Increase in Penicillin and multidrug resistance in Streptococcus pneumoniae (1993-2016): report from a tertiary care hospital laboratory, Pakistan

Background: Streptococcus pneumoniae is a major cause of morbidity and mortality worldwide. With the emergence of penicillin-resistant S. pneumoniae (PRSP), treatment has become challenging. The Clinical and Laboratory Standards Institute (CLSI) in 2008 revised its guidelines for S. pneumoniae and recommended separate penicillin breakpoints for meningeal and non-meningeal strains. Similar to penicillin’s, resistance to other classes of antibiotics has emerged globally. Objective: The objective of this study is to determine the trend of resistance to antimicrobials in S. pneumoniae infections and the impact of new CLSI guidelines on penicillin susceptibility among meningeal isolates. Methodology: Twenty-four years (1993-2016) data from S. pneumoniae isolates and their antimicrobial susceptibility was retrieved from the computerized database. Data was divided into two groups for analysis, pre-2008 and post 2008. Results: Penicillin resistance remained unchanged in non-meningeal isolates during both study periods. A significant rise in penicillin resistance in meningeal isolates was observed in the second period 2008-2016 (2.9% vs 36.2%). High resistance rates were observed for co-trimoxazole, tetracycline and erythromycin. Increased trend of multi-drug resistant (MDR) strains were also noted, from 11% in 1999 to 36% in 2016. Conclusion: The emergence of MDR strains is evident from our dataset. It seems like the rise in PRSP in meningeal isolates is due to revised CLSI guidelines. Overall low resistance to penicillin in non-meningeal isolates and no resistance to ceftriaxone is encouraging and will assist in drafting local guidelines. Cautious use of antimicrobials are essential to reduce further emergence of antimicrobial resistance in indigenous isolates.

Genetic Characterization of Staphylococcus aureus From Subclinical Mastitis Cases in Dairy Cows in Rwanda

Whole-genome sequencing was carried out on 30 Staphylococcus (S.) aureus isolates from dairy cows with subclinical mastitis from all five provinces of Rwanda. Twenty-five of the isolates produced enough sequence to be analyzed using core genome multilocus sequence typing (cg-MLST). The isolates group into three main clusters. The largest cluster contain isolates of sequence type (ST) 152 (n = 6) and the closely related ST1633 (n = 2). These sequence types have previously mainly been encountered in humans. The isolates of the second-largest cluster belong to ST5477 (n = 5),so far exclusively isolated from cows in Rwanda. The third cluster consists of isolates of ST97 (n = 4), which is a well-known bovine-adapted sequence type. These three clusters were all widespread over the country. Isolates of the usually human-adapted sequence types 1 (n = 2) and 5 (n= 1) were found and a single isolate of ST2430, previously found among humans in Africa. Finally, four isolates of novel sequence types were found: ST7108 (n = 2), ST7109 (n = 1), and ST7110 (n = 1). The blaZ penicillin resistance gene was found in 84% of the isolates and was in all cases corroborated by phenotypic resistance determination. Five (20%) of the isolates carried a tetracycline resistance gene, tet(K) or tetM, and three of these five also displayed phenotypic resistance while two isolates carried a tetM-gene but were yet tetracycline susceptible. Seven (28%) isolates carried the dfrG gene conferring resistance to trimethoprim. Four of these isolates indeed were resistant to trimethoprim while three isolates were sensitive. The str gene conferring resistance to aminoglycosides was found in three isolates; however, none of these displayed resistance to gentamycin. Our data revealed a high diversity of the sequence types of S. aureus isolates from cows with subclinical mastitis in Rwanda. Two major clusters of ST97 and ST5477 are likely to be bovine adapted and cause mastitis while the third cluster of ST152 usually have been found in humans and may signify a recent transmission of these types from human to cows, for example from hand milking. The high prevalence of this sequence type among dairy cows may pose zoonotic threat. The sequence types were widely distributed without any geographic correlation. Penicillin resistance, the most common type of resistance with a prevalence over 80%, but also tetracycline and trimethoprim resistance were displayed by several isolates.

