in a human immunodeficiency virus (HIV)-negative man presenting with inguinal lymphadenopathy. He reported unprotected insertive anal intercourse with two male partners in Croatia. Variant L2c of Chlamydia trachomatis was detected in clinical samples. Although the patient was eventually cured, the recommended treatment regimen with doxycycline had to be prolonged.

The effect of LDL particles on the behaviour of epithelial noncancer and cancer cell lines after in vitro induced injury

Cell spreading capability and cell proliferation are the major processes in wound healing of injured epithelia as well as in tumour progression. The effect of low-density lipoprotein (LDL) particles as a major extracellular source of cholesterol was evaluated in the re-epithelisation assay of in vitro induced injury. We selected two noncancer cell lines with different dependence on LDL concentrations, the kidney epithelial cells (MDCK) with higher dependence and keratinocytes (HaCaT) with lower dependence on LDL, and three cancer cell lines originating from epithelial cells: A549 (alveolar), CaCo-2 (intestinal) and RT4 (urothelial). All cells were incubated in a control medium, in an LDL-enriched medium or in an LDL-deficient medium. The LDL-enriched medium stimulated cell spreading of MDCK cells which, together with increased proliferation of these cells, resulted in an enhanced re-epithelisation of in vitro induced injury. LDL deficiency caused lower cell spreading which resulted in a decreased re-epithelisation despite the higher proliferation of MDCK cells in this medium. The re-epithelisation of keratinocytes (HaCaT) was not affected by altered LDL concentrations. In cancer cell lines A549, CaCo-2 and RT4, wide heterogeneity regarding cell proliferation and spreading capability was observed after treatment with different LDL concentrations. LDL had no influence on actin filament and tight junction distribution in any of the tested cell lines. The cholesterol content of all cell types, except for CaCo-2 cells, proved to be independent of the LDL level. Further research of the beneficial effects of LDL is needed to prove LDL as a safe enhancer of epithelial wound healing.