Australian Gonococcal Surveillance Programme Annual Report, 2020

The Australian Gonococcal Surveillance Programme (AGSP), established in 1981, has continuously monitored antimicrobial resistance in clinical isolates of Neisseria gonorrhoeae for more than 40 years. In 2020, a total of 7,222 clinical isolates of gonococci from patients in the public and private sectors, in all jurisdictions, were tested for in vitro antimicrobial susceptibility by standardised methods. Current treatment recommendations for gonorrhoea, for the majority of Australia, continues to be dual therapy with ceftriaxone and azithromycin. In 2020, decreased susceptibility (DS) to ceftriaxone (minimum inhibitory concentration [MIC] value ≥ 0.06 mg/L) was found nationally in 0.9% of isolates. There was one isolate, reported from Victoria in 2020, that was resistant to ceftriaxone (MIC value ≥ 0.25 mg/L). Resistance to azithromycin (MIC value ≥ 1.0 mg/L) was found nationally in 3.9% of N. gonorrhoeae isolates, continuing a downward trend observed and reported since 2017. Isolates with high-level resistance to azithromycin (MIC value ≥ 256 mg/L) are identified sporadically in Australia; in 2020, there was one such isolate reported in Queensland. In 2020, penicillin resistance was found in 27% of gonococcal isolates nationally, and ciprofloxacin resistance in 36%; however, there is considerable variation by jurisdiction. In some remote settings, penicillin resistance remains low, and this drug continues to be recommended as part of an empiric therapy strategy. In 2020, in remote Northern Territory, no penicillin resistance was reported, and in remote Western Australia 5/116 of gonococcal isolates (4.3%) were penicillin resistant. There was one ciprofloxacin-resistant isolate reported from remote Northern Territory, and ciprofloxacin resistance rates remain comparatively low in remote Western Australia (4/116; 3.4%).

Occurrence and aetiology of subclinical mastitis in water buffalo in Bangladesh

Subclinical mastitis (SCM) in water buffalo is a production disease associated with decreased milk yield and impaired milk quality and safety. Water buffalo is an important livestock species in Bangladesh, but information about the occurrence and aetiology of SCM in this species is scarce. A cross-sectional study was conducted as part of the Udder Health Bangladesh Programme to (i) determine the occurrence of SCM and bulk milk somatic cell count (SCC) in water buffalo in Bangladesh, (ii) identify pathogens causing SCM and (iii) evaluate penicillin resistance in isolated staphylococci strains. Sixteen buffalo farms in the Bagerhat and Noakhali regions of Bangladesh were selected for study and a bulk milk sample was collected from each farm. In addition, 299 udder quarter milk samples were collected from 76 animals. The bulk milk samples were assessed by direct SCC and the quarter milk samples by California mastitis test (CMT). The occurrence of SCM calculated at quarter and animal level was 42.5 and 81.6%, respectively. Milk samples from 108 CMT-positive quarters in 48 animals and 38 randomly selected CMT-negative quarters in 24 animals were investigated using bacteriological culture. Estimated mean bulk milk SCC was 195 000 cells/ml milk (range 47 000– 587 000 cells/ml milk). On culture, estimated quarter-level intramammary infection (IMI) was 40.4%. The identity of isolated bacteria was confirmed by MALDI-TOF mass spectrometry. Non-aureus staphylococci (NAS) were the most common pathogens (24.7%) and, among 36 NAS tested, 36.1% were resistant to penicillin. Thus there was high occurrence of SCM on the study farms, with relatively high penicillin resistance in NAS. Further studies are needed to identify underlying risk factors and develop an udder health control strategy for water buffalo in Bangladesh.

Correlation between Antibiotic Consumption and Resistance of Invasive Streptococcus pneumoniae

There is a lack of long-term studies that correlate different metrics of antibiotic consumption and resistance of invasive S. pneumoniae. The present study aims to investigate the correlation between national outpatients total antibiotic, penicillin and broad spectrum penicillins consumption expressed in daily doses per 1000 inhabitants per day (DID) with the ATC/DDDs, WHO version of 2019 (new version) and 2018 (old version), number of prescriptions per 1000 inhabitants per year (RxIDs) and number of packages per 1000 inhabitant per day (PIDs) with the resistance of invasive S. pneumoniae in Slovenia in the period from 2000 to 2018. The prevalence of penicillin resistance of invasive S. pneumoniae decreased by 47.13%, from 19.1% to 10.1%. Decline of resistance showed the highest correlation (R = 0.86) between RxIDs followed by PID (R = 0.85) and resistance of S. pneumoniae. Higher correlation between total use of antibiotics expressed in DID WHO version 2019 (R = 0.80) than for WHO version 2018 (R = 0.78) was found. Very high (R = 0.84) correlation between use of β-lactams expressed in PID, and RxIDs (R = 0.82) and reasonable (R = 0.59) correlation expressed in DIDs version 2019 was shown as well. The consumption of broad -spectrum penicillins (J01CA and J01CR02) expressed in PID (R = 0.72) and RxIDs (0.57) correlated significantly with the resistance of S. pneumoniae as well. A new finding of this study is that RxIDs correlated better with the resistance of S. pneumoniae than total consumption of antibiotics expressed in DID and significant correlations exist between use of broad-spectrum penicillins expressed in PID and RxIDs.

Australian Gonococcal Surveillance Programme Annual Report, 2020

The Australian Gonococcal Surveillance Programme (AGSP), established in 1981, has continuously monitored antimicrobial resistance in clinical isolates of <i>Neisseria gonorrhoeae</i> for more than 40 years. In 2020, a total of 7,219 clinical isolates of gonococci from patients in the public and private sectors, in all jurisdictions, were tested for in vitro antimicrobial susceptibility by standardised methods. Current treatment recommendations for gonorrhoea, for the majority of Australia, continues to be dual therapy with ceftriaxone and azithromycin. In 2020, decreased susceptibility (DS) to ceftriaxone (minimum inhibitory concentration [MIC] value ≥ 0.06 mg/L) was found nationally in 0.9% of isolates. There was one isolate, reported from Victoria in 2020, that was resistant to ceftriaxone (MIC value ≥ 0.25 mg/L). Resistance to azithromycin (MIC value ≥ 1.0 mg/L) was found nationally in 3.9% of <i>N. gonorrhoeae</i> isolates, continuing a downward trend observed and reported since 2017. Isolates with high-level resistance to azithromycin (MIC value ≥ 256 mg/L) are identified sporadically in Australia; in 2020, there was one such isolate reported in Queensland. In 2020, penicillin resistance was found in 27% of gonococcal isolates nationally, and ciprofloxacin resistance in 36%; however, there is considerable variation by jurisdiction. In some remote settings, penicillin resistance remains low, and this drug continues to be recommended as part of an empiric therapy strategy. In 2020, in remote Northern Territory, no penicillin resistance was reported, and in remote Western Australia 5/116 of gonococcal isolates (4.3%) were penicillin resistant. There was one ciprofloxacin-resistant isolate reported from remote Northern Territory, and ciprofloxacin resistance rates remain comparatively low in remote Western Australia (4/116; 3.4%).

β-lactam resistance in coagulase-negative Staphylococcus isolated from subclinical goat mastites

The objective of this work was to evaluate resistance mechanisms to β-lactam antimicrobials in 251 strains of coagulase-negative Staphylococcus (CoNS) isolated from subclinical goat mastitis, as well as to determine the sensitivity and specificity of the nitrocefin and disk diffusion methods to detect penicillin resistance, in comparison with the polymerase chain reaction (PCR). The isolates were evaluated for the presence of the blaZ and mecA genes, β-lactamase production, and susceptibility to penicillin. Of the total isolates, 228 (91%) carried the blaZ gene and, among these, 144 (63%) were positive for β-lactamase production. Resistance to penicillin was observed in 125 of the isolates, of which 96.8% carried the blaZ gene. The sensitivity of the phenotypic methods to detect β-lactamase production was low, but their specificity was high; the Kappa coefficient showed a poor agreement between the phenotypic methods and PCR. The mecA gene was detected in only 3% of the isolates, which were identified as belonging to the species: S. capitis subsp. ureolyticus, S. caprae, S. warneri, S. sciuri, S. simulans, and S. cohnii subsp. urealyticum. Coagulase-negative Staphylococcus are important mastitis-causing pathogens in goat and harbor the blaZ and mecA genes related to resistance to β-lactam antimicrobials. The sensitivity of the nitrocefin and disk diffusion methods to detect penicillin resistance is low in relation to that of PCR.

Post-Vaccination Streptococcus pneumoniae Carriage and Virulence Gene Distribution among Children Less Than Five Years of Age, Cape Coast, Ghana

In 2012, Ghana introduced PCV13 into its childhood immunization program. To monitor the pneumococcus after PCV13 vaccination, we analyzed serotypes, antibiotic resistance, and virulence genes of pneumococcal carriage isolates among children under five years of age. We obtained nasopharyngeal swabs from 513 children from kindergartens and immunization centers in Cape Coast, Ghana. Pneumococcal serotypes were determined by multiplex-PCR and Quellung reaction. Antibiotic resistance and virulence genes prevalence were determined by disc diffusion and PCR respectively. Overall, carriage prevalence was 29.4% and PCV13 coverage was 38.4%. Over 60% of the isolates were non-PCV13 serotypes and serotype 23B was the most prevalent. One isolate showed full resistance to penicillin, while 35% showed intermediate resistance. Resistance to erythromycin and clindamycin remained low, while susceptibility to ceftriaxone, levofloxacin and vancomycin remained high. Penicillin resistance was associated with PCV13 serotypes. Forty-three (28.5%) strains were multidrug-resistant. Virulence genes pavB, pcpA, psrP, pilus-1, and pilus-2 were detected in 100%, 87%, 62.9%, 11.9%, and 6.6% of the strains, respectively. The pilus islets were associated with PCV13 and multidrug-resistant serotypes. PCV13 vaccination had impacted on pneumococcal carriage with a significant increase in non-PCV13 serotypes and lower penicillin resistance. Including PcpA and PsrP in pneumococcal protein-based vaccines could be beneficial to Ghanaian children.

Relationship between MLSB resistance and the prevalent virulence genotypes among Bulgarian Staphylococcus aureus isolates

The aim of this study was to investigate the rate of resistance to macrolide-lincosamide-streptogramin B (MLSB) antibiotics, the mechanisms underlying this resistance and to evaluate their relationship with virulence genes profiles of 435 Bulgarian clinical isolates Staphylococcus aureus. The highest resistance was observed to penicillin (96.09%), followed by resistance to erythromycin and clindamycin (34.02 and 22.76%, respectively). Of the tested clinical strains of S. aureus, 96.09% contained the blaZ gene associated with penicillin resistance and 11.03%, the mecA gene responsible for methicillin resistance. The most prevalent were the erm genotypes associated with the presence mainly of ermA and ermC genes followed by ermB. The frequency rates of these genes, alone or in combinations were ermA 41.89%, ermB 27.70%, ermC 43.99%. The majority of Bulgarian macrolide resistant S. aureus exhibited cMLS phenotype, in 58.78% (P = 0.0036). The following virulence genotypes were present significantly more often in the macrolide resistant S. aureus isolates among the studied ones: hlg; hlg,seb; hlg,seb,sec; hlg,seb,seh; hlg,sec; hlg,sec,sei; hlg,sec,sei; hlg,sei; hlg,sei,sej; hlg,sej. This survey found correlation between the virulence profiles with a small number of genes and macrolide resistance among Bulgarian clinical S. aureus isolates, in contrast to sensitive strains, which possessed profiles predominantly with multiple genes.